NERSCPowering Scientific Discovery Since 1974

2010 Publications Resulting from the Use of NERSC Resources

On their Allocation Year 2011 ERCAP Request Forms Principal Investigators reported 1,528 refereed publications (published or in press) - as well as 262 publications submitted to refereed journals - for the preceding 12 months, based on using, at least in part, NERSC resources.

A 

PI Paul Adams

Liu H., Pereira J. H., Adams P. D.,Sapra R., Simmons B. A. and Sale K. L. Molecular Simulations Provide New Insight into Role of Accessory Immunoglobulin-like Domain of Cel9A, FEBS Letters 584(15),3431-3435, 2010.

Liu H., Sale K.L., Holmes B.M., Simmons B.A., Singh S. Understanding the Interactions of Cellulose with Ionic Liquids: A Molecular Dynamics Study. Journal of Physical Chemistry B, 114(12), 4293-4301, 2010.

Liu H., Sale K.L., Simmons B.A., Singh S. Interaction between polysaccharides and ionic liquid/water solutions. submitted to Journal of Physical Chemistry.

 PI Deborah Agarwal

D. Agarwal, M. Humphrey, N. Beekwilder, K. Jackson, M. Goode, and C. van Ingen, "A Data-Centered Collaboration Portal to Support Global Carbon-Flux Analysis," to appear in Concurrency and Computation: Practice and Experience, Wiley & Sons.

J. Li, D. Agarwal, M. Humphrey, C. van Ingen, K. Jackson, and Y. Ryu. eScience in the Cloud: A MODIS Satellite Data Reprojection and Reduction Pipeline in the Windows Azure Platforma. In Proceedings of the 24th IEEE International Parallel and Distributed Processing Symposium (IPDPS 2010), Apr 19-23, 2010. Atlanta, Georgia.

M. Humphrey, D. Agarwal, and C. van Ingen. Fluxdata.org: Publication and Curation of Shared Scientific Climate and Earth Sciences Data. In Proceedings of the 5th IEEE international Conference on e-Science (e-science 2009). Dec 7-9, 2009. Oxford, UK.

PI Greg Aldering

Amanullah, R., Lidman, C., Rubin, D., Aldering, G., Astier, P., Barbary, K., Burns, M. S., Conley, A., Dawson, K. S., Deustua, S. E., Doi, M., Fabbro, S., Faccioli, L., Fakhouri, H. K., Folatelli, G., Fruchter, A. S., Furusawa, H., Garavini, G., Goldhaber, G., Goobar, A., Groom, D. E., Hook, I., Howell, D. A., Kashikawa, N., Kim, A. G., Knop, R. A., Kowalski, M., Linder, E., Meyers, J., Morokuma, T., Nobili, S., Nordin, J., Nugent, P. E., \"Ostman, L., Pain, R., Panagia, N., Perlmutter, S., Raux, J., Ruiz-Lapuente, P., Spadafora, A. L., Strovink, M., Suzuki, N., Wang, L., Wood-Vasey, W. M. and Yasuda, N. (2010), "Spectra and Hubble Space Telescope Light Curves of Six Type Ia Supernovae at 0.511 < z < 1.12 and the Union2 Compilation", Astrophysical Journal, 716, 712.

Scalzo, R. A., Aldering, G., Antilogus, P., Aragon, C., Bailey, S., Baltay, C., Bongard, S., Buton, C., Childress, M., Chotard, N., Copin, Y., Fakhouri, H. K., Gal-Yam, A., Gangler, E., Hoyer, S., Kasliwal, M., Loken, S., Nugent, P., Pain, R., Pecontal, E., Pereira, R., Perlmutter, S., Rabinowitz, D., Rau, A., Rigaudier, G., Runge, K., Smadja, G., Tao, C., Thomas, R. C., Weaver, B. and Wu, C. (2010), "Nearby Supernova Factory Observations of SN 2007if" First Total Mass Measurement of a Super-Chandrasekhar-Mass Progenitor", Astrophysical Journal, 713, 1073.

Gal-Yam, A., Mazzali, P., Ofek, E. O., Nugent, P. E., Kulkarni, S. R., Kasliwal, M. M., Quimby, R. M., Filippenko, A. V., Cenko, S. B., Chornock, R., Waldman, R., Kasen, D., Sullivan, M., Beshore, E. C., Drake, A. J., Thomas, R. C., Bloom, J. S., Poznanski, D., Miller, A. A., Foley, R. J., Silverman, J. M., Arcavi, I., Ellis, R. S. and Deng, J. (2009), "Supernova 2007bi as a pair-instability explosion", Nature, 462, 624.

Morokuma, T., Tokita, K., Lidman, C., Doi, M., Yasuda, N., Aldering, G., Amanullah, R., Barbary, K., Dawson, K., Fadeyev, V., Fakhouri, H. K., Goldhaber, G., Goobar, A., Hattori, T., Hayano, J., Hook, I. M., Howell, D. A., Furusawa, H., Ihara, Y., Kashikawa, N., Knop, R. A., Konishi, K., Meyers, J., Oda, T., Pain, R., Perlmutter, S., Rubin, D., Spadafora, A. L., Suzuki, N., Takanashi, N., Totani, T., Utsunomiya, H., and Wang, L. (2010), "Subaru FOCAS Spectroscopic Observations of High-Redshift Supernovae", Pub. Astronomical Society of Japan, 62, 19.

Huang, X., Morokuma, T., Fakhouri, H. K., Aldering, G., Amanullah, R., Barbary, K., Brodwin, M., Connolly, N. V., Dawson, K. S., Doi, M., Faccioli, L., Fadeyev, V., Fruchter, A. S., Goldhaber, G., Gladders, M. D., Hennawi, J. F., Ihara, Y., Jee, M. J., Kowalski, M., Konishi, K., Lidman, C., Meyers, J., Moustakas, L. A., Perlmutter, S., Rubin, D., Schlegel, D. J., Spadafora, A. L., Suzuki, N., Takanashi, N. and Yasuda, N. (2009), "Hubble Space Telescope Discovery of a z = 3.9 Multiply Imaged Galaxy Behind the Complex Cluster Lens Warps J1415.1+36 at z = 1.026" Astrophysical Journal, 700, L12.

PI Vitali Alexandrov

V. Alexandrov, N. Gr??nbech-Jensen, A. Navrotsky, and M. Asta, Physical Review B, submitted (2010).

PI Yoram Alhassid

Shell model Monte Carlo approach: the heavy nuclei, Y. Alhassid, L. Fang and H. Nakada, accepted for publication in Journal of Physics (2010).

PI Hanna Annamalai

H. Annamalai, J. Hafner. K.P. Sooraj, and P. Pillai, 2010: Drying trends over south Asia: Is it human-influenced? (submitted)

P. Pillai and H. Annamalai, 2010: Moist dynamical linkage between ENSO and Monsoon (submitted)

H. Annamalai, 2010: Will the monsoon collapse in a warming planet? (submitted)

PI Jonathan Arons

Riquelme, M. & Spitkovsky, A. 2010a, "Magnetic Amplification by Magnetized Cosmic Rays in  Supernova Remnant Shocks," ApJ, 717, 1054

Sironi, L. & Spitkovsky, A. 2010, "Particle Acceleration in Relativistic Magnetized Collisionless  Electron-Ion Shocks," ApJ, submitted, arXiv:1009.0024

Riquelme, A. & Spitkovsky, A. 2010b, "Electron Injection by Whistler Waves in Non-relativistic  Shocks," ApJ, submitted, arXiv:1009.3319

Giannios, D. & Spitkovsky, A. 2009, "Signatures of a Thermal Component in Shock-Accelerated Electrons in GRBs," MNRAS, 400, 330

Sironi, L. & Spitkovsky, A. 2009a, "Particle Acceleration in Relativistic Magnetized Collisionless Pair Shocks: Dependence of Shock Acceleration on Magnetic Obliquity," ApJ, 698, 1523

Sironi, L., & Spitkovsky, A. 2009b, "Synthetic Spectra from PIC Simulations of Relativistic Collisionless Shocks", ApJ Lett., 707, L92

Riquelme, M. & Spitkovsky, A. 2009, "Non-Linear Study of Bell's Cosmic Ray Current-Driven Instability," ApJ, 694, 626

Medvedev, M. & Spitkovsky, A. 2009, "Radiative Cooling in Relativistic Collisionless Shocks: Can Simulations and Experiments Probe Relevant GRB Physics?" ApJ, 700, 956

Jiang, Y. F., Ciotti, L., Ostriker, J. P., Spitkovsky, A. 2009, "Synchrotron Emission from Elliptical Galaxies Consequent to AGN outbursts," ApJ, 711, 125

PI Alan Aspuru-Guzik

R. Sanchez-Carrera, S. Atahan, J. Schrier, and Alan Aspuru-Guzik, "Theoretical Characterization of the Air-Stable, High-Mobility Dinaphtho[2,3-b:2'3'-f]thieno[3,2-b]-thiophene Organic Semiconductor" J. Phys. Chem. C. 114, 2334 (2010)

J. McClain, J. Schrier, "Multiple Exciton Generation in Graphene Nanostructures" J. Phys. Chem. C 114, 14332 (2010)

Roel S. Sanchez-Carrera, M. Carmen Ruiz Delgado, Cristina Capel Ferron, Reyes Malave Osuna, Victor Hernandez, Juan T. Lopez Navarrete, Alan Aspuru-Guzik, "Optical absorption and emission properties of end-capped oligothienoacenes: A joint theoretical and experimental study" Organic Electronics 11, 1701 (2010).

PI Dilip Asthagiri

Dixit and Asthagiri: "Potential distribution theorem and ion selectivity in the KcsA K+ channel" (Invited Perspective) J. General Physiology (under review 2010).

Weber et al. "Molecular packing and chemical association in liquid water simulated using ab initio hybrid Monte Carlo and different exchange-correlation functionals", J. Chem. Phys. 132, 204509, 2010

Weber and Asthagiri "Thermodynamics of water modeled using ab initio potentials", J. Chem. Phys. (under review 2010).


B

PI Dmitri Babikov

D. Babikov and B. Kendrick, "The Infrared Spectrum of Cyclic-N3: Theoretical Prediction", accepted by J. Chem. Phys.

D. Babikov and B. Kendrick, "Perturbation theory treatment of pseudo-rotation in cyclic- N3", submitted to J. Chem. Phys.

PI Zhaojun Bai

E. Khatami, C.-R. Lee, Z. Bai, R. T. Scalettar and M. Jarrell, Dynamical mean field theory cluster solver with linear scaling in inverse temperature. Phys. Rev. E, Vol.81, 056703, 2010

R.-C. Lee, I.H. Chung, Z. Bai, Parallelization of Determinant Quantum Monte Carlo Simulation of Strongly Correlated Electron Systems, in the Proceedings of 24th IEEE International Parallel and Distributed Processing Symposium (IPDPS 2010), Atlanta, USA, April 2010.

PI David Bailey

A. Tiwari, J. K. Hollingsworth, "Online Adaptive Code Generation and Tuning", submitted to IPDPS 2011.

A. Tiwari, J. K. Hollingsworth, "End-to-end Auto-tuning with Active Harmony" in Performance Tuning in Scientific Computing, D. Bailry & S. Williams, ed., (to appear 2010)

N. Scherer III, Laksono Adhianto, Guohua Jin, John Mellor-Crummey, and Chaoran Yang. Hiding Latency in Coarray Fortran 2.0. The 4th Conference on Partitioned Global Address Space Programming Models, New York, NY. October 12-15, 2010. To appear.

Guohua Jin, John Mellor-Crummey, William N. Scherer III, Laksono Adhianto, and Chaoran Yang. Implementation and Performance Evaluation of the HPC Challenge Benchmarks in Coarray Fortran 2.0., submitted to  International Symposium on Parallel and Distributed Systems, May 2011.

Sean Peisert, "Fingerprinting Communication and Computation on HPC Machines," Lawrence Berkeley National Laboratory Technical Report LBNL-3483E, June 2010.

PI Krishnan Balasubramanian

K. Balasubramanian, W. Sikehaus, W. McLean II, “Uranium Hydriding: Mechanisms, Trends and Influence of Impurities”, In: Uranium: Compounds, Isotopes and Applications, Chapter 3, 23 pages, ISBN: 978-1-60692-573-7, Editor: Gerhardt H. Wolf, 2009 Nova Science Publishers, Inc.

K. Balasubramanian, and Zhiji Cao, ““Spectroscopic Properties and Potential Energy Surfaces for Curium Hydrides: CmH2, CmH2+, CmH and CmH+”, Journal of Physical Chemistry, Invited Article, Special Russell Pitzer Issue, J. Phys. Chem. A, Article ASAP DOI: 10.1021/jp903795q Publication Date (Web): September 8, 2009

M. G. Benavides-Garcia and K. Balasubramanian,” Structural Insights into the Toxicity of Uranyl: Interaction with Human Serum Protein Apotransferrin-Structure and Spectra”, ACS Journal Chemical Research in Toxicology, Chem. Res. Toxicol., 22 (9), pp 1613–1621(2009)

Z. Cao, K. Balasubramanian, M. Calvert and H. Nitsche, “Solvation Effects and Time Resolved Laser Fluorescence Spectroscopic Studies on Isomeric Preferences of Curium (III) Complexes with Multidentate phosphonopropionic Acid Ligands: CmH2PPA2+ and CmHPPA+ Complexes, Inorg. Chem., 48 (20), 9700–9714 (2009)

Z. Cao and K. Balasubramanian, “Theoretical studies of UO2(OH)(H2O)4+, UO2(OH)2(H2O)3, NpO2(OH)(H2O)4, and PuO2(OH)(H2O)4+”, Journal of Chemical Physics, 2009, in press

K. Balasubramanian, “Electronic Structure of Environmental Actinide Complexes”, American Physical Society Meeting, Pittsburgh, March 2009.

K. Balasubramanian, Group theoretical treatment of Jahn-Teller versus spin-orbit effects on geometries, rovibronic levels and nuclear spin species of bismuth and antimony clusters”, Molecular Physics, Volume 107, Issue 8 - 12 , 797 - 807 (2009)

T. Simeon, K. Balasubramanian, and C. Welch, “Computational Studies of Interaction of In and In3+ with Stone-Wales Defect Single-Walled Carbon nanotubes”, J. Phys. Chem. Lett., Jan 2010, published

D. M. David Jaba Singh, T. Pradeep, K. Thirumoorthy and K. Balasubramanian, “Closed cage Tungsten oxide Clusters in the Gas Phase”, J. Phys. Chem. A., (2010)

PI Perla Balbuena

Julibeth M. Martinez de la Hoz, Diego F. Leon-Quintero, Pussana Hirunsit, and Perla B. Balbuena, "Evolution of a Pt(111) surface at high oxygen coverage in acid medium,??? Chem. Phys. Lett., in press.G. E. Ramirez-Caballero, P. Hirunsit, and P. B. Balbuena, "Shell-anchor-core structures for enhanced stability and catalytic oxygen reduction activity," J. Chem. Phys., in press.

Pussana Hirunsit and Perla B. Balbuena, "Stability of Pt monolayers on Ir-Co cores with and without a Pd interlayer," J. Phys. Chem. C, 114, 13055-13060, (2010).

Gustavo Ramirez-Caballero and Perla B. Balbuena, "Confinement effects on alloy reactivity," Phys. Chem. Chem. Phys., in press.

Gustavo Ramirez-Caballero and Perla B. Balbuena, "Dissolution-resistant core-shell materials for acid medium oxygen reduction electrocatalysts," J. Phys. Chem. Letters, 1, 724-728, (2010).

Kuanping Gong, Wei-Fu Chen, Kotaro Sasaki, Dong Su, Miomir B. Vukmirovic, Weiping Zhu, Elise L. Izzo, Carmen Perez-Acosta, Pussana Hirunsit, Perla B. Balbuena, and Radoslav R. Adzic, "Platinum monolayer electrocatalysts: Improving the activity for the oxygen reduction reaction with palladium interlayer on IrCo alloy core," J. Electronal. Chem. in press.

Juan C. Burgos, Humberto Reyna, Boris I. Yakobson and Perla B. Balbuena, "Interplay of Catalyst Size and Metal-Carbon Interactions on the Growth of Single-Wall Carbon Nanotubes," J. Phys. Chem. C,114, 6952-6958, (2010).

Yuguang Ma and Perla B. Balbuena, "Surface adsorption and stabilization effect of Iridium in Pt-based alloy catalysts for PEM fuel cell cathodes," ECS Transactions, 25, 1, 1037-1044, (2009).

Yuguang Ma and Perla B. Balbuena, "Role of Iridium in Pt-based Alloy Catalysts for the ORR: Surface Adsorption and Stabilization Studies," J. Electrochem. Soc., 157, B959-B963, (2010).

Gustavo E. Ramirez-Caballero, Yuguang Ma, Rafael Callejas-Tovar, and Perla B. Balbuena, "Surface segregation and stability of core-shell alloy catalysts for oxygen reduction in acid medium," Phys. Chem. Chem. Phys.,12, 2209-2218, (2010).

Gustavo E. Ramirez-Caballero, Perla B. Balbuena, Paula R. Alonso, Pablo H. Gargano, and Gerardo H. Rubiolo "Carbon adsorption and absorption in L12 Fe3Al surfaces," J. Phys Chem. C.,113, 18321-18330, (2009).

Morgana A. Ribas, Ding Feng, Perla B. Balbuena, and Boris I. Yakobson, "Nanotube nucleation versus carbon-catalyst adhesion: Probed by molecular dynamics simulations," J. Chem. Phys., 131, 224501, (2009).

Pussana Hirunsit and Perla B. Balbuena, "Surface atomic distribution and water adsorption on PtCo alloys," Surf. Sci., 603, 911-919, (2009).

Yuguang Ma and Perla B. Balbuena, "Surface segregation in bimetallic Pt3M (M=Fe, Co, Ni) alloys with adsorbed oxygen," Surf. Sci.,603, 349-353, (2009).

Diego A. Gomez-Gualdrin and Perla B. Balbuena, "Effect of metal cluster-cap interactions on the catalyzed growth of single-wall carbon nanotubes," J. Phys. Chem. C, 113, 698-709, (2009).

PI Alan Balch

Franco, J. U., Hammons, J. C., Rios, D. Olmstead, M. M. Inorg. Chem., 49, 11, 5120-2125.

PI Arun Bansil

H. Lin, L. A. Wray, Y. Q. Xia, S. Y. Xu, S. A. Jia, R. J. Cava, A. Bansil and M. Z. Hasan (Half-Heusler ternary compounds as new multifunctional experimental platforms for topological quantum phenomena) Nature Materials 9, 546 (2010).

H. Lin, R. S. Markiewicz, L. A. Wray, L. Fu, M. Z. Hasan and A. Bansil (Single-Dirac-Cone Topological Surface States in the TlBiSe2 Class of Topological Semiconductors) Physical Review Letters 105, 036404 (2010).

Y. Xia, D. Qian, D. Hsieh, L. Wray, A. Pal, H. Lin, A. Bansil, D. Grauer, Y. S. Hor, R. J. Cava and M. Z. Hasan (Observation of a large-gap topological-insulator class with a single Dirac cone on the surface) Nature Physics 5, 398 (2009).

D. Hsieh, Y. Xia, D. Qian, L. Wray, F. Meier, J. H. Dil, J. Osterwalder, L. Patthey, A. V. Fedorov, H. Lin, A. Bansil, D. Grauer, Y. S. Hor, R. J. Cava and M. Z. Hasan, (Observation of Time-Reversal-Protected Single-Dirac-Cone Topological-Insulator States in Bi2Te3 and Sb2Te3) Physical Review Letters 103, 146401 (2009).

S. Mukherjee, M. P. Nadesalingam, P. Guagliardo, A.D. Sergeant, B. Barbiellini, J.F. Williams, N.G. Fazleev, A.H. Weiss (Auger mediated sticking of positrons to surfaces: Evidence for single step transition from a scattering state to a surface image potential bound state) Physical Review Letters 104, 247403 (2010).

R. S. Markiewicz, J. Lorenzana, G. Seibold and A. Bansil (Gutzwiller magnetic phase diagram of the cuprates), Physical Review B 81, 014509 (2010).

R. S. Markiewicz, J. Lorenzana and G. Seibold, (Gutzwiller magnetic phase diagram of the undoped t-t '-U Hubbard model) Physical Review B 81, 0140 (2010).

T. Das, R. S. Markiewicz and A. Bansil (Emergence of non-Fermi-liquid behavior due to Fermi surface reconstruction in the underdoped cuprate superconductors), Physical Review B 81, 184515 (2010).

T. Das, R. S. Markiewicz, and A. Bansil (Optical model-solution to the competition between a pseudogap phase and a charge-transfer-gap phase in high-temperature cuprate superconductors), Physical Review B 81, 174504 (2010).

S. Basak, T. Das, Hsin Lin, J. Nieminen, M. Lindroos, R. S. Markiewicz, and A. Bansil (Origin of the high-energy kink in the photoemission spectrum of the high-temperature superconductor Bi2Sr2CaCu2O8), Physical Review B 80, 214520 (2009).

J. Nieminen, I. Suominen, R. S. Markiewicz, H. Lin and A. Bansil (Spectral decomposition and matrix element effects in scanning tunneling spectroscopy of Bi2Sr2CaCu2O8+delta) Physical Review B 80, 134509 (2009).

Y. J. Wang, H. Lin, B. Barbiellini, P. E. Mijnarends, S. Kaprzyk, R. S. Markiewicz and A. Bansil (Proposal to determine the Fermi-surface topology of a doped iron-based superconductor using bulk-sensitive Fourier-transform Compton scattering), Physical Review B 81, 092501 (2010).

Y. J. Wang, H. Lin, B. Barbiellini, P. E. Mijnarends, S. Kaprzyk, W. Al-Sawai, R. S. Markiewicz and A. Bansil (High Resolution Compton Scattering as a Probe of the Fermi Surface in the Iron-based Superconductor LaO(1-x) F(x) FeAs) Journal of Superconductivity and Novel Magnetism 22, 596 (2009).

H. Kobayashi, T. Nagao, M. Itou, S. Todo, B. Barbiellini, P. E. Mijnarends, A. Bansil and N. Sakai, (Direct observation of localization of the minority-spin-band electrons in magnetite below the Verwey temperature) Physical Review B 80,104423 (2009).

PI Edward Baron

Soma De, E. Baron, & P. H. Hauschildt, On the Hydrogen Recombination Time in Type II Supernova Atmospheres, MNRAS, (2010), 401, 2081--2092.

P. H. Hauschildt, & E. Baron, A 3D Radiative Transfer Framework: VI. PHOENIX/3D example applications, A&A, (2010) 509, A260000.

Soma De, E. Baron, & P. H. Hauschildt, The effects of multi-level atoms, composition, and non-resonant processes on
hydrogen recombination: A full radiative transfer calculation, MNRAS, (2010), 403, 936--946.

S. James & E. Baron, Searching for Hydrogen in Type Ib Supernovae, ApJ, (2010), 718, 957--962.

A. Seelmann, P. H. Hauschildt, & E. Baron, A 3D Radiative Transfer Framework: VII. Arbitrary
Velocity Fields in the Eulerian Frame, A&A, (2010) in press.

D. Jack, P. H. Hauschildt, & E. Baron, Theoretical light curves of type Ia supernovae, A&A, (2010), submitted.

PI Don Batchelor

T. G. Jenkins, S. E. Kruger, C. C. Hegna, D. D. Schnack, and C. R. Sovinec, Calculating electron cyclotron current drive stabilization of resistive tearing modes in a nonlinear MHD model, Phys. Plasmas 17, 012502 (2010).

PI Victor Batista

Ann. Rev. Phys. Chem. 60:293-320, 2009 Luis G.C. Rego, Lea F. Santos and Victor S. Batista.

Photosynth. Res. 102:455-470, 2009 Eduardo M. Sproviero, Michael B. Newcomer, Jose A. Gascon, Enrique R. Batista, Gary W. Brudvig and Victor S. Batista.

Israel J. Chem. 49: 187-197, 2009 Justin Kim, Yinghua Wu, Jean-Luc Bredas and Victor S. Batista.

Energy & Environ. Sci. 2, 1173-1175, 2009 William R. McNamara, Robert C. Snoeberger III, Gonghu Li, Christiaan Richter, Laura J. Allen, Rebecca L. Milot, Charles A. Schmuttenmaer, Robert H. Crabtree, Gary W. Brudvig, and Victor S. Batista.

J. Phys. Chem. A 113,12532-12540, 2009 Elena Jakubikova, Robert C. Snoeberger III, Victor S. Batista and Enrique R. Batista.

Proc. SPIE 7396, 739604, 2009 Robert C. Snoeberger III, Tianquan Lian, and Victor S. Batista.

Dalton Trans. 45, 10078-10085, 2009 Honghu Li, Christian P. Richter, Rebecca L. Milot, Lawrence Cai, Charles A. Schmuttenmaer, Robert H. Crabtree, Gary W. Brudvig and Victor S. Batista.

J. Phys. Chem. B (in press) 2010 Shengye Jin, Robert C. Snoeberger III, Abey Issac, Victor S. Batista and Tianquan Lian.

J. Phys Chem. C 114:1317-1325, 2010 Luis G. C. Rego, Robson da Silva, Jos?? A. Freire, Robert C. Snoeberger and Victor S. Batista.

J. Phys. Chem. B (in press) 2010 Gonghu Li, Eduardo M. Sproviero, William R. McNamara, Robert C. Snoeberger III, Robert H. Crabtree, Gary W. Brudvig, and Victor S. Batista.

J. Chem. Theory Comput. 6:755-760, 2010 Ting Wang, Gary Brudvig, and Victor S. Batista.

Energy & Environ. Sci. 3, 917-923, 2010 William R. McNamara, Rebecca L. Milot, Hee-eun Song, Robert C. Snoeberger III, Victor S. Batista, Robert H. Crabtree and Gary W. Brudvig.

J. Chem. Theory Comput. 6, 2395-2401, 2010 Ting Wang, Gary Brudvig, and Victor S. Batista.

J. Phys. Chem. C. accepted (2010) Robson da Silva, Luis G.C. Rego, Jose A. Freire, Javier Rodriguez, Daniel Laria and Victor S. Batista.

NanoLett. submitted (2010) Steven J. Konezny, Christiaan Richter, Robert C. Snoeberger, Alexander R. Parent, Gary W. Brudvig, Charles A. Schmuttenmaer and Victor S. Batista.

Adgewandte Chemie submitted (2010) Theoretical EXAFS studies of a model of the oxygen evolving complex of photosystem II obtained with the quantum cluster approach, Xichen Li, Eduardo M. Sproviero, Ulf Ryde, Per E. M. Siegbahn, Victor S. Batista and Guangju Chen.

PI John Bell

J. B. Bell, M. S. Day, X. Gao, M. J. Lijewski, "Simulation of Nitrogen Emissions in a Low Swirl Burner," SciDAC 2010, J. of Physics: Conference Series, Chattanooga, Tennessee, July 2010.

A. Almgren, J. Bell, D. Kasen, M. Lijewski, A. Nonaka, P. Nugent, C. Rendleman, R. Thomas, M. Zingale, "MAESTRO, CASTRO and SEDONA -- Petascale Codes for Astrophysical Applications," SciDAC 2010, J. of Physics: Conference Series, Chattanooga, Tennessee, July 2010.

J. Nordhaus, A. Burrows, A. Almgren, and J. Bell, "Dimension as a Key to the Neutrino Mechanism of Core-Collapse Supernova Explosions," Astrophysical Journal, to appear.

A. Nonaka, A.S. Almgren, J. B. Bell, M. J. Lijewski, C. M. Malone, and M. Zingale, "MAESTRO: An Adaptive Low Mach Number Hydrodynamics Algorithm for Stellar Flows", Astrophysical Journal Supplement Series, 188, 358-383, June 2010.

A. S. Almgren, V.E. Beckner, J.B. Bell, M.S. Day, L.H. Howell, C.C. Joggerst, M.J. Lijewski, A. Nonaka, M. Singer, M. Zingale, "CASTRO: A New Compressible Astrophysical Solver. I. Hydrodynamics and Self-Gravity", Astrophysical Journal, 715, 1221-1238, June 2010.

A. J. Aspden, M. S. Day, and J. B. Bell, "Turbulence-flame interaction in lean premixed hydrogen", submitted for publication.

C. C. Joggerst, A. Almgren, and S. E. Woosley, "Three-dimensional simulations of Rayleigh-Taylor mixing in core collapse supernovae with CASTRO", to appear in Astrophysical Journal.

G. S. H. Pau, J. B. Bell, K. Pruess, A. S. Almgren, M. J. Lijewski, K. Zhang, "High resolution simulation and characterization of density-driven flow in CO2 storage in saline aquifers'', Advances in Water Resources, 33(4):443-455, 2010.

A. J. Aspden, M. S. Day, and J. B. Bell, "Characterization of Low Lewis Number Flames", accepted for publication in the Proceedings of the Combustion Institute.

A. J. Aspden, M. S. Day, and J. B. Bell, "Lewis Number Effects in Distributed Flames", accepted for publication in the Proceedings of the Combustion Institute.

M. S. Day, J. B. Bell, X. Gao and P. Glarborg "Numerical Simulation of Nitrogen Oxide Formation in Lean Premixed Turbulent Flames", accepted for presentation at the 33rd International Symposium on Combustion.

M. S. Day, X. Gao, and J. B. Bell, "Properties of Lean Turbulent Methane-Air Flames with Significant Hydrogen Addition", accepted for publication in Proceedings of the Combustion Institute.

A. J. Aspden, J. B. Bell, and S. E. Woosley, "Distributed Flames in Type Ia Supernovae", Astrophysical Journal, 710, 1654-1663, February 2010.

C. C. Joggerst, A. Almgren, J. Bell, Alexander Heger, Daniel Whalen, and S. E. Woosley, ``Primordial Core-Collapse Supernovae and the Chemical Abundances of Metal-Poor Stars,'' Astrophysical Journal, 709, 11-26, January 2010.

PI Roy Benedek

"Pourbaix-like phase diagram for lithium manganese spinels in acid", R. Benedek, M. M. Thackeray and A. van de Walle, J. Mater. Chem. 20, 369-374 (2010)

"Simulation of the surface structure of lithium manganese oxide spinel", R. Benedek and M. M. Thackeray (Physical Review B, submitted; revised version in preparation).

PI Bernd Berg

B.A. Berg, A. Bazavov, and Hao Wu, Deconfining Phase Transition on a Double Layered Torus, PoS (LAT2009) 91 (2010) 164.

PI Zvi Bern

C. F. Berger et al., ``Next-to-Leading Order QCD Predictions for Z,gamma^*+3-Jet Distributions at the Tevatron,'' arXiv:1004.1659 [hep-ph], to appear in Physical Review D.

C. F. Berger et al., ``Next-to-Leading Order QCD Predictions for W+3-Jet Distributions at Hadron Colliders,'' Phys. Rev. D 80, 074036 (2009)

PI Wes Bethel

Interactive Exploration and Analysis of Large Scale Simulations Using Topology-based Data Segmentation (article). P.-T. Bremer and G. Weber and J. Tierny and V. Pascucci and M. Day and J. B. Bell. IEEE Trans. on Visualization and Computer Graphics (2010, to appear)

Mark Howison, Andreas Adelmann, E. Wes Bethel, Achim Gsell, Benedikt Oswald, Prabhat. H5hut: A High-Performance I/O Library for Particle-based Simulations. In IASDS10 Workshop on Interfaces and Abstractions for Scientific Data Storage, Heraklion, Crete, Greece. September 2010.

Oliver Robel, Sean Ahern, E. Wes Bethel, Mark. D Biggin, Hank Childs, Estelle Cormier-Michel, Angela DePace, Michael B. Eisen, Charless C. Fowlkes, Cameron G. R. Geddes, Hans Hagen, Bernd Hamann, Min-Yu Huang, Soile V. E. Kernen, David W. Knowles, Cris L. Luengo Hendriks, Jitendra Malik, Jeremy Meredith, Peter Messmer, Prabhat, Daniela Ushizima, Gunther H. Weber, and Kesheng Wu. Coupling Visualization and Data Analysis for Knowledge Discovery from Multi-dimensional. In Procedia Computer Science, Proceedings of International Conference on Computational Science, ICCS 2010, May 2010. LBNL-3669E.

M. Howison. Comparing GPU Implementations of Bilateral and Anisotropic Diffusion Filters for 3D Biomedical Datasets. Technical Report LBNL-3425E, Lawrence Berkeley National Laboratory, Berkeley, CA, USA, 94720, 2010

T. Fogal, H. Childs, S. Shankar, J. Kruger, R.D. Bergeron, and P. Hatcher. Large Data Visualization on Distributed Memory Multi-GPU Clusters. High Performance Graphics 2010, Saarbruken, Germany, June 2010.

Daniela Ushizima, Cameron Geddes, Estelle Cormier-Michel, E. Wes Bethel, Janet Jacobsen, Prabhat, Oliver Rbel, Gunther Weber, Bernard Hamann, Peter Messmer, Hans Hagen. "Automated Detection and Analysis of Particle Beams in Laser-plasma Accelerator Simulations", In-Tech, 367-389, 2010.LBNL-3845E.

Mark Howison, E. Wes Bethel, and Hank Childs. "MPI-hybrid Parallelism for Volume Rendering on Large, Multi-core Systems." In Proceedings of the Eurographics Symposium on Parallel Graphics and Visualization, May 2???3, 2010, Norkopping, Sweden. LBNL-3297E. Best Paper Award.

P.-T. Bremer, G.H. Weber, V. Pascucci, M.S. Day and John B. Bell, Analyzing and Tracking Burning Structures in Lean Premixed Hydrogen Flames. In: : IEEE Transactions on Visualization and Computer Graphics, 16(2): 248-260, 2010. LBNL-2276E

G. H. Weber, S. Ahern, E.W. Bethel, S. Borovikov, H.R. Childs, E. Deines, C. Garth, H. Hagen, B. Hamann, K.I. Joy, D. Martin, J. Meredith, Prabhat, D. Pugmire, O. R??bel, B. Van Straalen and K. Wu. "Recent Advances in VisIt: AMR Streamlines and Query-Driven Visualization." In: Numerical Modeling of Space Plasma Flows: Astronum-2009 (Astronomical Society of the Pacific Conference Series). LBNL-3185E. Vol. 429, pp. 329-334, 2010

C. Garth, E. Deines, K. Joy, E. W. Bethel, H. Childs, G. Weber, S. Ahern, D. Pugmire, A. Sanderson, C. Johnson. "Twists and Turns: Vector Field Visual Data Analysis for Petascale Computational Science." SciDAC Review, Number 15, Winter 2009.

E. Wes Bethel, Hank Childs, Ajith Mascarenhas, Valerio Pascucci, and Prabhat. Scientific Data Managment Challenges in High Performance Visual Data Analysis. In Arie Shoshani and Doron Rotem, editors, Scientific Data Management: Challenges, Existing Technology, and Deployment. Chapman & Hall/CRC Press, 2009. (LBNL-1449E)

P.-T. Bremer, G.H. Weber, J. Tierny, V. Pascucci, M.S. Day and J.B. Bell. "A Topological Framework for the Interactive Exploration of Large Scale Turbulent Combustion," In: Proceedings of the 5th IEEE International Conference on e-Science, Oxford UK, 2009.

M. Howison, E. W. Bethel, and H. Childs. "Hybrid Parallelism for Volume Rendering on Large, Multi-core Systems." In Journal of Physics: Conference Series, Proceedings of SciDAC 2010, July 2010, Chattanooga TN, USA. LBNL-4024E.

M. Howison, E. W. Bethel, and H. Childs. "Hybrid Parallelism for Volume Rendering on Large, Multi-core Systems." In Astronum 2010, 5th International Conference on Numerical Modeling of Space Plasma Flows, June 2010, San Diego, CA, USA. LBNL-4024E-Conf.

A.Uselton, K.Antypas, D.M.Ushizima, J.Sukharev, "File System Monitoring as a Window Into User I/O Requirements", CUG-2010, Edinburgh, UK, May 24-27th, 2010. (possibly to be counted as a NERSC staff paper rather than a research group paper, you guys can decide)

Hank Childs, David Pugmire, Sean Ahern, Brad Whitlock, Mark Howison, Prabhat, Gunther Weber, E. Wes Bethel. "Extreme Scaling of Production Visualization Software on Diverse Architectures." IEEE Computer Graphics and Applications, 30(3):22-31, May/June 2010. LBNL-3403E.

Martin Isenburg, Peter Lindstrom, and Hank Childs, "Parallel and Streaming Generation of Ghost Data for Structured Grids." IEEE Computer Graphics and Applications, 30(3):32-44, May/June 2010.

P.-T. Bremer, G.H. Weber, V. Pascucci, M.S. Day and John B. Bell, Analyzing and Tracking Burning Structures in Lean Premixed Hydrogen Flames. In: : IEEE Transactions on Visualization and Computer Graphics, 16(2): 248-260, 2010. LBNL-2276E

O. R\"{u}bel, "Linking Automated Data Analysis and Visualization with Applications in Developmental Biology and High-energy Physics," Schriftenreihe Informatik, Band 28, Der Dekan (hrsg), Fachbereich Informatik, Technische Universität Kaiserslautert, December, 2009, ISBN 978-3-941438-35-4, ISSN 1610-2673. LBNL-3155E.

PI Amitava Bhattacharjee

A. Bhattacharjee, Y.-M. Huang, H. Yang, and B. Rogers, "Fast reconnection in high-Lundquist-number plasmas due to the plasmoid instability", Physics of Plasmas 16, 112102 (2009).

Brian P. Sullivan, A. Bhattacharjee, Yi-Min Huang, "Extension of the Electron Dissipation Region in Collisionless Hall MHD Reconnection", Phys. Plas 16, 102111 (2009)

Yi-Min Huang and A. Bhattacharjee, "Scaling Laws of Resistive Magnetohydrodynamic Reconnection in the High-Lundquist-Number, Plasmoid-Unstable Regime", Phys. Plasmas 17, 062104 (2010)

Yi-Min Huang, A. Bhattacharjee, and Brian P. Sullivan, "Onset of Fast Reconnection in Hall Magnetohydrodynamics Mediated by the Plasmoid Instability", submitted to Phys. Rev. Lett.

B. Sullivan, A. Bhattacharjee, and Yi-Min Huang, "On the question of hysteresis in Hall MHD", submitted to Physics of Plasmas, April 2010

N. Bessho and A. Bhattacharjee, "Fast reconnection in low-density hydrogen and pair plasmas", accepted by Plasma and Fusion Research.

N. Bessho and A. Bhattacharjee, "Fast magnetic Reconnection in low-density electron-positron plasmas", accepted by Physics of Plasmas.

J. Raeder, P. Zhu, Y. Ge, and G. Siscoe, "Tail Force Imbalance and Ballooning Instability Preceding Substorm Onset", submitted to J. Geophys. Res. (2010)

W. Fox, A. Bhattacharjee, K. Germaschewski, "Fast magnetic reconnection in laser-produced plasma bubbles", submitted to PRL, Sept 2010.

PI Paul Bonoli

Austin, T.M., Smithe, D.N., Ranjbar, V., "Computing quasi-linear diffusion coefficients using the delta-f particle-in-cell method," in Proceedings of the 18th Topical Conference on Radio Frequency Power in Plasmas, Vol. 1187, edited by V. Bobkov and J.-M. Noterdaeme (American Institute of Physics, Melville, NY, 2009) 585 (2009).

Choi, M., Chan, V.S., Berry, L.A., Jaeger, E.F., Green, D., Bonoli, P., Wright, J., and RF SciDAC Team, "Comparison of the Monte Carlo ion cyclotron heating model with the full-wave linear absorption model," Physics of Plasmas 16, 052513 (2009).

Choi, M., Green, D., Heidbrink, W.W., Harvey, R.W., Liu, D., Chan, V.S., Berry, L.A., Jaeger, E.F., Lao, L.L., Pinsker, R.I., Podesta, M., Smithe, D.N., Park, J.M., and Bonoli, P., RF SciDAC, and SWIM Team, "Iterated finite-orbit Monte Carlo simulations with full-wave fields for modeling tokamak," Phys. Plasmas 17, 056102 (2010).

Harvey, R.W., Petrov, Yu., Jaeger, E.F., Berry, L.A., Batchelor, D. B., Bonoli, P.T., and Wright, J.C., "Comparison of ICRF-Induced Ion Diffusion Coefficients Calculated with the DC and AORSA Codes," Proc. of 18th Topical Conference on. Radio Frequency Power in Plasmas, Ghent, (2009).

Lee, J.-P., and Wright, J.C., "A versatile parallel block tri-diagonal solver for spectral codes," to be submitted to Journal of Computational Physics (2010).

Phillips, C.K., Bell, R.E., Berry, L.A., Bonoli, P.T., Harvey, R.W., Jaeger, E.F., LeBlanc, B.P., Ryan, P.M., Taylor, G., Valeo, E.J., Wilson, J.R., Wright, J.C., Yuh, H., and the NSTX Team, "Spectral effects on fast wave core heating and current drive," Nuclear Fusion 49, 075015 (2009).

Smithe, D., Carlsson, J. and Austin, T., "Time-domain simulation of RF couplers on NERSC computers", 2009 Sherwood Fusion Theory Conference, Bulletin of the American Physical Society 54, 197 (2009).

Smithe, D., Carlsson, J. and Austin, T., "Time-Domain Simulation of RF Couplers," in Proceedings of the 18th Topical Conference on Radio Frequency Power in Plasmas, AIP Conference Proceedings, Volume 1187, pp. 609-612 (2009).

Taylor, G., Bell, R. E., Hosea, J. C., LeBlanc, B. P., Phillips, C. K., Podesta, M., Valeo, E. J., Wilson, J. R., Ahn, J-W., Chen, G., Green, D. L., Jaeger, E. F., Maingi, R., Ryan, P. M., Wilgen, J., Heidbrink, W. W., Liu, D., Bonoli, P. T., Brecht, T., Choi, M. and Harvey, R. W., "Advances in high-harmonic fast wave physics in the National Spherical Torus Experiment", Physics of Plasmas 17, 056114 (2010).

Tusijii, N., Porkolab, M., Edlund, E. M., Lin, L., Lin, Y., Wright, J. C. and Wukitch, S. J., "Measurements of mode converted ion cyclotron wave with phase contrast imaging in Alcator C-Mod and comparisons with synthetic PCI simulation in TORIC", in Proceedings of the 18th Topical Conference on Radio Frequency Power in Plasmas, Vol. 1187, edited by V. Bobkov and J.-M. Noterdaeme (American Institute of Physics, Melville, NY, 2009) pp. 65-68.

Wright, J.C., Bonoli, P.T., Schmidt, A.E., Phillips, C.K., Valeo, E.J., Harvey, R.W., and Brambilla, M.W., "An assessment of full wave effects on the propagation and absorption of lower hybrid waves," Physics of Plasmas 16, 072502 (2009).

Wright, J.C., Lee, J.P., Bonoli, P., Valeo, E., Phillips, C.K., and Harvey, R.H., "Challenges in self-consistent full wave simulations of lower hybrid waves," IEEE Transactions on Plasma Science on Plasma Science in Special Issue on Numerical Simulation of Plasmas, Vol. 38, 2136 (2010).

PI Julian Borrill

Cantalupo et al, ApJS 187:212, "MADmap: A Massively Parallel Maximum-Likelihood Cosmic Microwave Background Map-Maker"

Dickinson et al, ApJ, 705:1607, "Bayesian Component Separation and Cosmic Microwave Background Estimation for the Five-Year WMAP Temperature Data"

Hall et al, ApJ 718:632, "Angular Power Spectra of the Millimeter Wavelength Background Light from Dusty Star-forming Galaxies with the South Pole Telescope"

Leuker et al, ApJ 719:1045, "Measurements of Secondary Cosmic Microwave Background Anisotropies with the South Pole Telescope"

Stivoli et al, MNRAS in press, "Maximum likelihood, parametric component separation and CMB B-mode detection in suborbital experiments"

Huffenberger et al, A&A 510:A58, "Measuring Planck Beams with Planets"

Keskitalo et al, A&A in press, "Residual noise covariance for Planck low-resolution data analysis"

Meinhold et al, JINST 4:T12009, "Noise properties of the Planck-LFI receivers"

Mitra et al, submitted to A&A, "Fast Pixel Space Convolution for CMB Surveys with Asymmetric Beams and Complex Scan Strategies"

Prezeau et al, ApJ in press, "Algorithm for the evaluation of reduced Wigner matrices"

Ricciardi et al, MNRAS 406:1644, "Correlated Component Analysis for diffuse component separation with error estimation on simulated Planck polarization data"

Rocha et al, A&A 513:A23, "Markov Chain Beam Randomization: a study of the impact of PLANCK beam measurement errors on cosmological parameter estimation"

Rocha et al, MNRAS in press, "Application of XFaster power spectrum and likelihood estimator to Planck"

Rocha et al, submitted to MNRAS, "A high-l Likelihood for Planck - Xfaster"

PI James Boyle

J. Boyle and S. A. Klein, Impact of horizontal resolution on climate model forecasts of tropical precipitation and diabatic heating for the TWP-ICE period. Journal of Geophysical Research, in press

PI Linda Broadbelt

Konstantinov, I. and Broadbelt, L.J., "The Role of Oxazolidinones in L-Proline-Assisted Aldol-Type Reactions", Topics in Catalysis, 2010, 53, 1031-1038.

Konstantinov, I.A. and Broadbelt, L.J., "Reaction Free Energies in Organic Solvents: Comparing Different Quantum Mechanical Methods", Molecular Simulation, 2010, accepted.

Ivan A. Konstantinov, John M. Galloway, Michael M. Massaghi, Linda J. Broadbelt, Harold H. Kung "Selective Oxidation Palladium Complex Catalysts: Bonding and Configuration of Bis(meta-) and Bis(para-pyridyl)methylsiloxane Palladium Acetate Ring Complexes", J. Phys. Chem. C, submitted

PI David Bruhwiler

B.T. Schwartz, D.L. Bruhwiler, V.N. Litvinenko, S. Reiche, G.I. Bell, A. Sobol, G. Wang and Y. Hao, "Massively parallel simulation of anisotropic Debye shielding in the modulator of a coherent electron cooling system and subsequent amplication in a free electron laser," Journal of Physics: Conference Series (2010), in press.

J. Qiang et al., "Particle-field decomposition and domain decomposition in parallel particle-in-cell beam dynamics simulation," Computer Physics Communications (2010), in press.

PI Charles Brush

"Error Control of Iterative Linear Solvers for Integrated Groundwater Models" by M.F. Dixon, Z. Bai, C.F. Brush, F.I. Chung, E.C. Dogrul and T.N. Kadir,  Ground Water, accepted.


C

PI Roberto Car

X-Ray Absorption Signatures of the Molecular Environment inWater and Ice “, PRL 105, 017802(2010).

PI Joseph Carlson

"Ab initio nuclear structure simulations: the speculative 14F nucleus," P. Maris, A. M. Shirokov and J. P. Vary, Phys. Rev. C 81, 021301(R) (2010).

"Augmented Lagrangian Method for Constrained Nuclear Density Functional Theory," A. Staszczak, M.Stoitsov, A. Baran, and W. Nazarewicz, arXiv:1006.4137 (2010).

"Quadrupole collective inertia in nuclear fission: cranking approximation", A. Baran, J.A. Sheikh, J. Dobaczewski, W. Nazarewicz, arXiv:1007.3763 (2010).

"Nuclear Energy Density Optimization," M. Kortelainen, T. Lesinski, J. More, W. Nazarewicz, J. Sarich, N. Schunck, M. V. Stoitsov, and S. Wild, Phys. Rev. C 82, 024313 (2010).

"Natural Units For Nuclear Energy Density Functional Theory",  M. Kortelainen, R.J. Furnstahl, W. Nazarewicz, M.V. Stoitsov, Phys. Rev. C 82, 011304 (2010).

"One-quasiparticle States in the Nuclear Energy Density Functional Theory," N. Schunck, J. Dobaczewski, J. McDonnell, J. More, W. Nazarewicz, J. Sarich, and M.V. Stoitsov, Phys. Rev. C 81, 024316 (2010).

"Microscopically-based energy density functionals for nuclei using the density matrix expansion: Implementation and pre-optimization", M. Stoitsov, M. Kortelainen, S. K. Bogner, T. Duguet, R. J. Furnstahl, B. Gebremariam, N. Schunck, arXiv:1009.3452 (2010).

"Isospin-symmetry restoration within the nuclear density functional theory: Formalism and applications," W. Satula, J. Dobaczewski, W. Nazarewicz, M. Rafalski, Phys. Rev. C 81, 054310 (2010).

"Self-consistent symmetries in the proton-neutron Hartree-Fock-Bogoliubov approach," S. G. Rohozi??ski, J. Dobaczewski, and W. Nazarewicz, Phys. Rev. C 81, 014313 (2010).

"Spatial symmetries of the local densities," S.G. Rohozinski, J. Dobaczewski, and W. Nazarewicz, Int. J. Mod. Phys. E 19, 640 (2010).

`Low-Density Neutron Matter', A. Gezerlis and J. Carlson, Phys. Rev. {\bf C}81, 025803 (2010).

`Heavy-Light Fermion Mixtures at Unitarity', A. Gezerlis, S. Gandolfi, K. E. Schmidt, and J. Carlson', Phys. Rev. Lett. 103:060403, (2009).

Solution of the Skyrme-Hartree-Fock-Bogolyubov equations in the Cartesian deformed harmonic-oscillator basis. (VI) HFODD (v2.38j): a new version of the programJ. Dobaczewski, W. Satula, B.G. Carlsson, J. Engel, P. Olbratowski, P. Powalowsk, M. Sadziak, N. Schunk, A Staszczak, M. Stoitsov, M. Zalewski, and H. Zdunczuk, Comp. Phys. Comm. 180, 2361-2391 (2009).

'Self-consistent Skyrme QRPA for use in axially-symmetric nuclei of arbitrary mass', J. Terasaki and J. Engel, arXiv:1006.0010 [nucl-th], to appear in Phys. Rev. C (2010).

'Coupled-channels calculations of nonelastic cross sections using a density-functional structure model', G.P.A. Nobre, F.S. Dietrich, J.E. Escher, I.J. Thompson, M. Dupuis, J. Terasaki, and J. Engel, arXiv:1006.0267 [nucl-th], submitted to Phys. Rev. Lett. (2010).

'Effective 3-body interaction for mean-field and density-functional theory', Alexandros Gezerlis and G.F. Bertsch, to appear in Physical Review Letters (2010).

PI Paul Cassak

P. A. Cassak, M. A. Shay, and J. F. Drake, "Scaling of Sweet-Parker Reconnection with Secondary Islands," Phys. Plasmas, 16, 120702, 2009.

P. A. Cassak and J. F. Drake, "Secondary Islands in Embedded Sweet-Parker Reconnection and Energy Storage in the Corona," Ap. J. Lett., 707, L158, 2009.

P. A. Cassak, M. A. Shay, and J. F. Drake, "A saddle-node bifurcation model of magnetic reconnection  onset," Phys. Plasmas, 17, 062105, 2010.

L. S. Shepherd and P. A. Cassak, "Comparison of secondary islands in collisional reconnection to Hall reconnection," Phys. Rev. Lett., 105, 015004, 2010.

K. Malakit, M. A. Shay, P. A. Cassak, and C. Bard, "Scaling of asymmetric magnetic reconnection:  Kinetic particle-in-cell simulations," J. Geophys. Res., in press.

R. Schreier, M. Swisdak, J. F. Drake, and P. A. Cassak, "Three-dimensional simulations of the orientation and structure of reconnection X-lines," Phys. Plasmas, in press.

PI Paola Cessi

Wolfe, C.L., and P. Cessi, 2010: The Adiabatic Pole-to-Pole Overturning Circulation. Journal of Physical Oceanography, submitted.

Cessi, P., C.L. Wolfe, and B. C. Ludka, 2010: Eastern-boundary contribution to the meridional overturning circulation. Journal of Physical Oceanography, 40, 2075-2090. (Early Online Release)

Wolfe, C.L., and P. Cessi, 2010: What Sets the Strength of the Mid-Depth Stratification and Overturning Circulation in Eddying Ocean Models? Journal of Physical Oceanography, 40, 1520-1538.

Cessi, P., and C.L. Wolfe, 2009: Eddy-driven buoyancy gradients on eastern boundaries. Journal of Physical Oceanography, 39, 1595-1614.

PI Yuen-Dat Chan

MAGE - a GEANT4-based Monte Carlo Application Framework for Low-background Germanium Experiments, submitted to Nuclear Instruments and Method

PI Choong-Seock Chang

H.R. Strauss, L. Sugiyama, G.Y. Park, C.S.Chang, S. Ku, and I. Joseph, ``Extended MHD simulation or resonant magnetic perturbations,'' Nucl. Fusion 49, 055025 (2009)

S. Ku, C.S. Chang, and P.H. Diamond, "Full-f gyrokinetic particle simulation of centrally heated global ITG turbulence from magnetic axis to edge pedestal top in a realistic tokamak geometry," Nuclear Fusion 49, 115021 (2009)

X. Q. Xu, E. Belli, K. Bodi, J. Candy, C. S. Chang, B. I. Cohen, R. H. Cohen, P. Colella, A. M. Dimits, M. R. Dorr, Z. Gao, J. A. Hittinger, S. Ko, S. Krasheninnikov, G. R. McKee, W. M. Nevins, T. D. Rognlien, P. B. Snyder, J. Suh, M. V. Umansky, "Dynamics of kinetic Geodesic-Acoustic modes and the radial electric field in tokamak neoclassical plasmas," Nuclear Fusion, 49 065023 (2009).

S.H. Park, Suk Jae Yoo, Choong-Seock Chang, "Molecular dynamics simulation of hyperthermal neutrals generated by energetic ion impact on a metal plate," Appl. Phys. Lett. 107, 13304 (2009)

D.A. Gates, et al, C. Chang among many authors, "Overview of results from the National Spherical Torus Experiment (NSTX)," Nucl. Fusion 49, 104016 (2009)

R. Maingi, S.M. Kaye, R.E. Bell, T.M. Biewer, C.S. Chang, D.A. et al, "Overview of L-H power threshold studies, in NSTX," Nucl. Fusion 50, 064010 (2010)

G.Y. Park, C.S. Chang, I. Joseph, and R. Moyer, "Plasma transport in stochastic magnetic field caused by vacumm resonant magnetic perturbations at diverted tokamak edge," Physics of Plasmas, accepted for publication.

Seung-Hoon Park and C.S. Chang, "Numerical study of the plasma wall-bias effect on the ion flux through acceleration grid hole," Phys. Plasmas 17, 073505 (2010)

G. Dif-Pradalier* and P. H. Diamond, V. Grandgirard, Y. Sarazin, J. Abiteboul, X. Garbet, Ph. Ghendrih, and A. Strugarek, S. Ku and C. S. Chang, "On the validity of the local diffusive paradigm in turbulent plasma transport," PHYSICAL REVIEW E 82, 025401(R) (2010)

(Cover) L. E. Sugiyama and H. Staruss, "Magnetic X-point, Edge Localized Modes, and Magnetic Stochasticity," Phys. Plasmas 17, 062505 (2010)

Y. Chen and S. E. Parker, Phys. Plamas 16, 052305 (2009)

W. Wan, S. E. Parker, Y. Chen and F. W. Perkins, Phys. Plasmas. 17, 040701 (2010)

PI James Chelikowsky

I. Vasiliev, M. Lopez del Puerto, M. Jain, A. Lugo-Solis, J.R. Chelikowsky: Application of Time-Dependent Density Functional Theory to Molecules and Nanostructures, Theochem 914, 115 (2009).

T.-L. Chan and J.R. Chelikowsky: Controlling diffusion in semiconductor nanostructures by size and dimensionality, Nano Letters 10, 821 (2010).

J.-H. Eom, T.-L. Chan and J.R. Chelikowsky: The role of vacancies on B doping in Si nanocrystals, Solid State Commun. 150, 130 (2010).

M. Lopez del Puerto, M. Jain, and J.R. Chelikowsky: Time-dependent density functional theory calculation of the Stokes shift in hydrogenated silicon clusters,'' Phys. Rev. B 81, 035309 (2010).

L. V. Besteiro, L. Tortajada, M. L. Tiago, L.J. Gallego, J.R.Chelikowsky, and M.M.G. Alemany: Efficient n-type doping of zinc-blende III-V semiconductor quantum dots, Phys. Rev. B 81, 121307 (2010).

T.-L. Chan, H. Kwak, J.-H. Eom, S. Zhang, and J. R. Chelikowsky: A theory of self-purification in Si nanocrystals, Phys. Rev. 82, 115421 (2010)

K.H. Khoo, M. Kim, G. Schofield and J.R. Chelikowsky: Ab initio molecular dynamics simulations using a Chebyshev-filtered subspace iteration technique, Phys. Rev. B 82, 064201 (2010).

K.H. Khoo, A.T. Zayak, H. Kwak and J.R. Chelikowsky: First-principles study of confinement effects on the Rahman spectra of Si Nanocrystals, Phys. Rev. Lett. 105, 115504 (2010).

I. Vasliev and J.R. Chelikowsky: Real-space calculations of atomic and molecular polarizabilities using asymptotically correct exchange-correlation potentials, Phys. Rev. A 81, 012502 (2010).

T.-L. Chan, J. R. Chelikowsky and S. B. Zhang: Universality of formation energies in doping Si nanostructures, Phys. Rev. Lett. (submitted).

H. Kwak and J.R. Chelikowsky: Size-dependent Spin-polarization of Carbon-doped ZnO Nanocrystals, Applied Phys. Lett. 95, 263108 (2009).

M. Jain, J.R. Chelikowsky and S.G. Louie: Quasiparticle Excitations, Charge Transition Levels, and Optical Response of Oxygen Vacancies in Hafnia, Phys. Rev. Lett. (submitted).

M. Jain, J.R. Chelikowsky and S.G. Louie: Band gaps in bulk and reduced-dimensional systems: Variability and reliability of different hybrid functionals, Phys. Rev. Lett. (submitted).

J.K. Lee, N. Sai, and A.A. Demkov, Spin-polarized 2DEG through electrostatic doping in LaAlO3-EuO heterostructures, Phys. Rev. B (submitted).

G. Schofield, J.R. Chelikowsky and Y. Saad: Using Chebyshev-Filtered Subspace Iteration and Windowing Methods to Solve the Kohn-Sham Problem, Comp. Phys. Comm. (submitted).

PI Jackie Chen

J. H. Chen, "Petascale Direct Numerical Simulation of Turbulent Combustion - Fundamental Insights Towards Predictive Models," Proc. Combust. Inst. 33 (2011) 99-123.

PI Liu Chen

Properties of microturbulence in toroidal plasmas with reversed magnetic shear, Wenjun Deng and Zhihong Lin, Phys. Plasmas 16, 102503 (2009).

The importance of parallel nonlinearity in the self-interaction of geodesic acoustic mode, H. S. Zhang, Z. Qiu, L. Chen, and Z. Lin, Nuclear Fusion 49, 125009 (2009).

Electromagnetic formulation of global gyrokinetic particle simulation in toroidal geometry, I. Holod, W. L. Zhang, Y. Xiao, and Z. Lin, Phys. Plasmas 16, 122307 (2009).

Effects of electron dynamics in toroidal momentum transport driven by ion temperature gradient turbulence, I. Holod and Z. Lin, Plasma Phys. Contr. Fusion 52, 035002 (2010).

Fluctuation characteristics and transport properties of collisionless trapped electron mode turbulence, Yong Xiao, Ihor Holod, Wenlu Zhang, Scott Klasky, and Zhihong Lin, Phys. Plasmas 17, 022302 (2010).

Scalings of energetic particle transport by ion temperature gradient Microturbulence, Wenlu Zhang, Viktor Decyk, Ihor Holod, Yong Xiao, Zhihong Lin, and Liu Chen, Phys. Plasmas 17, 055902 (2010).

Trapped Electron Damping of Geodesic Acoustic Mode, Huasen Zhang and Zhihong Lin, Phys. Plasmas 17, 072502 (2010).

Gyrokinetic particle simulations of reversed shear Alfven eigenmode excited by antenna and fast ions, Wenjun Deng, Zhihong Lin, Ihor Holod, Xin Wang, Yong Xiao, and Wenlu Zhang, Phys. Plasmas, 2010 October issue, in press.

Gyrokinetic particle simulation of beta-induced Alfven eigenmode, H. S. Zhang, Z. Lin, I. Holod, X. Wang, Y. Xiao, W. L. Zhang, Phys. Plasmas, 2010 October issue, in press.

Gyrokinetic Simulation of Turbulence Driven Geodesic Acoustic Modes in Edge Plasmas of HL-2A Tokamak, Feng Liu, Z. Lin, J. Q. Dong, K. J. Zhao, Phys. Plasmas, 2010 October issue, in press.

PI Shentan Chen

Yang, J. Y.; Chen, S.; Dougherty, W. G.; Kassel, W. S.; Bullock, R. M.; DuBois, D. L.; Raugei, S.; Rousseau, R.; Dupuis, M.; Rakowski DuBois, M. Chem. Comm. 2010, 46, 8618.

Chen, S.; DuBois, D. L.; Raugei, S.; Rousseau, R.; Dupuis, M.; Bullock, R. M. J. Phys. Chem. A 2010, in press

Chen, S.; Raugei, S.; Rousseau, R.; Dupuis, M.; Bullock, R. M. "Homogeneous Ni Catalysts for H2 Oxidation and Production: An Assessment of Theoretical Methods, from Density Functional Theory to Post Hartree-Fock Correlated Wavefunction Theory." J. Phys. Chem. A, submitted.

Yang, J. Y.; Chen, S.; Dougherty, W. G.; Kassel, W. S.; Bullock, R. M.; Dubois, D. L.; Raugei, S.; Rousseau, R.; Dupuis, M.; Rakowski Dubois, M. "Hydrogen Oxidation Catalysis by a Nickel Diphosphine Complex with Pendant t-Butyl Amines." Chem. Coumm. submitted.

PI Yang Chen

W. Wan, S. E. Parker, Y. Chen and F. Perkins, "Natural fueling of a tokamak fusion reactor," Physics of Plasmas 17, 040701 (2010)

Y. Chen, S. E. Parker, J. Land and G. Fu, "High n stability of toroidal Alfven eigenmodes in a burning plasma," in press, Physics of Plasmas.

PI Hai-Ping Cheng

Sensitivity of the superconducting state and magnetic susceptibility to key aspects of electronic structure in ferropnictides, A.F. Kemper, T.A. Maier, H.-P. Cheng, P.J. Hirschfeld, D.J. Scalapino, New J. Phys. 12, 073030, (2010).

Modulation of pairing interaction in Bi2Sr2CaCu2O8+delta by an O dopant: A density functional theory study, K. Foyevtsova, H.C. Kandpal, H.O. Jeschke, S. Graser, H.-P. Cheng, R. Valenti, P.J. Hirschfeld, Phys. Rev. B82, 054514(2010).

First-principles study of Fe/MgO based magnetic tunnel junctions with Mg interlayers, Y. Wang, J. Zhang, X.G. Zhang, H.-P. Cheng. X.-F. Han, Phys. Rev. B82, 054405(2010).

Spin fluctuations and superconductivity in a three-dimensional tight-binding model for BaFe2As2, S. Grase, A.F. Kemper, T.A. Maier, H.-P. Cheng, P.J. Herschfeld, and D.J. Scalapino, Phys.Rev. B81, 214503 (2010).

Transition metal adatom and dimer adsorbed on graphene: Induced magnetization and electronic structures, C. Cao, M. Wu, JZ Jiang, and H.-P. Cheng, Phys. Reb. B81, 205424 (2010).

First-Principles Calculations of Fe-doped monolayer C60 on h-BN/Ni(111) SurfaceFe@C60, L. Li,  Y.-N. Wu, and H.-P. Cheng, J. Chem Phys. 132, 074702 (2010).

Manipulating I-V Characteristics of a Molecular Switch with Chemical Modifications, J. Palma, J.L. X.G. Zhang, J.L. Krause, and H.-P. Cheng, J. Phys. Chem. C114, 1655 (2010).

Surface Geometry of C-60 on Ag(111), H.I. Li, K. Pussi, K.J. Hanna, et al., Phys. Rev. Lett. 103, 056101(2009).

Chapter of Handbook of Nanophysics, "Supported Fullerenes" (Talyor and Francis Group, in press).

Working at interface, Hai-Ping Cheng (submitted to Molecular Physics)

Structure and stability of thin water films on quartz surfaces, Yun-Peng Chen and Hai-Ping Cheng
(submitted to APL).

PI Wai-Yim Ching

Antonio Siber, R. F. Rajter, R.H. French, W.Y. Ching, A. Parsegian and R. Podgornik, "Dispersion interactions between optically anisotropic cylinders at all separations: retardation effect for insulating and semiconducting single wall carbon nanotubes", Phys. Rev. B. 80, 165414/1-10 (2009).

Paul Rulis, A.R. Rupini, S.J. Pennycook, and W.Y. Ching, "Spectroscopic imaging of EELS using ab initio data and function field visualization", Ultromicroscopy, 109, 1472-1478 (2009).

Lei Liang, Paul Rulis, Bart Kahr, W.Y. Ching, "Theoretical study of the large linear dichroism of herapathite", Phys. Rev. B80, 235132-1-5 (2009).

Lei Liang, Paul Rulis and W.Y. Ching, "Mechanical properties, electronic structure and bonding of alpha- and beta- tri-calcium phosphates with surface characterization", Acta Biomaterialia, 6, 3763-3771 (2010). doi:10.1016.

R. H. French, V. A. Parsegian, Rudolf Podgornik, Rick Rajter, Anand Jagota, Jian Luo, Dilip Asthagiri, Manoj Chaudhury, Yet-Ming Chiang, Steve Granick, Mehran Kardar, Roland Kjellander, David Langreth, Jennifer Lewis, Steve Lustig, David Wesolowski, John Wettlaufer, Wai-Yim Ching, Mike Finnis, Frank Houlihan, O. Anatole von Lilienfeld, Carel Jan van Oss, Thomas Zemb, "Long Range Interactions In Nanoscale Science", Review of Modern Physics, 82:2, 1887-1944, (2010).

A. Siber, R. F. Rajter, R.H. French, W.Y. Ching, A. Parsegian and R. Podgornik, "Optically anisotropic infinite cylinder above an optically anisotropic half-space: Dispersion interaction of a single-walled carbon nanotube with a substrate", J. Vac Sci. Tech. B 28(3), C4A17-C4A24 (2010).

W.Y. Ching, Paul Rulis, Lizhi Ouyang, S. Aryal, and A. Misra, "Theoretical study of the elasticity, of the mechanical, behavior, electronic structure, interatomic bonding, and dielectric function of an intergranular glassy film model in prismatic beta-Si3N4", Phys. Rev. B 81, 214120-1-14. (2010).

A. Altay, C.B. Carter, P. Rulis, W.Y. Ching, I. Arslan and M.A. Gulgun, "Characterizing CA2 and CA6 using ELNES", J. Solid State Chemistry J. Solid State Chem, 183(8), 1776-1784 (2010).

R. F. Rajter, R.H. French, R. W.Y. Ching, Podgornik,and A. Parsegian, "Analyzing Chirality-dependent property trends in carbon nanotube systems Part1: Electronic structure and optical properties", (submitted to Phys. Rev. B).

R. F. Rajter, R.H. French, R. W.Y. Ching, Podgornik, and A. Parsegian, "Analyzing Chirality-dependent property trends in carbon nanotube systems Part2: Hamaker Coefficients and van der Waals London dispersion interactions". (submitted to Phys. Rev. B).

Yang Yang, W.Y. Ching, and A. Misra, "Higher-Order continuum theory applied to fracture simulation of nano-scale intergranular glassy film", J. of Nanomechanics and Micromechanics. (accepted)

Lei Liang, Paul Rulis, L. Ouyang, and W.Y. Ching, "Ab initio investigation of H- bonding and network structure in bulk water", submitted to Phys. Rev. B .

Paul Rulis and W.Y. Ching, ???Theoretical XANES spectra of Si-K, Si-L, N-K and O-K edges of a prismatic model of intergranular glassy films in beta-Si3N4", submitted to J. of materials Science.

Sitaram Aryal, Paul Rulis, Lizhi Ouyang, Liaoyuan Wang, and W.Y, Ching, "Ab initio calculations of the elastic, thermodynamic, electronic and spectroscopic properties of B6O crystals", submitted to Phys. Rev. B.

PI Mei-Yin Chou

S. Barraza-Lopez, M. Vanevic, M. Kindermann, and M. Y. Chou, "Effects of Metallic Contacts on Electron Transport through Graphene," Phys. Rev. Lett. 104, 076807/1-4 (2010).

J.-A. Yan and M. Y. Chou, "Oxidation Functional Groups on Graphene: Structural and Electronic Properties," Phys. Rev. B 82, 125403/1-10 (2010).

Feng Zhang, Yan Wang, and M. Y. Chou, "Theoretical Investigation of Intermediate Phases between Li2NH and LiNH2," Physical Review B 82, 094112 (2010).

Yan Wang, Feng Zhang, Roland Stumpf, and M. Y. Chou, "Catalytic Effect of Near-Surface Alloying on Hydrogen Interaction on the Aluminum Surface," submitted to Physical Review Letters.

Feng Zhang, Yan Wang, and M. Y. Chou, "Stability of the Hydrogen-storage Compound Li6Mg(NH)4 from First Principles," submitted to Physical Review B.

PI Alok Choudhary

Arifa Nisar, Wei-keng Liao and Alok Choudhary. Delegation-based I/O Software Architecture for High Performance Computing Systems. submitted to the IEEE Transactions on Parallel and Distributed Systems.

PI Daryl Chrzan

Shuo Chen, Elif Ertekin and D. C. Chrzan, Plasticity in Carbon Nanotubes: Cooperative Conservative Dislocation Motion, Physical Review B 81, 155417/1-8 (2010).

D. C. Chrzan, M. P. Sherburn, Yuranan Hanlumyuang, T. Li and J. W. Morris, Jr., Disocation Core Spreading in Elastically Anisotropic BCC Materials, submitted to Physical Review B.

PI Jhih-Wei Chu

Gross, A.G. and Chu, J.-W., "On the Molecular Origins of Biomass Recalcitrance: The Interaction Network and Solvation Structures of Cellulose Microfibrils", Journal of Physical Chemistry B, in press.

Brokaw, J.B. and Chu, J.-W., "On the Molecular Origins of Biomass Recalcitrance: The Interaction Network and Solvation Structures of Cellulose Microfibrils", Biophysical Journal, in press.

PI Catherine Chuang

Chuang, C. C., J. S. Boyle, S. Xie, and J. T. Kelly, 2010, Sensitivity of Aerosol Indirect Effects to Cloud Nucleation and Autoconversion Parameterizations in Short-Range Weather Forecasts over the Southern Great Plains During May 2003 Intensive Operations Period, submitted to JGR.

Chin, H-N S., P.M. Caldwell, and D.C. Bader, 2010, Preliminary Study of California Wintertime Model Wet Bias, Mon. Wea. Rev., accepted.

PI Bruce Cohen

B. I. Cohen, A. J. Kemp, and L. Divol, "Hybrid Simulation of Laser-Plasma Interactions in Inhomogeneous Plasmas," J. Computational Physics 229, 4591, (2010). (LLNL-JRNL-413523)

D. J. Strozzi, D. P. Grote, M. Tabak, B. I. Cohen, R. P. J. Town, A. J. Kemp, "Fast Ignition transport simulations for NIF," submitted to IFSA 2009 International Conference Proceedings, Journal of Physics, 2009.

B. I. Cohen, A. M. Dimits, A. Friedman, and R. E. Caflisch, "Time-step Considerations in Particle Simulation Algorithms for Coulomb Collisions in Plasmas," accepted for publication in IEEE Transactions on Plasma Science and Numerical Simulation of Plasmas, to appear Sept. 2010 (LLNL-JRNL-419386).

A. J. Kemp, B. I. Cohen, and L. Divol, "Integrated Kinetic Simulation of Laser-Plasma Interactions, Fast-Electron Generation and Transport in Fast Ignition," Phys. Plasmas 17, 056702 (2010)

R.E. Waltz, "Nonlinear Subcritical MHD Beta Limit," Phys. Plasmas 17, 072501 (2010).

R.E. Waltz, A. Casati, and G. Staebler, "Gyrokinetic Simulation Tests of Quasilinear and Tracer Transport," Phys. Plasmas 16, 072303 (2009).

E.A. Belli and J. Candy, "An Eulerian Method for Solution of the Multispecies Drift-Kinetic Equation," Plasmas Phys. Control. Fusion 51, 075018 (2009).

J. Candy, C. Holland, R. E. Waltz, M. R. Fahey, and E. Belli, "Tokamak profile prediction using direct gyrokinetic and neoclassical simulation" . Phys Plasmas 16, 060704 2009

A. Casati, T. Gerbaud, P. Hennequin, C, Bourrdelle, J. Candy, F. Garbet, V. Grandgirard, O. D. Gurcan, S, Heurausx, G. T. Hoang, C. Honore, F, Imbeaux, R. Sabot, Y, Sarazin, L. vermare, and R.E. Waltz, "Turbulence in TORE SUPRA Tokamak: Measurement and Validation of Nonlinear Simulations", Phys. Rev. Lett. 102, 165005 (2009)

C. Angioni, A.G. Peeters, G.V. Pereverzev, A. Bottino, J. Candy, R. Dux, E. Fable, T.Hein, and R.E. Waltz, "Gyrokinetic simulations of impurites, He ash and alpha particle transport and consequences for ITER", Nucl. Fusion 49 (2009) 055013

C. Angioni, J. Candy, E. Fable. m. Maslov, A.G. Peeters. R.E. Waltz and H. Weissn, "Particle pinch and collisionality in gyrokinetic simulations of tokamak plasma turbulence", Phys. Plasmas 16, 060702 (2009)

L. Lin, M. Porkolab, E.M. Edlund, J.C. Rost, C.L. Fiore, M. Greenwald, Y. Lin, D. R. Mikkelssen, N. Tsuji, and S. J. Wukitch, "Studies of turbulence and transport in Alcator C-Mod H-mode plasma with phase contrast imaging and Comparisons with GYRO", Phys. Plasmas 16, 012502 (2009)

L. Lin, M. Porkolab, E.M. Edlund, J.C. Rost, M. Greenwald, N. Tsuji, J. Candy, R.E. Waltz, and D. Mikkelssen, "Studies of turbulence and transport in Alcator C-Mod Ohmic plasmas with phase contrast imaging and carparsons with GYRO", PPCF 51, 065006 (2009)

E. M. Bass and R. E. Waltz, "Gyrokinetic simulations of mesoscale energetic particle driven Alfvenic turbulent transport embedded in microturbulence". submitted to Phys Plasmas 2010

PI Marvin Cohen

J.D. Sau, S.R. Leslie, D.M. Stamper-Kurn, and M.L. Cohen, "Theory of domain formation in inhomogeneous ferromagnetic dipolar condensates within the truncated Wigner approximation," Phys. Rev. A 80, 023622 (2009).

H. Lee, J. Ihm, M.L. Cohen, and S.G. Louie, "Calcium-decorated Carbon Nanotubes for High Capacity Hydrogen Storage," Phys. Rev. B 80, 115412 (2009).

L. Yang, J. Deslippe, C.-H. Park, M.L. Cohen, and S.G. Louie, "Excitonic Effects on the Optical Response of Graphene and Bilayer Graphene," Physical Review Lett. 103, 186802 (2009).

C. Tao, J. Sun, X. Zhang, R. Yamachika, D. Wegner, Y. Bahri, G. Samsonidze, M.L. Cohen, S.G. Louie, T.D. Tilley, R.A. Segalman, and M.F. Crommie, "Spatial Resolution of a Type II Heterojunction in a Single Bipolar Molecule," Nano Lett. 9, 3963 (2009).

C.-H. Park, F. Giustino, C.D. Spataru, M.L. Cohen, and S.G. Louie, "Angle-resolved Photoemission Spectra of Graphene from First-principles", Nano Lett. 9, 4234 (2009).

J. L. Janssen, M. Cote, S.G. Louie, and M.L. Cohen, "Electron-Phonon Coupling In C60 Using Hybrid Functionals," Phys. Rev. B 81, 073106 (2010).

J. Noffsinger and M. L. Cohen, "Electronic and structural properties of ununquadium from first principles," Phys. Rev. B 81, 073110 (2010).

F. Giustino, M.L. Cohen, and S.G. Louie, "GW Method with the Self-Consistent Sternheimer Equation," Phys. Rev. B 81, 115105 (2010).

B.D. Malone, S.G. Louie, and M.L. Cohen, "Electronic and Optical Properties of Body-Centered Tetragonal Si and Ge," Phys. Rev. B 81, 115201 (2010).

H.K. Lee, J. Ihm, M.L. Cohen, and S.G. Louie, "Calcium-Decorated Graphene-Based Nanostructures for High-Capacity Hydrogen Storage," Nano Lett. 10, 793 (2010).

Noffsinger and M.L. Cohen, "First-principles calculation of the electron-phonon coupling in ultrathin Pb superconductors: Suppression of the transition temperature by surface phonons," Phys. Rev. B 81, 214519 (2010).

J.D. Sau, S.R. Leslie, M.L. Cohen, and D.M. Stamper-Kurn, "Spin squeezing of high-spin, spatially extended quantum fields," New J. of Physics 12, 085011 (2010).

G.-S. Do, J. Kim, S.-H. Jhi, C.-H. Park, S.G. Louie, and M.L. Cohen, "Ab initio calculations of pressure-induced structural phase transitions of GeTe," Phys. Rev. B 82, 054121 (2010).

O.V. Yazyev and S.G. Louie, Topological Defects in Graphene: Dislocations and Grain Boundaries," Phys. Rev. B 81, 195420 (2010).

[O. V. Yazyev and S. G. Louie, "Electronic transport in polycrystalline graphene", Nature Materials, advance online publication (2010)

 L.Z. Tan, C.-H. Park, and S.G. Louie, "Graphene Dirac Fermions in One-dimensional Inhomogeneous Field Profiles: Transforming Magnetic to Electric Field," Phys. Rev. B 81, 195426 (2010).

T. Bazhirov, J. Noffsinger, and M. L. Cohen "Superconductivity and electron-phonon coupling in lithium at high pressures", Submitted to PRB (August 2010).

V. W. Brar, R. Decker, H.-M. Solowan, Y. Wang, L. Maserati, K. Chan, H. Lee, C. Girit, A. Zettl, S. G. Louie, M. L. Cohen, and M. F. Crommie, Nature Physics (accepted).

PI Phil Collela

P. McCorquodale and P. Colella, "A high-order finite-volume method for hyperbolic conservation laws on locally-refined grids" , submitted to CAMCoS.

R.K. Crockett, P. Colella, and D.T. Graves, "A Cartesian grid embedded boundary method for solving the Poisson and heat equations with discontinuous coefficients in three dimensions" Submitted to Journal of Computational Physics .

R.H. Cohen, J. Compton, M. Dorr, J. Hittinger, W.M Nevins, T.D. Rognlien, Z.Q. Xu, P. Colella, and D. Martin, "Testing and Plans for the COGENT edge kinetic code" , (abstract) submitted to Sherwood 2010.

P. Colella, M.R. Dorr, J.A.F. Hittinger, and D.F. Martin "High-Order Finite-Volume Methods in Mapped Coordinates" Submitted to Journal of Computational Physics .

B. Kallemov, G. H. Miller and D. Trebotich "Numerical Simulation of Polymer Flow in Microfluidic Devices" 2009 Proceedings of the Fourth SIAM Conference on Mathematics for Industry (MI09) pp. 93-98 (2010).

E. Ateljevich, P. Colella, D.T. Graves, T.J. Ligocki, J. Percelay, P.O. Schwartz, Q. Shu "CFD Modeling in the San Francisco Bay and Delta" 2009 Proceedings of the Fourth SIAM Conference on Mathematics for Industry (MI09), pp. 99-107 (2010).

Caroline Gatti-Bono, Phillip Colella and David Trebotich "A Second-Order Accurate Conservative Front-Tracking Method in One Dimension", SIAM J. Sci. Comput., 31(6):4795-4813 (2010)

Schwartz, P., and Colella P., "A Second-Order Accurate Method for Solving the Signed Distance Function Equation", Communications in Applied Mathematics and Computational Science, Vol. 5 (2010), No. 1, 81-97.

Prateek Sharma, Phillip Colella, and Daniel F. Martin "Numerical Implementation of Streaming Down the Gradient: Application to Fluid Modeling of Cosmic Rays" to appear in SIAM Journal on Scientific Computing .

PI William Collins

Dukowicz, J. K., S.F. Price, and W. H. Lipscomb, 2010a. Consistent approximations and boundary conditions for ice-sheet dynamics from a principle of least action. J. Glaciol., 56(197), 480-496.

Dukowicz, J. K., S.F. Price, and W. H. Lipscomb, 2010b. Incorporating arbitrary basal topography in variational formulation of ice sheet models. J. Glaciol. (submitted).

Elliott, S.M., Reagan, M.T., Moridis, G.J., Cameron-Smith, P.J., Geochemistry of Clathrate-Derived Methane in Arctic Ocean Waters, LBNL-3389E, Geophys. Res. Lett., 37, L12607, doi:10.1029/2010GL043369, 2010.

Elliott, S.M., Maltrud, M., Reagan, M.T., Moridis, G.J., Cameron-Smith, P.J., Marine Methane Cycle Simulations for the Period
of Early Global Warming, J. Geophysical Res. Biogeo., in revision, 2010.

Leung, L.R., M. Huang, Y. Qian, and X. Liang. 2010. Climate-Soil-Vegetation Control on Groundwater Table
Dynamics and its Feedbacks in a Climate Model.Clim. Dyn., DOI 10.1007/s00382-010-0746-x.

Reagan, M.T. and Moridis, G.J., Large-Scale Simulation of Oceanic Gas Hydrate Dissociation in Response to Climate Change, LBNL-2908E, Geophys. Res. Lett., 36, L23612, doi:10.1029/2009GL041332, 2009.

Zhao, C., X. Liu, L.R. Leung, B. Johnson, S. McFarlane, W.I. Gustafson, J.D. Fast, and R. Easter. 2010. The Spatial
Distribution of Dust and its Shortwave Radiative Forcing Over North Africa: Modeling Sensitivities to Dust Emissions and Aerosol Size Treatments. Atmos. Chem. and Phys., revised.

Chang, C.-Y., J. Chiang, M.F. Wehner (2010), Sulfate aerosol control of Tropical Atlantic climate over the 20th century, submitted to Journal of Climate.

Easterling, D. R., and M. F. Wehner (2009), Is the climate warming or cooling?, Geophys. Res. Lett., 36, L08706, doi:10.1029/2009GL037810.

Santer, B.D., K.E. Taylor, P.J. Gleckler, C. Bon???ls, T.P. Barnett, D.W. Pierce, T.M.L. Wigley, C. Mears, F.J. Wentz, W. Brueggemann, N.P. Gillett, S.A. Klein, S. Solomon, P.A. Stott, and M.F. Wehner (2009) Incorporating Model Quality Information in Climate Change Detection and Attribution Studies. Proceeding of the National Academy of Sciences. doi:10.1073/pnas.0901736106.

Wehner, M., T.R. Karl, J.M. Melillo, and T. C. Peterson, eds. (2009), Global Climate Change Impacts in the United States, Cambridge University Press.

Wehner, M.F., G. Bala, P. Duffy, A. Mirin, R. Romano (2010): Towards direct simulation of future tropical cyclone statistics in a high-resolution global atmospheric model. In press, Adv. in Meteorology.

Wehner, M.F., David R. Easterling, Jay H. Lawrimore, Richard R. Heim Jr., Russell S. Vose, Benjamin Santer (2010) Projections of Future Drought in the Continental United States and Mexico. Submitted to Journal of Hydrometeorology.

Wehner, M.F. (2010) Sources of uncertainty in the extreme value statistics of climate data. Extremes 13, 205-217,
doi:10.1007/s10687-010-0105-7.

Wehner, M.F., R. Smith, P. Duffy, G. Bala, (2010) The effect of horizontal resolution on simulation of very extreme US precipitation events in a global atmosphere model. Climate Dynamics 32, 241-247, doi:10.1007/s00382-009-0656-y.

PI Gil Compo

Baird, M.E., J.D. Everett, and I.M. Suthers, 2010: Analysis of southeast Australian zooplankton observations of 198-1942 using synoptic oceanographic conditions. Deep Sea Res. II, in press.

Bronnimann, S., A. Stickler, T. Griesser, A. M. Fischer, A. Grant, T. Ewen, T. Zhou, M. Schraner, E. Rozanov, and T. Peter, 2009: Variability of large-scale atmospheric circulation indices for the Northern Hemisphere during the past 100 years. Meteorol. Z., 18, 365-368, doi: 10.1127/0941-2948/2009/0392.

Compo, G.P., J.S. Whitaker, P.D. Sardeshmukh, N. Matsui, R.J. Allan, X. Yin,B.E. Gleason, R.S. Vose, G. Rutledge, P. Bessemoulin, S. Bronnimann, M. Brunet, R.I. Crouthamel, A.N. Grant, P.Y. Groisman, P.D. Jones, M.C. Kruk, A.C. Kruger, G.J. Marshall, M. Maugeri, H.Y. Mok, O. Nordli, T.F. Ross, R.M. Trigo, X.L. Wang, S.D. Woodruff, S.J. Worley, 2010: The Twentieth Century Reanalysis Project. Quart. J. Roy. Meteor. Soc., submitted at the editor's invitation.

Cook, B.I, R. Seager, and R.L. Miller, 2010: Atmospheric circulation anomalies during two persistent north american droughts: 1932-1939 and 1948-1957. Clim. Dyn., in press, doi: 10.1007/s00382-010-0807-1

Emanuel, K., 2010: Tropical Cyclone Activity Downscaled from NOAA-CIRES Reanalysis, 1908-1958. J. Adv. Model. Earth Syst., Vol. 2, Art. #1, 12 pp., doi:10.3894/JAMES.2010.2.1

Giese B.S., G.P. Compo, N.C. Slowey, P.D. Sardeshmukh, J.A. Carton, S. Ray, and J.S. Whitaker, 2010:The 1918/1919 El Ni??o. Bull. Amer. Meteor. Soc., 91, 177-183, doi: 10.1175/2009BAMS2903.

Whitaker, J.S., G.P. Compo, and J.-N. Thepaut, 2009: A comparison of variational and ensemble-based data assimilation systems for reanalysis of sparse observations. Mon. Wea. Rev., 137, 1991-1999.

Wood, K. R., and J.E. Overland, 2009: Early 20th century Arctic warming in retrospect, Int. J. of Climatol., 30, 1269-1279, doi: 10.1002/joc.1973.

PI Valentino Cooper

F. W. Averill, J. R. Morris and V. R. Cooper, "Calculated properties of hydrogenated single layers of BN, BC2N and graphene: Graphane and its BN-containing analogues," Phys. Rev. B 80, 195411 (2009).

V. R. Cooper "Van der Waals density functional: an appropriate exchange functional" Phys. Rev. B 81, 161104(R) (2010)

V. R. Cooper, L. Kong and D. C. Langreth "Computing dispersion interactions in density functional theory" Physics Procedia 3, 1417 (2010)

L. J. Peng and J. R. Morris, "Efficient calculations of hydrogen physisorption in expanded graphite and in amorphous carbon," J. Phys. Chem. C 114, 15522 (2010).

L. J. Peng and J. R. Morris, "Hydrogen adsorption calculations in expanded graphite and amorphous carbons," in Hydrogen Storage Materials, edited by E. Akiba, W. Tumas, P. Chen, M. Fichtner, S. Zhang (Mater. Res. Soc. Symp. Proc. Volume 1216E, Warrendale, PA, 2010), 1216-W01-08.

J. R. Morris, F. W. Averill, H. Han, B. C. Pan, V. R. Cooper and L.J. Peng, "Lattice strain effects in graphane and partially-hydrogenated graphene sheets," in Hydrogen Storage Materials, edited by E. Akiba, W. Tumas, P. Chen, M. Fichtner, S. Zhang (Mater. Res. Soc. Symp. Proc. Volume 1216E, Warrendale, PA, 2010), 1216-W03-10.

PI Silvia Crivelli

N. Max, C. Hu, O. Kreylos & S. Crivelli. BuildBeta - A system for automatically constructing beta-sheets.  Proteins. 2010 Feb 15;78(3):559-74.

PI Peter Cummings

P.S. Redmill, and C. McCabe, Molecular Dynamics Study of the Behavior of Selected Nanoscale Building Blocks in a Gel-Phase Lipid Bilayer. J. Phys. Chem. B.,114(28), 9165-9172 (2010).

P. T. Cummings, H. Docherty, C. R. Iacovella and J. K. Singh, "Phase Transitions in Nanoconfined Fluids: The Evidence from Simulation and Theory." Aiche Journal 56(4): 842-848 (2010).

H. Docherty and P. T. Cummings, "Direct evidence for fluid-solid transition of nanoconfined fluids," Soft Matter 6(8): 1640-1643 (2010).

Y. S. Leng, Y. J. Lei and P. T. Cummings, "Comparative studies on the structure and diffusion dynamics of aqueous and nonpolar liquid films under nanometers confinement," Modelling and Simulation in Materials Science and Engineering 18(3): Art. No. 034007 (2010).

Q. Pu, Y. S. Leng, X. C. Zhao and P. T. Cummings, "Molecular Simulation Studies on the Elongation of Gold Nanowires in Benzenedithiol" Journal of Physical Chemistry C 114(23) 10365-10372 (2010).

K. R. Hadley and C. McCabe, ???A Coarse-Grained Model for Amorphous and Crystalline Fatty Acids,??? Journal of Chemical Physics, 132, 134505 (2010).

K. R. Hadley and C. McCabe, ???A Structurally Relevant Coarse-Grained Model for Cholesterol,??? Biophysical Journal, in press (2010).

P. Fenter, S. S. Lee, A. A. Skelton, P. T. Cummings, "Direct and Quantitative Comparison of Simulated Density Profiles with High Resolution X-ray Reflectivity Data," J. Synchrotron Radiation, accepted for publication.

C.R. Iacovella, W.R French, P.T. Cummings, " The formation of polyhedral structures in elongated gold nanowires, " ACS Nano, submitted (2010)

A. A. Skelton, J. D. Kubicki, P. Fenter, D. J. Wesolowski, and P. T. Cummings, "Simulations of the Quartz/Water Interface: A Comparison of Classical Force Fields, Ab initio Molecular Dynamics and X-ray Reflectivity Experiments, " J. Phys. Chem. C, submitted (2010).

G. T. Beckham, Y. J. Bomble, J. F. Matthews, M. G. Resch, J. S. Yarbrough, S. R. Decker, L. Bu1, C. B. Taylor, X. C. Zhao, C. McCabe, J. Wohlert, M. Bergenstr??hle, J. W. Brady, W. S. Adney, M. E. Himmel, M. F. Crowley, ???The linker peptide from the Trichoderma reesei Family 7 cellulase is a flexible, disordered tether between the catalytic domain and carbohydrate-binding module further extended by O-linked glycosylation,??? Biophysical Journal, submitted (2010).

J. L. Rivera, G. K. Jennings and C. McCabe, "Frictional Forces in Mixed Hydrophobic ??? Hydrophilic Alkoxysilane Monolayers on Silica," Langmuir, submitted (2010).

Matthew Neurock, "Engineering Molecular Transformations," Industrial and Engineering Chemistry Research, 2010 accepted.


D

PI Valerie Daggett

Van der Kamp M.W., Schaeffer R.D., Jonsson A.L., Scouras A.D., Simms A.M., Toofanny R.D., Benson N.C., Anderson P.C., Merkley E.D., Rysavy S., Bromley D., Beck D.A.C., and Daggett V. Dynameomics: A Comprehensive Database of Protein Dynamics. Structure 18:423-435, 2010. (Journal cover)

McCully M.E., Beck D.A.C., Fersht A.R., and Daggett V. Refolding the Engrailed Homeodomain: Structural Basis for the Accumulation of a Folding Intermediate. Biophysical Journal 99:1628-1636, 2010.

Toofanny R.D., Jonsson A.L., and Daggett V. A Comprehensive Multidimensional-Embedded, One-Dimensional Reaction Coordinate for Protein Unfolding/Folding. Biophysical Journal 98:2671-2681, 2010.

Rutherford K. and Daggett V. Polymorphisms and disease: hotspots of inactivation in methyltransferases. Trends in Biochemical Sciences, In Press, 2010.

Law P.B. and Daggett V. The relationship between water bridges and the polyproline II conformation: a large-scale analysis of molecular dynamics simulations and crystal structures. Protein Engineering Design & Selection 23: 27-33, 2010.

Jonsson A.L., Scott K.A., and Daggett V. Dynameomics: A consensus view of the protein unfolding/folding transition state ensemble across a diverse set of protein folds. Biophysical Journal 97: 2958-2966, 2009.

Key J., Scheuermann T.H., Anderson P.C., Daggett V., and Gardner K.H. Principles of Ligand Binding within a Completely Buried Cavity in HIF2?? PAS-B. Journal of the American Chemical Society 131: 17647-17654, 2009.

Scouras A.D., and Daggett, V.. The dynameomics rotamer library: amino acid side chainconformations and dynamics from molecular dynamics simulations in water. Submitted, 2010.

Schaeffer R.D., Jonsson A.L., Simms A.M., Daggett V. Generation of a Consensus Protein Domain Dictionary, submitted, 2010.

Benson N.C., Daggett V. Wavelet analysis of protein motions. Submitted, 2010.

PI Niels Damrauer

Vallet, P. J.; Damrauer, N. H. "Computational Exploration of Heterolytic Halogen-Carbon Bond Scission Photoreactions in Ruthenium Polypyridyl Complexes" (2010), Submitted to The Journal of Physical Chemistry A.

PI Ronald Davidson

E. V. Belova, R. C. Davidson, C. Myers, Two-Fluid Mechanism of Plasma Rotation in Field-Reversed Configuration, Proceedings of the 23th Int. Conf. Daejeong, Korea, 2010, paper IAEA-IC/P4-3 (International Atomic Energy Agency, Vienna, 2010).

C. Myers, E. V. Belova, M. R. Brown, T. Grey, C. D. Cothran, M. Schaffer, Three-dimensional MHD simulations of counter-helicity spheromak merging in the Swarthmore Spheromak Experiment, submitted to Physics of Plasmas (2010).

"Advanced Numerical Modeling of Collective final focus for Intense Ion Beams", M. Dorf, I. D. Kaganovich, E. A. Startsev and R. C. Davidson, Poceedings of the 2010 International Accelerator Conference , in press (2010).

"Centroid and Envelope Dynamics of High-Intensity Charged Particle Beams in an External Focusing Lattice and Oscillating Wobbler", H. Qin, R. C. Davidson and B. G. Logan, Physical Review Letters 104, 254801 (2010).

"Whistler Wave Excitation and Effects of Self-Focusing on Ion Beam Propagation Through a Background Plasma along a Solenoidal Magnetic Field", M. A. Dorf, I. D. Kaganovich, E. A. Startsev and R. C. Davidson, Physics of Plasmas 17, 023103 (2010).

"New Spectral Method for Halo Particle Definition in Intense Mismatched beams" M. A. Dorf, R. C. Davidson and E. A. Startsev, submitted for publication (2010).

"Experimental Program for the Princeton Ion Source Test Facility", L. R. Grisham, E. P. Gilson, I. Kaganovich and A. Stepanov, submitted for publication (2010).

"Model Describing Thin Foil Transformation into Liquid Droplets", E. A. Startsev, I. D. Kaganovich and R. C. Davidson, submitted for publication (2010).

"Stability Properties of the Electron Return-Current for Intense Ion Beam Propagation Through Background Plasma", E. A. Startsev, R. C. Davidson and V. N. Khudik, submitted for publication (2010).

"Plasma Source Development for the NDCX-I and NDCX-II Neutralized Drift Compression Experiments", E. P. Gilson, R. C. Davidson, P. C. Efthimion and I. D. Kaganovich, submitted for publication (2010).

"Centroid and Envelope Dynamics of High-Intensity Charged Particle Beams in an External Focusing Lattice and Oscillating Wobbler for Heavy Ion Fusion", H. Qin, R. C. Davidson and B. G. Logan, submitted for publication (2010).

"Approximate Matched Kinetic Quasi-Equilibrium Solutions for an Intense Charged Particle Beam Propagating Through a Periodic Focusing Quadrupole Lattice", E. A. Startsev, R. C. Davidson and M. Dorf, Physical Review Special Topic on Accelerators and Beams, in press (2010).

"Twiss Parameters and Beam Matrix Formulation of Generalized Courant-Snyder Theory for Coupled Transverse Dynamics and their Application to Helical Transport Channels", M. Chung, H. Qin, and R. C. Davidson, Physics of Plasmas 17, 084502 (2010).

"Physics of Neutralization of Intense Charged Particle Beam Pulses by a Background Plasma", I. D. Kaganovich, R. C. Davidson, M. A. Dorf, E. A. Startsev, A. B Sefkow, A. F. Friedman and E. P. Lee, Physics of Plasmas 17, 056703 (2010).

"Beam Dynamics of the Neutralized Drift Compression Experiment-II ??? a Novel Pulse-Compressing Ion Accelerator", A. Friedman, J. J. Barnard, R. H. Cohen, D. P. Grote, S. M. Lund, W. M. sharp, A Faltens, E. Henestroza, J. Y. Jung, J. W. Kwan, E. P. Lee, M. A. Leitner, B. G. Logan, J.-L. Vay, W. L Waldron, R. C. Davidson, M. Dorf, E. P. Gilson and I. D. Kaganovich, Physics of Plasmas 17, 056704 (2010).

"Studies of Emittance Growth and Halo Particle Production in Intense Charged Particle Beams Using the Paul Trap Simulator Experiment", E. P. Gilson, R. C. Davidson, M. A. Dorf, P.C. Efthimion, R. Majeski, M. Chung, M. S. Gutierrez and A. N. Kabcanell, Physics of Plasmas 17, 056707 (2010).

PI Wibe De Jong

Groenewold GS, WA De Jong, J Oomens, and MJ Van Stipdonk. 2010. "Variable Denticity in Carboxylate Binding to the Uranyl Coordination Complexes." Journal of the American Society for Mass Spectrometry 21(5):719-727.

De Jong WA, EJ Bylaska, N Govind, CL Janssen, K Kowalski, T Muller, I Nielsen, HJJ van Dam, VV Veryazov, and R Lindh. 2010. "Utilizing High Performance Computing for Chemistry: Parallel Computational Chemistry." Physical Chemistry Chemical Physics. PCCP 12(26):6896-6920. (Journal Cover)

Kowalski K, S Krishnamoorthy, O Villa, JR Hammond, and N Govind. 2010. "Active-space completely-renormalized equation-of-motion coupled-cluster formalism: Excited-state studies of green fluorescent protein, free-base porphyrin, and oligoporphyrin dimer ." Journal of Chemical Physics 132(15):Article Number: 154103

Valiev M, EJ Bylaska, N Govind, K Kowalski, TP Straatsma, HJJ van Dam, D Wang, J Nieplocha, E Apra, TL Windus, and WA De Jong. 2010. "NWChem: a Comprehensive and Scalable Open-Source Solution for Large Scale Molecular Simulations." Computer Physics Communications 181(9):1477-1489

PI Lutgard De Jonghe

N. Adelstein, H. L. Ray, B. S. Mun, P. N. Ross, J. B. Neaton and L. C. De Jonghe, Phys Rev B (August 2010 submitted).

PI Viktor Decyk

R. Sanchez, D.E. Newman, J.-N. Leboeuf, B.A. Carreras, and V.K. Decyk, "On the nature of radial transport across radially-sheared poloidal zonal flows in electrostatic ion-temperature-gradient gyrokinetictokamak plasma turbulence", Phys. Plasmas 16, 055905 (2009).

V. I. Sotnikov, V. V. Ivanov, R. Presura, E. Yassin, J. Kindel, J. N. Leboeuf, O. G. Onishchenko, B. V. Oliver, B. Jones, T. A. Mehlhorn, and C. Deeney, "Investigation of flute instability in appplication to laboratory astrophysics and z-pinch experiments", Astrophysics and Space Science, Volume 322, Numbers 1-4, p. 209-213, August 2009.
http://www.springerlink.com/content/gn42147054308397/fulltext.pdf

P.-A. Gourdain, and J.-N. Leboeuf, "Hollow Current Profile Scenarios for Advanced Tokamak Operations", Physics of Plasmas 16, 112506 (2009).

V. I. Sotnikov, J. N. Leboeuf, and S. Mudaliar, "Scattering of Electromagnetic Waves in the Presence of Wave Turbulence Excited by a Flow with Velocity Shear", Plasma Science, IEEE Transactions on: Special issue on Numerical Simulation of Plasmas, Volume: PP , Issue: 99, Page(s): 1 - 11 (2010).

D. Schriver, M. Ashour-Abdalla, F. V. Coroniti, J. N. LeBoeuf, V. Decyk, P. Travnicek, O. Santolik, D. Winningham, J. Pickett, and M. L. Goldstein, "The Generation of Whistler Mode Emissions in the Inner Magnetosphere: An Event Study", J. Geophys. Res., 115, A00F17, August 2010.

PI William Detmold

Bottom hadrons from lattice QCD with domain wall and NRQCD fermions. Stefan Meinel, William Detmold,C.-J.David Lin, Matthew Wingate, Talk given at 27th International Symposium on Lattice Field Theory (Lattice 2009), Beijing, China, 25-31
Jul 2009. Published in PoS LAT2009:105,2009.

Bottomonium spectrum at order $v^6$ from domain-wall lattice QCD: Precise results for hyperfine splittings. Stefan Meinel,
e-Print: arXiv:1007.3966 [hep-lat], submitted to Phys. Rev. D.

Prediction of the Omega_bbb mass from lattice QCD. Stefan Meinel, e-Print: arXiv:1008.3154 [hep-lat], submitted to Phys. Rev. D.

PI Ram Devanathan

R. Devanathan and W. J. Weber, "Simulation of collision cascades and thermal spikes in ceramics," Nuclear Instruments and Methods in Physics Research B 268 (2010) 2857-2862.

J. Yu, R. Devanathan and W. J. Weber, "First principles study of defects and phase transition in UO2," Journal of Physics: Condensed Matter 21 (2009) 435401.

R. Devanathan, "Radiation damage evolution in ceramics," Nuclear Instrumnts and Methods in Physics Research B 267 (2009) 3017-3021.

R. Devanathan, J. Yu and W. J. Weber, "Energetic recoils in UO2 simulated using five different potentials", Journal of Chemical Physics 130 (2009) 174502.

J. Yu, R. Devanathan and W. J. Weber, "Unified interatomic potential for zircon, zirconia and silica systems", Journal of Materials Chemistry 19 (2009) 3923-3930.

PI Thomas Devereaux

C-C. Chen, B. Moritz, F. Vernay, J. N. Hancock, S. Johnston, C. J. Jia, G. Chabot-Couture, M. Greven, I. Elfimov, G. A. Sawatzky, and T. P. Devereaux, "Unraveling the nature of charge excitations in La2CuO4 with momentum-resolved Cu K-edge resonant inelastic X-ray scattering," arXiv:1002.4683v1 [cond-mat.str-el] (Accepted in Phys. Rev. Lett.)

C.-C. Chen, J. Maciejko, A. P. Sorini, B. Moritz, R. R. P. Singh, and T. P. Devereaux, "Orbital order and spontaneous orthorhombicity in iron pnictides," Phys. Rev. B 82, 100504(R) (2010) (Editors' Suggestion)

C.-C. Chen, B. Moritz, C. J. Jia, S. Johnston, A. P. Sorini, L.-Q. Lee, K. Ko, T. P. Devereaux, "Numerical studies of photon-based spectroscopies on high-Tc superconductors," Comp. Phys. Comm. (2010) DOI:10.1016/j.cpc.2010.08.017 (Available online: 26 August 2010)

B. Moritz, S. Johnston, and T. P. Devereaux, "Insights on the cuprate high energy anomaly observed in ARPES," J. Electron Spec. Rel. Phenom. 181, 31-34 (2010)

S. Johnston, W. S. Lee, Y. Chen, E. A. Nowadnick, B. Moritz, Z.-X. Shen, and T. P. Devereaux, "Material and doping dependence of the nodal and anti-nodal dispersion renormalizations in single and multi-layer cuprates," Adv. Cond. Matter Phys. 2010, 968304 (2010) (Review Article)

C.-C. Chen, B. Moritz, J. van den Brink, T. P. Devereaux, and R. R. P. Singh, "Finite-temperature spin dynamics and phase transitions in spin-orbital models," Phys. Rev. B 80, 180418(R) (2009)

S. Wang, W. L. Mao, A. P. Sorini, C.-C. Chen, T. P. Devereaux, Y. Ding, Y. Xiao, P. Chow, N. Hiraoka, H. Ishii, Y. Q. Cai, C.-C. Kao, "High pressure evolution of Fe2O3 electronic structure revealed by X-ray absorption," arXiv:1006.2612v1 [cond-mat.str-el] (Submitted to PRB)

PI Pat Diamond

Malkov, M.A. and P.H. Diamond, "Wave Dynamics and Particle Acceleration in Shock Precursors", in American Institute of Physics Conference Series, X., Ao & G.Z.R. Burrows, Ed., 183(1), 66, 2009 (8pp)

Tynan, G.R., P.H. Diamond, C. Holland, S.H. Muller, M. Xu, Z. Yan and J. Yu, "Nonlinear Dynamics of Shear Flows and Plasma Rotation in a Simple Laboratory Plasma System", Plasma Phys. Control. Fusion 51(12), 124055, 2009 (6pp).

McDevitt, C.J., P.H. Diamond, O.D. Gurcan and T.S. Hahm, "Toroidal Rotation Driven by the Polarization Drift", Phys. Rev. Lett. 103, 205003, 2009 (6pp).

Gurcan, O.D., P. Hennequin, L. Vermare, X. Garbet and P.H. Diamond, "Shell Models and the Possibility of Application to Fusion Plasmas", Plasma Phys. Control. Fusion 52(4), 045002, 2010 (21pp).

Diamond, P.H., S.-I. Itoh and K. Itoh, "Modern Plasma Physics: Volume 1, Physical Kinetics of Turbulent Plasmas, Cambridge University Press, 2010 (434 pp). BOOK

Dif-Pradalier, G., P.H. Diamond, V. Grandgirard, Y. Sarazin, J. Abiteboul, X. Garbet, Ph. Ghendrih, A. Strugerek, S. Ku and C.S. Chang, "On the Validity of the Local Diffusive Paradigm in Turbulent Plasma Transport", Phys. Rev. E 82, 025401, 2010 (4 pp.).

Ishizawa, A. and P.H. Diamond, "Ion-Temperature Gradient Modes Affected by Helical Magnetic Field of Magnetic Islands", Phys. Plasmas 17, 074503, 2010 (3 pp).

Kosuga, Y. and P.H. Diamond, "Collisionaless Dynamical Friction and Relaxation in a Simple Drift Wave-Zonal Flow Turbulence", Plas. Fusion Research, Accepted for Publication (2010).

Wang, W.X., P.H. Diamond, T.S. Hahm, S. Ethier, G. Rewoldt and W.M. Tang, "Nonlinear Flow Generation by Electrostatic Turbulence in Tokamaks", Accepted Phys. Plasmas 2010

McDevitt, C.J., P.H. Diamond, O.D. Gurcan and T.S. Hahm, "Poloidal Rotation and Its Relation to the Potential Vorticity Flux", Accepted Phys. Plasmas 2010

Kosuga, Y., P.H. Diamond and O.D. Gurcan, "On the Efficiency of Intrinsic Rotation Generation in Tokamaks", Submitted Phys. Plasmas 2010

PI Dimitre Dimitrov

D. A. Dimitrov, R. Busby, J. R. Cary, I. Ben-Zvi, T. Rao, J. Smedley, X. Chang, J. Keister, Q. Wu, E. Muller, Multiscale 3D simulations of charge gain and transport in diamond, accepted for publication in Journal of Applied Physics (2010).

X. Chang, Q. Wu, I. Ben-Zvi, A. Burril, J. Kewisch, T. Rao, J. Smedley, E. Wang, E. M. Muller, R. Busby, and D. A. Dimitrov, Electron Beam Emission from a Diamond-Amplified Cathodes, accepted for publication in the Physical Review Letters (2010)

D. A. Dimitrov, R. Busby, J. R. Cary, I. Ben-Zvi, J. Smedley, X. Chang, T. Rao, J. Keister, E. Muller, and A. Burrill, Simulations of Charge Gain and Collection Efficiency from Diamond Amplifiers, In P. Bergonzo et al., Diamond Electronics and Bioelectronics ??? Fundamentals of Applications III, MRS Proceedings vol. 1203, paper # 1203-J17-43, (2010), DOI: 10.1557/PROC-1203-J17-43

J. W. Keister, J. Smedley, D. A. Dimitrov, and R. Busby, Charge Collection and Propagation in Diamond X-ray Deterctors, IEEE Transactions on Nuclear Science, 57, 2400 (2010), DOI:
http://dx.doi.org/10.1109/TNS.2010.2052288

PI William Dorland

T. Tatsuno, M. Barnes, S. C. Cowley, W. Dorland, G. G. Howes, R. Numata, G. G. Plunk and A. A.
Schekochihin, Gyrokinetic simulation of entropy cascade in two-dimensional electrostatic turbulence, J.
Plasma Fusion Res. SERIES 9, 509 (2010).

M. Barnes, W. Dorland and T. Tatsuno: Resolving velocity space dynamics in continuum gyrokinetics,
Phys. Plasmas 17, 032106, 2010 [Figure 7 is used for the cover page of the issue].

R. Numata, G. G. Howes, T. Tatsuno, M. Barnes and W. Dorland, AstroGK: astrophysical gyrokinetics
code, J. Comp. Phys., in press (2010); preprint arXiv:1004.0279.

M. Barnes, I. G. Abel, G. Colyer, W. Dorland, T. Goerler, G. W. Hammett, E. Highcock, F. Jenko, F. I. Parra,
and A. A. Schekochihin, ???First-principles simulations of momentum transport and pro???le evolution
within the multi-scale gyrokinetic framework,??? Invited paper, Theory Of Fusion Plasmas Joint Varenna
-
Lausanne International Workshop, Villa Monastero, Varenna, Italy, August 30 - September 3, 2010,
submitted to Plasma Phys. Contr. Fusion.

H. Che, J.F. Drake, M. Swisdak, and P.H. Yoon, Breaking magnetic field lines during reconnection,
submitted to Nature (2010).

R. Schreier, M. Swisdak, J.F. Drake, and P.A. Cassak, Three-dimensional simulations of the orientation
and structure of reconnection X-lines, Phys. Plasmas, in press.

R. Fermo, J.F. Drake, and M. Swisdak,`A statistical model of magnetic islands in a current layer" Phys.
Plasmas 17, 010702, 2010.

H. Che, J.F. Drake, M. Swisdak, and P.H. Yoon, ``Electron holes and heating in the reconnection
dissipation region,'' Geophys. Res. Lett. 37, L11105, 2010.

J.F. Drake, M. Opher, M. Swisdak, and J.N. Chamoun,``A magnetic reconnection mechanism for the
generation of anomalous cosmic rays,'' ApJ, 709, 963--974, 2010.

H. Che, J.F. Drake, M. Swisdak and P.H. Yoon, ``Nonlinear development of streaming instabilities in
strongly magnetized plasmas,'' Phys. Rev. Lett. 102, 145004, 2009.

J.F. Drake, P.A.Cassak, M.A.Shay, M.Swisdak, and E.Quataert, ``A magnetic reconnection mechanism for
ion acceleration and abundance enhancements in impulsive flares,'' Astrophys. J. Lett. 700, L16, 2009.

J.F. Drake, M. Swisdak, T.D. Phan, P.A. Cassak, M.A. Shay, S.T. Lepri, R.P. Lin, E. Quataert and T.H.
Zurbuchen, ``Ion heating resulting from pickup in magnetic reconnection exhausts,'' J. Geophys. Res.
114, A05111, 2009.

R.G. Kleva and P. N. Guzdar, The disparate impact of the ion temperature gradient and the density
gradient on edge transport and the low-high transition in tokamaks, Phys. Plasmas 16, 032305 (2009).

R. G. Kleva and P. N. Guzdar, Suppression of edge-localized modes by magnetic field perturbations,
submitted to Phys. Plasmas.

PI German Drazer

"Partition-Induced Vector Chromatography in Microfluidic Devices", J. Bernate and G. Drazer, submitted to J. Colloid Interface Science (2010).

PI Michel Dupuis

R. Devanathan, A. Venkatnathan, R. J. Rousseau, M. Dupuis, T. Frigato, W. Gu and V. Helms, "Atomistic simulation of water percolation and proton hopping in Nafion fuel cell membrane," Journal of Physical Chemistry B, doi: 10.1021/ jp103398b (Journal cover article to be published on November 4, 2010).

N. B. Idupulapati, R. Devanathan and M. Dupuis, "Ab initio study of hydration and proton dissociation in ionomer membranes," Journal of Physical Chemistry A 114(25) (2010) 6904-6912.

N. B. Idupulapati, R. Devanathan and M. Dupuis, "Molecular structure and transport dynamics in perfluoro sulfonyl imide membranes," submitted to Journal of Physics: Condensed Matter (2010; under review).

T. M. Chang, L. X. Dang, R. Devanathan and M. Dupuis, "Structure and Dynamics of N, N-diethyl-N-methyl Ammonium-Triflate Ionic Liquid, Neat and with Water, from Molecular Dynamics Simulations", submitted to Journal of Physical Chemistry A (2010; under review)

R. Devanathan, "Proton exchange membranes for fuel cells" in Energy Production and Storage - Inorganic Chemical Strategies for a Warming World (Ed. Robert H. Crabtree) pp 89-100 (2010). ISBN: 978-0-470-74986-9.


E

PI Charlotte Elster

The Two-Nucleon System in Three Dimensions, J. Golak, W. Glockle, R. Skibinski, H. Witaa, D. Rozpedzik, K. Topolnicki, I. Fachruddin, Ch. Elster, A. Nogga, arXiv:1001.1264 [nucl-th]; Phys. Rev. C 81, 034006 (2010).

3N Scattering in a Three-Dimensional Operator Formulation, W. Glockle, I. Fachruddin, Ch. Elster, J. Golak, R. Skibinski, H. Witaa, arXiv:0910.1144 [nucl-th], Eur. Phys. J. A 43, 339 (2010).

A new way to perform partial wave decomposition of few-nucleon forces, J. Golak, D. Rozpedzik, R. Skibinski, K. Topolnicki, H. Witala, W. Glockle, A. Nogga, E. Epelbaum, H. Kamada, Ch. Elster, I. Fachruddin, arXiv:0911.4173 [nucl-th], Eur. Phys. J. A 43, 241 (2010).

A New Treatment of 2N and 3N Bound States in Three Dimensions, W. Glockle, Ch. Elster, J. Golak, R. Skibinski, H. Witaa, H. Kamada, Few-Body Syst 47, 25 (2010).

Poincare-invariant Three-Body Scattering, Ch. Elster, T. Lin, W.N. Polyzou, W. Glockle, Few Body Syst. 45, 157 (2009).

PI Paul Erhart

"The influence of short range order on the thermodynamics of Fe???Cr alloys",G Bonny, P Erhart, A Caro, R C Pasianot, L Malerba and M Caro, Modelling Simul. Mater. Sci. Eng. 17, 025006 (2009)

"A scalable parallel Monte Carlo algorithm for atomistic simulation of precipitation in alloys", B Sadigh, P Erhart, A Stukowski, A Caro, E Martinez, and L Zepeda-Ruiz, submitted to Physical Review B

"An efficient algorithm for calculating free energies of interfaces: The variance-constrained semi-grandcanonical ensemble Monte-Carlo method", B Sadigh and P Erhart, submitted to Journal of Chemical Physics


F

PI Roland Faller

Ian G. Elliott, Tonya L. Kuhl, Roland Faller: A Molecular Simulation Study of the Structure of High Density Polymer Brushes in Good Solvent accepted into Macromolecules

PI Alexey Fedorov

A. V. Fedorov, C. M. Brierley and K. Emanuel (2010). "Tropical cyclones and permanent El Nino in the early Pliocene epoch", Nature, 463, 1066-1070, DOI: 10.1038/nature08831. This article was also featured on the cover of Nature on 25th February, 2010

PI Andrew Felmy

Stuart Bogatko, E. J. Bylaska and J. H. Weare (2010), First principles simulation of the bonding, vibrational, and electronic properties of the hydration shell of the high spin Fe3+ ion in aqueous solutions, Journal of Physical Chemistry A, 114, 2189-2200, Highlighted as Journal cover.

Eric J. Bylaska, Kevin Glass, Doug Baxter, Scott B. Baden and John H. Weare (2009) Hard scaling challenges for ab initio molecular dynamics capabilities in NWChem: Using 100,000 CPUs per second, Journal of Physics: Conference Series, vol. 180, art. No. 012028, Proceedings of SciDAC 2009, San Diego, CA, 14-18 June 2009, Ed. Horst Simon., work highlighted in cover.

Eric J. Bylaska, Kurt R. Glaesemann, Andrew R. Felmy, Monica Vasiliu and David A. Dixon, and Paul G. Tratnyek (2010) Free Energies for Degradation Reactions of 1,2,3-Trichloro-Propane from ab initio Electronic Structure Theory, Journal of Physical Chemistry A, in press

Eric J. Bylaska, Kiril Tsemekhman, Scott B. Baden, John H. Weare, and Hannes Jonsson (2010) Parallel Implementation of G-point Pseudopotential Plane-Wave DFT with Exact Exchange, Journal of Computational Chemistry, in press, doi: 10.1002/jcc.21598

Cauet, E.; Bogatko, S.; Weare, J.H.; Fulton, J.; Schenter, G.; Bylaska, E.J. Structure and Dynamics of the Hydration Shells of Zn2+ ion from ab-initio Molecular Dynamics and Combined ab intio and classical molecular dynamics simulations. J. Chem. Phys. 2010, 132, art. 194502.

Eric J. Bylaska et al. (2010) Large Scale Plane Wave Density Functional Theory: Formalism, Parallelization, and Applications in Computational Methods for Large Systems: Electronic Structure Approaches for Biotechnology and Nanotechnology, (John Wiley & Sons, Inc.) Ed. J.R. Reimers. (in press).

PI Graham Fleming

A Ishizaki, GR Fleming, Quantum superpositions in photosynthetic light harvesting: delocalization and entanglement, New J. Phys. 12, 055004 (2010).

A Ishizaki, TR Calhoun, GS Schlau-Cohen, GR Fleming, Theoretical examination of quantum coherence in a photosynthetic system at physiological temperature, Phys. Chem. Chem. Phys. 106, 17255 (2010). (Selected as the cover graphics.)

PI Alberto Franceschetti

S. J. Clark, J. Robertson, S. Lany, and A. Zunger, "Intrinsic defects in ZnO calculated by screened exchange and hybrid density functionals", PHYSICAL REVIEW B 81, 115311 (2010)

Stephan Lany and Alex Zunger, "Many-body GW calculation of the oxygen vacancy in ZnO", PHYSICAL REVIEW B 81, 113201 (2010).

Vladan Stevanovic, Mayeul d'Avezac, and Alex Zunger, "Simple Point-Ion Electrostatic Model Explains the Cation Distribution in Spinel Oxides", PHYSICAL REVIEW LETTERS, 105, 075501 (2010)

Xiuwen Zhang, Giancarlo Trimarchi, Mayeul d'Avezac, and Alex Zunger, "Long-range order instead of phase separation in large lattice-mismatch isovalent AX-BX systems", PHYSICAL REVIEW B 80, 241202(R) (2009)

Xiuwen Zhang and Alex Zunger, "Altered Reactivity and the Emergence of Ionic Metal Ordered Structures in Li-Cs at High Pressures" PHYSICAL REVIEW LETTERS, 104, 245501 (2010)

Xiuwen Zhang and Alex Zunger, "Diagrammatic Separation of Different Crystal Structures of A2BX4 Compounds Without Energy Minimization: A Pseudopotential Orbital Radii Approach", Adv. Funct. Mater. 2010, 20, 1944

Z. Lin, A. Franceschetti, and M. Lusk, "Size dependence of multiple-exciton generation rates in CdSe quantum dots" (submitted).

PI Stuart Freedman

A. Gando et al. [KamLAND Collaboration], "Enhanced Constraints on ??13 from A Three-Flavor Oscillation Analysis of Reactor Antineutrinos at KamLAND", submitted to PRC.

S. Abe et al. [KamLAND Collaboration], "Production of Radioactive Isotopes through Cosmic Muon Spallation in KamLAND", Phys. Rev. C81, 025807 (2010).

B.E. Berger et al. [KamLAND Collaboration], "The KamLAND Full-Volume Calibration System", JINST 4, P04017 (2009).

E. Andreotti et al. [CUORICINO Collaboration], "Muon-induced backgrounds in the CUORICINO experiment", Astropart. Phys. 34, 18 (2010).

PI Arthur Freeman

Interface two-dimensional metallicity but lack of superconductivity in heterobonded semiconductors: ZnS/Si and GaP/Si,
S. H. Rhim, R. Saniz, and A. J. Freeman, Phys. Rev. B 79, 045313 (2009)

Surface-Stabilized Nonferromagnetic Ordering of a Layered Ferromagnetic Manganite, V. B. Nascimento, J. W. Freeland, R. Saniz, R. G. Moore, D. Mazur, H. Liu, M. H. Pan, J. Rundgren, K. E. Gray, R. A. Rosenberg, H. Zheng, J. F. Mitchell, A. J. Freeman, K. Veltruska, and E. W. Plummer, Phys. Rev. Lett. 103, 227201 (2009)

Interfacial Dirac Cones from Alternating Topological Invariant Superlattice Structures of Bi2Se3, Jung-Hwan Song, Hosub Jin, and Arthur J. Freeman, Phys. Rev. Lett. 105, 096403 (2010)

Role of an interfacial FeO layer in the electric-field-driven switching of magnetocrystalline anisotropy at the Fe/MgO interface, Kohji Nakamura, Toru Akiyama, Tomonori Ito, M. Weinert, and A. J. Freeman, Phys. Rev. B 81, 220409 (2010)

PI James Freericks

B. Moritz, T. P. Devereaux, and J. K. Freericks, "Temporal response of nonequilibrium correlated electrons," Comp. Phys. Comm. (2010) DOI:10.1016/j.cpc.2010.05.020 (Available online: 9 June 2010)

B. Moritz, T. P. Devereaux, and J. K. Freericks, "Time-resolved photoemission of correlated electrons driven out of equilibrium," Phys. Rev. B 81, 165112 (2010) (Also appears in Virt. J. Ultrafast Sci. 9 (5) (May 2010))

PI Ann Fridlind

A. Varble, E. J. Zipser, A. M. Fridlind, A. S. Ackerman, J.-P. Chaboureau, J. Fan, A. Hill, J.-P. Pinty, and B. Shipway, Evaluation of TWP-ICE cloud-resolving simulations using observations, Part I: Precipitation and cloud structure, J. Atmos. Sci. (September 2010, submitted)

A. M. Fridlind, A. S. Ackerman, J.-P. Chaboureau, J. Fan, W. W. Grabowski, A. Hill, T. Jones, H. Morrison, S. Park, J. C. Petch, J.-P. Pinty, C. Schumacher, X. Wu, S. Xie, and M. Zhang , A cloud-resolving model intercomparison based on the Tropical Warm Pool-International Cloud Experiment, Part I: Specification and results versus domain-wide observations. J. Geophys. Res. (October 2010, submitted)

A. M. Fridlind, B. van Diedenhoven, A. S. Ackerman, A. Avramov, H. Morrison, Entrainment limitations on heterogeneous ice formation in mixed-phase boundary layer clouds: A FIRE-ACE/SHEBA Arctic case study, J. Atmos. Sci. (October 2010, submitted)

A. Avramov, A. S. Ackerman, A. S. Ackerman, A. M. Fridlind, B. van Diedenhoven, A. V. Korolev, J. W. Strapp, G. M. McFarquhar, R. Jackson, S. D. Brooks, A. Glen, and J. Verlinde, Modeling study of ice formation closure during ISDAC, J. Geophys. Res. (November 2010, submitted)

PI Alex Friedman

A. Friedman, J. J. Barnard, R. H. Cohen, D. P. Grote, S. M. Lund, W. M. Sharp, A. Faltens, E. Henestroza, J.-Y. Jung, J. W. Kwan, E. P. Lee, M. A. Leitner, B. G. Logan, J.-L. Vay, W. L. Waldron, R. C. Davidson, M. Dorf, E. P. Gilson, and I. D. Kaganovich, "Beam dynamics of the Neutralized Drift Compression Experiment-II, a novel pulse-compressing ion accelerator," Phys. Plasmas 17, 056704 (2010).

A. Friedman, J. J. Barnard, R. H. Cohen, D. P. Grote, S. M. Lund, W. M. Sharp, A. Faltens, E. Henestroza, J.-Y. Jung, J. W. Kwan, E. P. Lee, M. A. Leitner, B. G. Logan, J.-L. Vay, W. L. Waldron, R. C. Davidson, M. Dorf, E. P. Gilson, and I. D. Kaganovich, "Developing the Physics Design for NDCX-II, a Unique Pulse-Compressing Ion Accelerator," Proceedings of the 2009 International Computational Accelerator Physics Meeting, 31 August - 4 September 2009, San Francisco (to be published).

J.-L. Vay, J. M. Byrd, M. A. Furman, R. Secondo, M. Venturini, J. D. Fox, C. H. Rivetta, W. H??fle, CERN, Switzerland, "Simulation of E-Cloud Driven Instability and its Attenuation using a Feedback System in the CERN SPS", Proceedings for the 10th International Particle Accelerator Conference, Kyoto, Japan, 23-28 May 2010, p. 2438.

W. M. Fawley and J.-L. Vay, "Full Electromagnetic Simulation of Coherent Synchrotron Radiation via the Lorentz-Boosted Frame Approach," Proceedings for the 10th International Particle Accelerator Conference, Kyoto, Japan, 23-28 May 2010, p. 1874.

S. M. Lund, T. Kikuchi, and R. C. Davidson, "Generation of Initial Vlasov Distributions for Simulation of Charged Particle Beams With High Space-Charge intensity", Physical Review Special Topics on Accelerators and Beams 12, 114801 (2009).

J. J. Barnard, J. Armijo, D. S. Bailey, A. Friedman, F. M. Bieniosek, E. Henestroza, I. Kaganovich, P. T. Leung, B. G. Logan, M.M. Marinak, R. M. More, S. F. Ng, G. E. Penn, L. J. Perkins, P. Stoltz, S. Veitzer, J. S. Wurtele, S. S. Yu, A. B. Zylstra, "Ion beam heated target simulations and analysis for warm dense matter physics and inertial fusion energy" Nuclear Instruments and Methods in Physics Research A 606, 134 (2009).

A. Friedman, J. J. Barnard, R. J. Briggs, R. C. Davidson, M. Dorf, D. P. Grote, E. Henestroza, E. P. Lee, M. A. Leitner, B. G. Logan, A. B. Sefkow, W. M. Sharp, W. L. Waldron, D. R. Welch, and S. S. Yu, "Towards a Physics Design for NDCX-II, an Ion Accelerator for Warm Dense Matter and HIF Target Physics Studies," Nuclear Instruments and Methods in Physics Research A 606, 6 (2009).

R. H. Cohen, A. Friedman, D. P. Grote, and J.-L. Vay, "An Implicit 'Drift-Lorentz' Particle Mover for Plasma and Beam Simulations," Nuclear Instruments and Methods in Physics Research A 606, 53 (2009).

S. M. Lund, C. J. Wootton, and E. P Lee, "Transverse Centroid Oscillations in Solenoidally Focused Beam Transport Lattices," Nuclear Instruments and Methods in Physics Research A 606, 56 (2009).

W. M. Sharp, A. Friedman, D. P. Grote, E. Henestroza, M. A. Leitner, and W. L. Waldron, "Developing Acceleration Schedules for NDCX-II," Nuclear Instruments and Methods in Physics Research A 606, 97 (2009).

PI Guoyong Fu

Lang, JY; Fu, GY; Chen, Y, "onlinear simulation of toroidal Alfven eigenmode with source and sink" PHYSICS OF PLASMAS 17, 042309 (2010);

Chen, Y; Parker, SE; Lang, JY; Fu, GY, "yrokinetic Simulation of High-n Toroidal Alfven Eigenmodes in a Burning Plasma" Physics of Plasmas, accepted, August, 2010;

Lang, JY, Chen, Y; Parker, SE; Fu, GY, "yrokinetic delta_f particle simulations of toroidicity-induced Alfven eigenmode" Physics of Plasmas 16, 102101 (2009).

PI Inez Fung

Boyce, C.K., and J.E. Lee, “Could land plant evolution have fed the marine revolution?” Paleontological Research, submitted.

Lee, J.E., C.K. Boyce, “The impact of hydraulic capacity on water and carbon cycles in tropical South America,” J. Geophys. Res., in press.

C.K. Boyce, J.E. Lee, T. J. Brodribb, T. S. Feild, and M. A. Zwieniecki, “Angiosperms put the rain in the rainforests: The impact of plant physiological evolution on tropical biodiversity,” Annal. Mo. Bot. Gard. in press.

C.K. Boyce, and J.E. Lee, “A unique role for flowering plants in modifying tropical climate and biodiversity,” Proceedings of Royal Society, B., doi:10.1098/rspb.2010.0485.

Lee, J.E., A. Swann, “Evaluation of using the “amount effect” to interpret speleothem data: Asian monsoon study,” IOP Conf. Series: Earth and Environmental Science, 9, L23801 (2010).

Lee, J.E., R. Pierrehumbert, B. Lintner, and A. Swann, “Sensitivity of the stable water isotopic values on the convective parameterization schemes,” Geophy. Res. Lett, 36, L23801, doi:10.1029/2009GL040880 (2009).

Lee, J.E., K. Johnson, and I. Fung, “Precipitation over South America during the Last Glacial Maximum: An analysis of the “amount effect” with a water isotope-enabled General Circulation Model,” Geophy. Res. Lett, 36, L19701, doi:10.1029/2009GL039265 (2009).

Tseng, Y. H. (2010), "Diagnosing Sahel Drought in the Ensemble Community Atmospheric Model 3.5" (submitted to Climate Dynamics).

Boyce, C.K., and J.E. Lee, “Could land plant evolution have fed the marine revolution?” Paleontological Research, submitted.

Lee, J.E., C.K. Boyce, “The impact of hydraulic capacity on water and carbon cycles in tropical South America,” J. Geophys. Res., in press.

C.K. Boyce, J.E. Lee, T. J. Brodribb, T. S. Feild, and M. A. Zwieniecki, “Angiosperms put the rain in the rainforests: The impact of plant physiological evolution on tropical biodiversity,” Annal. Mo. Bot. Gard. in press.

C.K. Boyce*, and J.E. Lee,* “A unique role for flowering plants in modifying tropical climate and biodiversity,” Proceedings of Royal Society, B., doi:10.1098/rspb.2010.0485. (*: equal contributions).

Lee, J.E., A. Swann, “Evaluation of using the “amount effect” to interpret speleothem data: Asian monsoon study,” IOP Conf. Series: Earth and Environmental Science, 9, L23801 (2010).

Lee, J.E., R. Pierrehumbert, B. Lintner, and A. Swann, “Sensitivity of the stable water isotopic values on the convective parameterization schemes,” Geophy. Res. Lett, 36, L23801, doi:10.1029/2009GL040880 (2009).

Lee, J.E., K. Johnson, and I. Fung, “Precipitation over South America during the Last Glacial Maximum: An analysis of the “amount effect” with a water isotope-enabled General Circulation Model,” Geophy. Res. Lett, 36, L19701, doi:10.1029/2009GL039265 (2009).

Tseng, Y. H. (2010), "Diagnosing Sahel Drought in the Ensemble Community Atmospheric Model 3.5" (submitted to Climate Dynamics).

PI Miguel Furman

ILC DAMPING RINGS STATUS: RECOMMENDATION FOR THE FEASIBILITY OF MORE COMPACT RINGS, M. T.F. Pivi, S. Guiducci, M. Palmer, J. Urakawa et al. In preparation for submission to Physical Review Special Topics AB, (2010)

BEAM DYNAMICS PARALLEL SIMULATION CODE FOR NON-LINEAR SINGLE-BUNCH INSTABILITIES IN PARTICLE ACCELERATORS: CMAD, M. T.F. Pivi, in preparation for submission to Physical Review Special Topics AB, (2010)

TESTS OF PROTOTYPE CHAMBERS WITH GROOVES IN THE PEP-II ACCELERATOR, M. T.F. Pivi, F. King, R. E. Kirby, T. Markiewicz, T. O. Raubenheimer, J. Seeman, L. Wang, in preparation for submission to Nuclear Instruments and Methods A, (2010)

EMITTANCE GROWTH AND RESONANCES CROSSING OF PARTICLE BEAMS BELOW THE SINGLE-BUNCH INSTABILITY THRESHOLD, K. Sonnad and M. T.F. Pivi, In preparation for submission to Physical Review ST AB, (2010)

PRESENT STATUS AND FIRST RESULTS OF THE FINAL FOCUS BEAM LINE AT THE KEK ACCELERATOR TEST FACILITY, P. Bambade et al., Physical Review ST Accel. Beams 13, 042801 (2010).

EXPERIMENTAL OBSERVATIONS OF IN-SITU SECONDARY ELECTRON YIELD REDUCTION IN THE PEP-II PARTICLE ACCELERATOR BEAM LINE,
M. T.F. Pivi, et al. G. Collet, F. King, R. E. Kirby, T. Markiewicz, T. O. Raubenheimer, J. Seeman, F. Le Pimpec,
Nuclear Instruments and Methods in Physics Research A 621 (1-3), 47???56, (2010).

OBSERVATION OF MAGNETIC RESONANCES IN AN ELECTRON CLOUD, M. T.F. Pivi, J. S. T. Ng, F. Cooper, D. Kharakh, F. King, R. E. Kirby, B. Kuekan, C. M. Spencer, L. Wang, T. O. Raubenheimer, Nuclear Instruments and Methods in Physics Research A, 621 (1-3), 33???38, (2010).

M. A. Furman, R. De Maria, Y. Papaphilippou and G. Rumolo, "Electron-Cloud Build-Up Simulations in the Proposed PS2: Status Report (PDF)", LBNL-xxx/CBP Note 851, May 25, 2010. To be published in the Proc. IPAC10 (Kyoto, Japan, 23-28 May, 2010), paper TUPD018.

M. A. Furman, "How to generate random numbers with a power (or any other) density (PDF)", CBP-Technote-406, 8 Oct. 2009.


G

PI Giulia Galli

A. Splendiani, L. Sun, Y. Zhang, T. Li, J. Kim, C.-Y. Chim, G.Galli, and F. Wang, "Emerging Photoluminescence in Monolayer MoS2",  Nano Lett., 10, 1271 (2010)

A. Gali, M. Voros, D. Rocca, G. Zimanyi and G. Galli, "High energy excitations in silicon nanoparticles" , Nano Lett. 9, 3780 (2009).

D. Donadio and G. Galli, "Temperature dependence of the thermal conductivity of thin silicon nanowires" , Nano Lett. 10, 847 (2010).

L. Spanu, S. Sorella and G. Galli, "Nature and strength of interlayer binding in graphite", Phys. Rev. Lett., 103, 196401 (2009).

Y. Li, D. Lu, H-V Nguyen and G. Galli, "Van der Waals interactions in molecular assemblies from first-principles calculations", , J. Phys. Chem. A, 114, 1944-1952 (2010).

PI Bruce Garrett

F. Paesani, S. S. Xantheas and G. A. Voth, "Infrared Spectroscopy and Hydrogen-Bond Dynamics of Liquid Water from Centroid Molecular Dynamics with an Ab Initio-Based Force Field", Journal of Physical Chemistry B 113, 13118 (2009)

X. Sun, S. Yoo, S. S. Xantheas, L. X. Dang, "The reorientation mechanism of hydroxide ions in water: A molecular dynamics study", Frontiers article (invited), Chemical Physics Letters 481, 9 (2009)

S. Yoo, S. S. Xantheas, X. C. Zeng, "The melting temperature of Bulk Silicon from Ab initio Molecular Dynamics Simulations", Chemical Physics Letters 481, 88 (2009)

J. R. Hammond, N. Govind, K. Kowalski, J. Autschbah, S. S. Xantheas, "Accurate dipole polarizabilities for water clusters n=2-12 at the coupled cluster level of theory and benchmarking of various density functionals", Journal of Chemical Physics 131, 214103 (2009). Featured in the Virtual Journal of Biological Physics Research. 11th most downloaded paper in December 2009.

N. Hontama, Y. Inokuchi, T. Ebata, C. Dedonder-Lardeux, C. Jouvet, and S. S. Xantheas, "Structure of the Calix[4]arene-(H2O) cluster: The World's Smallest Cup of Water", Journal of Physical Chemistry A 114, 2967 (2010)

X.-B. Wang, K. Kowalski, L.-S. Wang and S. S. Xantheas, "Stepwise hydration of the cyanide anion: A temperature-controlled photoelectron spectroscopy and ab-initio computational study of CN-(H2O)n (n = 2-5)", Journal of Chemical Physics 132, 124306 (2010)

R. Kusaka, Y. Inokuchi, S. S. Xantheas and T. Ebata, "Structures and Encapsulation Motifs of Functional Molecules Probed by Laser Spectroscopic and Theoretical Methods", Invited Review article, Special issue on Laser Spectroscopy and Sensing, Sensors 10, 3519 (2010)

T. Ebata, N. Hontama, Y. Inokuchi, T. Haino, E. Apra and S. S. Xantheas, "Encapsulation of Arn clusters by Calix[4]arene: Endo- vs. exo-complexes", Physical Chemistry Chemical Physics 12, 4569 (2010)

F. Paesani, S. Yoo, H. J. Bakker and S. S. Xantheas, "Nuclear Quantum Effects in the reorientation of water", Journal of Physical Chemistry Letters 1, 2316 (2010)

E. G. Bakalbassis, E. Malamidou-Xenikaki, S. Spyroudis and S. S. Xantheas, "Dimerization of Indanedioneketene to Spiro-oxetanone: A Theoretical Study", Journal of Organic Chemistry 75, 5499 (2010)

V.-A. Glezakou, S. T. Elbert, S. S. Xantheas and K. Ruedenberg, "Analysis of bonding patterns in the valence isoelectronic series O3, S3, SO2 and OS2 in terms of oriented quasi-atomic molecular orbitals", Klaus Ruedenberg special issue (invited), Journal of Physical Chemistry A 114, 8923 (2010)

S. Pandelov, J. C. Werhahn, B. M. Pilles, S. S. Xantheas, and H. Iglev, "An empirical correlation between the enthalpy of solution of aqueous salts and their ability to form hydrates", Journal of Physical Chemistry A 114, 10454 (2010). Journal cover

PI Cameron Geddes

J.-L. Vay, C. G. R. Geddes, E. Cormier-Michel, D. P. Grote, "Modeling laser wakefield accelerators in a Lorentz boosted frame," In arXiv:1009.2727v2

W.B. Mori, W. An, V.K. Decyk, W. Lu, F.S. Tsung, R.A. Fonseca, S.F. Martins, J. Vieira, L.O Silva, M. Chen, E. Esarey, C.G.R. Geddes, W.P. Leemans, C.B. Schroeder, J-L. Vay, K. Amyx, D.L. Bruhwiler, J. R.Cary, E. Cormier-Michel, B. Cowan, P. Messmer, C. Huang and T. Antonsen, "Dream beams: Extreme-scale computing enabling new accelerator technologies for the energy and intensity frontiers," Journal of Physics: Conference Series (2010), submitted.

O. Ruebel, S. Ahearn, E.W. Bethel, M. Biggin, H. Childs, E. Cormier-Michel, A. DePace, M.B. Eisen, C.C. Fowlkes, C.G.R. Geddes, H. Hagen, B. Hamann M-Y Huang, S.V.E. Keranen, D.W. Knowles, C.L Luengo Hendriks, J. Malik, J. Meredith, P. Messmer, Prabhat, D. Ushizima, G.H. Weber, K. Wu, "Coupling visualization and data analysis for knowledge discovery from multi-dimensional scientific data," Proc. International Conference on Computational Science (2010). LBNL-3669E.

PI Phillip Geissler

JL Baker, A Widmer-Cooper, M Toney, P Geissler, AP Alivisatos, Device-scale perpendicular alignment of colloidal nanorods, Nano Letters 10 (2010) 195.

PI Robert Gerber

Sugar-salt and sugar-salt-water complexes: structure and dynamics of glucose-KNO3-(H2O), Madeleine Pincu, Brina Brauer, Robert Benny Gerber and Victoria Buch, Phys. Chem. Chem. Phys., 2010, 12, 3550-3558

PI Alexandros Gezerlis

Alexandros Gezerlis and G. F. Bertsch, "Effective 3-body interaction for mean-field and density-functional theory", to appear in Phys. Rev. Lett. (2010).

Alexandros Gezerlis and J. Carlson, "Low-density neutron matter", Phys. Rev. C 81, 025803 (2010).

A. Gezerlis, S. Gandolfi, K. E. Schmidt, and J. Carlson "Heavy-Light Fermion Mixtures at Unitarity", Phys. Rev. Lett. 103, 060403 (2009).

PI Steven Ghan

Qian, Y., W. I. Gustafson Jr., and Fast, J. D., 2010, An investigation of the sub-grid variability of trace gases and aerosols for global climate modeling, Atmos. Chem. Phys., 10, 6917-6946, doi:10.5194/acp-10-6917-2010.

PI Yousry Gohar

Yan Cao and Yousry Gohar, "A Conceptual Design of a Fusion-Fission Hybrid System", ANS 2010.

PI Javad  Golji

Golji J, Collins R, Mofrad MRK. Molecular Mechanics of the alpha-Actinin Rod Domain: Bending, Torsional,
and Extensional Behavior, PLOS Computational Biology, 2009.

Golji J, Mofrad MRK, A Molecular Dynamics Investigation of Vinculin Activation. Biophysical Journal,
99(3)August 2010a.

Golji J, Lam J, Mofrad MRK, Talin Binds Activated Vinculin. Biophysical Journal, ACCEPTED 2010b.

PI Stephen Gray

X. Wu, S. K. Gray, and M. Pelton, Quantum dot induced transparency in a nanoscale resonator, Optics Express, submitted (2010).

T. W. Lee and S. K. Gray,Remote grating-assisted excitation of narrow-band surface plasmons, Optics Express, submitted (2010).

PI Chris Greene

Potential energy and dipole moment surfaces of H3- molecule M. Ayouz, O. Dulieu, R. Guerout, J. Robert, V. Kokoouline; J. Chem. Phys. 132, 194309 [11pp] (2010)

Formation of the simplest stable negative molecular ion H3- in interstellar medium V. Kokoouline, M. Ayouz, R. Guerout, M. Raoult, J. Robert, O. Dulieu; submitted to Phys. Rev. A arXiv:0910.2330 (2009)

Temperature dependence of binary and ternary recombination of D3+ ions with electrons T. Kotrik, P. Dohnal, I. Korolov, R. Plasil, S. Roucka, J. Glosik, C.H. Greene, V. Kokoouline; J. Chem. Phys. 133, 034305 [8pp] (2010)

Binary and ternary recombination of H3+ and D3+ ions with electrons in low temperature plasma T.J. Glosik, R. Plasil, T. Kotrik, P. Dohnal, J. Varju, M. Hejduk, I. Korolov, S. Roucka, V. Kokoouline; Molec. Phys. 108, 2253 [12pp] (2010)

Calculation of rate constants for vibrational and rotational excitation of the H3+ ion by electron impact V. Kokoouline, A. Faure, J. Tennyson, and C.H Greene; Mon. Not. R. Astron. Soc. 405, 1195 [8pp] (2010)

Photoassociation of a cold atom-molecule pair: long-range quadrupole-quadrupole inter- actions, M. Lepers, O. Dulieu, V. Kokoouline; Phys. Rev. A, in press [8pp] (2010) arXiv:1006.5314

Laser control of complete vibrational transfer in Na2 using resonance coalescence O. Atabek, R. Lefebvre, M. Lepers, A. Jaouadi, O. Dulieu, and V. Kokoouline; submitted to Phys. Rev. A [6pp] (2010)

Theoretical study of dissociative recombination H3O+ ion with electrons N. Douguet, I. Mikhailov, A. Orel, I. Schneider, C.H. Greene, V. Kokoouline; submitted [4pp] (2010)

Resonant structure of low-energy H3+ dissociative recombination A. Petrignani, S. Al- tevogt, M. H. Berg, D. Bing, M. Grieser, J. Hoffmann, B. Jordon-Thaden, C. Krantz, M. B. Mendes, O. Novotny, S. Novotny, D. A. Orlov, R. Repnow, T. Sorg, J. Stutzel, A. Wolf, H. Buhr, H. Kreckel, V. Kokoouline, C. H. Greene; submitted [10pp] (2010)

PI Jeffrey Grossman

J.-H. Lee, J. Wu and J. C. Grossman, Phys. Rev. Lett. 104, 016602 (2010).

Y. Kanai, V. Srinivasan, S. K. Meier, K. P. C. Vollhardt and J. C. Grossman, Angewandte Chemie (2010)  (accepted for publication).

Y. Kanai, Z. Wu, and J. C. Grossman, J. Mater. Chem. 20, 1053 (2010).

PI Hua Guo

S. C. Farantos, R. Schinke, H. Guo, and M. Joyeux, Chem. Rev., 109, 4248 (2009), Energy localization in molecules, bifurcation phenomena and their spectroscopic signatures: The global view.

Z. Li, D. Xie, Z. Sun, D. H. Zhang, S. Y. Lin and H. Guo, J. Chem. Phys., 131, 124313 (2009), NH( ) + H/D(2S) ??? H(2S) + NH/ND( ) exchange reactions: State-to-state quantum scattering and applicability of statistical model.

F. Lique, M. Jorfi, P. Honvault, P. Halvick, S. Y. Lin, H. Guo, D. Xie, J. K??os, P. J. Dagdigian, and M. H. Alexander, J. Chem. Phys., 131, 221104 (2009), O + OH ??? O2 + H: A key, and exemplary, reaction for interstellar chemistry. New theoretical results and comparison with experiment. (One of 20 most downloaded articles from J. Chem. Phys., December 2009)

Z. Sun, L. Liu, S. Y. Lin, R. Schinke, H. Guo and D. H. Zhang, Proc. Natl. Acad. Sci. USA, 107, 555 (2010), State-to-state quantum dynamics of O + O2 isotope exchange reactions reveals non-statistical behavior at atmospheric conditions.

Z. Sun, H. Guo and D. H. Zhang, J. Chem. Phys., 132, 084112 (2010), Extraction of state-to-state reactive scattering attributes from wave packet in reactant Jacobi coordinates.

W. Lai, S. Y. Lin, D. Xie and H. Guo, J. Phys. Chem. A (invited article in the Soep Festschrift), 114, 3121 (2010), Non-adiabatic dynamics of -state photodissociation of ammonia: a four-dimensional wave packet study.

J. Ma, S. Y. Lin, H. Guo, Z. Sun, D. H. Zhang, D. Xie, J. Chem. Phys., 133, 054302 (2010), State-to-state quantum dynamics of the O(3P) + OH(2???) ??? H(2S) + O2(3???-g) reaction. (Cover article)

A. Li, D. Xie, R. Dawes, A. W. Jasper, J. Ma, and H. Guo, J. Chem. Phys., accepted, Global potential energy surface, vibrational spectrum, and reaction dynamics of the first excited (A2A???) state of HO2.

S. Y. Lin, H. Guo, B. Jiang, S. Zhou, and D. Xie, J. Phys. Chem. A (invited article in the Schinke Festschrift), in press, Non-Born-Oppenheimer state-to-state dynamics of the N(2D) + H2 ??? NH( ) + H reaction: Influence of the Renner-Teller coupling.

G. K. Smith, S. Lin, W. Lai, A. Datye, D. Xie, and H. Guo, J. Phys. Chem. C, submitted, Density functional theory studies of the initial steps in methanol steam reforming on PdZn and ZnO surfaces.

PI William Gutowski

J.M. Prusa and W.J. Gutowski, 2010. "Multi-Scale Features of Baroclinic Waves in Sound-Proof, Global Simulations With EULAG", Proceedings of European Conference on Computational Fluid Dynamics, ECCOMAS CFD 2010, Lisbon, Portugal, 14-17 June 2010, paper # 1453.


H

PI Stephan Haas

Revealing Novel Quantum Phases in Quantum Antiferromagnets on Random Lattices, R. Yu, T. Roscilde, and S. Haas, Condensed Matter Physics 12, 519 (2009).

Adaptation and Performance of the Cartesian Coordinates Fast Multipole Method for Nanomagnetic Simulations, W. Zhang and S. Haas, Journal of Magnetism and Magnetic Materials 321, 3687 (2009).

Plasmonic excitations in tight-binding nanostructures, R. Muniz, S. Haas, A.F.J. Levi, and I. Grigorenko, Phys. Rev. B 80, 045413 (2009).

Electron-phonon bound states and impurity band formation in quantum wells, B.P.W. de Oliveira and S. Haas, Phys. Rev. B 79, 155102 (2009).

Magnetic and metallic state at intermediate Hubbard U coupling in multiorbital models for undoped iron pnictides, R. Yu, K.T. Trinh, A. Moreo, M. Daghofer, J. A. Riera, S. Haas, and E. Dagotto, Phys. Rev. B 79, 104510 (2009).

PI Maciej Haranczyk

S. Ling, M. Gutowski, SSC: A Tool for Constructing Libraries for Systematic Screening of Conformers, J. Chem. Inf. Model., submitted for publication.

S. Ling, Z. Keolopile, A.V. Abramov, M. Gutowski, Suppressing Energy Barriers between Conformers on Molecular Potential Energy Surfaces, J. Chem. Theory Comput., submitted.

Katherine Harkay

Karoly Nemeth, Katherine C. Harkay, Michel van Veenendaal, Linda Spentzouris, Marion White, Klaus Attenkofer, George Srajer, "High brightness photocathodes through ultra-thin surface layers on metals," Phys. Rev. Lett. 104, 046801 (2010).

PI Bruce Harmon

"Comparing efficiencies of genetic and minima hopping algorithms for crystal structure prediction", M. Ji, C. Z. Wang, and K. M. Ho, Phys. Chem. Chem. Phys. in press (2010).

"The Role of Pentagon-Heptagon Pair Defect in Carbon Nanotube : The Center of Vacancy Reconstruction", Gun-Do Lee, C. Z. Wang, Euijoon Yoon, Nong-Moon Hwang, and K. M. Ho, Appl. Phys. Lett. 97, 093106 (2010).

"Appearance of bulk-like motifs in Si, Ge, and Al clusters", Wen-Cai Lu, C. Z. Wang , Li-Zhen Zhao , Wei Zhang , Wei Qin , K. M. Ho, Phys. Chem. Chem. Phys. 12, 8551 (2010).

"Charge localization in [112] Si/Ge and Ge/Si core-shell nanowires", Nuo Liu , Yan-Rong Li , Ning Lu , Yong-Xin Yao , Xiao-Wei Fang , Cai-Zhuang Wang and Kai-Ming Ho, J. Phys. D: Appl. Phys. 43, 275404 (2010).

"Chemical bonding analysis for solid-state systems using intrinsic oriented quasiatomic minimal-basis-set orbitals", Y. X. Yao, C. Z. Wang, and K. M. Ho, Phys. Rev. B 81, 235119 (2010).

"Reconstruction and evaporation at graphene nanoribbon edges", Gun-Do Lee, C. Z. Wang, Euijoon Yoon, Nong-Moon Hwang, and K. M. Ho, Phys. Rev. B 81, 195419 (2010).

"Geometric structures of Ge-n (n=34-39) clusters", Wei Qin, Wen-Cai Lu, Qing-Jun Zang, Li-Zhen Zhao, Guang-Ju Chen, C. Z. Wang, and K. M. Ho, J. Chem. Phys. 132, 214509 (2010).

"Core properties of dislocations in YCu and YAg B2 intermetallic compounds", Q. Chen, M. Ji, C. Z. Wang, K. M. Ho, B. B. Biner, Intermetallics, 18, 312 (2010)

"Statistical model of defects in Al-H system", M. Ji, C. Z. Wang, K. M. Ho, S. Adhikari, and K. R. Hebert, Phys. Rev. B 81, 024105 (2010).

"Platelike structures of semiconductor clusters Ge-n (n=40-44)", Wei Qin, Wen-Cai Lu, Li-Zhen Zhao, Qing-Jun Zang, Guang-Ju Chen, C. Z. Wang, and K. M. Ho, J. Chem. Phys., 131, 124507 (2009).

"Stabilities and fragmentation energies of Sin clusters (n=2-33)", Wei Qin, Wen-Cai Lu, Li-Zhen Zhao, Qing-Jun Zang, C. Z. Wang, and K. M. Ho, J. Phys.: Condens. Matter, 21, 455501 (2009).

"Finding Low Energy Structure of Si[001] Symmetric Tilted Grain Boundaries With A Genetic Algorithm", J. Zhang, C. Z. Wang, and K. M. Ho, Phys. Rev. B 80, 174102 (2009).

"Influence of the electronic structure on the ductile behavior of B2 CsCl-type AB intermetallics", K.A. Gschneidner, Jr., Min Ji, C.Z. Wang, K.M. Ho, A.M. Russell, Ya. Mudryk, A.T. Becker and J.L. Larson, Acta Mater 57, 5876 (2009).

"Stochastic coarsening model for Pb islands on a Si(111) surface", G. P. Zhang, M. Hupalo, M. Li, C. Z. Wang, J.W. Evans, M. Tringides, and K. M. Ho, Phys. Rev. B, accepted.

B. Curtin, R. Biswas, V. Dalal, Photonic crystal based back reflectors for light management and enhanced absorption in amorphous silicon solar cells, Appl. Phys. Lett. 95, 231102 (2009).

Photonic Crystal Back Reflectors for Enhanced Absorption in Amorphous Silicon Solar Cells, Rana Biswas, Benjamin Curtin, Vikram Dalal, MRS 1245-A07-21 (2010).

R. Biswas, C. Xu, W. Zhao, r. Liu, R. Shinar, J. Shinar. Simulation of tandem organic light emitting diodes, submitted to journal of photonics for energy applications.

R. Biswas and D. Zhou, Simulation and modeling of photonic and plasmonic crystal back reflectors for efficient light trapping, Phys. Status Solidi A 207, No. 3, 667 (2010).

 PI Charles Harris

K.R. Sawyer, J.F. Cahoon, J.E. Shanoski, E.A. Glascoe, M.F. Kling, J.P. Schlegel, M.C. Zoerb, M. Hapke, J.F. Hartwig, C.E. Webster, and C.B. Harris, "Time-resolved IR Studies on the Mechanism for the Functionalization of Primary C-H Bonds by Photoactivated Cp*W(CO)3(Bpin)", J. Am. Chem. Soc., 132, 1848-1859 (2010).

PI Martin Head-Gordon

Willard, AP, Chandler, D, "Instantaneous Liquid Interfaces." JOURNAL OF PHYSICAL CHEMISTRY B, v 114, is 5. (2010)

Patel, AJ, Varilly, P, Chandler, D, "Fluctuations of Water near Extended Hydrophobic and Hydrophilic
Surfaces. " JOURNAL OF PHYSICAL CHEMISTRY B, v 114, is 4. (2010)

Thom, AJW, Sundstrom, EJ, Head-Gordon, M, "LOBA: a localized orbital bonding analysis to calculate oxidation states, with application to a model water oxidation catalyst". PHYSICAL CHEMISTRY CHEMICAL PHYSICS, v 11, i 47 (2009)

PI Teresa Head-Gordon

J. W. Ponder, C.J. Wu, V.S. Pande, I. Haque, R.A. Distasio Jr., D. Lambrecht, M. Head-Gordon, G.N.I. Clark, M.E. Johnson, T. Head-Gordon (2010). Current status of the AMOEBA polarizable force field. J. Phys. Chem. B (Feature Article and Cover) 114, 2549-2564.

J. Z. Ruscio, N. Lux Fawzi & T. Head-Gordon (2010). How hot? Systematic convergence of the replica exchange method using multiple reservoirs. J. Comp. Chem. 31, 620-627.

C. Malardier-Jugroot, D. T. Bowron, A. K. Soper, M. E Johnson, and T. Head-Gordon (2010). Structure and dynamics of aqueous peptide solutions in the presence of co-solvents. Phys. Chem. Chem. Phys. (Journal Cover) 12, 382-392.

M. E Johnson, C. Malardier-Jugroot, and T. Head-Gordon (2010). Effects of co-solvents on peptide hydration water structure and dynamics. Phys. Chem. Chem. Phys. (Journal cover) 12, 393-405.

C. Peng, L. Zhang & T. Head-Gordon (2010). Instantaneous normal modes as a reaction coordinate for protein conformational transitions. Biophys. J. 98, 2356-2364.

A. K. Soper, J. Teixeira, and T. Head-Gordon (2010). Is ambient water inhomogeneous on the nanometre length scale? Proc. Natl. Acad. Sci. Letter to editor published online.

G. N. I. Clark, C. D. Cappa, J. D. Smith, R. J. Saykally, T. Head-Gordon (2010). The structure of ambient water. Mol. Phys. (Review) 108 (11), 1415- 1433.

A. Sodt and T. Head-Gordon (2010). An implicit solvent coarse-grained lipid model with correct stress profile. J. Chem. Phys. 132, 205103-205310.

A. Sodt and T. Head-Gordon (2010). Driving forces for transmembrane alpha-helix oligomerization. Biophys. J. 99, 227-237.

E.-H. Yap and T. Head-Gordon (2010). A multipole-based Poisson Boltzmann solver for simulation of large protein complexes. J. Chem. Theory Comput. (Journal cover) 6, 2214-2224.

G. N. I. Clark, G. L. Hura, J. Teixeira, A. K. Soper, T. Head-Gordon (2010). Small angle scattering and the structure of ambient liquid water. Proc. Natl. Acad. Sci. Published online July 20; 1073/pnas.1006599107.

J. E. Kohn, P. Afonine, J. Z. Ruscio, P. D. Adams, T. Head-Gordon (2010). Evidence of functional protein dynamics from X-ray crystallography. PLoS Computational Biology 6(8): e1000911.

M. Lin and T. Head-Gordon (2010). Reliable protein structure refinement using a physically derived energy function. J. Comp. Chem. In press.

R. M. Lynden-Bell, N. Giovambattista, P. G. Debenedetti, T. Head-Gordon, P. J. Rossky (2010). Hydrogen bond strength and network effects on hydration of nonpolar molecules. Phys. Chem. Chem. Phys. submitted

J. Z. Ruscio, J. E. Kohn, K. A. Ball, T. Head-Gordon (2009). The influence of protein dynamics on the success of computational enzyme design. J. Am. Chem. Soc. 131, 14111-14115.

M.E. Johnson and T. Head-Gordon (2009). Assessing thermodynamic-dynamic relationships for water-like liquids. J. Chem. Phys. 130, 214510-21.

M.E. Johnson, C. Malardier-Jugroot, R.K. Murarka, and T. Head-Gordon (2009). Hydration water dynamics near biological interfaces. J. Phys. Chem. B 113, 4082-4092.

PI Graeme Henkelman

J. A. Farmer, C. T. Campbell, L. Xu, and G. Henkelman, Defect sites and their distributions on MgO(100) by Li and Ca adsorption calorimetry, J. Am. Chem. Soc. 131, 3098-3103 (2009).

W. Tang and G. Henkelman, Charge redistribution in core-shell nanoparticles to promote oxygen reduction, J. Chem. Phys. 130, 194504 (2009).

D. Mei, L. Xu, and G. Henkelman, Potential energy surface of methanol decomposition on Cu(110), J. Phys. Chem. C 113, 4522-4537 (2009).

N. S. Froemming and G. Henkelman, Optimizing core-shell nanoparticle catalysts with a genetic algorithm, J. Chem. Phys. 131, 234103 (2009).

L. Xu, D. Mei, and G. Henkelman, Adaptive kinetic Monte Carlo simulation of methanol decomposition on Cu(100), J. Chem. Phys. 131, 244520 (2009).

D. Sheppard, G. Henkelman, and O. A. von Lilienfeld, Alchemical derivatives of reaction energetics, J. Chem. Phys. 133, 084104 (2010).

L. Xu and G. Henkelman, Calculations of Li adsorption and diffusion on MgO(100) in comparison to Ca, Phys. Rev. B , in press (2010).

PI Ian Hinchliffe

Phys.Lett.B688:21-42,2010.

PI Brian Hingerty

Broyde S, Patel DJ. DNA repair: How to accurately bypass damage. Nature. 2010  Jun 24;465(7301):1023-4. PubMed PMID: 20577203.

Cai Y, Kropachev K, Xu R, Tang Y, Kolbanovskii M, Kolbanovskii A, Amin S, Patel DJ, Broyde S, Geacintov NE. Distant neighbor base sequence context effects  in human nucleotide excision repair of a benzo[a]pyrene-derived DNA lesion. J Mol Biol. 2010 Jun 11;399(3):397-409. Epub 2010 Apr 22. PubMed PMID: 20399214; PubMed Central PMCID: PMC2923096.

Rechkoblit O, Kolbanovskiy A, Malinina L, Geacintov NE, Broyde S, Patel DJ. Mechanism of error-free and semitargeted mutagenic bypass of an aromatic amine lesion by Y-family polymerase Dpo4. Nat Struct Mol Biol. 2010 Mar;17(3):379-88. Epub 2010 Feb 14. PubMed PMID: 20154704.

Ding S, Kolbanovskiy A, Durandin A, Crean C, Shafirovich V, Broyde S, Geacintov NE. Absolute configurations of DNA lesions determined by comparisons of experimental ECD and ORD spectra with DFT calculations. Chirality. 2009;21 Suppl  1:E231-41. Review. PubMed PMID: 19937959.

Donny-Clark K, Broyde S. Influence of local sequence context on damaged base conformation in human DNA polymerase iota: molecular dynamics studies of nucleotide incorporation opposite a benzo[a]pyrene-derived adenine lesion. Nucleic Acids Res. 2009 Nov;37(21):7095-109. Epub . PubMed PMID: 19767609; PubMed Central PMCID: PMC2790882.

Jia L, Kropachev K, Ding S, Van Houten B, Geacintov NE, Broyde S. Exploring damage recognition models in prokaryotic nucleotide excision repair with a benzo[a]pyrene-derived lesion in UvrB. Biochemistry. 2009 Sep 29;48(38):8948-57. PubMed PMID: 19681599.

Zhang N, Ding S, Kolbanovskiy A, Shastry A, Kuzmin VA, Bolton JL, Patel DJ, Broyde S, Geacintov NE. NMR and computational studies of stereoisomeric equine estrogen-derived DNA cytidine adducts in oligonucleotide duplexes: opposite orientations of diastereomeric forms. Biochemistry. 2009 Aug 4;48(30):7098-109. PubMed PMID: 19527068; PubMed Central PMCID: PMC2916639.

Ding S, Jia L, Durandin A, Crean C, Kolbanovskiy A, Shafirovich V, Broyde S, Geacintov NE. Absolute configurations of spiroiminodihydantoin and allantoin stereoisomers: comparison of computed and measured electronic circular dichroism spectra. Chem Res Toxicol. 2009 Jun;22(6):1189-93. PubMed PMID: 19485408.

Rechkoblit O, Malinina L, Cheng Y, Geacintov NE, Broyde S, Patel DJ. Impact of conformational heterogeneity of OxoG lesions and their pairing partners on bypass fidelity by Y family polymerases. Structure. 2009 May 13;17(5):725-36. PubMed PMID: 19446528.

Wang L, Broyde S, Zhang Y. Polymerase-tailored variations in the water-mediated and substrate-assisted mechanism for nucleotidyl transfer: insights from a study of T7 DNA polymerase. J Mol Biol. 2009 Jun 19;389(4):787-96. Epub 2009 Apr 21. PubMed PMID: 19389406; PubMed Central PMCID: PMC2801548.

Xu P, Oum L, Lee YC, Geacintov NE, Broyde S. Visualizing sequence-governed nucleotide selectivities and mutagenic consequences through a replicative cycle: processing of a bulky carcinogen N2-dG lesion in a Y-family DNA polymerase. Biochemistry. 2009 Jun 9;48(22):4677-90. PubMed PMID: 19364137; PubMed Central PMCID: PMC2929011.

PI Kai-Ming Ho

"Contrasting Behavior of Carbon Nucleation in the Initial Stages of Graphene Epitaxial Growth on Stepped Metal Surfaces", H. Chen, W. G. Zhu and Z. Y. Zhang, Phys. Rev. Lett. 104, 186101 (2010).

"First-principles study of quantum size effects in ultrathin Pb-Bi metal alloy films",Y. Jia, S. Y. Wang, W. G. Chen, Q. Sun, H. H. Weitering and Z. Y. Zhang, Phys. Rev. B 81, 245425 (2010).

"Strong Quantum Size Effects in Pb(111) Thin Films Mediated by Anomalous Friedel Oscillations", Y. Jia, B. A. Wu, C. Li, T. L. Einstein, H. H. Weitering and Z. Y. Zhang, Phys. Rev. Lett. 105, 066010 (2010).

"Adsorbate-induced restructuring of Pb mesas grown on vicinal Si(111) in the quantum regime",A. A. Khajetoorians, W. G. Zhu, J. Kim, S. Y. Qin, H. Eisele, Z. Y. Zhang and C. K. Shih Phys. Rev. B 80(24), 245426 (2009).

"Quantum Size Effects in the Growth, Coarsening, and Properties of Ultra-thin Metal Films and Related Nanostructures",M. M. Ozer, C. Z. Wang, Z. Y. Zhang and H. H. Weitering, J. of Low Temperature Physics 157, 221-251 (2009).

"Ab initio study on noncompensated CrO codoping of GaN for enhanced solar energy conversion", H. Pan, B. H. Gu, G. Eres and Z. Y. Zhang, J. Chem. Phys. 132(10), 104501 (2010).

"Phase-Dependent Photocatalytic Ability of TiO2: A First-Principles Study",
H. Pan, B. H. Gu and Z. Y. Zhang, J. of Chem. Theory and Computation 5(11): 3074-3078 (2009).

"Fabrication and characterization of brookite-rich, visible light-active TiO2 films for water splitting",H. Pan, X. F. Qiu, I. N. Ivanovc, H. M. Meyer, W. Wang, W. G. Zhu, M. P. Paranthaman, Z. Y. Zhang, G. Eres and B. H. Gu, Appl. Catalysis B-Environmental 93(1-2): 90-95 (2009).

"Kinetic Monte Carlo simulations of nanocolumn formation in two-component epitaxial growth", S. Zheng, W. G. Zhu, Y. F. Gao, G. M. Stocks and Z. Y. Zhang  Appl. Phys. Lett. 96, 071913 (2010).

"Band Gap Narrowing of Titanium Oxide Semiconductors by Noncompensated Anion-Cation Codoping for Enhanced Visible-Light Photoactivity", W. G. Zhu, X. F. Qiu, V. Iancu, X. Q. Chen, H. Pan, W. Wang, N. M. Dimitrijevic, T. Rajh, H. M. Meyer, M. P. Paranthaman, G. M. Stocks, H. H. Weitering, B. H. Gu, G. Eres and Z. Y. Zhang, Phys. Rev. Lett. 103, 226401 (2009).

"Finding Low Energy Structure of Si[001] Symmetric Tilted Grain Boundaries With A Genetic Algorithm", J. Zhang, C. Z. Wang, and K. M. Ho, Phys. Rev. B 80, 174102 (2009).

"Charge localization in [112] Si/Ge and Ge/Si core-shell nanowires", Nuo Liu , Yan-Rong Li , Ning Lu , Yong-Xin Yao , Xiao-Wei Fang , Cai-Zhuang Wang and Kai-Ming Ho, J. Phys. D: Appl. Phys. 43, 275404 (2010).

"Stochastic coarsening model for Pb islands on a Si(111) surface", G. P. Zhang, M. Hupalo, M. Li, C. Z. Wang, J.W. Evans, M. Tringides, and K. M. Ho, Phys. Rev. B, accepted.

Graphene Oxide as an Ideal Substrate for Hydrogen Storage", L Wang, K Lee, Y-Y Sun, M Lucking, Z Chen, J J Zhao, and S B Zhang, ACS Nano 3, 2995 (2009).

"Self-purification in Si nanocrystals: An energetics study", T.-L. Chan, H. Kwak, J.-H. Eom, S. B. Zhang, and J. R. Chelikowsky, Phys. Rev. B 82, 115421 (2010).

"Type B epitaxy of Ge on CaF2(111) surface", T.-L. Chan, C. Gaire, T.-M. Lu, G.-C. Wang, and S. B. Zhang Surf. Sci. 604, 1645-1648 (2010)

"Morphology and texture evolution of nanostructured CaF2 films on amorphous substrates under oblique incidence flux", C. Gaire, P. Snow, T.-L. Chan, W. Yuan, M. Riley, Y. Liu, S. B. Zhang, G.-C. Wang, and T.-M. Lu, Accepted.

 

 

 

 

 

 

 


I

PI Hong Im

P. G. Arias, H. G. Im, P. Narayanan, A. Trouve, "A computational study of nonpremixed flame extinction by water spray," Proceedings of the Combustion Institute, v. 33, in press, (2011).

S.M. Sarathy, W.J. Pitz, M.J. Thomson, and T.F. Lu, "An Experimental and Kinetic Modeling Study of Methyl Decanoate Combustion," Proceedings of the Combustion Institute, v. 33, in press (2011).

P. Narayanan, H.R. Baum and A. Trouve, "Effect of soot addition on extinction limits of luminous laminar counterflow diffusion flames," Proceedings of the Combustion Institute, v. 33, in press (2011).

Z. Luo, C.S. Yoo, E. Richardson, J.H. Chen, C.K. Law, and T.F. Lu, "Chemical Explosive Mode Analysis for a Turbulent Lifted Ethylene Jet Flame in Highly-Heated Coflow," Combustion and Flame, submitted (2010).

Z. Luo, T.F. Lu, and J. Liu, "A Reduced Mechanism for Ethylene/Methane Mixtures with Excessive NO Enrichment," Combustion and Flame, submitted (2010).

PI Talgat  Inerbaev

T. M. Inerbaev, S. Seal and A.E. Masunov, Density functional study of oxygen vacancy formation and spin density distribution in octahedral ceria nanoparticles Journal of Molecular Modeling 16(10) 1617-1623 (2010)

A. Vincent, T.M. Inerbaev, S. Babu, A.S. Karakoti, W.T. Self, A.E. Masunov and S. Seal, Tuning Hydrated Nanoceria Surfaces: Experimental/Theoretical Investigations of Ion Exchange and Implications in Organic and Inorganic Interactions Langmuir 26(10) 7188-7198 (2010)

T. Inerbaev, A.S. Karakoti, S. V. N. T., Kuchibhatla, A.E. Masunov, and S. Seal, Water Induced Blue Shift of Cerium Oxide Nanoparticles (submitted)

PI Jennifer Irish

Udoh, I. E., and Irish, J. L., "Improvements in hurricane surge response functions: Incorporating the effects of forward speed, approach angle, and sea level rise," Proc. 1st International Conference on Vulnerability and Risk Analysis and Management, College Park, MD, accepted.

 Irish, J. L., Ferreira*, C. M., Song*, Y. K., Udoh*, I., Olivera, F., and Chang, K.-A., "Rapid probabilistic hurricane surge and damage forecasting using hydrodynamics-based surge response functions," Proc. International Conference on Coastal Engineering in Shanghai, China (2009), in press.

PI Valerie Izzo

V.A. Izzo and P.B. Parks, "Plasma current spikes due to internal reconnection during tokamak disruptions" Nucl. Fusion 50, 058001

T. G. Jenkins, S. E. Kruger, C. C. Hegna, D. D. Schnack, and C. R. Sovinec, "Calculating electron cyclotron current drive stabilization of resistive tearing modes in a nonlinear MHD model", Phys. Plasmas 17, 012502 (2010).


J

PI Stephen Jardin

L.E. Sugiyama and H.R. Strauss, "Magnetic X-points, edge localized modes, and stochasticity", Phys. Plasmas 17, 062505 (2010).

J.A. Breslau and G.Y. Fu, "Implementation of an implicit shear Alfven operator in the M3D code," Comp. Phys. Communications 181, 1661-1670 (2010).

H.R. Strauss, R. Paccagnella, and J. Breslau, "Wall forces produced during ITER disruptions", Phys. Plasmas 17, 082505 (2010).

PI Julius Jellinek

J. R. Green, J. Jellinek, and R. S. Berry, SPACE-TIME PROPERTIES OF GRAM-SCHMIDT VECTORS IN CLASSICAL HAMILTONIAN EVOLUTION, Phys. Rev. E 80, 066205 (1-10) (2009)

R. Santamaria, J. Soullard, and J. Jellinek, THERMAL BEHAVIOR OF A 13-MOLECULE HYDROGEN CLUSTER UNDER PRESSURE, J. Chem. Phys. 132, 124505 (1-7) (2010).

M. Yang, F. Yang, K. A. Jackson, and J. Jellinek, PROBING THE STRUCTURAL EVOLUTION OF CuN-, N = 9 - 20, THROUGH A COMPARISON OF COMPUTED ELECTRON REMOVAL ENERGIES AND EXPERIMENTAL PHOTOELECTRON SPECTRA, J. Chem. Phys. 132, 064306 (1-6) (2010).

R. Perez de Tudela, D. Lopez-Duran, M. P. de Lara-Castells, R. Prosmiti, O. Roncero, G. Delgado-
Barrio, F. A. Gianturco, J. Jellinek, and P. Villareal, A QUANTUM CHEMISTRY APPROACH TO ENERGIES, STRUCTURES, AND SPECTROSCOPY OF DOPED HELIUM CLUSTERS, In Computational Methods in Science and Engineering, Vol. 1, G. Maroulis and T. E. Simos, Eds., AIP Conference Proceedings (in press)

Li Ma, K. A. Jackson, and J. Jellinek, SITE-SPECIFIC POLARIZABILITIES AS PREDICTORS OF FAVORABLE BINDING SITES ON Na_n CLUSTERS, Submitted

C. Wang, R. S. Berry, and J. Jellinek, RANGE EFFECTS OF INTER-PARTICLE FORCES ON STRUCTURES, THERMODYNAMIC PROPERTIES AND POTENTIAL ENERGY LANDSCAPES: (KCl)_32 AND RELATED SYSTEMS, Submitted

PI Puru Jena

Sa Li, Rajeev Ahuja, C. Moys??s Ara??jo, B??rje Johansson and Puru Jena, Dehydrogenation associated with Ti catalyst in sodium alanate, J. Phys. Chem. Solids, 71, 1073 (2010).

Oleksandr Dolotko, Haiqiao Zhang, Sa Li, Puru Jena, and Vitalij Pecharsky, Mechanochemically driven nonequilibrium processes in MNH2???CaH2 systems (M= Li or Na), Journal of Alloys and Compounds, 506, 224 (2010).

Jian Zhou, Qian Wang, Qiang Sun, and Puru Jena , Electronic and magnetic properties of a BN sheet decorated with hydrogen and fluorine, Phys. Rev. B 81, 085442, (2010)

Qian Wang, Qiang Sun, and Puru Jena, First-principles study of the effect of vacancies on magnetic properties of Zn1-xCoxO thin films, J. Phys.: Condens. Matter 22, 076002 (2010)

Miao Miao Wu, Xiao Zhou, Jian Zhou, Qiang Sun, Qian Wang and Puru Jena , Interaction of C59Si with Si based clusters:a study of Janus nanostructures , J. Phys.: Condens. Matter 22, 275303 (2010)

Sa Li, Mary Willis, and P. Jena, Reaction intermediates during the dehydrogenation of metal borohydrides: A cluster perspective, J. Phys.Chem. C. (In press).

Wang, Q., Sun, Q., and Jena, P.: "Probing the Existence of Energetically Degenerate Cluster Isomers by Chemically Tagging", Appl. Phys. Lett. (submitted).

Wu, M. M., Wang, Q., Sun, Q., and Jena, P., Reaction induced magnetic transition in Mn2 dimer,  J. Chem. Phys. (submitted).

Wu, M. M., Wang, H., Ko, Y. J., Kandalam, A. K., B. Kiran, Wang, Q., Sun, Q., Bowen, K. H., and Jena, P., The Discovery of a New Class of Magnetic Superhalogens, J. Am. Chem. Soc. (submitted).

PI Chueng Ryong Ji

H.~M.~Choi and C.~R.~Ji, ``Light-front dynamic analysis of transition form factors in the process of P to V nu'' arXiv:1007.2502 [hep-ph].

B.Bakker and C.~R.~Ji, ``Spin Filter in DVCS amplitudes,'' arXiv:1002.0443 [hep-ph].

M. Blasone, A. Capolupo, C.-R. Ji and G. Vitiello, Ref.: Ms. No. IJMPA-D-10-00124R1 ``On flavor conservation in weak interaction decays involving mixed neutrinos", International Journal of Modern Physics A, in press.

H.-M. Choi, C.-R. Ji, ``Non-leptonic two-body decays of the B(c) meson in light-front quark model and QCD factorization approach" , Published in Phys.Rev .D 80:114003,2009.

C.~R.~Ji, W.~Melnitchouk and A.~W.~Thomas, ``Equivalence of pion loops in equal-time and light-front dynamics,'' Phys. Rev. D 80, 054018 (2009), [arXiv:0906.3497 [nucl-th]].

H.~M.~Choi and C.~R.~Ji, ``Semileptonic and radiative decays of the B_c meson in light-front quark model,'' Phys. Rev.D 80, 054016 (2009), [arXiv:0903.0455 [hep-ph]].

PI De-en Jiang

Jiang, D. E.*; Cooper, V. R.*; Dai, S. "Porous Graphene as the Ultimate Membrane for Gas Separation." Nano Lett., 9, 4019 (2009).

Jiang, D. E.*; Walter, M.; Dai, S. "Gold Sulfide Nanoclusters: A Unique Core-in-cage Structure" Chem. Euro. J., 16, 4999 (2010).

Jiang, D. E.* "Understanding and Predicting Thiolated Gold Nanoclusters from First Principles" Acta Physico-Chimica Sinica, 26, 999 (2010). (Invited review).

Jiang, D. E.*; Walter, M.*; Akola, J.*. "On the Structure of Thiolate-Protected Au44 Cluster." J. Phys. Chem. Special Issue, "Symposium on Protected Metallic Clusters, Quantum Wells, and Metal-nanocrystal Molecules", ASAP (Invited article).


K

PI Andrey Kalinichev

A.G.Kalinichev, P.Kumar, R.J.Kirkpatrick (2010) Effects of hydrogen bonding on the properties of layered double hydroxides intercalated with organic acids: Molecular dynamics computer simulations. (Invited). Philosophical Magazine, published on-line, April 13, 2010.

I.S.Ufimtsev, A.G.Kalinichev, T.J.Martinez, R.J.Kirkpatrick (2009) A multistate empirical valence bond model for solvation and transport simulations of OH in aqueous solutions. Phys.Chem.-Chem.Phys., 11, 9420-9430.

J.Wang, A.G.Kalinichev, R.J.Kirkpatrick (2009) Asymmetric hydrogen bonding and orientational ordering of water at hydrophobic and hydrophilic surfaces: A comparison of water/vapor, water/talc, and water/mica interfaces. J.Phys.Chem.C, 113, 11077???11085.

P.Kumar, A.G.Kalinichev, R.J.Kirkpatrick (2009) Hydrogen bonding structure and dynamics of aqueous carbonate species from Car-Parrinello molecular dynamics simulations. J.Phys.Chem.B, 113, 794-802.

PI Martin Karplus

B. R. Brooks, C. L. Brooks III, A. D. MacKerell, Jr., L. Nilsson, R. J. Petrella, B. Roux, Y. Won, G. Archontis, C. Bartels, S. Boresch, A. Caflisch, L. Caves, Q. Cui, A. R. Dinner, M. Feig, S. Fischer, J. Gao, M. Hodoscek, W. Im, K. Kuczera, T. Lazaridis, J. Ma. V. Ovchinnikov, E. Paci, R. W. Pastor, C. B. Post, J. Z. Pu, M. Schaefer, B. Tidor, R. M. Venable, H. L. Woodcock, X. Wu, W. Yang, D. M. York, and M. Karplus. CHARMM: The Biomolecular Simulation Program,  J. Comput. Chem. 30, 1545-1614 (2009),

P. Maragakis, A. van der Vaart, and M. Karplus. Gaussian-Mixture Umbrella Sampling, J. Phys. Chem. B 113, 4664-4673 (2009),

M. Cecchini, S. Krivov, M. Spichty, and M. Karplus. Calculation of Free-Energy Differences by Confinement Simulations. Application to Peptide Conformers, J. Phys. Chem. B 113, 9728-9740 (2009),

I. V. Kalgin, M. Karplus, and S. F. Chekmarev. Folding of a SH3 Domain: Standard and "Hydrodynamic" Analyses, J. Phys. Chem. B 113, 12759-12772 (2009),

M. Lei, J. Velos, A. Gardino, A. Kivenson, M. Karplus, and D. Kern. Segmented Transition Pathway of the Signaling Protein Nitrogen Regulatory Protein C, J. Mol. Biol. 392, 823-836 (2009),

Y. Qi, M. C. Spong, K. Nam, A. Banerjee, S. Jiralerspong, M. Karplus, and G. L. Verdine. Encounter and Extrusion of an Intrahelical Lesion by a DNA Repair Enzyme, Nature 462, 762-769 (2009),

M. Karplus and J. Pu. How Biomolecular Motors Work: Synergy between Single Molecule Experiments and Single Molecule Simulations, in Single Molecule Spectroscopy in Chemistry, Physics and Biology: Nobel Symposium 138, A. Graslund, R. Rigler, and J. Widengren, editors, 3-22 (Springer Series in Chemical Physics, 2009),

K. Nam, G. Verdine, and M. Karplus. Analysis of an Anomalous Mutant of MutM DNA Glycosylase Leads to New Insights into the Catalytic Mechanism, J. Am. Chem. Soc. 131, 18208-18209 (2009),

V. Ovchinnikov, B.L. Trout, and M. Karplus. Mechanical Coupling in Myosin V: A Simulation Study, J. Mol. Biol. 395, 815-833 (2010),

Y. Qi, M. C. Spong, K. Nam, M. Karplus, and G. Verdine. Entrapment and Structure of an Extrahelical Guanine Attempting to Enter the Active Site of a Bacterial DNA Glycosylase, MutM, J. Biol. Chem. 285, 1468-1478 (2010),

A. Grinthal, I. Adamovic, B. Weiner, M. Karplus and N. Kleckner. PR65, the HEAT-Repeat Scaffold of Phosphatase PP2A, Is an Elastic Connector that Links Force and Catalysis, Proc. Natl. Acad. Sci. USA 107, 2467-2472 (2010),

M. Karplus. Dynamical Aspects of Molecular Recognition, J. Mol. Recognit. 23, 102-104 (2010),

A. A. Golosov, J. J. Warren, L. S. Beese, and M. Karplus. The Mechanism of the Translocation Step in DNA Replication by DNA Polymerase I: A Computer Simulation Analysis, Structure 18, 83-93 (2010),

M. Cecchini, Y. Alexeev, and M. Karplus. Pi Release from Myosin: A Simulation Analysis of Possible Pathways Structure 18, 458-470 (2010),

M. Karplus. Role of Conformation Transitions in Adenylate Kinase, Proc. Natl. Acad. Sci. USA 107, E71 (2010),

F. Rao and M. Karplus. Protein Dynamics Investigated by Inherent Structure Analysis, Proc. Natl. Acad. Sci. USA 107, 9152-9157 (2010),

M. Spichty, M. Cecchini, and M. Karplus. Conformational Free-Energy Difference of a Miniprotein from Nonequilibrium Simulations, J. Phys. Chem. Lett. 1, 1922-1926 (2010),

PI Daniel Kasen

D. Kasen, ``Seeing the Collision of a Supernova with its Companion Star'', ApJ, 708, 1025 (2010).

D. Kasen and L.~Bildsten ``Supernova Light Curves Powered by Young Magnetars", ApJ, 717, 245 (2010).

D. Kasen, S.E. Woosley, and A. Heger ``Pair Instability Supernovae: Light Curves, Spectra, and Shock Breakout", ApJ, submitted (2010).

D. Kasen, F. Ropke, and S.E. Woosley ``The Diversity of Type Ia Supernovae from Broken Symmetries'', Nature, 460, 869 (2009).

D.Kasen and S.E. Woosley, "Type II Supernovae: Model Light Curves and Standard Candle Relationships", ApJ, 702, 2205 (2009).

PI Paul Kent

M. Bajdich, M. L. Tiago, R. Q. Hood, P. R. C. Kent, and F. A. Reboredo. "Systematic reduction of sign errors in many-body calculations of atoms and molecules". Physical Review Letters 104 193001 (2010).

O. Delaire, K. Marty, M. B. Stone, P. R. C. Kent, M. S. Lucas, D. L. Abernathy, D. Mandrus, and B. C. Sales. "Phonon softening and metallization of a narrow-gap semiconductor by thermal disorder". Submitted to Physical Review Letters (2010)

N. Kumar, P. R. C. Kent, A. V. Bandura, J. D. Kubicki, D. J. Wesolowski, D. R. Cole and J. O. Sofo. "Faster Proton Transfer Dynamics of Water on SnO2 Compared to TiO2". Submitted to J. Chem. Phys. (2010).

M. Bajdich, F. A. Reboredo, and P. R. C. Kent. "Quantum Monte Carlo Calculations of dihydrogen binding energetics on Ca cations: an assessment of errors in density functionals for weakly bonded systems". Physical Review B (Rapid Communications) 82 081405 (2010).

H.-Y. Kim and P. R. C. Kent, "van der Waals force: Accurate calculation and assessment of approximate methods in dielectric nanocolloids up to 16 nm," J. Chem. Phys. 131, 144705 (2009) - published (10/14/2009).

Matthew Neurock, "Engineering Molecular Transformations", Industrial and Engineering Chemistry Reseach, (2010) accepted.

H. Olcay, L. Xu, Y. Xu, and G.W. Huber, "Aqueous-phase hydrogenation of acetic acid over transition metal catalysts", ChemCatChem; doi:/10.1002/cctc.201000134 (2010)

D.C. Ford, A.U. Nilekar, Y. Xu, M. Mavrikakis, "Partial and complete reduction of O2 by hydrogen on transition metal surfaces", Surface Science, 604 (2010) 1565???1575; doi: 10.1016/j.susc.2010.05.026.

A. Govindasamy, K. Muthukumar, J. Yu, Y. Xu, and V.V. Guliants, "Adsorption of propane, isopropyl, and hydrogen on cluster models of the M1 phase of Mo-V-Te-Nb-O mixed metal oxide catalyst", Journal of Physical Chemistry C, 114 (2010) 4544-4549; doi: 10.1021/jp910382x.

Beckham, Gregg; Bomble, Yannick; Matthews, James; Resch, Michael; Yarbrough, John; Decker, Steve; Bu, Lintao; Zhao, Xiongce; McCabe, Clare; Wohlert, Jakob; Bergenstr??hle, Malin; Brady, John; Adney, William; Himmel, Mike; Crowley, Michael, "The linker peptide from the Trichoderma reesei Family 7 cellulase is a flexible, disordered tether between the catalytic domain and carbohydrate-binding module further extended by O-linked glycosylation", submitted to JPC (2010)

Qing Pu, Yongsheng Leng, Xiongce Zhao, Peter T. Cummings, "Molecular Simulation Studies on the Elongation of Gold Nanowires in Benzenedithiol", J. Phys. Chem. B, in press. (2010)

Xiongce Zhao, "Self assembly of DNA segments on graphene and carbon nanotube arrays in aqueous solution: a molecular dynamics study", submitted to JPC. (2010)

Clare McCabe, Xiongce Zhao, "Energy storage in cellulase linker peptides", (Invited paper), in "Computational Modeling in Lignocellulosic Biofuel Production", Editors: M. Nimlos, M. F. Crowley, ACS symposium series, ACS Publishing, in press. (2010)

A.F. Kemper, T.A. Maier, H.-P. Cheng, P.J. Hirschfeld, D.J. Scalapino. "Sensitivity of the superconducting state and magnetic susceptibility to key aspects of electronic structure in ferropnictides", New J. Phys. 12, 073030, (2010).

K. Foyevtsova, H.C. Kandpal, H.O. Jeschke, S. Graser, H.-P. Cheng, R. Valenti, P.J. Hirschfeld, "Modulation of pairing interaction in Bi2Sr2CaCu2O8+delta by an O dopant: A density functional theory study" Phys. Rev. B82, 054514(2010).

"First-principles study of Fe/MgO based magnetic tunnel junctions with Mg interlayers", Y. Wang, J. Zhang, X.G. Zhang, H.-P. Cheng. X.-F. Han, Phys. Rev. B82, 054405(2010).

S. Grase, A.F. Kemper, T.A. Maier, H.-P. Cheng, P.J. Herschfeld, and D.J. Scalapino, "Spin fluctuations and superconductivity in a three-dimensional tight-binding model for BaFe2As2", Phys.Rev. B81, 214503 (2010).

C. Cao, M. Wu, JZ Jiang, and H.-P. Cheng "Transition metal adatom and dimer adsorbed on graphene: Induced magnetization and electronic structures", Phys. Rev. B81, 205424 (2010).

L. Li, Y.-N. Wu, and H.-P. Cheng "First-Principles Calculations of Fe-doped monolayer C60 on h-BN/Ni(111) Surface Fe@C60", J. Chem Phys. 132, 074702 (2010).

J. Palma, J.L. X.G. Zhang, J.L. Krause, and H.-P. Cheng, "Manipulating I-V Characteristics of a Molecular Switch with Chemical Modifications", J. Phys. Chem. C114, 1655 (2010).

H.I. Li, K. Pussi, K.J. Hanna, et al. "Surface Geometry of C-60 on Ag(111)", Phys. Rev. Lett. 103, 056101(2009).  

Hai-Ping Cheng "Working at interfaces", submitted to Molecular Physics (2010)

Yun-Peng Chen and Hai-Ping Cheng "Structure and stability of thin water films on quartz surfaces". Submitted to Applied Physics Letters (2010)

G. Reddy, J.E. Straub, D. Thirumalai, "Dry amyloid fibril assembly in a yeast prion peptide is mediated by long-lived structures containing water wires", Proc. Natl. Acad. Sci. (in review, 2010).

Sponer JE, Vazquez-Mayagoitia A, Sumpter BG, Leszczynski J, Sponer J, Otyepka M, Banas P, Fuentes-Cabrera M, "Theoretical Studies on the Intermolecular Interactions of Potentially Primordial Base-Pair Analogues" CHEMISTRY-A EUROPEAN JOURNAL    16    3057-3065    (2010)   

Vazquez-Mayagoitia A, Huertas O, Brancolini G, Migliore A, Sumpter BG, Orozco M, Luque FJ, Di Felice R, Fuentes-Cabrera M, "Ab initio Study of the Structural, Tautomeric, Pairing, and Electronic Properties of Seleno-Derivatives of Thymine Context Sensitive Links" JOURNAL OF PHYSICAL CHEMISTRY B 113 14465-14472    (2009)

W. Donner, C. L. Chen, and A. J. Jacobson "Epitaxial Strain-Induced Chemical Ordering of LSC on STO" Submitted to Chemistry of Materials (2010)

PI Richard Klein

Krumholz, Mark R.; Klein, Richard I.; McKee, Christopher F.; Offner, Stella S. R.; Cunningham, Andrew J., The Formation of Massive Star Systems by Accretion, cience, Volume 323, Issue 5915 (2009)

 Offner, Stella S. R.; Klein, Richard I.; McKee, Christopher F.; Krumholz, Mark R., The Effects of Radiative Transfer on Low-Mass Star Formation, The Astrophysical Journal, Volume 703, Issue 1, pp. 131-149 (2009).

 Kratter, Kaitlin M.; Matzner, Christopher D.; Krumholz, Mark R.; Klein, Richard I., On the Role of Disks in the Formation of Stellar Systems: A Numerical Parameter Study of Rapid Accretion, The Astrophysical Journal, Volume 708, Issue 2, pp. 1585-1597 (2010).

 Krumholz, Mark R.; Cunningham, Andrew J.; Klein, Richard I.; McKee, Christopher F., Radiation Feedback, Fragmentation, and the Environmental Dependence of the Initial Mass Function, The Astrophysical Journal, Volume 713, Issue 2, pp. 1120-1133 (2010).

PI  Emmanouil Kioupakis

Q. Yan, P. Rinke, M. Scheffler, and C. G. Van de Walle, "Strain effects in group-III nitrides: Deformation potentials for AlN, GaN, and InN", Appl. Phys. Lett. 95, 121111 (2009)

E. Kioupakis, P. Rinke, A. Schleife, F. Bechstedt, and C. G. Van de Walle, "Free-carrier absorption in nitrides from first principles", Phys. Rev. B 81, 241201 (2010)

E. Kioupakis, P. Rinke, and C. G. Van de Walle, "Determination of internal loss in nitride lasers from first principles", Appl. Phys. Express 3, 082101 (2010)

P. G. Moses and C. G. Van de Walle, "Band bowing and band alignment in InGaN alloys", Appl. Phys. Lett. 96, 021908 (2010)

P. G. Moses, M. Miao, Q. Yan, and C. G. Van de Walle, "Hybrid functional investigations of band gaps and band alignments for AlN, GaN, InN, and InGaN", submitted.

E. Kioupakis, P. Rinke, K. T. Delaney, and C. G. Van de Walle, "Efficiency droop in nitride light emitters: the case of indirect Auger recombination", submitted.

PI Joanna Kiryluk

R. Abassi et al., Search for Muon Neutrinos from Gamma-Ray Bursts with the IceCube Neutrino Telescope, Astrophysical Journal 710, 346 (2010).

R. Abassi et al., Measurement of sound speed vs. depth in South Pole ice: pressure waves and shear waves, Astroparticle Phys. 33, 277 (2010).

R. Abassi et al.,The Energy Spectrum of Atmospheric Neutrinos between 2 and 200 TeV with the AMANDA-II Detector, Astroparticle Phys. 34, 48 (2010).

R. Abassi et al., Search for High-Energy Muon Neutrinos from the "Naked-Eye" GRB 080319B with the IceCube Neutrino Telescope, Astrophys. J. 701, 1721 (2009).

R. Abassi et al., First Neutrino Point-Source Results From the 22-String IceCube Detector, Astrophys. J. Lett. 701, L47 (2009).

R. Abassi et al., Calibration and Characterization of the IceCube Photomultiplier Tube, Nucl. Instrum. Meth.A618, 139 (2010).

R. Abassi et al., Extending the search for neutrino point sources with IceCube above the horizon, Phys. Rev. Lett.103, 221102 (2009).

R. Abassi et al., Limits on a muon flux from Kaluza-Klein dark matter annihilations in the Sun from the IceCube 22-string detector, Phys. Rev. D81, 057101 (2010).

R. Abassi et al., Measurement of the Anisotropy of Cosmic Ray Arrival Directions with IceCube, arXiv:1005.2960, accepted by Astrophys. J. Lett.

PI Richard Klein

Krumholz, Mark R.; Klein, Richard I.; McKee, Christopher F.; Offner, Stella S. R.; Cunningham, Andrew J., The Formation of Massive Star Systems by Accretion, cience, Volume 323, Issue 5915 (2009)

 Offner, Stella S. R.; Klein, Richard I.; McKee, Christopher F.; Krumholz, Mark R., The Effects of Radiative Transfer on Low-Mass Star Formation, The Astrophysical Journal, Volume 703, Issue 1, pp. 131-149 (2009).

 Kratter, Kaitlin M.; Matzner, Christopher D.; Krumholz, Mark R.; Klein, Richard I., On the Role of Disks in the Formation of Stellar Systems: A Numerical Parameter Study of Rapid Accretion, The Astrophysical Journal, Volume 708, Issue 2, pp. 1585-1597 (2010).

 Krumholz, Mark R.; Cunningham, Andrew J.; Klein, Richard I.; McKee, Christopher F., Radiation Feedback, Fragmentation, and the Environmental Dependence of the Initial Mass Function, The Astrophysical Journal, Volume 713, Issue 2, pp. 1120-1133 (2010).

PI Kwok Ko

C.-K. Ng, R.J. England, L.-Q. Lee. R. Noble, V. Rawat and J. Spencer, Transmission and Radiation of an Accelerating Mode in a Photonic Bandgap Fiber, SLAC-PUB-14156, submitted to PRST-AB (2010).

L.-Q. Lee, A. Candel, C.-K. Ng and K. Ko, On Using Moving Windows in Finite Element Time Domain Simulation for Long Accelerator Structures, accepted for publication in J. Comput. Physics (2010).

L.-Q. Lee, C. Ng, A. Candel, L. Xiao, G. Schussman, L. Ge, Z. Li, V. Rawat and K. Ko, Wakefield Computations at Extreme-Scale for Ultra-Short Bunches Using Parallel hp-Refinement, SciDAC Conference 2010, July 11-15, Chattanooga, Tennessee.

PI V. Rao Kotamarthi

Drewniak, B., Song J., Prell J., Kotamarthi V.R., and Jacob, R., Modeling Impact of Agriculture Land Use and Management on U.S. Carbon Budgets. Submitted to Global Change Biology.

PI Petr Kral

L. Vukovic and P. Kral, Coulombically Driven Rolling of Nanorods on Water, Phys. Rev. Lett. 103, 246103 (2009); highlighted: Nature Nanotechnology (18. Dec. 2009) and Virtual Journal of Nanoscale Sci. & Technol. Vol. 21, Issue 25.

N. Patra, B. Wang and P. Kral, Nanodroplet Activated and Guided Folding of Graphene Nanostructures, Nano Letters 9, 3766 (2009); highlighted: Nature 462, 658 (2009).

A. Titov B. Wang, K. Sint and P. Kral, Controllable synthetic molecular channels: Biomimetic ammonia switch, J. Phys. Chem. B 114, 1174 (2010).

N. Patra and P. Kral, Nanotube-assisted Encapsulation of Molecules inside Micelles, submitted.

N. Patra, Y. Song and P. Kral, Self-assembly of Graphene Nanostructures on Nanotubes, submitted.

PI Arnold Kritz

A.Y. Pankin, G.Y. Park, J. Cummings, et al. (2010) Kinetic modeling of H-mode pedestal with effects from anomalous transport and MHD stability (submitted to Problems of Atomic Science and Technology. Series: Plasma Physics).

A.Y. Pankin, G. Bateman, J.R. Cary et al.$(2010) Simulation of anomalous transport in tokamaks using the FACETS code. (Accepted for publication in Comp. Phys. Comm.)

A.H. Hakim, J.R. Cary, J. Candy, ..., A Pankin, et al. Coupled whole device simulations of plasma transport in tokamaks with the FACETS code (Accepted for publication in J. Physics: Conf. Series, 2010).

PI Leeor Kronik

S. Sharifzadeh, A. Biller, L. Kronik, and J. B. Neaton, "First-principles study of the electronic structure of organic semiconductors", presented at the 22nd Annual Workshop on Electronic Structure Methods, Austin, TX, June 2010.


L

PI Andrew Lacis

Q. Ma, R. H. Tipping, and R. R. Gamache, Uncertainties Associated with Theoretically Calculated N2-broadened Half-widths of H2O lines, Mol. Phys. Vol. 108, 2225 (2010).

C. Leforestier, R. H. Tipping, and Q. Ma, Temperature Dependence of Mechanisms Responsible for the Water-Vapor Continuum Absorption: II Dimers and collision-induced absorption. J. Chem. Phys. 132,164302 (2010).

PI Uzi Landman

"Oxidation of DNA: Damage to Nucleobases", S. Kanvah, J. Joseph, G. B. Schuster, R.N. Barnett, C.L. Cleveland, U. Landman, Accounts of Chemical Research, 43, 280 (2010).

"Size dependent binding energies of methane to small god clusters", S.M. Lang, T.M. Bernhardt, R.N. Barnett, U. Landman, ChemPhysChem 11, 1570 (2010).

"Methane Activation and Catalytic Ethylene Formation on Free Au2+",S.M. Lang, T.M. Bernhardt, R.N. Barnett, U. Landman, Angew. Chem. Int. Ed. 49, 980 (2010) (cover article).

"Ultrathin magnesia films as support for molecules and metal custers: tuning reactivity by thickness and composition", M.E. Vaida, T.M. Bernhardt, C. Barth, F. Esch, U. Heiz, U. Landman,

(feature article), Physica Status Solidi B 247, No. 5, 1001 (2010).

PI Michael Langston

B. Andersson, M. Benson, L. O. Cardell, J. Erjefal, M. Hahn-Zoric, M. A. Langston, R. Mobini and A. D. Perkins, "A Module-Based Analytical Strategy to Identify Novel Disease-Associated Genes Shows an Inhibitory Role for Interleukin 7 Receptor in Allergic Inflammation," BMC Systems Biology 3:19 (2009).

E. J. Chesler, R. Kirova, M. A. Langston, X. Peng and A. D. Perkins, "A Systems Genetic Analysis of Chronic Fatigue Syndrome: Combinatorial Data Integration from SNPs to Differential Diagnosis of Disease," in Methods of Microarray Data Analysis VI (J. Cuticchia and S. M. Lin, editors), CreateSpace Publishing, 2009, 81-98.

J. D. Eblen, I. C. Gerling, A. M. Saxton, J. Wu, J. R. Snoddy and M. A. Langston, "Graph Algorithms for Integrated Biological Analysis, with Applications to Type 1 Diabetes Data," in Clustering Challenges in Biological Networks (S. Butenko, W. A. Chaovalitwongse and P. Pardalos, editors), World Scientific, 2009, 207-222.

G. L. Rogers, A. D. Perkins, C. A. Phillips, J. D. Eblen, F. N. Abu-Khzam, and M. A. Langston, "Using Out-of-Core Techniques to Produce Exact Solutions to the Maximum Clique Problem on Extremely Large Graphs," Proceedings, ACS/IEEE International Conference on Computer Systems and Applications, Rabat, Morocco; 2009.

S. E. Bergeson, E. J. Chesler, R. Kirova, E. R. Lance, M. A. Langston, C. K. Lewis, K. H. Lodowski and J. Song "Reconstructing Generalized Logical Networks of Transcriptional Regulation in Mouse Brain from Temporal Gene Expression Data," EURASIP Journal on Bioinformatics and Systems Biology, 2009.

A. D. Perkins and M. A. Langston, "Threshold Selection in Gene Co-Expression Networks Using Spectral Graph Theory Techniques," BMC Bioinformatics 10 (2009).

B. J. Aronow, C. Auffray, M. Benson, G. Clermont, D. Dalevi, F. Dehne, D. Dubhashi, M. A. Langston, D. R. Marshall, Y. Moreau, P. Provero, P. Raasch, D. M. Rocke and J. Tegner. "Translating Between Systems Biology and Medicine: Report of the 3rd Bertinoro Systems Biology Workshop," Genome Medicine 1 (2009).

E. J. Baker, E. J. Chesler, J. J. Jay, R. Kirova, Z. Li, V. M. Philip and Y. Zhang. "Ontological Discovery Environment: A System for Integrating Gene-Phenotype Associations," Genomics 94 (2009), 377-387.

B. R. Borate, E. J. Chesler, A. M. Saxton and B. H. Voy. "Comparison of Thresholding Approaches for Microarray Gene Co-Expression Matrices," BMC Research Notes 2 (2009).

E. J. Chesler, S. Das, S. A. Kania, R. M. Lynch, S. Naswa, G. L. Rogers, A. M. Saxton and B. H. Voy. "Identifying Genetic Loci and Spleen Gene Coexpression Networks Underlying Immunophenotypes in BXD Recombinant Inbred Mice," Physiological Genomics 41 (2010), 244-253.

F. N. Abu-Khzam, H. Fernau, S. Lee-Cultura and U. Stege. "A Fixed-Parameter Algorithm for String-to-String Correction," Proceedings, Computing: the Australasian Theory Symposium (CATS), Brisbane, Australia, January, 2010.

G. Kempermann, L. Lu, M. K. Mulligan, R. W. Overall, G. L. Rogers Jr. and R. W. Williams. "Genetic Analysis of BDNF Expression Cliques and Adult Neurogenesis in the Hippocampus," Proceedings, ORNL Biomedical Science and Engineering Conference: Biomedical Sciences Research and Analysis in Neurosciences, Oak Ridge, Tennessee, May, 2010.

F. N. Abu-Khzam, A. E. Mouawad and C. P. Nolan. "A Hybrid Graph Representation for Recursive Backtracking Algorithms," Proceedings, International Frontiers of Algorithmics Workshop, Wuhan, China, August, 2010.

PI Stephan Lany

K. Biswas and S. Lany, "Energetics of quaternary III-V alloys described by incorporation and clustering of impurities", Phys. Rev. B 80, 115206 (2009).

PI Jean-Noel Leboeuf

R. Sanchez , D. E. Newman, J.-N. Leboeuf , V. K. Decyk , and B. A. Carreras, "Nature of transport across sheared zonal flows in electrostatic ion-temperature-gradient gyrokinetic plasma turbulence", Phys. Rev. Letts. 101, 205002, 14 November 2008.

R. Sanchez, D.E. Newman, J.-N. Leboeuf, B.A. Carreras, and V.K. Decyk, "On the nature of radial transport across radially-sheared poloidal zonal flows in electrostatic ion-temperature-gradient gyrokinetictokamak plasma turbulence", Phys. Plasmas 16, 055905 (2009).

R. Sanchez, D.E. Newman, J.N. Leboeuf, and V. Decyk, "Mechanisms responsible for the emergence of non-diffusive transport features across zonal flows in ITG gyro-kinetic simulations", Paper P1.1087, 37th EPS Conference on Plasma Physics, European Physical Society, Dublin, Ireland, 21 - 25 June, 2010. http://ocs.ciemat.es/EPS2010PAP/html/

PI Dung-Hai Lee

Fan Yang, Hui Zhai, Fa Wang, Dung-Hai Lee, The electronic instabilities of the Iron-based superconductors: a variational Monte-Carlo study, accepted by Phys. Rev. B

PI Frank Lee

A. Li, A. Alexandru, X. Meng and K.F. Liu, Study of QCD critical point using canonical ensemble method, Nucl. Phys. A830, 633 (2009)

Lai Wang, F.X. Lee, N to Delta transition amplitudes from QCD sum rules Phys. Rev. D 80, 034003 (2009).

F.X. Lee, S. Moerschbacher, W. Wilcox, Magnetic moments of vector, axial, and tensor mesons in lattice QCD, Phys. Rev. D 78, 094502 (2008).

Anyi Li, Andrei Alexandru, Keh-Fei Liu, Xiangfei Meng, Finite density phase transition of QCD with $N_f=4$ and $N_f=2$ using canonical ensemble method, submitted to Phys. Rev. D

Lai Wang and Frank X. Lee, MathQCDSR: a Mathematica package for QCD sum rules calculations, submitted to Computer Physics Communications

J.P. Singh, F.X. Lee, and Lai Wang, Eta-nucleon coupling constant in QCD with SU(3) symmetry breaking, submitted to Nuclear Physics A.

(xQCD Collaboration) A. Li, A. Alexandru , Y. Chen , T. Doi , S.J. Dong , T. Draper , M. Gong , A. Hasenfratz, I. Horvath , F.X. Lee , K.F. Liu , N. Mathur , T. Streuer , and J.B. Zhang, Overlap Valence on 2 + 1 Flavor Domain Wall Fermion Configurations with Deformation and Low-mode Substitution, submitted to Physical Review D.

Andrei Alexandru, Urs Wenger, QCD at non-zero density and canonical partition functions with Wilson fermions, submitted to Physical Review D.

PI T. S. Harry Lee

B. Julia-Diaz, H. Kamano, T.-S. H. Lee, A. Matsuyama, T. Sato, N. Suzuki, 'Dynamical coupled-channels analysis of $p(e,e'\pi)N$ reaction,'  Phys. Rev. C80, 025207 (2009)

Hovhannes R. Grigoryan, T.-S.H. Lee, Ho-Ung Yee, 'Electromagnetic Nucleon-to-Delta Transition in Holographic QCD,' Phys.Rev. D80, 055006 (2009)

B. Julia-Diaz, H. Kamano, T.-S. H. Lee, A. Matsuyama, T. Sato, N. Suzuki, 'Double and single pion photoproduction within a dynamical coupled-channelsmodel,' Phys. Rev. C80, 025207 (2009)

N. Suzuki, B. Julia-Diaz, H. Kamano, T.-S. H. Lee, A. Matsuyama, T. Sato, 'Disentangling the Dynamical Origin of $P_{11}$ Nucleon Resonances.' Phys. Rev. Lett. 104, 042302 (2010)

H. Kamano, S. Nakamura, T.-S. H. Lee, T. Sato, 'On the extraction of $P_{11}$ resonances from $\pi N$ data.' Phys. Rev. C 81, 065207 (2010)

N. Suzuki, T. Sato , T.-S.H. Lee, 'Extraction of Electromagnetic Transition Form Factors for Nucleon Resonances within a Dynamical Coupled-Channels Model' accepted by Phys. Rev. C, Sept., (2010);arXiv:1006.2196 [nucl-th]

PI Wei-li Lee

"Drift-kinetic studies of neoclassical poloidal rotation with finite orbits," R. A. Kolesnikov, W. X. Wang, F. L. Hinton, G. Rewoldt, and W. M. Tang, Plasma Phys. Control. Fusion 52 042002 (2010)

"Drift-kinetic simulation of neoclassical transport with impurities in tokamaks," R. A. Kolesnikov, W. X. Wang, F. L. Hinton, G. Rewoldt, and W. M. Tang, Phys. Plasmas 17, 022506 (2010)

"Comparison of poloidal velocity measurements to neoclassical theory on the National Spherical Torus Experiment," R. E. Bell, R. Andre, S. M. Kaye, R. A. Kolesnikov, B. P. LeBlanc, G. Rewoldt, W. X. Wang, and S. A. Sabbagh, Phys. Plasmas, in press (August 2010)

"Nonlinear flow generation by electrostatic turbulence in tokamaks," W. X. Wang, P. H. Diamond, T. S. Hahm, S. Ethier, G. Rewoldt, W. M. Tang, Phys. Plasmas, 17, 072511 (July 2010)

"A Synthetic Diagnostics for Validation of Electron Gyro-radius-scale Turbulence Simulations against Coherent Scattering Measurements," F.M. Poli, S. Ethier, W.X. Wang, T.S. Hahm, E. Mazzucato, and D.R. Smith, Phys. Plasmas, accepted and in print (August 2010)

"Properties of Freely Decaying and Driven Turbulence of Fusion Plasmas using Gyrokinetic Particle Simulation," R. Ganesh, W. W. Lee, S. Ethier and J. Manickam, Supplementary Special Issue of the Jornal of Japan Society of Plasma Science and Nuclear Fusion (to appear).

PI Xuhui Lee

Huang, J., X. Lee, E. G. Patton, 2010: Entrainment and Budget of Heat, Water Vapor and Carbon Dioxide in a Convective Boundary Layer Driven by Time-Varying Solar Radiation, Journal of Geophysical Research - Atmospheres, submitted.

PI Sanjiva Lele

J. Larsson, Effect of shock-capturing errors on turbulence statistics, AIAA J. 48, 1554-1557, 2010.

E. Johnsen, J. Larsson, A.V. Bhagatwala, W.H. Cabot, P. Moin, B.J. Olsson, P.S. Rawat, S.K. Shankar, B. Sjogreen, H.C. Yee, X. Zhong and S.K. Lele, Assessment of high-resolution methods for numerical simulations of compressible turbulence with shock waves, J. Comput. Phys. 229, 1213-1237, 2010. (This paper has been among the top-10 most downloaded from the journal)

J. Larsson and S. K. Lele, Direct numerical simulation of canonical shock/turbulence interaction,Phys. Fluids. 21, 126101, 2009. (This paper has been among the top-20 most downloaded from the journal)

J. Larsson, Blending technique for compressible inflow turbulence: algorithm localization and accuracy assessment, J. Comput. Phys. 228, 933-937, 2009.

PI Yongsheng Leng

Lei, Y. J. and Leng, Y. S., "Force oscillation and phase transition of simple fluids under confinement", Physical Review E (Rapid Communication), in press.

Pu, Q., Leng, Y. S., Zhao, X. C., and Cummings, P. T., "Molecular simulation studies on the elongation of gold nanowires in benzenedithiol", J. Phys. Chem. C 114 (2010).

Leng, Y. S., Lei, Y. J., and Cummings, P. T., "Comparative studies on the structure and diffusion dynamics of aqueous and nonpolar liquid films under nanometers confinement", Modeling Simul. Mater. Sci. Eng. 18, 034007 (2010).

PI William Lester

R. Whitesides, D. Domin, R. Salomon-Ferrer, W.A. Lester, Jr., and M. Frenklach, "Embedded-Ring Migration on Graphene Zigzag Edge," Proc. Int. Symp. Combustion, 32, 577 (2009).

D. Yu Zubarev, N. Robertson, D. Domin, J. McClean, J. Wang, W. A Lester, Jr., R. Whitesides, X. You, and M. Frenklach, "Local Electronic Structure and Stability of Pentacene Oxyradicals," J. Phys. Chem. C 114,  5429 (2010) (part of the Barbara J. Garrison Festschrift).

M. R. Philpott, S. Vukovic, Y. Kawazoe, and W. A. Lester, Jr., "Edge versus Interior in the Chemical Bonding and Magnetism of Zigzag Edged Triangular Graphene Molecules," J. Chem. Phys., 133, 044708 (2010).

D. Yu Zubarev, N. Robertson, D. Domin, J. McClean, J. Wang, W. A Lester, Jr., R. Whitesides, X. You, and M. Frenklach, "Polyaromatic Hydrocarbon Oxyradical Stability," J. At. Mol. Sci. 1, 48 (2010).

D. Yu Zubarev, D. Domin, W. A Lester, Jr., "Quantitative Characteristics of Qualitative Localized Bonding Patterns," J. Phys. Chem. A 114, 3074 (2010) (part of the Benoit Soep Festschrift).

J. Wang, D. Domin, B. Austin, D. Yu Zubarev, J. McClean, M. Frenklach, T. Cui, W. A. Lester, Jr., "A Diffusion Monte Carlo Study of the O-H Bond Dissociation of Phenol," J. Phys. Chem. A 114, 9832 (2010) (part of the Reinhard Schinke Festschrift).

J. Wang, D. Yu Zubarev, M. R. Philpott, S. Vukovic, W. A Lester, Jr., T. Cui, Y. Kawazoe, "Onset of Diradical Character in Small Nanosized Graphene Patches," Phys. Chem. Chem. Phys. 12, 9839 (2010).

L. Castiglioni, S. Vukovic, P. E. Crider, W. A. Lester, Jr., and D. M. Neumark, "Intramolecular Competition in the Photodissociation of C3D3 Radicals at 248 and 193 nm," Phys. Chem. Chem. Phys. 12, 10714 (2010).

X. You, R. Whitesides, D. Zubarev, W. A. Lester, Jr., M. Frenklach, "Bay-Capping Reactions: Kinetics and Influence on Graphene-Edge Growth," Proc. Combust. Inst. doi:10.1016/j.proci.2010.05.110 (in press).

PI Xin-Zhong Liang

Liang, X.-Z., M. Xu, X. Yuan, T. Ling, H.I. Choi, F. Zhang, L. Chen, S. Liu, S. Su, F. Qiao, J.X.L. Wang, K.E. Kunkel, W. Gao, E. Joseph, V. Morris, T.-W. Yu, J. Dudhia, and J. Michalakes, 2010: Development of CWRF for regional weather and climate prediction: General model description and basic skill evaluation. J. Climate (submitted).

PI Guang Lin

G. Lin and A. M. Tartakovsky, An Efficient, High-order Probabilistic Collocation Method on Sparse Grids for Three-dimensional Flow in Random Porous Media, Advances in Water Resources, Volume 32, Issue 5, 2009, Pages 712-722.

G. Lin and A. M. Tartakovsky, Numerical studies of three-dimensional stochastic Darcy's equation and stochastic advection-diffusion-dispersion equation, Journal of Scientific Computing, Volume 43, Issue 1, 2010, Pages 92-117.

G. Lin, D. M. Tartakovsky, and A. M. Tartakovsky, Random Domain Decomposition for Probabilistic Collocation on Sparse Grids, Journal of Computational Physics, Volume 229, Issue 19, 20 September 2010, Pages 6995-7012.

Z. Xu and G Lin. Hierarchical reconstruction for spectral/hp element methods for solving hyperbolic conservation laws, Acta Mathematica Scientia, Volume 29, Issue 6, 2009, Pages 1737-1748.

W. Wu, G. Lin, Basic function scheme of polynomial type, Applied Mathematics and Mechanics, 2009, 30(9).

D. Mei, G. Lin. Effects of heat and mass transfer on the reaction kinetics of CO oxidation on the RuO2(110) catalyst, Catalysis Today, in review.

Z. Xu, Y. Liu, H. du, G. Lin, and CW. Shu, Point-wise Hierarchical Reconstruction for Discontinuous Galerkin and Finite Volume Methods for Solving Conservation Laws, Journal of Computational Physics, in review.

G. Lin and G.E. Karniadakis, Stochastic Simulations and Sensitivity Analysis of Plasma Flow, International Journal for Numerical Methods in Engineering, Volume 80, Issue 6-7, 2009, Pages 738 ??? 766.

G. Lin, A. M. Tartakovsky, and CH Henager, Jr., A phase field model for crystal growth in the Bridgman furnace, International Journal of Heat and Fluid Flow, in review.

PI Yu Lin

Y. Lin, X. Y. Wang, L. Chen, X. Lu, W. Kong, and Z. Lin, Development of Gyrokinetic Electron and Fully Kinetic Ion (GeFi) Particle Simulation Scheme for Investigation of Magnetic Reconnection, PPCF, submitted, 2010.

PI Zhihong Lin

Z. H. Guo, L. Chen and F. Zonca. "Radial Spreading of Drift-Wave-Zonal-Flow Turbulence via Soliton Formation." Physical Review Letters 103, 055002 (2009).

I. Holod, W. L. Zhang, Y. Xiao and Z. Lin. "Electromagnetic formulation of global gyrokinetic particle simulation in toroidal geometry." Physics of Plasmas 16, 122307 (2009).

Y. Nishimura. "Excitation of low-n toroidicity induced Alfven eigenmodes by energetic particles in global gyrokinetic tokamak plasmas." Physics of Plasmas 16, 030702 (2009).

Y. Nishimura, Z. Lin and L. Chen. "Full torus electromagnetic gyrokinetic particle simulations with kinetic electrons." Communications in Computational Physics 5, 183 (2009).

Z. Y. Qiu, L. Chen and F. Zonca. "Collisionless damping of short wavelength geodesic acoustic modes." Plasma Physics and Controlled Fusion 51, 012001 (2009).

R. E. Waltz, A. Casati and G. M. Staebler. "Gyrokinetic simulation tests of quasilinear and tracer transport." Physics of Plasmas 16, 072303 (2009).

Y. Xiao and Z. H. Lin. "Turbulent Transport of Trapped-Electron Modes in Collisionless Plasmas." Physical Review Letters 103, 085004 (2009).

H. S. Zhang, Z. Qiu, L. Chen and Z. Lin. "The importance of parallel nonlinearity in the self-interaction of geodesic acoustic mode." Nuclear Fusion 49, 125009 (2009).

E. M. Bass and R. E. Waltz. "Gyrokinetic simulations of mesoscale energetic particle driven Alfvenic turbulent transport embedded in microturbulence." submitted to Phys. Plasmas with pre-print available on the GYRO website: https://fusion.gat.com/theory/Gyropub (2010).

I. Holod and Z. Lin. "Effects of electron dynamics in toroidal momentum transport driven by ion temperature gradient turbulence." Plasma Physics and Controlled Fusion 52, 035002 (2010).

D. A. Spong, E. D'Azevedo and Y. Todo. "Clustered frequency analysis of shear Alfveacuten modes in stellarators." Physics of Plasmas 17, 022106 (2010).

R. E. Waltz. "Nonlinear Subcritical MHD Beta Limit." General Atomics Report GA-A26625, accepted for publication in Phys. Plasmas. Preprint on GYRO website: https://fusion.gat.com/theory/Gyropub ( 2010).

Y. Xiao, I. Holod, W. L. Zhang, S. Klasky and Z. Lin. "Fluctuation characteristics and transport properties of collisionless trapped electron mode turbulence." Physics of Plasmas 17, 022302 (2010).

W. L. Zhang, V. Decyk, I. Holod, Y. Xiao, Z. Lin and L. Chen. "Scalings of energetic particle transport by ion temperature gradient microturbulence." Physics of Plasmas 17, 055902 (2010).

H. S. Zhang and Z. Lin. "Trapped electron damping of geodesic acoustic mode." Physics of Plasmas 17, 072502 (2010).

Wenjun Deng, Zhihong Lin, Ihor Holod, Xin Wang, Yong Xiao, and Wenlu Zhang, "Gyrokinetic particle simulations of reversed shear Alfven eigenmode excited by antenna and fast ions", Phys. Plasmas, 2010 October issue, in press.

H. S. Zhang, Z. Lin, I. Holod, X. Wang, Y. Xiao, W. L. Zhang, "Gyrokinetic particle simulation of beta-induced Alfven eigenmode", Phys. Plasmas, 2010 October issue, in press.

Feng Liu, Z. Lin, J. Q. Dong, K. J. Zhao, "Gyrokinetic Simulation of Turbulence Driven Geodesic Acoustic Modes in Edge Plasmas of HL-2A Tokamak", Phys. Plasmas, 2010 October issue, in press.

PI Da-Jiang Liu

"Formation of complex wedding-cake morphologies during homoepitaxial film growth of Ag on Ag9111): atomistic, step-dynamics, and continuum modeling," M. Li, Y. Han, P.A. Thiel, and J. W. Evans, J. Phys. Cond. Mat., 21, 084216 (2009).

"The effect of chalcogens (O, S) on coarsening of nanoislands on metal surfaces," M. Shen, D.-J. Liu, C. J. Jenks, J. W. Evans, and P. A. Thiel, Surf. Sci. 603, 1486 (2009).

"Interactions between oxygen on Pt(100): Implications for ordering during chemisorption and catalysis," D.-J. Liu and J. W. Evans, ChemPhysChem, 11, 2174 (2010).

"DFT analysis of key energetics in metal homoepitaxy: quantum size effects in periodic slab calculations," D.-J. Liu, Phys. Rev. B, 81, 035415 (2010).

"Formation and coarsening of Ag(110) bilayer islands on NiAl(110): STM analysis and atomistic lattice-gas modeling," Y. Han, B. Unal, D. Jing, F. Qin, C. J. Jenks, D.-J. Liu, P. A. Thiel, and J. W. Evans, Phys. Rev. B, 81 115462 (2010).

"Quantum size effects in metal nanofilms: comparison of an electron-gas model and density functional theory calculations," Y. Han, and D.-J. Liu, Phys. Rev. B , 80, 155404 (2009).

"Low temperature adsorption of H2S on Ag(111)," S. Russell, D.-J. Liu, M. Kawai, Y. Kim, and P. A. Thiel, J. Chem. Phys., in press.

"Formation and coarsening of Ag(110) bilayer islands on NiAl(110): STM analysis and atomistic lattice-gas modeling," Phys. Rev. B, 81, 115462 (2010)

PI Feng Liu

L. Ci, L. Song, C. Jin, D. Jariwala, D. Wu, Y. Li, A. Srivastava, Z. Wang, K. Storr, L. Balicas, F. Liu, P. M. Ajayan "Atomic layers of hybridized boron nitride and graphene domains." Nature Mat. 9, 430 (2010)

Z. Liu, J. Wu, W. Duan, M. G. Lagally, F. Liu "Electronic Phase Diagram of Single-Element Silicon 'Strain' Superlattices." Phys. Rev. Lett. 105, 016802 (2010)

Z. F. Wang and Feng Liu "Manipulation of Electron Beam Propagation by Hetero-Dimensional Graphene Junctions." ACS Nano. 4, 2459 (2010)

Y. Zhang, M. Yu, D. E. Savage, Max G. Lagally, R. H. Blick, and Feng Liu "Effect of Surface Bonding on Semiconductor Nanoribbon Wiggling Structure." Appl. Phys. Lett. 96, 111904 (2010)

M. Gao, Y. Pan, C. Zhang, H. Hu, R. Yang, H. Lu, J. Cai, S. Du, Feng Liu, and H.-J. Gao "Tunable interfacial properties of epitaxial graphene on metal substrates." Appl. Phys. Lett. 96, 053109 (2010)

J. Zhu, Feng Liu, and G. B. Stringfellow "Enhanced cation-substituted p-type doping in GaP from dual surfactant effects/" J. Crys. Growth 312, 174 (2010)

PI Keh-Fei Liu

K.F. Liu, `Neutron Electric Dipole Moment at Fixed Topology', Mod. Phys. Lett. A24, 1971 (2009), [arXiv:0807.1365].[UK/08-07]

M. Deka, T. Streuer, T. Doi, S.J. Dong, T. Draper, K.F. Liu, N. Mathur, and A.W. Thomas, `Moments of Nucleon's Parton Distribution for the Sea and Valence Quarks from Lattice QCD', Phys. Rev. D79, 094502 (2009), [arXiv:0811.1779]. [UK/08-08]

T. Doi, M. Deka, S.J. Dong, T. Draper, K.F. Liu, D. Mankame, N. Mathur, T. Streuer, `Nucleon strangeness form factors from N(f) = 2+1 clover fermion lattice QCD', Phys. Rev. D80, 094503 (2009), [arXiv:0903.3232].[UK/09-01]

A. Li, A. Alexandru, K.F. Liu, and X.F. Meng, `Finite density phase transition of QCD with N_f=4 and N_f=2 using the canonical ensemble method', Accepted for publication in Phys. Rev. D, [arXiv:1005.4158].[UK/10-04]

A. Li, A. Alexandru, Y. Chen, T. Doi, S.J. Dong, T. Draper, Ming Gong, I. Horvath, F.X. Lee, K.F. Liu, N. Mathur, T. Streuer, and J.B. Zhang, `Overlap Valence on $2+1$ Flavor Domain Wall Fermion Configurations with Deflation and Low-mode Substitution', Submitted to Phys. Rev. D, [arXiv:1005.5424]. [UK/10-01]

S. Prelovsek, T. Draper, C.B. Lang, M. Limmer, K.f. Liu, N. Mathur, D. Mohler,  `Lattice study of light scalar tetraquarks with I=0,2,1/2,3/2: Are \sigma and \kappa tetraquarks?' Submitted to PHys. Rev. D, [arXiv:1005.0948]. [UK/10-06]

PI Ping Liu

K. Sasaki, H. Naohara, Y. Cai, Y. Choi, P. Liu, M. Vukmirovic, J. Wang, R. R. Adzic, "Core-protected Core-shell Electrocatalysts: Potential for Automotive Applications of Fuel Cells", Angewandte Chemie International Edition, accepted as Very Important Paper (VIP).

F. Yang, Y. Choi, P. Liu, J. Hrbek, J. A. Rodriguez, "The Autocatalytic Reduction of a Cu2O/Cu(111) Surface by CO: STM, XPS and DFT Studies", The Journal of Physical Chemistry C, in press.

P. Liu, Y. Choi, Y. Yang, M.G. White, "Methanol synthesis from H2 and CO2 on a Mo6S8 cluster: a density functional study", The Journal of Physical Chemistry A 114 (2010) 3888-3895. (This paper is highlighted on the cover of JPCA.)

J. X. Wang, H. Inada, L. Wu, Y. Zhu, Y. Choi, P. Liu, W.P. Zhou, R. R. Adzic, " Oxygen Reduction on Well-Defined Core-Shell Nanocatalysts: Particle Size, Facet, and Pt Shell Thickness Effects", Journal of the American Chemical Society 131 (2009) 17298-17302 (This paper is highlighted in JACS select collection).

PI Steven Louie

H. Lee, J. Ihm, M.L. Cohen, and S.G. Louie, "Calcium-decorated Carbon Nanotubes for High Capacity Hydrogen Storage," Phys. Rev. B 80, 115412 (2009).

L. Yang, et.al., "Excitonic Effects on the Optical Response of Graphene and Bilayer Graphene," Physical Review Lett. 103, 186802 (2009).

S. Choi, et. al., "Localization of Metal-Induced Gap States at the Metal-Insulator Interface: Origin of Flux Noise in SQUIDs and Superconducting Qubits," Phys. Rev. Lett. 103, 197001 (2009).

S.Y. Quek, et. al., "Length Dependence of Conductance in Aromatic Single-Molecule Junctions," Nano Lett. 9, 3949 (2009).

C. Tao, et.al., "Spatial Resolution of a Type II Heterojunction in a Single Bipolar Molecule," Nano Lett. 9, 3963 (2009).

C.-H. Park, et.al., "Angle-resolved Photoemission Spectra of Graphene from First-principles," Nano Lett. 9, 4234 (2009).

D. Prendergast and S.G. Louie, "Bloch-state-based Interpolation: An Efficient Generalization of the Shirley Approach to Interpolating Electronic Structure," Phys. Rev B 80, 235126 (2009).

V.W. Brar, et.al., "Observation of Carrier-Density-Dependent Many-Body Effects in Graphene via Tunneling Spectroscopy," Phys. Rev. Lett. 104, 036805 (2010).

T.-T. Tang, et.al., "A Tunable Phonon-Exciton Fano System in Bilayer Graphene," Nat. Nanotechnol. 5, 32 (2010).

C-H. Park and S.G. Louie, "Tunable Excitons in Biased Bilayer Graphene," Nano Lett. 10, 426 (2010).

J. L. Janssen, et.al., "Electron-Phonon Coupling In C60 Using Hybrid Functionals," Phys. Rev. B 81, 073106 (2010).

F. Giustino, M.L. Cohen, and S.G. Louie, "GW Method with the Self-Consistent Sternheimer Equation," Phys. Rev. B 81, 115105 (2010).

B.D. Malone, S.G. Louie, and M.L. Cohen, "Electronic and Optical Properties of Body-Centered Tetragonal Si and Ge," Phys. Rev. B 81, 115201 (2010).

H.K. Lee, et.al., "Calcium-Decorated Graphene-Based Nanostructures for High-Capacity Hydrogen Storage," Nano Lett. 10, 793 (2010).

M.J. Comstock, et.al., "Determination of Photoswitching Dynamics through Chiral Mapping of Single Molecules Using a Scanning Tunneling Microscope," Phys. Rev. Lett. 104, 178301 (2010).

O.V. Yazyev and S.G. Louie, "Topological Defects in Graphene: Dislocations and Grain Boundaries," Phys. Rev. B 81, 195420 (2010).

L.Z. Tan, C.-H. Park, and S.G. Louie, "Graphene Dirac Fermions in One-dimensional Inhomogeneous Field Profiles: Transforming Magnetic to Electric Field," Phys. Rev. B 81, 195426 (2010).

M. Kamenetska, et.al., "Conductance and Geometry of Pyridine-linked Single-molecule Junctions," J. Am. Chem. Soc. 132, 6817 (2010).

F.D. Vila, et.al., "Basis Set Effects on the Hyperpolarizability of CHCl3: Gaussian-type Orbitals, Numerical Basis Sets and Real-space Grids," J. Chem. Phys. 133, 034111 (2010).

G.-S. Do, et.al., "Ab initio calculations of pressure-induced structural phase transitions of GeTe," Phys. Rev. B 82, 054121 (2010).

 


M

PI Chung-Pei Ma

J. DeBuhr, E. Quataert, and C.-P. Ma (2010), Monthly Notices of the Royal Astronomical Society, submitted. "The Growth of Massive Black Holes in Galaxy Merger Simulations with Feedback by Radiation Pressure"

J. DeBuhr, E. Quataert, C.-P. Ma, and P. Hopkins (2010), Monthly Notices of the Royal Astronomical Society, 406, L55. "Self-Regulated Black Hole Growth via Momentum Deposition in Galaxy Merger Simulations"

PI S. D. Mahanti

Mal-Soon Lee, Ferdinand P. Poudeu, and S. D. Mahanti, Electronic structure and thermoelectric properties of Sb-based semiconducting half-Heusler compounds, submitted to Physical Review B

 

PI Steven Manson

"Photoionization of the Be Isoelectronic Sequence: Total Cross Sections," W.-C. Chu, H.-L. Zhou, A. Hibbert and S. T. Manson, J. Phys. B 42, 205003-1-17 (2009).

"Satellite Lines in the Photoionization of Ions: The Be Isoelectronic Sequence," W.-C. Chu, H.-L. Zhou, A. Hibbert and S. T. Manson, Phys. Rev. A 81, 053412-1-5 (2010).

"Overlapping Resonances in Atomic Ions," W.-C. Chu, H.-L. Zhou, A. Hibbert and S. T. Manson, Phys. Rev. A 82, 013417-1-4 (2010).

"Photoionization of potassium-like transition metal ions: I. Ti3+ to Fe7+," A. M. Sossah, H.-L. Zhou, S. T. Manson, Phys. Rev. A (submitted).

PI Artem Masunov

Ganopadhyay, S; Masunov, AE; Inerbaev, T, et al., "Understanding oxygen vacancy migration and clustering in barium strontium cobalt iron oxide." SOLID STATE IONICS Volume: 181 Issue: 23-24 Pages: 1067-1073 Published: 2010

Workalemahu M., Mikhailov I., Masunov A. Are Density Functional Theory predictions of the Raman spectra accurate enough to distinguish conformational transitions during amyloid formation? Journal of Molecular Modeling. 2010, 16, 1093-1101

Workalemahu M. Berhanu, Artem E. Masunov. Natural polyphenols as inhibitors of amyloid aggregation. Molecular Dynamics study of GNNQQNY heptapeptide decamer, Biophysical Chemistry. 2010, 149, 12-21

Workalemahu M., Abd El-Maaboud I.M. Determination of Lamivudine and Stavudine in pharmaceutical preparations using chemometrics-assisted spectrophotometry Saudi Pharmaceutical Journal. 2009, 17, 286- 294

Author(s): Inerbaev, TM; Seal, S; Masunov, AE
Title: Density functional study of oxygen vacancy formation and spin density distribution in octahedral ceria nanoparticles
Source: JOURNAL OF MOLECULAR MODELING Volume: 16 Issue: 10 Pages: 1617-1623 Published: 2010

Author(s): Vincent, A; Inerbaev, TM; Babu, S, Masunov, AE et al.
Title: Tuning Hydrated Nanoceria Surfaces: Experimental/Theoretical Investigations of Ion Exchange and Implications in Organic and Inorganic Interactions
Source: LANGMUIR Volume: 26 Issue: 10 Pages: 7188-7198 Published: 2010

Author(s): Webster, S; Peceli, D; Hu, H, Masunov, AE, et al.
Title: Near-Unity Quantum Yields for Intersystem Crossing and Singlet Oxygen Generation in Polymethine-like Molecules: Design and Experimental Realization
Source: JOURNAL OF PHYSICAL CHEMISTRY LETTERS Volume: 1 Issue: 15 Pages: 2354-2360 Published: 2010

Author(s): Belfield, KD; Bondar, MV; Frazer, A; Mikhailov IA; Masunov AE, et al.
Title: Fluorene-Based Metal-Ion Sensing Probe with High Sensitivity to Zn2+ and Efficient Two-Photon Absorption
Source: JOURNAL OF PHYSICAL CHEMISTRY B Volume: 114 Issue: 28 Pages: 9313-9321 Published: 2010

Gangopadhyay, S., Masunov,* A. E., Poalelungi, E., Leuenberger,* M. Weak magnetic coupling in Mn12 molecular magnet is predicted correctly at DFT+U theory level. J. Chem. Phys 132, 244104 2010 (also published in Virtual Journal of Nanoscale Science and Technology)

PI Manos Mavrikakis

A. U. Nilekar, and A. V. Ruban, and M. Mavrikakis, "Surface segregation energies in low-index open surfaces of bimetallic transition metal alloys", Surface Science, 603, 91 (2009).

L. R. Merte, J. Knudsen, L. C. Grabow, R. T. Vang, E. Laegsgaard, M. Mavrikakis, and F. Besenbacher, "Correlating STM contrast and atomic-scale structure by chemical modification: Vacancy dislocation loops on FeO/Pt(111)", Surface Science, 603, L15 (2009).

P. Ferrin, S. Kandoi, J. Zhang, R. Adzic, and M. Mavrikakis, "Molecular and atomic hydrogen interactions with Au-Ir Near-Surface Alloys", Journal of Physical Chemistry C, 113, 1411 (2009).
HIGHLIGHTED IN THE JOURNAL COVER.

P. Ferrin, D. Simonetti, S. Kandoi, E. Kunkes, J. A. Dumesic, J. K. Norskov, and M. Mavrikakis, "Modeling ethanol decomposition on transition metals: A combined application of scaling and Bronsted-Evans-Polanyi Relations", Journal of the American Chemical Society, 131, 5809 (2009).

L. W. Bruch, R. P. Nabar, and M. Mavrikakis, "Weak molecular chemisorption of N2/Pt(111)", Journal of Physics: Condensed Matter, 21, 264009 (2009).

W. Zhou, X. Yang, M. B. Vukmirovic, B. E. Koel, J. Jiao, G. Peng, M. Mavrikakis, and R. R. Adzic, "Improving Electrocatalysts for O2 Reduction by Fine-tuning the Pt-support Interaction: Pt Monolayer on the Surfaces of a Pd3Fe(111) Single-crystal Alloy", Journal of the American Chemical Society, 131, 12755 (2009).

P. Ferrin and M. Mavrikakis, "Structure sensitivity of methanol electroxidation on transition metals", Journal of the American Chemical Society 131, 14381 (2009).

J. Rempel, J. Greeley, L. B. Hansen, O. H. Nielsen, M. Mavrikakis, and J. K. Norskov, "Effect of steps on the dissociation of NO on Rhodium close-packed surfaces", Journal of Physical Chemistry C, 113, 20623 (2009).

J. Knudsen, L. R. Merte, L. C. Grabow, F. M. Eichhorn, S. Porsgaard, H. Zeuthen, R. T. Vang, E. Laegsgaard, M. Mavrikakis and F. Besenbacher, "Reduction of FeO/Pt(111) thin films by exposure to atomic hydrogen", Surface Science 604, 11 (2010).

S. Kandoi, P. Ferrin, and M. Mavrikakis, "Hydrogen on and in selected overlayer near-surface alloys and the effect of subsurface hydrogen on the reactivity of alloy surfaces", Topics in Catalysis 53, 384 (2010).

M. Ojeda, R. Nabar, A. U. Nilekar, A. Ishikawa, M. Mavrikakis, and E. Iglesia, "CO activation pathways and the mechanism of the Fischer-Tropsch synthesis", Journal of Catalysis 272, 287 (2010).

A. U. Nilekar, S. Alayoglu, B. Eichhorn, and M. Mavrikakis, "Preferential CO oxidation in hydrogen: Reactivity of core-shell nanoparticles", Journal of the American Chemical Society 132, 7418 (2010).

D. C. Ford, A. U. Nilekar, Y. Xu, and M. Mavrikakis, "Partial and complete reduction of O2 by hydrogen on transition metal surfaces", Surface Science 604, 1565 (2010).

J. Knudsen, L. R. Merte, G. Peng, R. T. Vang, A. Resta, E. Laegsgaard, J. N. Andersen, M. Mavrikakis and F. Besenbacher, "Low temperature CO oxidation on Ni(111) and on Au/Ni(111) surface alloy", ACS Nano 4, 4380 (2010).
HIGHLIGHTED IN THE JOURNAL COVER.

PI William McCurdy

A. Palacios, T. N. Rescigno and C. W. McCurdy, "Time-dependent treatment of two-photon resonant single and double ionization of helium by ultrashort laser pulses" , Phys. Rev. A 79, 033402 (2009).

Liang Tao, W. Vanroose, B. Reps, T. N. Rescigno, and C. W. McCurdy, "Long-time solution of the time-dependent Schroedinger equation for an atom in an electromagnetic field using complex coordinate contours" Phys. Rev. A 80, 063419 (2009).

J. Fernandez, F. L. Yip, T. N. Rescigno, C. W. McCurdy and F. Martin, "Two-center effects in one-photon single ionization of H2+, H2 and Li2+ with circularly polarized light", Phys. Rev. A 79, 043409 (2009).

L. Tao, C. W. McCurdy and T. N. Rescigno, "Grid-based methods for diatomic quantum scattering problems II: Time-dependent treatment of single- and two-photon ionization of H2+", Phys. Rev. A 80, 013401 (2009).

A. Palacios, T. N. Rescigno and C. W. McCurdy, "Two-electron time-delay interference in atomic double ionization by attosecond pulses," Phys. Rev. Lett. 103, 253001 (2009).

M Kurka , J Feist , D A Horner , A Rudenko , Y H Jiang , K U Kuhnel , L Foucar , T N Rescigno, C W McCurdy , R Pazourek , S Nagele , M Schulz , O Herrwerth , M Lezius , M F Kling , M Schoeffler , A Belkacem , S Dusterer , R Treusch , B I Schneider , L A Collins , J Burgdoerfer , C D Schroeter , R Moshammer and J Ullrich, "Differential cross sections for non-sequential double ionization of He by 52 eV photons from the Free Electron Laser in Hamburg, FLASH" New J. Phys. 12, 073035 (2010).

D. A. Horner, T. N. Rescigno and C. W. McCurdy, "Nuclear Recoil Cross Sections from Time-dependent Studies of Two-Photon Double Ionization of Helium" Phys. Rev. A 81, 023410 (2010).

F. L. Yip, C. W. McCurdy and T. N. Rescigno, "Hybrid Orbital and Numerical Grid Representation for Electronic Continuum Processes: Double Photoionization of Atomic Beryllium", Phys. Rev. A 81, 053407 (2010).

F. L. Yip, C. W. McCurdy and T. N. Rescigno, "Double Photoionization of excited Lithium and Beryllium", Phys. Rev. A 81, 063419, (2010).

L. Tao, C. W.McCurdy and T. N. Rescigno, "Grid-based methods for diatomic quantum scattering problems III: Double photoionization of molecular hydrogen in prolate spheroidal coordinates", Phys. Rev. A 82, 023423 (2010).

A. Palacios, D. A. Horner, T. N. Rescigno and C. W. McCurdy, "Two-photon double ionization of the helium atom by ultrashort pulses", J. Phys. B: At. Mol. Opt. Phys. 43 (2010) 194003.

PI Donghai Mei

Xu, L., Mei, D. and Henkelman, G. "Adaptive kinetic Monte Carlo Simulation of Methanol Decomposition on Cu(100)", J. Chem. Phys., 131, 244520 (2010).

Mei, D., Rousseau, R., Kathmann, S. M., Glezakou, V. A., Engelhard, M. H., Jiang, W., Wang, C., Gerber, M. A., White, J. F. and Stevens, D. J. "Ethanol synthesis from syngas over Rh-based/SiO2 catalysts: A combined experimental and theoretical modeling study", J. Catal. , 271, 325-342 (2010).

Mei, D., Kwak, J. H., Szanyi, J., Ge, Q., and Charles H. F. Peden "Catalyst Size and Morphology Effects on the Interaction of NO2 with BaO/??-Al2O3 Materials", Catal. Today, 151, 304-313 (2010).

Mei, D. "Density Functional Theory Study of Surface Carbonate Formation on BaO(001)", J. Phys. Chem. C, 114, 1867-1874 (2010).

Mei, D., Kwak, J. H., Hu, J. Z., Cho, S. J., Szanyi J., Allard, L. and Peden, C. H. F. "The Unique Role of Anchoring Penta-coordinated Al3+ Sites in the Sintering of Al2O3-supported Pt Catalysts", J. Phys. Chem. Lett. 1, 2688-2691 (2010)

Chen, S.; Raugei, S.; Rousseau, R.; Dupuis, M.; Bullock, M. "Homogeneous Ni Catalysts for H2 Oxidation and Production: An Assessment of Theoretical Methods, from Density Functional Theory to Post Hartree-Fock Correlated Wavefunction Theory", J. Phys. Chem. A, submitted.

Yang, J. Y.; Chen, S.; Dougherty, W. G.; Kassel, W. S.; Bullock, M.; Dubois, D. L.; Raugei, S.; Rousseau, R.; Dupuis, M.; Rakowski Dubois, M. "Hydrogen Oxidation Catalysis by a Nickel Diphosphine Complex with Pendant t-Butyl Amines", Chem. Commun. submitted.

PI David Mikkelsen

C. Bourdelle, et al., "Collisionality scaling in Tore Supra: detailed energy confinement analysis, turbulence measurements and gyrokinetic modeling", submitted to Nuclear Fusion

W. Guttenfelder & J. Candy, "Resolving electron scale turbulence in spherical tokamaks with flow shear", submitted to Physics of Plasmas

PI Doug Miller

Miller, D.K., A.M. Wilson, G.J. Cutrell, A.P. Barros, and O.P. Prat, 2010: Observed precipitation associated with air mass thunderstorms over the southern Appalachian Mountains 28, 29 July 2008. Submitted to the Journal of the Natural Hazards and Earth System Sciences, in the process of revision.

PI Thomas Miller

Menzeleev AR and Miller TF. `Ring polymer molecular dynamics beyond the linear response regime: Excess electron injection and trapping in liquids.' J. Chem. Phys., 132 (2010) 034106.

Ananth N and Miller TF. `Exact quantum statistics for electronically nonadiabatic systems using continuous path variables.' J. Chem. Phys., submitted.

Zhang B and Miller TF. `A hydrophobically stabilized open state for the lateral gate of the Sec translocon.' Proc. Natl. Acad. Sci. USA, 107 (2010) 5399.

Adelman JL, Chodera JD, Kuo IFW, Miller TF, and Barsky D. `The mechanical properties of PCNA: Implications for the loading and function of sliding clamps.' Biophys. J., 98 (2010) 3062. Featured as cover art.

PI William Miller

Guohua Tao and William H. Miller, "Semiclassical Description of Electronic Excitation Population Transfer in a Model Photosynthetic System" JOURNAL OF PHYSICAL CHEMISTRY LETTERS 1, 891 (2010)

Alexey L. Kaledin, C. William McCurdy, and William H. Miller, " A semiclassical correction for quantum mechanical energy levels" J. Chem. Phys. 133, 054101 (2010)

Guohua Tao and William H. Miller, "Time-dependent importance sampling in semiclassical initial value representation calculations for time correlation functions", in preparation.

Jian Liu, William H. Miller, Georgios Fanourgakis, Sotiris S. Xantheas, Imoto Sho and Shinji Saito, "Dynamical properties of liquid water: Insights from quantum simulations with an ab intio based, flexible and polarizable force field" (in preparation)

Jian Liu and William H. Miller, "On the statistical mechanics of Hamiltonian and non-Hamiltonian trajectory-based dynamics for quantum systems" (in preparation)

Jian Liu and William H. Miller, "Three simple approaches to generate the trajectory-based dynamics which conserves the canonical distribution in the phase space formulation of quantum mechanics: III. Thermal Correlation Functions" (in preparation)

Jian Liu and William H. Miller, "Three simple approaches to generate the trajectory-based dynamics which conserves the canonical distribution in the phase space formulation of quantum mechanics: II. Methodologies" (in preparation)

Jian Liu and William H. Miller, "Three simple approaches to generate the trajectory-based dynamics which conserves the canonical distribution in the phase space formulation of quantum mechanics: I. Theories" (in preparation)

PI Jason Montgomery

Nanopost Plasmonic Crystals Fabricated via Soft Nanoimprinting for Surface Enhanced Raman Scattering, Journal of Physical Chemistry C, (submitted)

PI Warren Mori

W. Theobald, S. Ivancic, B. Eichman, P. M. Nilson, J. A. Delettrez, F. J. Marshall, D. D. Meyerhofer, J. F. Myatt, C. Ren, T. C. Sangster, C. Stoeckl, R. Yan, J. D. Zuegel, V. Ovchinnikov, L. Van Woerkom, and R. R. Freeman, K. U. Akli and R. B. Stephens, "High-intensity laser-plasma interaction with wedge-shaped cavity targets," to appear in Physics of Plasmas, 2010

R. Yan, A. Maximov, C. Ren, and F. Tsung, "Growth and saturation of convective modes of the two-plasmon decay instability in inertial confinement fusion," Phys. Rev. Lett. 103, 175002 (2009)

R. Yan, A. V. Maximov, and C. Ren, "The linear regime of the two-plasmon decay instability in inhomogeneous plasmas," Phys. Plasmas 17, 052701 (2010) C. Clayton, J. E. Ralph, F. Albert, R. A. Fonseca, S. H. Glenzer, C. Joshi, W. Lu, K. A. Marsh, S. F. Martins, W. B. Mori, A. Pak, F. S. Tsung, B. B. Pollock, J. S. Ross, L. O. Silva, and D. H. Froula, Self-guided laser wakefield acceleration beyond 1GeV using ionization-induced injection, Phys. Rev. Lett.,

J. E. Ralph et al, "Laser Wakefield Acceleration at Reduced Density in the Self-guided Regime", Phys. of Plas., 17, 056709 (2010).

S. F. Martins et al, "Modeling laser wakefield accelerator experiments with ultrafast particle-in-cll simulations in boosted frames", Phys. Plas., 17, 056705 (2010).

A. Pak et al, "Injection and trapping of tunnel-ionized electrons into laser-produced wakes", Phys. Rev. Lett., 104, 025003 (2010).

S. F. Martins et al, "Numerical Simulations of laser wakefield accelerators in optimal Lorentz Frames", Comp. Phys. Comm., 181, 869 (2010).

S. F. Martins et al, "Exploring laser wakefield accelerator regimes for near-term lasers using particle-in-cell simulation in Lorentz-boosted frames", Nature Physics, 6, 311 (2010).

J. Vieira, S. F. Martins, V. B. Pathak, R.A. Fonseca, L.O. Silva, W.B. Mori, "Magnetic control of particle-injection in plasma based accelerators", in preparation (2010)

F. S. Tsung et al, "CO2 laser acceleration of forward directed MeV protons in a gas target", in preparation (2010).

PI James Morris

F. W. Averill, J. R. Morris and V. R. Cooper, "Calculated properties of hydrogenated single layers of BN, BC2N and graphene: Graphane and its BN-containing analogues," Phys. Rev. B 80, 195411 (2009).

Min Xu, Y.Y. Ye, J.R. Morris, D.J. Sordelet and M.J. Kramer, "In situ observation of thermal expansion of tetragonal C11b phase in Zr2Cu(1-x)Pdx alloys," Intermetallics 18, 8 (2010).

Xing-Qiu Chen, C. L. Fu, and J. R. Morris, "The electronic, elastic, and structural properties of Ti-Pd intermetallics from first-principles calculation," Intermetallics 18, 998-1006 (2010).

T. Egami, V. Levashov, J. R. Morris, and O. Haruyama, "Statistical Mechanics of Metallic Glasses and Liquids," Mat. Trans. A 41A, 1628 (2010).

Xing-Qiu Chen, C.L. Fu, C. Franchini, and R. Podloucky, "Hybrid density functional calculation of the electronic and magnetic structure of tetragonal CuO," Physical Review B 80, 094527 (2009).

PI Adam Moule

Huang, D. M.; Faller, R.; Do, K.; Moule, A. J., Coarse-grained computer simulations of polymer/fullerene bulk heterojunctions for organic photovoltaic applications. Journal of Chemical Theory and Computation 2010, 6, 526-537.

Huang, D. M.; Moule, A. J.; Faller, R., Characterization of Polymer-Fullerene Mixtures for Organic Photovoltaics by Systematically Coarse-Grained Molecular Simulations. Fluid Phase Equilibria (In Press) 2010.

Do, K.; Huang, D. M.; Faller, R.; Moule, A. M., A comparitive MD study of the local structure of polymer semiconductors P3HT and PBTTT. Physical Chemistry Chemical Physics (In Press) 2010.

PI Alfred Msezane

Novel mechanism for nanoscale catalysis, A.Z. Msezane, Z. Felfli and D. Sokolovski, J. Phys. B, At Press (2010) (FAST TRACK)

Scaling Behavior of Heavy Fermion Metals, V.R. Shaginyan, M.Ya. Amusia, A.Z. Msezane, and K.G. Popov, Physics Reports 492, 31-109 (2010)

Resonances in Low-Energy Electron Elastic Cross Sections for Lanthanide Atoms, Z. Felfli, A.Z. Msezane and D. Sokolovski, Phys. Rev. A 79, 012714 (2009)

Differential Cross Sections for Low-Energy Electron Elastic Scattering by Lanthanide Atoms: La, Ce, Pr, Nd, Eu, Gd, Dy and Tm, Z. Felfli, A.Z. Msezane and D. Sokolovski, Phys. Rev. A 79,062709 (2009)

Complex angular momentum analysis of low-energy electron elastic scattering from lanthanide atoms, Z. Felfli, A.Z. Msezane and D. Sokolovski, Phys. Rev. A 81, 042707 (2010)

Low-energy electron elastic scattering cross sections for excited Au and Pt atoms, Z. Felfli, A. R. Eure, A. Z. Msezane and D. Sokolovski, NIMB 268, 1370 (2010)

Low-Energy Electron Elastic Scattering from Complex Atoms: Nd, Eu and Tm, Z. Felfli, A.Z. Msezane and D. Sokolovski, Can. J. Phys. 87, 321 (2009)

Energy Scales and Magnetoresistance at a Quantum Critical Point, V.R. Shaginyan, M. Ya. Amusia, A.Z. Msezane, K.G. Popov and V.A. Stephanovich, Physics Letters A 373, 986 (2009)

[Ti II] lines observed in eta-Carinae Sr- filament and lifetimes of the metastable states of Ti+, N. C. Deb, A. H. Hibbert, Z. Felfli and A. Z. Msezane, J. Phys. B 42, 015701 (2009)

Fast charged-particle impact ionization of endohedral atoms: e + He@C60, A. S. Baltenkov, V. K. Dolmatov, S. T. Manson, and A. Z. Msezane, Phys. Rev. A 79, 043201 (2009)

Large scale CIV3 calculations of fine-structure energy levels and radiative rates in Al-like Copper, G. P. Gupta and A. Z. Msezane, Can. J. Phys. 87, 895 (2009)

Photoionization of the I+ Ion, Zhifan Chen and Alfred Z. Msezane, J. Phys. B 42, 165203 (2009).

Magnetic-Field-induced Reentrance of Fermi-Liquid Behavior and Spin-Lattice Relaxation Rates in YbCu5-xAux, V.R. Shaginyan, A.Z. Msezane, K.G. Popov and V.A. Stephanovich, Physics Letters A 373, 3783 (2009)

Fine-structure energy levels, oscillator strengths and lifetimes in Al-like Vanadium, G. P. Gupta and A. Z. Msezane, Phys. Scripta 81, 045302 (2010).

Effects of the fullerene (C60) potential and position of the atom (A) on spectral characteristics of endohedral atoms A@C60, A. S. Baltenkov, U. Becker, S. T. Manson and A. Z. Msezane, J. Phys. B 43, 115102 (2010).

Photoionization of Ce3+ @C82 endohedral fullerene, Zhifan Chen, R.A. Phaneuf and A.Z. Msezane, J. Phys. B. At Press (2010)

PI James Muckerman

Wada, T.; Muckerman, J. T.; Fujita, E.; Tanaka, K. "Substituents Dependent Capability of Bis(ruthenium-dioxolene-terpyridine) Complexes Toward Water Oxidation," Dalton Trans. 2010, submitted.

Polyansky, D. E.; Rochford, J.; Muckerman, J. T.; Zong, R.; Thummel, R. P.; Fujita, E. "Mechanistic Study of Catalytic Water Oxidation: Unusual Pathway for O-O Bond Formation Avoiding a RuV=O Species," J. Am. Chem. Soc. 2010, submitted.

Muller, E.; Karim, A.; Muckerman, J. T.; Davies, T.; Ciobanu, C. V.; Sutter, P. "H-trapping near Ti/Al(111): Side-effects of catalysts in alanate hydrogen storage reactions," Phys. Rev. B 2010, submitted.

Karim, A.; Muckerman, J. T. "Density Functional Theory Based Kinetic Monte Carlo Study of Hydrogen Dissociative Adsorption and Diffusion on Ti-Doped Al(111), "J. Phys. Chem. C 2010, submitted.

Creutz, C.; Chou, M.; Hou, H.; Muckerman, J. T. "Hydride Ion Transfer from Ruthenium(II) Complexes in Water: Kinetics and Mechanism" Inorg. Chem. 2010, in press.

Shen, X. A.; Small, Y. A.; Wang, J.; Allen, P. B.; Fernandez-Serra, M. V.; Hybertsen, M. S.; Muckerman, J. T. "Photocatalytic Water Oxidation at the GaN (1010)-Water Interface" J. Phys. Chem. C 2010, 114, 13695-13704.

Concepcion, J. J.; Tsai, M.-K.; Muckerman, J. T.; Meyer, T. J. "Mechanism of Water Oxidation by Single-Site Ruthenium Complex Catalysts" J. Am. Chem. Soc. 2010, 132, 1545-1557.

Rochford, J.; Tsai, M.-K.; Szalda, D. J.; Boyer, J. L.; Muckerman, J. T.; Fujita, E. "Oxidation State Characterization of Ruthenium 2-Iminoquinone Complexes through Experimental and Theoretical Studies" Inorg. Chem. 2010, 49, 860-869.

Doherty, M. D.; Grills, D. C.; Muckerman, J. T.; Polyansky, D. E.; Fujita, E. "Toward more efficient photochemical CO2 reduction: Use of scCO2 or photogenerated hydrides" Coord. Chem. Rev. 2010, 254, 2472-2482.

Tsai, M. K.; Rochford, J.; Polyansky, D. E.; Wada, T.; Tanaka, K.; Fujita, E.; Muckerman, J. T. "Characterization of Redox States of Ru(OH2)(Q)(tpy)2+ (Q=3,5-di-tert-butyl-1,2-benzoquinone, tpy=2,2':6',2''-terpyridine) and Related Species through Experimental and Theoretical Studies" Inorg. Chem. 2009, 48, 4372-4383.

Fukushima, T.; Fujita, E.; Muckerman, J. T.; Polyansky, D. E.; Wada, T.; Tanaka, K. "Photochemical Stereospecific Hydrogenation of a Ru Complex with an NAD(+)/NADH-Type Ligand" Inorg. Chem. 2009, 48, 11510-11512.

Boyer, J. L.; Rochford, J.; Tsai, M.-K.; Muckerman, J. T.; Fujita, E. "Ruthenium Complexes with Non-innocent Ligands: Electron Distribution and Implications for Catalysis" Coord. Chem. Rev. 2009, 254, 309-330.

Achord, P.; Fujita, E.; Muckerman, J. T.; Scott, B.; Fortman, G. C.; Temprado, M.; Cai, X. C.; Captain, B.; Isrow, D.; Weir, J. J.; McDonough, J. E.; Hoff, C. D. "Experimental and Computational Studies of Binding of Dinitrogen, Nitriles, Azides, Diazoalkanes, Pyridine, and Pyrazines to M(PR3)2(CO)3 (M = Mo, W; R = Me, iPr)" Inorg. Chem. 2009, 48, 7891-7904.

PI Christopher Mundy

Hydroxide anion at the air-water interface, Mundy CJ, Kuo IFW, Tuckerman ME, et al., Chemical Physics Letters 481, 2-8 (2009) FRONTIERS ARTICLE

"Towards and understanding of complex chemical systems", C.J. Mundy, et al, SCIDAC REVIEW VOL. 17, Page 10 2010 (Cover article)

"Improving the density functional theory description of water with self-consistent polarization," Murdachaew G, Mundy CJ, Schenter GK, JOURNAL OF CHEMICAL PHYSICS Volume: 132 Issue: 16 Article Number: 164102

"The role of excluded spatial regions on the electrochemical surface potential of water," S. Kathmann, I.-F. Kuo, C.J. Mundy, G.K. Schenter, SUBMITTED TO THE JOURNAL OF THE AMERICAN CHEMICAL SOCIETY


N

PI Habib Najm

Safta, C., Ray, J., Najm, H.N., "A High-Order Low-Mach Number AMR Construction for Chemically Reacting Flows", J. Comput. Phys., in press.

PI Jeffrey Neaton

Y. Kanai, J. B. Neaton, and J. C. Grossman, "Theory and simulation of nanostructured materials for photovoltaic applications", Comp. Sci. Eng. 12, 18 (2010)

K. H. Khoo, A. T. Zayak, H. Kwak, and J. R. Chelikowsky, "First-Principles Study of Confinement Effects on the Raman Spectra of Si Nanocrystals", Phys. Rev. Lett. 105, 115504 (2010).

M. Kamenetska, S. Y. Quek, A. C. Whalley, M. L. Steigerwald, H. J. Choi, S. G. Louie, C. Nickolls, M. S. Hybertsen, J. B. Neaton, and L. Venkataraman, "Conductance and geometry of pyridine-linked single-molecule junctions", J. Am. Chem. Soc. 132, 6817 (2010)

M. Dell'Angela, G. Kladnik, A. Cossaro, A. Verdini, M. Kamanetska, I. Tamblyn, S. Y. Quek, J. B. Neaton, D. Cvetko, A. Morgante and L. Venkataraman, "Relating energy level alignment and amine-linked single molecule junction conductance", Nano Letters 10, 2470 (2010)

S. Yang, D. Prendergast, and J. B. Neaton, "Strain-Induced Band Gap Modification in Coherent Core/Shell Nanostructures". Nano Lett. 10, 3156 (2010).

A. T. Zayak, Y. S. Hu, H. Choo, S. Cabrini, P. J. Schuck, and J. B. Neaton, "Origin of Chemical Raman Enhancement of Organic Adsorbates on Metal Surfaces", submitted to Nature Chemistry.

J. Bhattacharjee and J. B. Neaton, "Interfacial carbon nanotubes of arbitrary chiralities into linear heterojunctions" submitted to Phys. Rev. B

PI John Negele

C. Alexandrou, G. Koutsou, H. Neff, J.W. Negele, W. Schroers, A. Tsapalis, "The Nucleon to Delta electromagnetic transition in lattice QCD", Phys. Rev. D77 (2008) 085012, arXiv:0710.4621 [hep-lat].

C. Alexandrou, T. Korzec, G. Koutsou, C. Lorce, J. W. Negele, V. Pascalutsa, A. Tsapalis, M. Vanderhaeghen, "Quark transverse charge densities in the Delta(1232) from lattice QCD", Nucl. Phys. A825 (2009) 115, arXiv:0901.3457 [hep-ph].

C. Alexandrou, T. Korzec, G. Koutsou, Th. Leontiou, C. Lorce, J. W. Negele, V. Pascalutsa, A. Tsapalis, M. Vanderhaeghen, "Delta-baryon electromagnetic form factors in lattice QCD", Phys. Rev. D79 (2009) 014507 arXiv:0810.3976 [hep-lat].

C. Alexandrou, T. Korzec, G. Koutsou, J. W. Negele, Y. Proestos, "Electromagnetic form factors of the Omega^- in lattice QCD", Phys. Rev. D82 (2010) 034504 arXiv:1006.0558 [hep-lat].

C. Alexandrou, G. Koutsou, J. W. Negele, Y. Proestos, A. Tsapalis, "Nucleon to Delta transition form factors with Nf = 2+1 dynamical Domain-Wall fermions", (In preparation, 2010).

PI Karoly Nemeth

Karoly Nemeth, Katherine C. Harkay, Michel van Veenendaal, Linda Spentzouris, Marion White, Klaus Attenkofer, George Srajer, "High brightness photocathodes through ultra-thin surface layers on metals," Phys. Rev. Lett. 104, 046801 (2010).

Anders M. N. Niklasson, Matt Challacombe, C. J. Tymczak and Karoly Nemeth, Trace Correcting Density Matrix Extrapolation in Self-Consistent Geometry Optimization, Journal of Chemical Physics, 132, 124104 (2010)

Karoly Nemeth, Matt Challacombe and Michel van Veenendaal, The Choice of Internal Coordinates in Complex Chemical Systems, Journal of Computational Chemistry, 31, 2078-2086 (2010)

PI Gregory Newman

Newman G.A., Commer M. and Carazzone J., 2010, Imaging CSEM data in the presence of electrical anisotropy: Geophysics, 75, F51-F61.

Commer M., Newman G.A., Williams K.H. and Hubbard S.S., 2010, Three-dimensional spectral induced polarization data inversion for complex resistivity: Geophysics, submitted.

PI Esmond Ng

Pietro Cicotti, Xiaoye S. Li and Scott B. Baden, "Performance modeling tools for parallel sparse linear algebra computations", Proc of the International Conference on Parallel Computing (ParCo2009) Sept. 1-4, 2009, ENS-Lyon, France.

X. S. Li and Meiyue Shao, "A Supernodal Approach to Incomplete LU factorization". Submitted to ACM Transaction on Math. Software.

X. S. Li, M. Shao, I. Yamazaki, and E. G. Ng, "Factorization-based sparse solvers and preconditioners", Journal of Physics: Conference Series 180 (2009) 012015. Proc. of SciDAC 2009, June 14-18, 2009.

I. Yamazaki and X. Li, "On techniques to improve robustness and scalability of the Schur complement method". To appear in the Proc. International Conference on High Performance Computing for Computational Science (VECPAR???????10), June 22-24, 2010. Lecture Notes in Computer Science.

I. Yamazaki, X. Li, F.-H. Rouet and B. Ucar, "Partitioning, ordering, and load balancing in a parallel hybrid solver". In preparation.

I. Yamazaki, X. Li, T. Sakurai, H. Tadano, and T. Ikegami, "Performance study of a parallel nonlinear eigensolver based on a contour integral method with an application to accelerator cavity designs". Submitted to SC10.

I. Yamazaki, X. Li, and E. Ng, "Preconditioning Schur complement systems of highly-indefinite linear systems for a parallel hybrid solver". To appear in Numerical Mathematics: Theory, Methods and Applications, 2010.

I. Yamazaki, X. Li, and E. Ng, "A parallel hybrid linear solver for accelerator cavity designs". To appear in the proceedings of International Computational Accelerator Physics Conference.

J. P. Vary, P. Maris. E. Ng, C. Yang and M. Sosonkina, "Ab initio nuclear structure - the large sparse matrix eigensolver problem". J. Physics, 2009.

PI Jerry Nolen

Itacil C. Gomes, Jerry Nolen, Thomas Kroc, and James T. Harvey, "A New Approach for Production of Ac-225"

Itacil C. Gomes and Jerry Nolen, "Concept development of a compact accelerator-driven neutron multiplier for 99Mo production"

PI Michael Notaro

Notaro, M., and D. Gutzler, 2010: Simulated impact of vegetation across the North American monsoon region in CCSM3.5. Climate Dynamics, in review.

PI Peter Nugent

Kasliwal et al., Rapidly Decaying Supernova 2010X: A Candidate ".Ia" Explosion 2010 submitted to ApJL

Ofek et al., Supernova PTF 09uj: A Possible Shock Breakout from a Dense Circumstellar Wind, 2010 accepted, ApJ

Law et al., The Palomar Transient Factory Survey Camera: 1st Year Performance and Results 2010 SPIE 7735

Rau et al., PTF10fqs: A Luminous Red Nova in the Spiral Galaxy Messier 99 (submitted to ApJ)

Acarvi et al., Core-Collapse Supernovae from the Palomar Transient Factory: Indications for a Different Population in Dwarf Galaxies ApJ 2010 721 777-784

Quimby et al., Mysterious transients unmasked as the bright blue death throes of massive stars submitted to Nature (embargoed for discussion in the press).

Rau et al., The Palomar Transient Factory: System Overview, Performance and First Results PASP 121 1395L.

Kulkarni et al., Exploring the Optical Transient Sky with the Palomar Transient Factory PASP 121 1334R.

Walters et al., The 12Kx8K CCD mosaic camera for the Palomar Transient Factory 2008 SPIE 7014 (1.5MB pdf)


O

PI Grazyna Odyniec

Balance Functions from Au+Au, d+Au, and p+p Collisions at $\sqrt{s_{NN}}$ = 200 GeV, Phys. Rev. C 82 (2010) 24905

Higher Moments of Net-proton Multiplicity Distributions at RHIC, Phys. Rev. Lett. 105 (2010) 22302

Azimuthal di-hadron correlations in d+Au and Au+Au collisions at $\sqrt{s_{NN}}=200$ GeV from STAR , Phys. Rev. C 82 (2010) 24912

Longitudinal scaling property of the charge balance function in Au + Au collisions at 200 GeV , Phys. Lett. B 690 (2010) 239

Charged and strange hadron elliptic flow in Cu+Cu collisions at $\sqrt{s_{NN}}$ = 62.4 and 200 GeV, Phys. Rev. C 81 (2010) 44902

Upsilon cross section in p+p collisions at sqrt(s) = 200 GeV, Phys. Rev. D 82 (2010) 12004

Three-particle coincidence of the long range pseudorapidity correlation in high energy nucleus-nucleus collisions , Phys. Rev. Lett. 105 (2010) 22301

Inclusive pi^0, eta, and direct photon production in p+p and d+Au collisions at sqrt(s_NN) = 200 GeV , Phys. Rev. C 81 (2010) 64904

Observation of pi^+pi^-pi^+pi^- photoproduction in ultraperipheral heavy-ion collisions at sqrt(s_NN) = 200 GeV at the STAR detector, Phys. Rev. C 81 (2010) 44901

Identified high-$p_T$ spectra in Cu+Cu collisions at $\sqrt{s_{NN}}$=200 GeV ,Phys. Rev. C 81 (2010) 54907

Observation of an Antimatter Hypernucleus , Science 328 (2010) 58

Identified particle production, azimuthal anisotropy, and interferometry measurements in Au+Au collisions at $\sqrt{\bm {s_{NN}}} =$ 9.2 GeV , Phys. Rev. C 81 (2010) 24911

Observation of charge-dependent azimuthal correlations and possible local strong parity violation in heavy ion collisions, Phys. Rev. C 81 (2010) 54908

PI Joseph Oefelein

A. M. Kempf, B. J. Geurts, and J. C. Oefelein. Error analysis of large eddy simulation of the turbulent non-premixed sydney bluff-body flame. Combustion and Flame, 2010. Submitted.

R. C. Knaus, C. Pantano, and J. C. Oefelein. Statistical analysis and modeling of scalar dissipation and its relation to the filtered mixture fraction. Physics of Fluids, 2010. Submitted.

J. H. Frank, S. A. Kaiser, and J. C. Oefelein. Analysis of scalar mixing dynamics in LES using high-resolution imaging of laser rayleigh scattering in turbulent non-reacting jets and non-premixed jet flames. Proceedings of the Combustion Institute, 33, 2010.

PI Serdar Ogut

K. Frey, J. C. Idrobo, M. L. Tiago, F. Reboredo, and S. Ogut, "Quasiparticle gaps and exciton Coulomb energies in Si nanoshells: First principles calculations", Phys. Rev. B 80, 153411 (2009) [Cited 1 time].

PI Leonid Oliker

R. Sudarsan, K. Madduri, J. Borrill, Y. Zheng, L. Oliker, "Cosmic Microwave Background Map Making At The Petascale And Beyond", submitted to 6th ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming, PPoPP 2011 (under review)

L. Oliker, J. Carter, V. Beckner, J. Bell, H. Wasserman, M. Adams, S. Ethier, E.Schnetter, "Large-Scale Numerical Simulations on High-End Computational Platforms", chapter in Performance Tuning of Scientific Applications, Editors D. H. Bailey, R. F. Lucas, S. W. Williams, to appear.

A. Uselton, M. Howison, N. Wright, D. Skinner, N. Keen, J. Shalf, K. Karavanic, L. Oliker"Parallel I/O Performance: From Events to Ensembles ", International Parallel & Distributed Processing Symposium (IPDPS) 2010.

S. Ethier, M. Adams, J. Carter, L. Oliker, ???Petascale Parallelization of the Gyrokinetic Toroidal Code???, VECPAR: High Performance Computing for Computational Science, June 2010.

S. Kamil, L. Oliker, A. Pinar, J. Shalf, ???Communication Requirements and Interconnect Optimization for High-End Scientific Applications??? , IEEE Transactions on Parallel and Distributed Systems (TPDS), 2009 .

PI Kostas Orginos

"Lattice Calculations of Nucleon Electromagnetic Form Factors at Large Momentum Transfer" H.-W. Lin, S. D. Cohen, R. G. Edwards, K. Orginos, and D. G. Richards (2010), arxiv:1005.0799 (submitted).

PI Vidvuds Ozolins

Y. Zhang, E. H. Majzoub, V. Ozolins, and C. Wolverton, "Theoretical prediction of different decomposition paths for Ca(BH4)2 and Mg(BH4)2,"submitted to Physical Review B (2010).

W. Sun, C. Wolverton, A. R. Akbarzadeh, and V. Ozolins, "First-principles prediction of high-capacity, thermodynamically reversible hydrogen storage reactions based on (NH4)2B12H12," submitted to Physical Review Letters (2010).

E. H. Majzoub, Fei Zhou, and V. Ozolins, "First-principles calculated phase diagram for nanoclusters in the Na-Al-H system: A single-step decomposition pathway for NaAlH4," submitted to Journal of the American Chemical Society (2010).

K. Michel, Y. Liu, and V. Ozolins, "The Atomic Structure and Silane-H2 Interactions of SiH4(H2)2 from First-Principles Calculations," submitted to Physical Review B (2010).


P 

PI Alexei Pankin

A.Y. Pankin, G.Y. Park, J. Cummings, et al. (2010) Kinetic modeling of H-mode  pedestal with effects from anomalous transport and MHD stability (submitted to  Problems of Atomic Science and Technology. Series: Plasma Physics). 

A.Y. Pankin, G. Bateman, J.R. Cary et al.$(2010) Simulation of anomalous  transport in tokamaks using the FACETS code. (Accepted for publication in Comp.  Phys. Comm.)

PI Bahram Parvin

J. Han, H. Chang, K. Anadarawewa, P. Yaswen, M.H. Barcellos-Hoff, and B. Parvin, "Multidimensional profiling of cell surface proteins and nuclear markers," IEEE Transaction on Computational Biology and Bioinformatics, March 2010

J. Han, H. Chang, G. Fontenay, T. Groesser, M.H. Barcellos-Hoff, and B. Parvin, "Multiscale iterative voting for differential analysis of stress response for 2D and 3D cell culture models," J. of Microscopy, in press.

H. Chang and B. Parvin, "Multiphase level set for automated delineation of membrane-bound macro-molecules," IEEE Int. Symp. On Biomedical Imaging: from nano to macro, April 2010.

PI Edward Patton

Patton, E. G. and G. G. Katul: 2009, Turbulent pressure and velocity perturbations induced by gentle hills covered with sparse and dense canopies, Boundary-Layer Meteorology, 133, pp. 189-217, DOI: 10.1007/s10546-009-9427-x.

Sullivan, P. P. and E. G. Patton: 2010, The effect of mesh resolution on convective boundary layer statistics an structures generated by large-eddy simulation, Journal of the Atmospheric Sciences, Submitted.

PI Joyce Penner

Lee, S. S., J.E. Penner, and M. Wang, 2009: Comparison of a global-climate model simulation to a cloud-system resolving model simulation for long-term thin stratocumulus clouds, Atmos. Chem. Phys., 9, 6497-6520.

Lee, S. S. and J. E. Penner, 2010: Comparison of a global-climate model to a cloud-system resolving model for the long-term response of thin stratocumulus clouds to preindustrial and present-day aerosol conditions, Atmos. Chem. Phys., 10, 6371-6389.

Lee, S.S., L.J. Donner, and J.E. Penner, 2010: Thunderstorm and stratocumulus: how does their contrasting morphology affect their interactions with aerosols?, Atmos. Chem. Phys., 10, 6819-6837.

Lee, S. S. and J. E. Penner, 2010: Aerosol effects on ice clouds: Can the traditional concept of aerosol indirect effects be applied to aerosol-cloud interactions in cirrus clouds?, Atmos. Chem. Phys. Discuss., 10429???10462.

Lee, S. S. and J. E. Penner, 2009: Factors determining the effect of aerosols on cloud mass and the dependence of these factors on liquid-water path, Atmos. Chem. Phys. Discuss., 9, 19313-19350.

Lee, S. S. and J. E. Penner, 2009: Impact of solar radiation on aerosol-cloud interactions in thin stratocumulus clouds, Atmos. Chem. Phys. Discuss., 9, 23791-23833.

Roesler, E. and J. E. Penner, 2010: Can global models ignore the chemical composition of aerosols?, Geophys. Res. Lett., submitted.

Liu, X., X. Han, J. E. Penner, and M. Wang, 2010: Sensitivity of Global Aerosol Size Distribution and Aerosol Direct Radiative Forcing to Input Meteorological Fields, J. Geophys. Res., submitted, March 2010.

Andronova, N.G., D. R. VandenBerg, Q. F. Stout, R. Oehmke, J. E. Penner and V. Zubov, Atmospheric Model Tracer Advection with 3-D Spherical AMR, submitted, 2010.

PI Stephen Pennycook

T.J. Pennycook, M.J. Beck, K. Varga, M. Varela, S.J. Pennycook and S.T. Pantelides, "Origin of Colossal Ionic Conductivity in Oxide Multilayers: Interface Induced Sublattice Disorder," Physical Review Letters 104, 115901 (2010).

T.J. Pennycook, G. Hadjisavvas, J.C. Idrobo, P.C. Keliresand and S.T. Pantelides, ???Optical gaps of free and embedded Si nanoclusters: Density functional theory calculations???, Phys. Rev. B 82, 125310 (2010).

O.L. Krivanek, M.F. Chisholm, V. Nicolosi, T.J. Pennycook, G.J. Corbin, N. Dellby, M.F. Murfitt, C.S. Own, Z.S. Szilagyi, M.P. Oxley, S.T. Pantelides and S.J. Pennycook, ???Atom-by-atom structural and chemical analysis by annular dark-field electron microscopy???, Nature 464, 571 (2010).

J. C. Idrobo and S.T. Pantelides, ???Origin of Bulk-Like Optical Response in noble-metal Ag and Au Nanoparticles???, Phys. Rev. B 82, 085420 (2010).

J. He, A. Borisevich, S. V. Kalinin, S. J. Pennycook, and S. T. Pantelides, ???Control of Octahedral Tilts and Magnetic Properties of Perovskite Oxide Heterostructures by Substrate Symmetry???, submitted to Physical Review Letters 2010.

PI Saul Perlmutter

An Intensive HST Survey for z > 1 Supernovae by Targeting Galaxy Clusters,Dawson et al. 2009 AJ, 138, 1271 (arXiv:0908.3928)

HST Discovery of a z=3.9 Multiply Imaged Galaxy Behind the Complex Cluster Lens WARPS J1415+36 at z=1.026, Huang et al. 2009 ApJL,707,12

Subaru FOCAS Spectroscopic Observations for High-Redshift Supernovae,Morokuma et al. 2010 PASJ, 62, 19

Hubble Space Telescope Weak-Lensing Study of the Galaxy Cluster XMMU J2235.3-2557 at z = 1.4: A Surprisingly Massive Galaxy Cluster when the Universe is One-Third of its Current Age, Jee et al. 2009 ApJ, 704, 672

Multi-wavelength study of XMMU J2235.3-2557: the most massive galaxy cluster at z > 1, Rosati et al. 2009 A&A, 508, 583

Multiwavelength observations of a rich galaxy cluster at z = 1. The HST/ACS colour-magnitude diagram, Santos et al. 2009 A&A, 501, 49

The XMM Cluster Survey: Galaxy Morphologies and the Color-Magnitude Relation in XMMXCS J2215.9-2013 1738 at z = 1.46, Hilton et al. 2009 ApJ, 697, 436

Discovery of an Unusual Optical Transient with the Hubble Space Telescope, Barbary et al. 2009, ApJ, 690, 1358

PI Per-Olof Persson

A. Uranga, P.-O. Persson, M. Drela, and J. Peraire, Implicit Large Eddy Simulation of transition to turbulence at low Reynolds numbers using a Discontinuous Galerkin method. Int. J. Num. Meth. Engrg., accepted.

P.-O. Persson, D. J. Willis, J. Peraire, The Numerical Simulation of Flapping Wings at Low Reynolds Numbers. Proc. of the 48th AIAA Aerospace Sciences Meeting and Exhibit, January 2010. AIAA-2010-724.

PI Steven Pieper

`Multi-angle Simulation of Flavor Evolution in the NeutronizationNeutrino Burst from an O-Ne-Mg Core-collapse Supernova', J. F. Cherry, G. M. Fuller, H. Duan, and Y. Qian, Phys. Rev. {\bf D}, in print (2010).

`Low-Density Neutron Matter', A. Gezerlis and J. Carlson, Phys. Rev. {\bf C}81, 025803 (2010).

`Heavy-Light Fermion Mixtures at Unitarity', A. Gezerlis, S. Gandolfi, K. E. Schmidt, and J. Carlson', Phys. Rev. Lett. 103:060403, (2009).

PI Mitch Pindzola

B. Sun and M. S. Pindzola, Dynamics of a two species Bose-Einstein condensates in a double well, Physical Review A 80, 033616 (September 2009)

M. S. Pindzola, J. A. Ludlow, F. J. Robicheaux, J. P. Colgan, and C. J. Fontes, Fully-relativistic time-dependent close-coupling method for electron-impact ionization of atomic ions, Physical Review A 80, 052706 (November 2009)

M. S. Pindzola, J. A. Ludlow, F. J. Robicheaux, J. P. Colgan, and D. C. Griffin, Electron-impact double ionization of Magnesium, Journal of Physics B 42, 215204 (November 2009)

J. A. Ludlow, T. G. Lee, M. S. Pindzola, F. J. Robicheaux, and J. P. Colgan, Double photoionization of He including quadrupole radiation effects, Journal of Physics B 42, 225204 (November 2009)

J. P. Colgan, D. C. Griffin, C. P. Ballance, and M. S. Pindzola, Total cross sections for the double photoionization of Li from the ground and excited states, Physical Review 80, 063414 (December 2009)

M. S. Pindzola, J. A. Ludlow, C. P. Ballance, and D. C. Griffin, Electron-impact ionization of Xe+24, Journal of Physics B 43, 025201 (January 2010)

B. Sun and M. S. Pindzola, Bogoliubov modes and the static structure factor for a two species Bose-Einstein condensate, Journal of Physics B 43, 055301 (March 2010)

J. A. Ludlow, C. P. Ballance, S. D.Loch, and M. S. Pindzola, Breit-Pauli R-matrix electron-impact excitation calculations along the Ar isonuclear sequence, Journal of Physics B 43, 074029 (April 2010)

M. S. Pindzola, C. P. Ballance, F. J. Robicheaux, and J. P. Colgan, Electron-impact double ionization of Beryllium, Journal of Physics B 43, 105204 (May 2010)

M. S. Pindzola, J. A. Ludlow, and J. P. Colgan, Photoionization of highly charged atomic ions, Physical Review A 81, 063431 (June 2010)

T. G. Lee, M. S. Pindzola, and F. J. Robicheaux, Double ionization of H2 by intense attosecond laser pulses, Journal of Physics B 43, 165601 (August 2010)

C. P. Ballance, S. D. Loch, M. S. Pindzola, and D. C. Griffin, Dielectronic recombination of W+35, submitted to Journal of Physics B (July 2010)

F. J. Robicheaux, S. D. Loch, M. S. Pindzola, and C. P. Ballance, Contribution of near threshold states to plasma processes, submitted to Physical Review Letters (July 2010)

T. G. Lee, S. D. Loch, C. P. Ballance, J. A. Ludlow, and M. S. Pindzola, Electron-impact ionization cross sections for excited states of B, B+, and B+2 and an investigation into n-scaling of ionization cross sections, submitted to Physical Review A (July 2010)

X. Ren, A. Senftlenen, T. Pfluger, A. Dorn, J. P. Colgan, M. S. Pindzola, O. Al-Hagan, D. H. Madison, I. Bray, D. V. Fursa, and J. Ullrich, Tracing multiple scattering patterns in absolute (e,2e) cross sections for H2 and He over a full solid angle, submitted to Physical Review A (August 2010)

PI Tomasz Plewa

Harding, E. C., Drake, R. P., Aglitskiy, Y., Plewa, T., Velikovich, A. L., Gillespie, R. S., Weaver, J. L., Visco, A., Grosskopf, M. J., & Ditmar, J. R., Laser driven supersonic flow over a compressible foam surface on the Nike laser,
2010, Phys. Plasmas, 17, pp. 056310-1-9

Kuranz, C. C., Drake, R. P., Grosskopf, M. J., Fryxell, B., Budde, A., Hansen, J. F., Miles, A. R., Plewa, T., Hearn, N., & Knauer, J., Spike morphology in blast-wave-driven instability experiments, 2010, Phys. Plasmas, 17, pp. 056310-1-9

Guzman, J., & Plewa, T., Non-spherical core-collapse supernovae: evolution towards homologous expansion, 2009, Nonlinearity, 22, pp. 2775-2797

Gawryszczak, A., Guzman, J., Plewa, T., & Kifonidis, K., Non-spherical core collapse supernovae III. Evolution towards homology and dependence on the numerical resolution, 2010, A&A, in press (http://adsabs.harvard.edu/abs/2010arXiv1007.0463G)

Odrzywolek, A., & Plewa, T., Probing thermonuclear supernova explosions with neutrinos, 2010, submitted (http://adsabs.harvard.edu/abs/2010arXiv1006.0490O)

PI Alan Poon

Energy Threshold Analysis of the Phase I and Phase II Data Sets of the Sudbury Neutrino Observatory. Phys. Rev. C 81, 055504 (2010)

B. Aharmim et al. (SNO Collaboration) Searches for High Frequency Variations in the 8B Solar Neutrino Flux at the Sudbury Neutrino Observatory. ApJ 710, 540-548 (2010)

PI Ruth Pordes

Hoang Khoa Ly, Marcelo A. Marti , Diego F. Martin, Damian Alvarez-Paggi, Wiebke Meister, Anja Kranich, Inez M. Weidinger, Peter Hildebrandt, and Daniel H. Murgida, "Thermal Fluctuations Determine the Electron-Transfer Rates of Cytochrome c in Electrostatic and Covalent Complexes", ChemPhysChem 2010, 11, 1225-1235.

Damian Alvarez Paggi, Diego F. Martin, Anja Kranich, Peter Hildebrandt, Marcelo A. Marti, Daniel H. Murgida, "Computer simulation and SERR detection of cytochrome c dynamics at SAM-coated electrodes", Electrochimica Acta 54 (2009) 4963-4970.

Pablo M. De Biase, Damian Alvarez Paggi, Fabio Doctorovich, Peter Hildebrandt, Dario A. Estrin, Daniel H. Murgida, and Marcelo A. Marti, "Molecular Basis for the Electric Field Modulation of Cytochrome c Structure and Function", J. Am. Chem. Soc. 2009, 131, 16248-16256

Damian Alvarez-Paggi, Diego F. Martin, Pablo M. DeBiase, Peter Hildebrandt, Marcelo A. Marti, and Daniel H. Murgida, "Molecular Basis of Coupled Protein and Electron Transfer Dynamics of Cytochrome c in Biomimetic Complexes", J. AM. CHEM. SOC. 2010, 132, 5769-5778.

Tao Wu, X. Sheldon Wang, Barry Cohen and Hongya Ge, "MOLECULAR MODELING OF NORMAL AND SICKLE HEMOGLOBINS", Journal for Multiscale Computational Engineering, 8(2), 237-244 (2010)

PI Larry Pratt

Lawrence M. Pratt, Stewart Voit, Fabian N. Okeke, Nobuaki Kambe, "Nickel Catalyzed Alkyl Coupling Reactions: Evaluation of Computational Methods." Submitted for publication

B. Ramachandran, Purnima Kharidehal,, Lawrence M. Pratt, Stewart Voit, Fabian N. Okeke, Monique Ewan, "Computational Strategies for Reactions of Aggregated and Solvated Organolithium Carbenoids."J. Phys. Chem. A, 2010, 114, 8423

Lawrence M. Pratt, Stewart Voit, Binh Khanh Mai, BichLien H. Nguyen, "Lithium Cuprate Coupling Reactions: Evaluation of Computational Methods for Determination of the Reaction Mechanisms."J. Phys. Chem. A, 2010, 114, 5005

PI Joel Primack

Ceverino, Daniel; Klypin, Anatoly. The Role of Stellar Feedback in the Formation of Galaxies. The Astrophysical Journal, 695, 292 (2009).

Dekel, Avishai; Sari, Re'em; Ceverino, Daniel. Formation of Massive Galaxies at High Redshift: Cold Streams, Clumpy Disks, and Compact Spheroids. The Astrophysical Journal, 703, 785 (2009).

Kacprzak, Glenn G.; Churchill, Christopher W.; Ceverino, Daniel; Steidel, Charles C.; Klypin, Anatoly; Murphy, Michael T. Halo Gas and Galaxy Disk Kinematics Derived from Observations and ??CDM Simulations of Mg II Absorption-selected Galaxies at Intermediate Redshift. The Astrophysical Journal, 711, 535 (2010).

Ceverino, Daniel; Dekel, Avishai; Bournaud, Frederic. High-redshift clumpy discs and bulges in cosmological simulations. MNRAS, 404, 2151 (2010).

Goerdt, Tobias; Dekel, A.; Sternberg, A.; Ceverino, D.; Teyssier, R.; Primack, J. R. Gravity-driven Ly?? blobs from cold streams into galaxies. MNRAS, 407, 613 (2010).

PI Fritz Prinz

Y. Zhou, T. Holme, J. Berry, T. Ohno, D. Ginley and R. O'Hayre, "Dopant-Induced Electronic Structure Modification of HOPG Surfaces: Implications for High Activity Fuel Cell Catalysts", J. Phys. Chem. C, vol. 114, pp. 506-515, 2010.

Timothy Holme, Yingke Zhou, Robert Pasquarelli and Ryan O'Hayre, " First principles study of doped carbon supports for enhanced platinum catalysts", Phys. Chem. Chem. Phys., vol. 12, pp. 9461-9468, 2010.

PI Philip Pritchett

P.L. Pritchett and F.S. Mozer, "Asymmetric Magnetic Reconnection in the Presence of a Guide Field," J. Geophys. Res., 114, A11210, doi:10.1029/2009JA014343, 2009.

PI Han Pu

L. O. Baksmaty, Hong Lu, C. J. Bolech, Han Pu, "Concomitant Modulated Superfluidity In Polarized Fermionic Gases." Under review at Physical Review Letters also on the archives at: arXiv:1003.4488

PI Dale Pullin

"An adaptive high-order hybrid scheme for compressive, viscous flows with detailed chemistry" Ziegler, J., Deiterding R., Pullin D., Shepherd J., submitted to Journal of Computational Physics

PI Alkesh Punjabi

One manuscript will be submitted to Physics of Plasmas in September 2010.

PI Yevgeniy Puzyrev

J. Gazquez*, W. Luo, M.P. Oxley, M. Prange, M.A. Torija, M. Sharma, C. Leighton, S.T. Pantelides, S.J. Pennycook, and M. Varela, "Atomic-resolution imaging of nanometer sized spin-state superlattices in cobaltite films" submitted to Advanced Materials.

X. Shen, M. P. Oxley1, Y. Puzyrev, B. R. Tuttle, G. Duscher, and S. T. Pantelides, "Excess Carbon in Silicon Carbide", submitted to Journal of Applied Physics.


R

PI Abhay Ram

Peter J. Catto and Darin R. Ernst, "Alternate form of Model Like Particle Collision Operator", Plasma Phys. Control. Fusion 51 No 6 (June 2009) 062001.

D. R. Ernst, J. Lang, W. M. Nevins, M. Hoffman, Y. Chen, W. Dorland, and S. Parker, "Role of zonal flows in trapped electron mode turbulence through nonlinear gyrokinetic particle and continuum simulation", Invited paper YI2 3, Bull. Am. Phys. Soc. 53, 323 (2008). Physics of Plasmas 16, 055906 (2009).

J. C. Wright, P. T. Bonoli, A. E. Schmidt, C. K. Phillips, E. J. Valeo, R. W. Harvey, and M. A. Brambilla, "An assessment of full wave effects on the propagation and absorption of lower hybrid waves", Phys. Plasmas 16, 072502 (2009). NOTE: indirect benefit from NERSC resources. From APS invited talk, featured on journal cover.

M. Barnes, I. G. Abel, W. Dorland, D. R. Ernst, G. W. Hammett, P. Ricci, B. N. Rogers, A. A. Schekochihin, and T. Tatsuno, "Linearized model Fokker--Planck collision operators for gyrokinetic simulations. II. Numerical implementation and tests", Phys. Plasmas 16, 072107 (2009).

J. C. Wright, E. J. Valeo, C. K. Phillips, P. T. Bonoli and M. Brambilla, "Full Wave Simulations of Lower Hybrid Waves in Toroidal Geometry with Non-Maxwellian Electrons", Commun. Comput. Phys., Vol. 4, No. 3, 545 (2008).

B. A. Nelson, T. R. Jarboe, R. D. Milroy, U. Shumlak, G. A. Cone, A. H. Glasser, G. J. Marklin, C. C. Kim, W. B. Lowrie, V. S. Lukin, E. T. Meier, C. R. Sovinec and R. A. Bayliss, E. D. Held and J. Y. Ji, "Activities of the Plasma Science and Innovation Center", Japanese Journal of Plasma and Fusion Research, Vol. 84, No. 11 (2008), pp. 775-780 (in Japanese).

PI David Randall

Khairoutdinov, M. F., S. K. Krueger, C.-H. Moeng, P. Bogenschutz, and D. A. Randall, 2010: Large-eddy simulation of maritime deep tropical convection. J. Adv. Modeling Earth Sys. (in press).

Moeng, C.-H., M. A. LeMone , M. Khairoutdinov , S. Krueger , P. Bogenschutzc and D. A. Randall, 2010: The tropical marine boundary layer under a deep convection system: a large-eddy simulation study. J. Adv. Modeling Earth Sys. (in press).

Moeng, C.-H., P. P. Sullivan, M. F. Khairoutdinov, and D. A. Randall, 2010: A two-part scheme for subgrid-scale transport in cloud-resolving models. J. Atmos. Sci. (in press).

Palmer, B., A. Koontz, K. Schuchardt, R. Heikes, and D. A. Randall, 2010: An IO API for a global cloud resolving model. Submitted to the International Journal of High Performance Computing Applications.

Benedict, J. J., and D. A. Randall, 2010: The effects of ocean coupling on the MJO. Submitted to J. Climate.

DeMott, C. A., D. A. Randall, C. Stan, and M. Khairoutdinov, 2011: Simulated Coupling of the Asian Monsoon with Tropical Wave Activity. Submitted to J. Climate.

PI Sergey Rashkeev

B. Beeler, B. Good, S. Rashkeev, C. Deo, M. Baskes, and M. Okuniewski. First principles calculations of defects in U. Journal of Physics. Condensed Matter (submitted 07.26.2010).

D. Gryaznov, S. Rashkeev, E.A. Kotomin, E. Heifets, Y. Zhukovskii. Helium behavior in oxide nuclear fuels: First principles modeling. Nuclear Instruments and Methods in Physics Research Section B: Beam Interactions with Materials and Atoms 268, Issue 19, 3090-3094 (2010); doi: 10.1016/j.nimb.2010.05.054.

Michael V. Glazoff and Sergey N. Rashkeev. Beryllium Adsorption at Transition Aluminas: Implications for Environmental Science and Oxidation of Aluminum Alloys. The Journal of Physical Chemistry C 114, N33, 14208???14212 (2010); doi: 10.1021/jp1044942.

Sokrates T. Pantelides, L. Tsetseris, M.J. Beck, S.N. Rashkeev, G. Hadjisavvas, I. Batyrev, B. Tuttle, A.G. Marinopoulos, X.J.Zhou, D.M.Fleetwood, and R.G.Schrimpf. Performance, reliability, radiation effects, and aging issues in microelectronics -- From atomic-scale physics to engineering-level modeling. Solid-State Electronics 54, N9, 841-848 (2010); doi: 10.1016/j.sse.2010.04.041.

Sergey N. Rashkeev, Sheng Dai, and Steven H. Overbury. Modification of Au/TiO2 nanosystems by SiO2 monolayers: Toward the control of the catalyst activity and stability. The Journal of Physical Chemistry C 114, N7, 2996-3002 (2010); doi: 10.1021/jp9091738.

Maija M. Kuklja and Sergey N. Rashkeev. Self-accelerated mechanochemically in nitroarenes. The Journal of Physical Chemistry Letters 1, N1, 363-367 (2010); doi: 10.1021/jz9001967.

S. J. Pennycook, M. F. Chisholm, A. R. Lupini, M. Varela, A. Y. Borisevich, M. P. Oxley, W. D. Luo, K. van Benthem, S.-H. Oh, D. L. Sales, S. I. Molina, J. Garc??a-Barriocanal, C. Leon, J. Santamara, S. N. Rashkeev, and S. T. Pantelides. Aberration-corrected scanning transmission electron microscopy: from atomic imaging and analysis to solving energy problems. Philosophical Transactions of the Royal Society A - Mathematical, Physical, and Engineering Sciences 367, issue 1903, 3709-3733 (2009); doi: 10.1098/rsta.2009.0112 (review article).

Yuri A. Mastrikov, Maija M. Kuklja, Eugene A. Kotomin, and Joachim Maier, First-principles modelling of complex perovskite (Ba1-xSrx)(Co1-yFey)O3-d for solid oxide fuel cell and gas separation membrane applications, Energy and Environmental Science, 2010, 1-8.

F.J.Zerilli and M.M.Kuklja, Ab initio equation of state of the organic molecular crystal: ??-octahydro-1,3,5,7-tetranitro-1,3,5,7-tetrazocine (beta-HMX), J. Phys. Chem. A, 2010, 114(16) 5372-5376.

Ligen Wang and Maija M. Kuklja, First-principles study of small aluminum clusters: Oxygen adsorptions, oxidation and phase stability, Journal of Physics and Chemistry of Solids,71(2), 140-144 (2010).

A.V.Kimmel, P.V.Sushko, and M.M.Kuklja , The structure and decomposition chemistry of isomer defects in a crystalline DADNE, Invited paper to appear in Journal of Energetic Materials, 28, 20-33, 2010.

Maija M. Kuklja and Sergey N. Rashkeev, Molecular mechanisms of Shear-strain Sensitivity of Energetic Crystals DADNE and TATB, Invited paper to appear in Journal of Energetic Materials, 28, 1-12, 2010.

O.Sharia and M.M.Kuklja, Ab initio kinetics of beta-octahydro-tetranitro-tetrazocine decomposition, submitted to the Journal of Physical Chemistry A.

PI Lawrence Rauchwerger

G. Tanase, X. Xu, A. Buss, Harshvardhan,I. Papadopoulos, O. Pearce, T. Smith, N. Thomas, M. Bianco, N. Aamato and L. Rauchwerger, ``The STAPL pList'',Proc. of the 22-th Workshop on Languages and Compilers for Parallel Computing (LCPC)}, Wilmington, DE, Sept. 2009.

A. Jula and L. Rauchwerger, ``Two Memory Allocators that Use Hints to Improve Locality'', ACM SIGPLAN Int. Symposium on Memory Management (ISMM'09), Dublin, Ireland, June 2009.

The STAPL pView, Antal Buss, Adam Fidel, Harshvardhan, Timmie Smith, Gabriel Tanase, Nathan Thomas, Xiabing Xu, Mauro Bianco, Nancy M. Amato, Lawrence Rauchwerger, Proc. of the 23-th Workshop on Languages and Compilers for Parallel Computing (LCPC)}, Houston, TX, Oct. 2010.

STAPL: Standard Template Adaptive Parallel Library, Antal Buss, Harshvardhan, Ioannis Papadopoulos, Olga Tkachyshyn, Timmie Smith, Gabriel Tanase, Nathan Thomas, Xiabing Xu, Mauro Bianco, Nancy M. Amato, Lawrence Rauchwerger, In Haifa Experimental Systems Conference, Haifa, Israel, May 2010.

PI John Rehr

J. J. Rehr, M. P. Prange, and J. J. Kas, Calculation of optical constants and related quantities from optical to x-ray frequencies, Journal of Physics: Conference Series 190, 012001 (2009).

K. Jorissen and J. J. Rehr, Calculations of electron energy loss and x-ray absorption spectra in periodic systems without a supercell, Phys. Rev. B 81, 245124 (2010).

K. Jorissen, J. J. Rehr, and J. Verbeeck, Multiple scattering calculations of relativistic electron energy loss spectra, Phys. Rev. B 81, 155108 (2010).

J. J. Kas, J. J. Rehr, J. L. Glover, and C. T. Chantler, Comparison of Theoretical and Experimental Cu and Mo K-edge XAS, Nuc. Inst. and Meth. in Phys. Res. A 619, 2832 (2010).

John J. Rehr, Joshua J. Kas Fernando D. Vila, Parameter-free calculations of x-ray spectra with FEFF9, PCCP 12, 5503 (2010).

G. Veronesi, C. Degli Esposti Boschi, L. Ferrari, G. Venturoli, F. Boscherini, F.D. Vila, and J.J. Rehr, Ab initio analysis of the x-ray absorption spectrum of the myoglobin-carbon monoxide complex: Structure and vibrations, Phys. Rev. B (R) 82, 020101 (2010).

PI Thomas Reichler

Pennell, C. and T. Reichler (2010): On the effective number of climate models, J. Climate, (submitted).

Martin G., C. Senior, S. Ineson, P. James, S. Milton, M. Brooks, T. Reichler, and J. Kim (2010): Analysis and reduction of systematic errors through a seamless approach to modelling weather and climate, J. Climate, (in press).

PI Chuang Ren

R. Yan, A. Maximov, C. Ren, and F. Tsung, "Growth and saturation of convective modes of the two-plasmon decay instability in inertial confinement fusion," Phys. Rev. Lett. 103, 175002 (2009)

R. Yan, A. V. Maximov, and C. Ren, "The linear regime of the two-plasmon decay instability in inhomogeneous plasmas," Phys. Plasmas 17, 052701 (2010)

PI Barrett Rogers

``Low-frequency turbulence in a linear magnetized plasma'', B. Rogers and P. Ricci, Phys. Rev. Lett. {\bf 104} (2010)

``Gyrokinetic simulations of a particle pinch regime in closed-fieldline systems'', S. Kobayashi and B. Rogers, submitted to Phys. Rev. Lett. (2010)

``Ion and electron heating in gyrokinetic simulations of the tearing instability'', R. Numata, W. Dorland, N. Loureiro, B. Rogers, A. Schekochihin, T. Tatsuno, submitted to Phys. Rev. Lett. (2010)

``Perpendicular Ion Heating by Low-Frequency Alfven-Wave Turbulence in the Solar Wind,'', B. Chandran, B. Li, B. Rogers,  E. Quataert, K. Germaschewski, to appear in Astrophys. J. (2010)  (eprint: arXiv:1001.2069)

``Turbulence Phase Space in Simple Magnetized Toroidal Plasmas'', P. Ricci and B. Rogers, PRL 104, 145001,  DOI: 10.1103/PhysRevLett.104.145001 (2010)

``Collisional damping of zonal flows due to finite Larmor radius effects'',  P. Ricci, B. Rogers, W. Dorland, Phys. Plasmas 17,  DOI: 10.1063/1.3447875 (2010)

``Magnetic Reconnection at the Dayside Magnetopause in Global LFM Simulations'', J. E. Ouellette, B. N. Rogers, M. Wiltberger, and J. G. Lyon,  to appear in JGR (2010)

``Fast Reconnection in High-Lundquist-Number Plasmas Due to Secondary Tearing Instabilities'' A. Bhattacharjee, Y. Hwang, H. Yang, B. Rogers, Physics of Plasmas 16, Issue 11, pp. 112102-112102-5 (2009)

``Plasma transport and turbulence in the Helimak: Simulation and  experiment'', B. Li, B. Rogers, K. Gentle, P. Ricci, Phys. Plasmas 16,  082510 (2009); doi:10.1063/1.3212591

``Three-dimensional fluid simulations of a simple magnetized toroidal  plasma'', P. Ricci and B.N. Rogers, Phys. Plasmas 16, 092307 (2009) doi:10.1063/1.3230119

``Transport scaling in an interchange-driven simple magnetized torus'',  P. Ricci and B.N. Rogers, Phys. Plasmas 16, 062303 (2009);  doi:10.1063/1.3139261

``Gyrokinetic Simulations of Turbulent Transport in a Ring Dipole Plasma'',  S. Kobayashi, B. N. Rogers, W. Dorland, Phys. Rev. Lett. 103, 055003 (2009),  DOI: 10.1103/PhysRevLett.103.055003

``Linearized model Fokker-Plank collision operators for gyrokinetic simulations. II. Numerical implementation and tests'',  M. Barnes, I. Abel, W. Dorland, D. Ernst, G. Hammett, P. Ricci,  B. Rogers, A. Schekochihin, T. Tatsuno, Phys. Plasmas 16, 072107 (2009);  OI: 10.1063/1.3155085

PI Tony Rollett

G. P. Purja Pun and Y. Mishin: Development of an interatomic potential for the  Ni-Al system, Philosophical Magazine 89, 3245-3267 (2009)

G. P. Purja Pun and Y. Mishin: Molecular dynamics study of self-diffusion in the  cores of edge and screw dislocations in aluminum, Acta Materialia 57, 5531-5542  (2009)

T. Frolov and Y. Mishin: Stable nanocolloidal structures in metallic systems,  Physical Review Letters 104, 055701 (2010)

T. Frolov, W. J. Boettinger and Y. Mishin: Atomistic simulation of hillock growth, Acta Materialia 58, 5471???5480 (2010)

T. Frolov and Y. Mishin: Orientation dependence of the solid-liquid interface stress: atomistic calculations for copper, Modeling and Simulation in Materials Science and Engineering 18, 074003 (2010)

G. P. Purja Pun and Y. Mishin: Molecular dynamics simulation of the martensitic phase transformation in NiAl alloys, Journal of Physics: Condensed Matter 22, 395403 (2010)

S. J. Fensin, D. Olmsted, D. Buta, M. Asta, A. Karma and J. J. Hoyt, "Structural disjoining potential for grain-boundary premelting and grain coalescence from molecular-dynamics simulations," Phys. Rev. E 81, 31601 (2010)

L. J. Peng, J. R. Morris and R.S. Aga, "A quantitative comparison of simulated crystal nucleation for the Lennard-Jones system with classical nucleation theory," J. Chem. Phys 133, 084505 (2010).

Chuck Henager, Jr., and J. R. Morris, "Atomistic simulation of CdTe solid-liquid coexistence equilibria," Phys. Rev. B 80, 245309 (2009).

PI Barbara Romanowicz

Lekic, V., Panning, M. & Romanowicz, B. A simple method for improving crustal corrections in waveform tomography. Geophys. J. Int. 182 (1), 265-278 (2010).

V. Lekic, B. Romanowicz, Inferring upper mantle structure by full waveform tomography with the Spectral Element Method, Geophys. J. Int. in revision.

Lekic, V. and B. Romanowicz (2010) Clustering Analysis of Global Tomographic Model Developed Using the Spectral Element Method, submitted to Nature Geosciences.

PI Robert Rosner

Hicks, Elizabeth and Rosner, Robert. "The effects of burning on the development of 2D turbulence", Physica Scripta T

PI Edward Rubin

Allgaier M et al. Targeted discovery of glycoside hydrolases from a switchgrass-adapted compost community. PLoS One. 2010 Jan 21;5(1):e8812.

Alverson AJ et al. Insights into the Evolution of Mitochondrial Genome Size from Complete Sequences of Citrullus lanatus and Cucurbita pepo (Cucurbitaceae). Mol Biol Evol. 2010 Jun;27(6):1436-48.

Anderson IJ et al. Complete genome sequence of Halorhabdus utahensis type strain (AX-2T). Standards in Genomic Sciences. 2009:1(3):218-225.

Ayala-Del-Rio HL et al. The genome sequence of Psychrobacter arcticus 273-4, a psychroactive Siberian permafrost bacterium reveals mechanisms for adaptation to low temperature growth. Appl Environ Microbiol. 2010 Apr;76(7):2304-12.

Baker SE. Selection to sequence: opportunities in fungal genomics. Environ Microbiol. 2009 Dec;11(12):2955-8.

Burnum KE et al. Proteome insights into the symbiotic relationship between a captive colony of Nasutitermes corniger and its hindgut microbiome. ISME J. 2010 Jul 8. [Epub ahead of print]

Cannon GC et al. Carboxysomal carbonic anhydrases: Structure and role in microbial CO2 fixation. Biochim Biophys Acta. 2010 Feb;1804(2):382-92. Epub 2009 Oct 8.

Chain PS et al. Genomics. Genome project standards in a new era of sequencing. Science. 2009 Oct 9;326(5950):236-7.

Chan YF et al. Adaptive evolution of pelvic reduction in sticklebacks by recurrent deletion of a Pitx1 enhancer. Science. 2010 Jan 15;327(5963):302-5. Epub 2009 Dec 10.

Chapman JA et al. The dynamic genome of Hydra. Nature. 2010 Mar 14. [Epub ahead of print]

Chertkov O et al. Complete genome sequence of Aminobacterium colombiense type strain (ALA-1T).  Standards in Genomic Sciences. 2010:2(3): 280-289

Chovatia M et al. Complete genome sequence of Thermanaerovibrio acidaminovorans type strain (Su883T). Standards in Genomic Sciences. 2009:1(3):254-261.

Clum A et al. Complete genome sequence of Pirellula staleyi type strain (ATCC 27377T). Standards in Genomic Sciences. 2009:1(3):308-316.

DeAngelis KM et al. Strategies for Enhancing the Effectiveness of Metagenomic-based Enzyme Discovery in Lignocellulolytic Microbial Communities. Bioenergy Res. Jun 2010; 3(2):Sp. Iss. SI, 146-148.

Dehal PS et al. MicrobesOnline: an integrated portal for comparative and functional genomics. Nucleic Acids Res. 2010 Jan;38(Database issue):D396-400.

Deli A et al. LmbE proteins from Bacillus cereus are de-N-acetylases with broad substrate specificity and are highly similar to proteins in Bacillus anthracis. FEBS J. 2010 Jul;277(13):2740-53. Epub 2010 May 19.

Ditty JL et al. (2010) Incorporating Genomics and Bioinformatics across the Life Sciences Curriculum. PLoS Biol 8(8): e1000448.

Donaher N et al. The Complete Plastid Genome Sequence of the Secondarily Nonphotosynthetic Alga Cryptomonas paramecium: Reduction, Compaction, and Accelerated Evolutionary Rate. Genome Biol  Evol. 2009 Nov 13;2009:439-48.

Du J et al. Bifurcation and enhancement of autonomous-nonautonomous retrotransposon partnership through LTR Swapping in soybean. Plant Cell. 2010 Jan;22(1):48-61.

Duncan KE. Biocorrosive Thermophilic Microbial Communities in Alaskan North Oil Slope Facilities. Environ Sci Technol. 2009 Oct 15;43(20):7977-7984.

Engelbrektson A et al. Experimental factors affecting PCR-based estimates of microbial species richness and evenness. ISME J. 2010 May;4(5):642-7.

Ferris P et al. Evolution of an expanded sex-determining locus in Volvox. Science. 2010 Apr 16;328(5976):351-4.

Foster B et al. Complete genome sequence of Xylanimonas cellulosilytica type strain (XIL07T). Standards in Genomic Sciences. 2010:2(1): 1-8.

Fritz-Laylin LK et al. The genome of Naegleria gruberi illuminates early eukaryotic versatility. Cell. 2010 Mar 5;140(5):631-42.

Glavina del Rio T et al. Complete genome sequence of Chitinophaga pinensis type strain (UQM 2034T). Standards in Genomic Sciences. 2010:2(1): 87-95.

Gowda M et al. Genome-wide characterization of methylguanosine-capped and polyadenylated small RNAs in the rice blast fungus Magnaporthe oryzae. Nucleic Acids Res. 2010 Jul 21. [Epub ahead of print]

Gronow S et al. Complete genome sequence of Veillonella parvula type strain (Te3T). Standards in Genomic Sciences. 2010:2(1): 57-65.

Guisinger MM et al. Implications of the Plastid Genome Sequence of Typha (Typhaceae, Poales) for Understanding Genome Evolution in Poaceae. J Mol Evol. 2010 Jan 21. [Epub ahead of print]

Haley BJ et al. Comparative genomic analysis reveals evidence of two novel Vibrio species closely related to V. cholerae. BMC Microbiol. 2010 May 27;10:154.

Han C et al. Complete genome sequence of Kangiella koreensis type strain (SW- 125T). Standards in Genomic Sciences. 2009:1(3):226-233.

Harmon-Smith M et al. Complete genome sequence of Sebaldella termitidis type strain (NCTC 11300T). Standards in Genomic Sciences. 2010:2(2): 220-227.

He SM et al. Metatranscriptomic array analysis of 'Candidatus Accumulibacter phosphatis'-enriched enhanced biological phosphorus removal sludge. Environ Microbiol. 2010 May;12(5):1205-17.

Hellsten U et al. The genome of the Western clawed frog Xenopus tropicalis. Science. 2010 Apr 30;328(5978):633-6.

Hemme CL et al. Metagenomic insights into evolution of a heavy metal-contaminated groundwater microbial community. ISME J. 2010 May;4(5):660-72.

Hill KK et al. Recombination and insertion events involving the botulinum neurotoxin complex genes in Clostridium botulinum types A, B, E and F and Clostridium butyricum type E strains. BMC Biol. 2009 Oct 5;7:66.

Hirschman L et al. Meeting Report: “Metagenomics, Metadata and Meta-analysis” (M3) Workshop at the Pacific Symposium on Biocomputing 2010 Standards in Genomic Sciences. 2010:2(3): 357-360.

Hooper S et al. Estimating DNA coverage and abundance in metagenomes using a gamma approximation. Bioinformatics. 2010 Feb 1;26(3):295-301.

Hyatt D et al. Prodigal: prokaryotic gene recognition and translation initiation site identification. BMC Bioinformatics. 2010 Mar 8;11(1):119. [Epub ahead of print]

Hyten DL et al. High-throughput SNP discovery through deep resequencing of a reduced representation library to anchor and orient scaffolds in the soybean whole genome sequence. BMC Genomics. 2010 Jan 15;11(1):38. [Epub ahead of print]

International Brachypodium Initiative. Genome sequencing and analysis of the model grass Brachypodium distachyon. Nature. 2010 Feb 11;463(7282):763-8.

Ivanova N et al. Complete genome sequence of Geodermatophilus obscurus type strain (G-20T). Standards in Genomic Sciences. 2010:2(2): 158-167.

Ivanova N et al. Complete genome sequence of Haliangium ochraceum type strain (SMP-2T). Standards in Genomic Sciences. 2010:2(1): 96-106.

Ivanova N et al. Complete genome sequence of Gordonia bronchialis type strain 3410T). Standards in Genomic Sciences. 2010:2(1): 19-28. 44. Ivanova N et al. A call for standardized classification of metagenome projects.

Environ Microbiol. 2010 Jul;12(7):1803-5. 45. Jackson DJ et al. Parallel Evolution of Nacre Building Gene Sets in Molluscs. Mol Biol Evol. 2010 Mar;27(3):591-608.

Janssen PJ et al. The complete genome sequence of Cupriavidus metallidurans strain CH34, a master survivalist in harsh and anthropogenic environments. PLoS One. 2010 May 5;5(5):e10433.

Junier P et al. The genome of the Gram-positive metal- and sulfate-reducing bacterium Desulfotomaculum reducens strain MI-1. Environ Microbiol. 2010 May 17. [Epub ahead of print]

Keim P et al. The genome and variation of Bacillus anthracis. Mol Aspects Med. 2009 Sep 1. [Epub ahead of print]

Kielak A et al. Phylogenetic and metagenomic analysis of Verrucomicrobia in former agricultural grassland soil. FEMS Microbiol Ecol. 2010 Jan;71(1):23-33.

Kiss H et al. Complete genome sequence of Denitrovibrio acetiphilus type strain (N2460T) Standards in Genomic Sciences. 2010:2(3): 270-279

Kouvelis VN et al. Complete genome sequence of ethanol producer Zymomonas mobilis NCIMB 11163. J Bacteriol. 2009 Nov;191(22):7140-1.

Kristiansson E et al. ShotgunFunctionalizeR: An R-package for functional comparison of metagenomes. Bioinformatics. 2009 Aug 20. [Epub ahead of print]

Kunin V et al. Wrinkles in the rare biosphere: pyrosequencing errors lead to artificial inflation of diversity estimates. Environ Microbiol. 2009 Aug 27. [Epub ahead of print]

Lail K et al. Complete genome sequence of Spirosoma linguale type strain (1T). Standards in Genomic Sciences. 2010:2(2): 176-185.

Land M et al. Complete genome sequence of Beutenbergia cavernae type strain (HK1 0122T). Standards in Genomic Sciences. 2009:1(1):21-28.

Liolios K et al. The Genomes On Line Database (GOLD) in 2009: status of genomic and metagenomic projects and their associated metadata. Nucleic Acids Res. 2009 Nov 13;19(4):682-9. [Epub ahead of print]

Liolios K et al. Complete genome sequence of Thermobispora bispora type strain (R51T) 3 Standards in Genomic Sciences. 2010:2(3): 18-326

Lykidis A et al. The Complete Multipartite Genome Sequence of Cupriavidus necator JMP134, a Versatile Pollutant Degrader. PLoS One. 2010 Mar 22;5(3):e9729.

Lykidis A et al. Multiple syntrophic interactions in a terephthalate-degrading methanogenic consortium. ISME J. 2010 Aug 05; doi:10.1038/ismej.2010.125. [Epub ahead of print.]

Ma LJ et al. Comparative genomics reveals mobile pathogenicity chromosomes in Fusarium. Nature. 2010 Mar 18;464(7287):367-73.

Macagno ER et al. Construction of a medicinal leech transcriptome database and its application to the identification of leech homologs of neural and innate immune genes. BMC Genomics. 2010 Jun 25;11:407.

Markowitz VM et al. The integrated microbial genomes system: an expanding comparative analysis resource. Nucleic Acids Res. 2009 Oct 28;25(17):2271-8. [Epub ahead of print]

Martin J et al. Bacillus anthracis genome organization in light of whole transcriptome sequencing. BMC Bioinformatics. 2010 Apr 29;11 Suppl 3:S10.

Martinez D et al. Annotation of protein-coding genes in fungal genomes. Appl. Comput. Math., V.9, Special Issue, 2010, 56-65.

Mavromatis K et al. Complete genome sequence of Alicyclobacillus acidocaldarius type strain (104-IAT). Standards in Genomic Sciences. 2010:2(1): 9-18.

Mavrommatis K et al. Gene Context Analysis in the Integrated Microbial Genomes (IMG) Data Management System. PLoS ONE. 2009 Nov 24:4(11):e7979.

Mavromatis K et al. Complete genome sequence of Coraliomargarita akajimensis type strain (04OKA010-24 T). Standards in Genomic Sciences. 2010:2(3): 290-299.

McBride MJ et al. Novel features of the polysaccharide-digesting gliding bacterium Flavobacterium johnsoniae revealed by genome sequence analysis. Appl Environ Microbiol. 2009 Aug 28. [Epub ahead of print]

McMurdie PJ et al. Localized Plasticity in the Streamlined Genomes of Vinyl Chloride Respiring Dehalococcoides. PLoS Genet. 2009 Nov;5(11):e1000714.

Munk C et al. Complete genome sequence of Stackebrandtia nassauensis type strain (LLR-40K-21T). Standards in Genomic Sciences. 2009:1(3):292-299.

Nalbantoglu U et al. Large Direct Repeats Flank Genomic Rearrangements between a New Clinical Isolate of Francisella tularensis subsp tularensis A1 and Schu S4. PLoS One. 2010 Feb 3;5(2):e9007.

Nelson KE et al. A Catalog of Reference Genomes from the Human Microbiome.Science. 2010 May 21;328(5981):994-9.

Nicolas FE et al. Endogenous short RNAs generated by Dicer 2 and RNA-dependent RNA polymerase 1 regulate mRNAs in the basal fungus Mucor circinelloides. Nucleic Acids Res. 2010 Apr 28. [Epub ahead of print]

Nolan M et al. Complete genome sequence of Rhodothermus marinus type strain (R- 10T). Standards in Genomic Sciences. 2009:1(3):283-291.

Nolan M et al. Complete genome sequence of Streptosporangium roseum type strain (NI 9100T). Standards in Genomic Sciences. 2010:2(1): 29-37.

Nolan M et al. Complete genome sequence of Streptobacillus moniliformis type strain (9901T). Standards in Genomic Sciences. 2009:1(3):300-307.

Novichkov PS et al. RegPrecise: a database of curated genomic inferences of transcriptional regulatory interactions in prokaryotes. Nucleic Acids Res. 2010 Jan;38(Database issue):D111-8.

Novichkov PS et al. RegPredict: an integrated system for regulon inference in prokaryotes by comparative genomics approach. Nucleic Acids Res. 2010 Jul 1;38 Suppl:W299-307.

Ohm RA et al. Genome sequence of the model mushroom Schizophyllum commune. Nat Biotechnol. 2010 July 11. [Epub ahead of print]

Pati A et al. Complete genome sequence of Sphaerobacter thermophilus type strain (S 6022T). Standards in Genomic Sciences. 2010:2(1): 49-56.

Pati A et al. GenePRIMP: a gene prediction improvement pipeline for prokaryotic genomes. Nat Methods. 2010 May 2. [Epub ahead of print]

Pati A et al. Complete genome sequence of Brachyspira murdochii type strain (56- 150T). Standards in Genomic Sciences. 2010:2(3): 260-269

Pati A et al. Complete genome sequence of Arcobacter nitrofigilis type strain (CIT). Standards in Genomic Sciences. 2010:2(3): 300-308.

Pearson T et al. Phylogeographic reconstruction of a bacterial species with high levels of lateral gene transfer. BMC Biol. 2009 Nov 18;7:78.

Penn K et al. Genomic islands link secondary metabolism to functional adaptation in marine Actinobacteria. ISME J. 2009 May 28. [Epub ahead of print]

Prochnik SE et al. Genomic analysis of organismal complexity in the multicellular green alga Volvox carteri. Science. 2010 Jul 9;329(5988):223-6.

Pukall R et al. Complete genome sequence of Slackia heliotrinireducens type strain (RSH 1T). Standards in Genomic Sciences. 2009:1(3):234-241.

Pukall R et al. Complete genome sequence of Jonesia denitrificans type strain (Prevot 55134T). Standards in Genomic Sciences. 2009:1(3):262-269.

Pukall R et al. Complete genome sequence of Conexibacter woesei type strain (ID131577T). Standards in Genomic Sciences. 2010:2(2): 212-219.

Pukall R et al. Complete genome sequence of Kribbella flavida type strain (IFO 14399T). Standards in Genomic Sciences. 2010:2(2): 186-193.

Raha D et al. Close association of RNA polymerase II and many transcription factors with Pol III genes. Proc Natl Acad Sci U S A. 2010 Feb 23;107(8):3639-44. Epub 2010 Feb 5.

Ran L et al. Genome erosion in a nitrogen-fixing vertically transmitted endosymbiotic multicellular cyanobacterium. PLoS One. 2010 Jul 8;5(7):e11486.

Reeve WG et al. Complete genome sequence of Rhizobium leguminosarum bv. trifolii strain WSM2304, an effective microsymbiont of the South American clover Trifolium polymorphum. Standards in Genomic Sciences. 2010:2(1): 66-76.

Reeve WG et al. Complete genome sequence of the Medicago microsymbiont Ensifer (Sinorhizobium) medicae strain WSM419. Standards in Genomic Sciences. 2010:2(1): 77-86.

Reeve WG et al. Complete genome sequence of Rhizobium leguminosarum bv. trifolii strain WSM1325, an effective microsymbiont of annual Mediterranean clovers. Standards in Genomic Sciences. 2010:2(3): 347-356

Saunders E et al. Complete genome sequence of Haloterrigena turkmenica type strain (4kT). Standards in Genomic Sciences. 2010:2(1): 107-116.

Schmutz J et al. Genome sequence of the palaeopolyploid soybean. Nature. 2010 Jan 14; 463(7278):178-83.

Sieber JR et al. The genome of Syntrophomonas wolfei: new insights into syntrophic metabolism and biohydrogen production. Environ Microbiol. 2010 May 12. [Epub ahead of print]

Seidl V et al. Transcriptomic response of the mycoparasitic fungus Trichoderma atroviride to the presence of a fungal prey. BMC Genomics;10:567.

Sikorski J et al. Complete genome sequence of Sulfurospirillum deleyianum type strain (5175T). Standards in Genomic Sciences. 2010:2(2): 149-157.

Sikorski J et al. Complete genome sequence of Segniliparus rotundus type strain (CDC 1076T). Standards in Genomic Sciences. 2010:2(2): 203-211.

Spring S et al. Complete genome sequence of Thermosphaera aggregans type strain (M11TLT). Standards in Genomic Sciences. 2010:2(3): 245-259

Spring S et al. Complete genome sequence of Desulfotomaculum acetoxidans type strain (5575T). Standards in Genomic Sciences. 2009:1(3):242-253.

Spring S et al. Complete genome sequence of Desulfohalobium retbaense type strain (HR100T). Standards in Genomic Sciences. 2010:2(1): 38-48.

Srivastava M et al. Early evolution of the LIM homeobox gene family. BMC Biol. 2010 Jan 18;8:4.

Srivastava M et al. the Amphimedon queenslandica genome and the evolution of animal complexity. Nature. 2010 Aug 05;466(7307): 470-726.

Strnad H et al. Complete genome sequence of the photosynthetic purple nonsulfur bacterium Rhodobacter capsulatus SB 1003. J Bacteriol. 2010 Apr 23. [Epub ahead of print]

Tagmount A et al. The Porcelain Crab Transcriptome and PCAD, the Porcelain Crab Microarray and Sequence Database. PLoS One. 2010 Feb 19;5(2):e9327.

Tice H et al. Complete genome sequence of Nakamurella multipartita type strain (Y-104T). Standards in Genomic Sciences. 2010:2(2): 168-175.

Tindall BJ et al. Complete genome sequence of Halomicrobium mukohataei type strain (arg-2T). Standards in Genomic Sciences. 2009:1(3):270-277.

Vanden Wymelenberg A et al. Comparative transcriptome and secretome analysis of wood decay fungi Postia placenta and Phanerochaete chrysosporium. Appl Environ Microbiol. 2010 Apr 16. [Epub ahead of print]

von Jan M et al. Complete genome sequence of Archaeoglobus profundus type strain (AV18T). Standards in Genomic Sciences. 2010:2(3): 327-346

Wagner-Dobler I et al. The complete genome sequence of the algal symbiont Dinoroseobacter shibae: a hitchhiker's guide to life in the sea. ISME J. 2009 Sep 10. [Epub ahead of print]

Walker CB et al. Nitrosopumilus maritimus genome reveals unique mechanisms for nitrification and autotrophy in globally distributed marine crenarchaea. Proc Natl Acad Sci U S A. 2010 May 11;107(19):8818-23.

Walsh DA et al. Metagenome of a Versatile Chemolithoautotroph from Expanding Oceanic Dead Zones. Science. 2009 Oct 23;326(5952):578-82.

Wang S et al. Assembly of 500,000 inter-specific catfish expressed sequence tags and large scale gene-associated marker development for whole genome association studies. Genome Biol. 2010 Jan 22;11(1):R8. [Epub ahead of print]

Wang Z et al. SoyDB: a knowledge database of soybean transcription factors. BMC Plant Biol. 2010 Jan 18;10(1):14. [Epub ahead of print]

Wei D et al. Laccase and its role in the production of extracellular reactive oxygen species during wood decay by the brown rot basidiomycete Postia placenta. Appl Environ Microbiol. 2010 Feb 12. [Epub ahead of print]

Wilson A et al. Structural determinants underlying photoprotection in the photoactive orange carotenoid protein of cyanobacteria. J Biol Chem. 2010 Jun 11;285(24):18364-75.

Wirth R et al. Complete genome sequence of Thermocrinis albus type strain (HI 11/12T). Standards in Genomic Sciences. 2010:2(2): 194-202.

Woyke T et al. One bacterial cell, one complete genome. PLoS One. 2010 Apr 23;5(4):e10314.

Wu D. A phylogeny-driven genomic encyclopedia of bacteria and archaea. Nature. 2009 Dec 24;462(7276):1056-60.

Wurtzel O et al. A single-base resolution map of an archaeal transcriptome. Genome Res. 2010 Jan;20(1):133-41.

Yilmaz S et al. Fixation-free fluorescence in situ hybridization for targeted enrichment of microbial populations. ISME J. 2010 May 27. [Epub ahead of print]

Young M et al. Genome sequence of the Fleming strain of Micrococcus luteus, a simple free-living actinobacterium. J Bacteriol. 2009 Nov 30:1(1):63-67. [Epub ahead of print]

PI Yoram Rubin

Murakami, H., X. Chen, M.S. Hahn, Y. Liu, M.L. Rockhold, V.R. Vermeul, J.M. Zachara, and Y. Rubin: Bayesian approach for three-dimensional aquifer characterization at the Hanford 300 area, Hydrol. Earth Syst. Sci. Discuss., 7, 2017-2052, 2010.

Rubin, Y., X. Chen, H. Murakami and M. Hahn: A Bayesian approach for inverse modeling, data assimilation and conditional simulation of spatial random fields, Water Resour. Res., doi:10.1029/2009WR008799, in press.

Murakami, H., X. Chen, M.S. Hahn, M.L. Rockhold, V.R. Vermeul, and Y. Rubin: Bayesian geostatistical inversion framework for probabilistic risk assessments of groundwater contamination, Japan Geoscience Union Meeting, Makuhari, Chiba, May 2010.

Rubin, Y., F. de Barros, X. Chen, H. Murakami and M.S. Hahn: Elements of a Comprehensive Approach for Modeling Uncertainty, Eos Trans. AGU, 90(52), Fall Meet. Suppl., Abstract H51N-01.

Chen, X., H. Murakami, M.S. Hahn, M.L. Rockhold, V.R. Vermeul, Y. Rubin: Integrating Tracer Test Data into Geostatistical Aquifer Characterization at the Hanford 300 Area, Eos Trans. AGU, 90(52), Fall Meet. Suppl., Abstract H43F-1095.

Murakami, H., X. Chen, M.S. Hahn, Y. Liu, M.L. Rockhold, V.R. Vermeul, Y. Rubin: Three-dimensional Characterization of A High-K Aquifer at the Hanford 300 Area and Retrospective Analysis of Experimental Designs, Eos Trans. AGU, 90(52), Fall Meet. Suppl., Abstract H43F-1082

PI Robert Ryne

J. Qiang, X. Li, "Particle-Field Decomposition and Domain Decomposition in Parallel Particle-In-Cell Beam Dynamics Simulation," submitted to Computer Physics Communication, (2010)

J. Qiang, "Short wavelength seeding through compression for free electron lasers," to appear in Nuclear Instruments & Methods in Physics Research A (2010).

J. Qiang, "Particle-In-Cell/Monte Carlo Simulation of Ion Back BomBardment in a High Average Current RF Photo-Gun," Nuclear Instruments & Methods in Physics Research A 614, 1 (2010).

J. Qiang, "A high-order fast method for computing convolution integral with smooth kernel," Computer Physics Communication, 181, 313 (2010).


S

PI Yousef Saad

Pierre Carrier, Yousef Saad, MSI Bulletin, Summer 2010,web address: http://static.msi.umn.edu/research_bulletin/2010-26-2.pdf [Best poster award from the 25th Anniversary of the Minnesota Supercomputing Institute.]

P. Carrier, Physical Review B, Vol 80, 075319 (2009)

Ab initio molecular dynamics simulations using a Chebyshev-filtered subspace iteration technique, K. H. Khoo, M. Kim, G. Schofield, and James R. Chelikowsky, Phys. Rev. B 82, 064201 (2010). http://prb.aps.org/abstract/PRB/v82/i6/e064201

First-Principles Study of Confinement Effects on the Raman Spectra of Si Nanocrystals, K. H. Khoo, A. T. Zayak, H. Kwak, and James R. Chelikowsky, Phys. Rev. Lett. 105, 115504 (2010). http://prl.aps.org/abstract/PRL/v105/i11/e115504

PI Sayeef Salahuddin

Ganapathi, Kartik; Yoon, Youngki; Salahuddin, Sayeef, "Comparative analysis of the performance of  InAs lateral and vertical band-to-band tunneling transistors", Device Research Conference (DRC), 2010 Issue Date: 21-23 June 2010, On page(s): 57 - 58

Y Yoon and S Salahuddin, "Barrier-free tunneling in a carbon heterojunction transistor," Appl. Phys. Lett. 97, 03310,2, 2010. [cover article]

K Ganapathi, Y Yoon, and S Salahuddin, "Analysis of InAs vertical and lateral band-to-band tunneling transistors: Leveraging vertical tunneling for improved performance," Appl. Phys. Lett. 97, 033504 ,2010.

Y. Yoon and S Salahuddin, "Inverse temperature dependence of subthreshold slope in graphene nanoribbon tunneling transistor," Appl. Phys. Lett. 96, 013510 (2010).

Y.Yoon and S. Salahuddin, ???Structure, channel dimension and doping effects in carbon heterojunction transistors towards barrier-free band-to-band tunneling,??? Proceedings of Device Research Conference, 2010.

PI Martin Savage

Aaron Torok, et al (NPLQCD Collaboration ) Meson-Baryon Scattering Lengths from Mixed-Action Lattice QCD. Phys.Rev.D81:074506,2010.

NPLQCD Collaboration (Silas R. Beane et al.), High Statistics Analysis using Anisotropic Clover Lattices: (III) Baryon-Baryon Interactions.Phys.Rev.D81:054505,2010.

William Detmold, Martin J. Savage, A method to study complex systems of mesons in Lattice QCD. Phys.Rev.D82:014511,2010.

S.R. Beane, W. Detmold, K. Orginos, M.J. Savage, Nuclear Physics from Lattice QCD.major review accepted for publication Progress in Particle and Nuclear Physics e-Print: arXiv:1004.2935 [hep-lat]

PI Richard Saykally

D. Prendergast and S. G. Louie, "Bloch-state-based interpolation: An efficient generalization of the Shirley approach to interpolating electronic structure," Phys. Rev. B 80, 235126 (2009).

S. Fatehi, C. P. Schwartz, R. J. Saykally, and D. Prendergast, Nuclear quantum effects in the structure and lineshapes of the N2 near-edge x-ray absorption fine structure spectrum, J. Chem. Phys. 132, 094302-094309 (2010).

C. P. Schwartz, R. J. Saykally and D. Prendergast An analysis of the NEXAFS spectra of a molecular crystal: alpha-glycine J. Chem. Phys. 133, 044507 (2010).

J. S. Uejio, C. P. Schwartz, A. M. Duffin, A. H. England, D. Prendergast, and R. J. Saykally, "Monopeptide versus Monopeptoid: Insights on Structure and Hydration of Aqueous Alanine and Sarcosine via X-ray Absorption Spectroscopy," J. Phys. Chem. B 114, 4702-4709 (2010).

C. P. Schwartz, J. S. Uejio, A. M. Duffin, A. H. England, D. N. Kelly, D. Prendergast, R. J. Saykally "Investigation of protein conformation and interactions with salts via X-ray absorption spectroscopy" PNAS 107, 14008-14013 (2010).

PI Henry Schaefer

Q. Cheng, A. C. Simmonett, F. A. Evangelista, Y. Yamaguchi, and H. F. Schaefer, "Characterization of the BNNO Radical", J. Chem. Theory Comput., 6, 1915 (2010).

J. C. Hargis, H. F. Schaefer, K. N. Houk, and Steven E. Wheeler, "Noncovalent Interactions of a Benzo[a]pyrene Diol Epoxide with DNA Base Pairs: Insight into the Formation of Adducts of (+)-BaP DE-2 with DNA", J. Phys. Chem. A, 114, 2038 (2010).

H. Feng and W. D. Allen, "The Problematic C2H4+F2 Reaction Barrier", J. Chem. Phys., 132, 094304, (2010).

T. Lu, Q. Hao, A. C. Simmonett, F. A. Evangelista, Y. Yamaguchi, D.-C. Fang, and H. F. Schaefer, "Low-Lying Triplet States of Diphosphene and Diphosphinylidene", J. Phys. Chem. A (2010, available online DOI:10.1021/jp105281w).

Q. Wu, Q. Hao, J. J. Wilke, A. C. Simmonett, Y. Yamaguchi, Q. Li, D.-C. Fang, and H. F. Schaefer, "Anharmonic Vibrational Analysis for the Propadienylidene Molecule (H2C=C=C:)", J. Chem. Theory Comput., (in press, 2010).

H. M. Jaeger, H. F. Schaefer, J. Demaison, A. G. Csaszar, and W. D. Allen, "Lowest-Energy Conformers of alpha-Alanine", J. Chem. Theory Comput., (submitted, 2010).

D. S. Hollman, A. C. Simmonett, and H. F. Schaefer, "The Benzene + OH Potential Energy Surface: Intermediates and Transition States", Phys. Chem. Chem. Phys., (submitted, 2010).

PI Rocco Schiavilla

S. Pastore, L. Girlanda, R. Schiavilla, M. Viviani, R.B. Wiringa, "Electromagnetic Currents and Magnetic Moments in $\chi$EFT", Phys. Rev. C80, 034004 (2009)

L. Girlanda, S. Pastore, R. Schiavilla, M. Viviani, "Relativity constraints on the two-nucleon contact interactions", Phys. Rev. C81, 034005 (2010)

E. Adelberger et al., "Solar fusion cross sections II: the pp chain and CNO cycles", Rev. Mod. Phys. in press (2010), arXiv:1004.2318

M. Viviani, R. Schiavilla, L. Girlanda, A. Kievsky, L.E. Marcucci, "The parity-violating asymmetry in the 3He(n,p)3H reaction" Phys. Rev. C in press (2010), arXiv:1007.2052

L. Girlanda, A. Kievsky, L.E. Marcucci, S. Pastore, R. Schiavilla, M. Viviani, "Thermal neutron captures on $d$ and $^3$He" submitted to Phys. Rev. Lett., arXiv:1008.0356

L.E. Marcucci et al., "Muon capture on deuteron and 3He" submitted to Phys. Rev. C, arXiv:1008.1172

PI Erik Schnetter

C. D. Ott, E. Schnetter, A. Burrows, E. Livne, E. O'Connor, F. Loeffler, Computational Models of Stellar Collapse and Core-CollapseSupernovae, to appear in the proceedings of the DOE/SciDAC 2009 conference, arXiv:0907.4043v1 [astro-ph.HE], http://stellarcollapse.org/papers/Ott_SciDAC2009.pdf .

Evan O'Connor, Christian D. Ott, A New Open-Source Code for Spherically-Symmetric Stellar Collapse to Neutron Stars and Black Holes, accepted for publication to the Classical and Quantum Gravity special issue for MICRA2009, arXiv:0912.2393v3 [astro-ph.HE].

Michael W. Thomas, Erik Schnetter, Simulation Factory: Taming Application Configuration and Workflow on High-End Resources, accepted by CBHPC 2010, arXiv:1008.4571v1 [cs.DC].

PI Joshua Schrier

J. Schrier, "Helium Separation Using Porous Graphene Membranes" J. Phys. Chem. Lett. 1, 2284 (2010)

PI Karen Schuchardt

"Efficient Extraction of Regional Subsets from Massive Climate Datasets using Parallel IO" submitted to Fall American Geophysical Union meeting

"An IO API for a Global Cloud Resolving Model" Environmental Modelling and Software

PI David Schultz

M. S. Pindzola, J. A. Ludlow, and J. P. Colgan, "Double ionization of H2 by fast bare ions," Physical Review A 80, 032707 (September 2009)

M. S. Pindzola, C. P. Ballance, J. A. Ludlow, S. D. Loch, and J. P. Colgan, "Electron-impact ionization of C2," Journal of Physics B 43, 065201 (March 2010)

D. R. Schultz, T. G. Lee, and S. D. Loch, "Calculations and analysis of cross sections required for Argon charge exchange recombination spectroscopy," Journal of Physics B 43, 144002 (July 2010)

J. P. Colgan, J. Abdallah, Jr., C. J. Fontes, and R. E. H. Clark, "Non-LTE studies of boron plasmas," Journal of Physics B 43, 144021 (July 2010)

M. A. Bautista, C. P. Ballance, and P. Quinet, "Atomic data and spectral model for Fe+2," Astrophysical Journal 718, L189 (August 2010)

I. Orban, S. Bohm, R. Schuch, S. D. Loch, and E. Smith,
"Recombination rate coefficients of Si+10," submitted to Astrophysical Journal (July 2010)

M. S. Pindzola, F. J. Robicheaux, and J. P. Colgan, "Single and double ionization in C+6 + He collisions," submitted to Physical Review (August 2010)

PI Annabella Selloni

Aschauer U., Chen J., Selloni A., "Peroxide and superoxide states of adsorbed O2 on anatase TiO2 (101) with subsurface defects", PCCP, in Press, DOI: 10.1039/C0CP00116C

Aschauer U., Selloni A., "Influence of subsurface Ti interstitials on the reactivity of anatase (101)", SPIE Optics & Photonics Proceedings, San Diego, 2010

"Simulation of electrocatalytic hydrogen production by a bioinspired catalyst anchored to a pyrite electrode", Zipoli F., Car R., Cohen M. H., and Selloni A., J. Am. Chem. Soc. 2010, 132, 8593.

"Theoretical design by first principles molecular dynamics of a bio-inspired electrode-catalyst system for electrocatalytic hydrogen production from acidified water", Zipoli F., Car R., Cohen M. H., and Selloni A. J. Chem. Theo. Comput. (in press)

"Electrocatalyst design from first principles: a hydrogen-production catalyst inspired by Nature", Zipoli F., Car R., Cohen M. H., and Selloni A. (Submitted)

PI John Shalf

Lavanya Ramakrishnan, Keith R. Jackson, Shane Canon, Shreyas Cholia, John Shalf: ???Defining future platform requirements for e-Science clouds.??? SoCC 2010: 101-106

S. Kamil, C. Chan, L. Oliker, J. Shalf, S. Williams"An Auto-Tuning Framework for Parallel Multicore Stencil Computations", International Parallel & Distributed Processing Symposium (IPDPS) 2010, (2010)

A. Uselton, M. Howison, N. Wright, D. Skinner, N. Keen, J. Shalf, K. Karavanic, L. Oliker"Parallel I/O Performance: From Events to Ensembles ", International Parallel & Distributed Processing Symposium (IPDPS) 2010

K. Madduri, S. Williams, S. Ethier, L. Oliker, J. Shalf, E. Strohmaier, K. Yelick, "Memory-Efficient Optimization of Gyrokinetic Particle-to-Grid Interpolation for Multicore Processors: SC09: International Conference for High-Performance Computing, Networking, Storage, and Analysis, Nov, 2009.

M. Mohiyuddin, M. Murphy, S. Williams, L. Oliker, J. Shalf, J. Wawrzynek"A Case for Hardware/Software Co-Tuning for Power Efficient Scientific Computing", SC09: International Conference for High-Performance Computing, Networking, Storage, and Analysis, Nov, 2009.

K. Datta, S. Williams, V. Volkov, J. Carter, L. Oliker, J. Shalf, K. Yelick"Auto-tuning the 27-point Stencil for Multicore", international Workshop on Automatic Performance Tuning (iWAPT), 2009.

Shoaib Kamil, Leonid Oliker, Ali Pinar, John Shalf: Communication Requirements and Interconnect Optimization for High-End Scientific Applications. IEEE Trans. Parallel Distrib. Syst. 21(2): 188-202 (2010)

PI Shunli Shang

S. L. Shang, H. Zhang, Y. Wang, and Z. K. Liu, "Temperature-dependent elastic stiffness constants of alpha- and theta-Al2O3 from first-principles calculations", J. Phys.: Condens. Matter Vol. 22 (2010) 375403.

S. L. Shang, Y. Wang, and Z. K. Liu, "Thermodynamic fluctuations between magnetic states from first-principles phonon calculations: The case of bcc Fe", Phys. Rev. B, Vol. 82 (2010) 014425.

S. L. Shang, A. Saengdeejing, Z. G. Mei, D. E. Kim, H. Zhang, S. Ganeshan, Y. Wang, and Z. K. Liu, "First-principles calculations of pure elements: Equations of state and elastic stiffness constants", Comput. Mater. Sci., Vol. 48 (2010) 813-826,

Y. Wang, J. J. Wang, H. Zhang, V. R. Manga, S. L. Shang, L. Q. Chen, and Z. K. Liu, "A first-principles approach to elasticity at finite temperatures", J. Phys.: Condens. Matter, Vol. 22 (2010) 225404.

D. E. Kim, S. L. Shang, and Z. K. Liu, "Effects of alloying elements on elastic properties of Ni3Al by first-principles calculations", Intermetallics, Vol. 18 (2010) 1163-1171.

S. L. Shang, Y. Wang, Y. Du, and Z. K. Liu, "Entropy favored ordering: Phase stability of Ni3Pt revisited by first-principles", Intermetallics, Vol. 18 (2010) 961-964.

S. L. Shang, Y. Wang, D. E. Kim, and Z. K. Liu, "First-principles thermodynamics from phonon and Debye model: Application to Ni and Ni3Al", Comp. Mater. Sci., Vol. 47 (2010) 1040-1048.

D. E. Kim, S. L. Shang, and Z. K. Liu, "Effects of alloying elements on elastic properties of Ni by first-principles calculations", Comput. Mater. Sci., Vol. 47 (2009) 254-260.

PI Michael Shay

Parashar, T. N., S. Servidio, B. Breech, M. A. Shay, and W. H. Matthaeus, Kinetic Driven Turbulence: Structure in Space and Time, Physics of Plasmas, In Press, 2010.

Cassak, P. A., and M. A. Shay, Magnetic reconnection for Coronal Conditions: Reconnection Rates, Secondary Islands, and Onset, Space Science Reviews, Submitted, 2010.

Malakit, K., M. A. Shay, P. A. Cassak, C. Bard, Scaling of asymmetric magnetic reconnection: Kinetic particle-in-cell simulations, Journal of Geophysical Research, In Press, 2010.

Eastwood, J. P., M. A. Shay, T. D. Phan, and M. Oieroset, Asymmetry of the ion diffusion region Hall electric and magnetic fields during guide field reconnection: Observations and comparison with simulations, Physical Review Letters, Vol. 104, 205001, 2010.

Eastwood, J. P., T. D. Phan, M. Oieroset, and M. A. Shay, Average properties of the magnetic reconnection ion diffusion region in the Earth's magnetotail: 2001-2005 Cluster observations and comparison with simulations, Journal of Geophysical Research , Vol. 115, A08215, 2010.

Cassak, P. A., M. A. Shay, and J. F. Drake, A saddle-node bifurcation model of magnetic reconnection onset, Physics of Plasmas , Vol. 17, 062105, 2010.

Servidio, S., W. H. Matthaeus, M. A. Shay, P. Dmitruk, P. A. Cassak, and M. Wan, Statistics of magnetic reconnection in Two-Dimensional Magnetohydrodynamic Turbulence, Physics of Plasmas , Vol.17, 032315, 2010.

Cassak, P. A., Shay, M. A., and J. F. Drake, Scaling of Sweet-Parker Reconnection with Secondary Islands, Physics of Plasmas, Vol. 16, 120702, 2009.

Servidio, S., M. A. Shay, W. H. Matthaeus, P. Dmitruk, P. A. Cassak, and M. Wan, Properties of magnetic reconnection in MHD turbulence, Proceedings of the Solar Wind 12 Conference, edited by M. Maksimovic, K. Issautier, N. Meyer-Vernet, M. Moncuquet and F. Pantellini, p. 198, 2010.

Parashar, T. N., S. Servidio, M. A. Shay, W. H. Matthaeus, and P. A. Cassak, Orszag Tang vortex - Kinetic study of a turbulent plasma, Proceedings of the Solar Wind 12 Conference, edited by M. Maksimovic, K. Issautier, N. Meyer-Vernet, M. Moncuquet and F. Pantellini, p. 304, 2010.

Drake, J. F., P. A. Cassak, M. A. Shay, M. Swisdak, E. Quataert, A Magnetic Reconnection Mechanism for Ion Acceleration and Abundance Enhancements in Impulsive Flares, The Astrophysics Journal, Vol. 700, p. L16, 2009.

Drake, J. F., M. Swisdak, T. D. Phan, P. A. Cassak, M. A. Shay, S. T. Lepri, R. P. Lin, E. Quartaert, T. H. Zurbuchen, Ion heating resulting from pickup in magnetic reconnection exhausts, Journal of Geophysical Research, Vol. 114, A05111, doi:10.1029/2008JA013701, 2009.

PI Junko Shigemitsu

C. McNeile et al, High Precision c and b masses and QCD coupling from current-current correlators in lattice and continuum QCD, Phys. Rev. D82:034512, 2010

CTH Davies et al, Precise charm to strange mass ratio and light quark masses from full lattice QCD, Phys. Rev. Lett. 104:132003, 2010.

CTH Davies et al, Precise determination of the lattice spacing in full lattice QCD, Phys. Rev. D.81:034506, 2010.

E. Gregory et al, A prediction of the B_c^* mass in full lattice QCD, Phys. Rev. Lett. 104:022001, 2010.

PI Alex Sim

"Efficient Bulk Data Replication for the Earth System Grid", A. Sim, D. Gunter, V. Natarajan, A. Shoshani, D. Williams, J. Long, J. Hick, J. Lee, E. Dart, Proceedings of International Symposium on Grid Computing, Data Driven e-Science: Use Cases and Successful Applications of Distributed Computing Infrastructures (ISGC 2010), 2010

PI Donald Sinclair

Thermodynamics of lattice QCD with 3 flavours of colour-sextet quarks. By J.B. Kogut and D.K.Sinclair. ANL-HEP-PR-10-46 (2010).

Thermodynamics of lattice QCD with 2 sextet quarks on N_t=8 lattices. By J.B. Kogut and D.K. Sinclair. ANL-HEP-PR-10-45 (2010).

Chiral symmetry breaking and monopole dynamics in non-compact QED3 coupled to a four-fermi interaction. By W. Armour, John B. Kogut, Costas Strouthos. Phys.Rev.D82:014503,2010,. [arXiv:1004.3053]

Thermodynamics of lattice QCD with 2 flavours of colour-sextet quarks: A model of walking/conformal Technicolor. By J.B. Kogut & D.K. Sinclair. Phys.Rev.D81:114507,2010,. [arXiv:1002.2988]

PI Berend Smit

M. Haranczyk, C.H. Rycroft, T.F. Willems "High-throughput analysis of the void space in crystalline porous materials using Voronoi decomposition", Molecular Informatics - submitted

M. Haranczyk, J.A. Sethian - "Automatic structure analysis in high-throughput characterization of porous materials", Journal of Chemical Theory and Computation - submitted

PI Jeremy Smith

Barbara Collignon, Roland Schulz, Jeremy Smith, and Jerome Baudry Task-parallel MPI implementation of Autodock4 for docking of very large databases of compounds using High Performance Super-Computers. Journal of Computational Chemistry, in Press

PI George Smoot

J.L. Christiansen, E. Albin, J. Goldman, I.P.W. Teng, M. Foley, G.F. Smoot, Search for Cosmic Strings in the COSMOS Survey, Submitted to Physical Review D, http://arxiv.org/abs/1008.0426.

PI Randall Snurr

P. Ryan, O.K. Farha, L.J. Broadbelt, and R.Q. Snurr, Computational Screening of Metal-Organic Frameworks for Xenon/Krypton Separation, AIChE Journal, 2010, in
press.

PI Masha Sosonkina

L. Seshagiri, M.-S. Wu, M. Sosonkina, and Z. Zhang, Exploring tuning strategies for quantum chemistry computations, Software Automatic Tuning, R. Suda, K. Naono, K. Teranishi and J. Cavazos, (eds.), Springer, 2010, pp. 193--208.

P. Maris, M. Sosonkina, J.P. Vary, E.G. Ng, and C. Yang, Scaling of {\em ab-initio nuclear} physics calculations on multicore computer architectures, In Proc. Int'l Conference on Computational Science (ICCS 2010), Amsterdam, Netherlands, Jun. 2010.

L. Seshagiri, M.-S. Wu, M. Sosonkina, Z. Zhang, M.S. Gordon, and M.W. Schmidt, Enhancing adaptive middleware for quantum chemistry applications with a database framework, In Proc. Int'l Parallel and Distributed Processing Symposium (IPDPS 2010), 11th Workshop on Parallel and Distributed Scientific and Engineering Computing, Atlanta, GA, Apr. 2010.

F. Liu, M. Sosonkina, and R. Bramley, A new approach: component-based multi-physics coupling through CCA-LISI, In Proc. Int'l Conference on Computational Science and Applications (ICCSA 2010), Fokuoka, Japan, Mar. 2010, pp. 503--518.

PI Ivo Souza

Theory of orbital magnetoelectric response, Andrei Malashevich, Ivo Souza, Sinisa Coh, and David Vanderbilt, New Journal of Physics 12, 053032 (2010)

Band theory of spatial dispersion in magnetoelectrics, Andrei Malashevich and Ivo Souza (Phys. Rev. B, in press)

PI Carl Sovinec

T. G. Jenkins, S. E. Kruger, C. C. Hegna, D. D. Schnack, and C. R. Sovinec, "Calculating Electron Cyclotron Current Drive Stabilization of Resistive Tearing Modes in a Nonlinear MHD Model," Physics of Plasmas 17, 12502 (2010).

B. J. Burke, S. E. Kruger, C. C. Hegna, P. Zhu, P. B. Snyder, C. R. Sovinec, and E. C. Howell, "Edge  localized linear ideal magnetohydrodynamic instability studies in an extended-magnetohydrodynamic code," Physics of Plasmas 17, 32103 (2010).

C. R. Sovinec, J. R. King, and the NIMROD Team, "Analysis of a Mixed Semi-Implicit/Implicit Algorithm for Low-Frequency Two-Fluid Plasma Modeling," Journal of Computational Physics 229, 5803 (2010).

R. D. Milroy, C. C. Kim, and C. R. Sovinec, "Extended magnetohydrodynamic simulations of field reversed configuration formation and sustainment with rotating magnetic field current drive," Physics of Plasmas 17, 62502 (2010).

PI Panagiotis Spentzouris

E. G. Stern, J. F. Amundson, P. G. Spentzouris, and A. A. Valishev, Phys. Rev. ST Accel. Beams 13, 024401 (2010).

C. E. Clayton, J. E. Ralph, F. Albert, R. A. Fonseca, S. H. Glenzer, C. Joshi, W. Lu, K. A. Marsh, S. F. Martins, W. B. Mori, A. Pak, F. S. Tsung, B. B. Pollock, J. S. Ross, L. O. Silva, and D. H. Froula, Phys. Rev. Lett. 105, 105003 (2010)

C.-K. Ng, R.J. England, L.-Q. Lee. R. Noble, V. Rawat and J. Spencer, Transmission and Radiation of an Accelerating Mode in a Photonic Bandgap Fiber, SLAC-PUB-14156, submitted to PRST-AB.

PI Frank Spera

Spera, F.J., Ghiorso, M., and Nevins, D. (2010) Structure, Thermodynamic and Transport Properties of Liquid MgSiO3: Comparison of Molecular Models and Laboratory Results, submitted Geochim. Cosmo. Acta, July 15, 2010.

Ghiorso, M. and Spera, F. (2010) Large Scale Simulations in Reviews in Mineralogy and Geochemistry (eds) Wentzcovitch, R. and Stixrude, L. 71, 437-463.

Spera, F.J., Nevins, D., Ghiorso, M. S., Cutler, I. (2009) Structure, thermodynamics and transport properties of CaA12Si2O8 liquid. Part I: Molecular dynamics simulations, Geochim. Cosmo. Acta 73, 6918-6936.

Ghiorso, M. S., Nevins, D., Cutler, I., Spera, F.J. (2009), Molecular dynamics studies of CaA12Si2O8 liquid. Part II: Equation of state and a thermodynamic model, Geochim. Cosmo. Acta 73, 6937-6951.

Nevins, D, Spera, FJ, Ghiorso, M., (2009) Shear Viscosity and diffusion in liquid MgSiO3: Transport properties and implications for terrestrial planet magma oceans, American Mineralogist 94, 975-980.

Martin, B, Spera, FJ, Ghiorso, M, Nevins, D. (2009) Structure, thermodynamic and transport properties of molten Mg2SiO4: Molecular dynamics simulations and model EOS, American Mineralogist, 94, 693-703.

PI Don Spong

D. A. Spong, B. N. Breizman, D. L. Brower, Ed D'Azevedo, C. B. Deng, A. Konies, Y. Todo, and K. Toi, "Energetic-Particle-Driven Instabilities in General Toroidal Configurations," Contributions to Plasma Physics, Vol. 50 (2010) 708-712.

D. A. Spong, E. D'Azevedo, and Y. Todo, "Clustered frequency analysis of shear Alfven modes in stellarators," Phys. of Plasmas Vol. 17 (2010) 022106.

D. A. Spong., J. H. Harris, "New QP/QI symmetric stellarator configurations," Plasma and Fusion Research (Japan Society of Plasma Research), Vol. 5, S2039 (2010).

J. Lore, W. Guttenfelder, A. Briesemeister, D. T. Anderson, F. S. B. Anderson, C. B. Deng, K. M. Likin, D. A. Spong, J. N. Talmadge, and K. Zhai, "Internal electron transport barrier due to neoclassical ambipolarity in the Helically Symmetric Experiment," Phys. of Plasmas 17, 056101 (2010).

Y. Todo, S. Murakami, T. Yamamoto, A. Fukuyama, D. A. Spong, S. Yamamoto, M. Osakabe, and N. Nakajima, "Numerical analyses of energetic particles in LHD," Fusion Science and Tech., Vol. 58 (2010) 277.

"Overview of Studies on Energetic-Ion-Driven MHD Instabilities in Stellarator/Helical Plasmas and Comparison with Tokamaks," K. Toi, M. Isobe, M. Osakabe, K. Ogawa, D. Spong, Y. Todo, and the LHD Experiment Group, Contributions to Plasma Physics, Vol. 50 (2010), 493-500.

Isobe, M.; Ogawa, K.; Toi, K.; Osakabe, M.; Nagaoka, K.; Shimizu, A.; Spong, D.A.; Okamura, S., "Effect of Energetic-Ion-Driven MHD Instabilities on Energetic-Ion-Transport in Compact Helical System and Large Helical Device,"Contributions to Plasma Physics, Vol. 50 (2010), 540-545.

K. Ogawa , M. Isobe , K. Toi , F. Watanabe , D.A. Spong , A. Shimizu , M. Osakabe , S. Ohdachi , S. Sakakibara and LHD Experiment Group, "Observation of energetic-ion losses induced by various MHD instabilities in the Large Helical Device (LHD), Nuclear Fusion Vol. 50 (2010) 084005.

K. Toi, F. Watanabe, T. Tokuzawa, K. Ida, S. Morita, T. Ido, A. Shimizu, M. Isobe, K. Ogawa, D.A. Spong, Y. Todo, T. Watari, S. Ohdachi, S. Sakakibara, S. Yamamoto, S. Inagaki, K. Narihara, M. Osakabe, K. Nagaoka, Y. Narushima, K.Y. Watanabe, H. Funaba, M. Goto, K. Ikeda, T. Ito, O. Kaneko, S. Kubo, S.Murakami, T. Minami, J. Miyazawa, Y. Nagayama, M. Nishiura, Y. Oka, R. Sakamoto, T. Shimozuma, Y. Takeiri, K. Tanaka, K. Tsumori, I. Yamada, M. Yoshinuma, K. Kawahata,A. Komori, "LHD Experimental Group Observation of Reversed Shear Alfv??n Eigenmodes Excited by Energetic Ions in a Helical Plasma," accepted for publication in Physical Review Letters (2010).

B. Tobias, I.G.J. Classen, C.W. Domier, W.W. Heidbrink, N.C. Luhmann, Jr., R. Nazikian, H.K. Park, D. Spong, and M.A. Van Zeeland, "Electron Cyclotron Emission Imaging of Fast Ion Induced Shearing of 2D Alfven Eigenmodes," submitted for publication in Physical Reveiw Letters (2010).

PI Garrison Sposito

Kwon, K.D., Refson, K., Bone, S., Qiao, R., Yang, W., Liu, Z., Sposito, G., Magnetic ordering in mackinawite (tetragonal FeS): evidence for strong itinerant spin fluctuations, submitted.

Kwon, K.D., Refson, K., Sposito, G., 2010. Surface complexation of Pb(II) by hexagonal birnessite nanoparticles. Geochimica et Cosmochimica Acta, in press (http://dx.doi.org/10.1016/j.gca.2010.09.002).

Kwon K.D., Sposito G., 2010. Reactivity of biogenic manganese oxide for metal sequestration and photochemistry: computational solid state physics study. Journal of the Mineralogical Society of Korea 23, 161-170.

Pena J., Kwon K.D., Refson K., Bargar J.R., Sposito G., 2010. Mechanisms of nickel sorption by a bacteriogenic birnessite. Geochimica et Cosmochimica Acta 74, 3076-3089.

Bourg I.C., Sposito G., 2010. Connecting the molecular scale to the continuum scale for diffusion processes in smectite-rich porous media. Environmental Science and Technology 44, 2085-2091.

Bourg I.C., Richter F.M., Christensen J.N., Sposito G., 2010. Isotopic mass-dependence of alkali metal cation diffusion coefficients in water. Geochimica et Cosmochimica Acta 74, 2249-2256.

PI Phillip Sprangle

M.H. Helle and D. Kaganovich and D.F. Gordon and A. Ting, "Measurement of electro-optic shock and electron acceleration in a strongly cavitated laser wakefield accelerator," Phys. Rev. Lett. 105, 105001 (2010) (note: simulations not explicitly discussed in this paper, but were highly relevant in motivating the work)

D. Kaganovich, M.H. Helle, D.F. Gordon, and A. Ting, "Measurements of colliding shock wave and supersonic gas flow," submitted to Appl. Phys. Lett.

PI Malcolm Stocks

Bevan, K. H., H. Guo, E. D. Williams and Z. Y. Zhang "First-principles quantum transport theory of the enhanced wind force driving electromigration on Ag(111)." Physical Review B 81(23).

Chen, H., W. G. Zhu and Z. Y. Zhang "Contrasting Behavior of Carbon Nucleation in the Initial Stages of Graphene Epitaxial Growth on Stepped Metal Surfaces." Physical Review Letters 104(18).

Jia, Y., S. Y. Wang, W. G. Chen, Q. Sun, H. H. Weitering and Z. Y. Zhang "First-principles study of quantum size effects in ultrathin Pb-Bi metal alloy films." Physical Review B 81(24).

Jia, Y., B. A. Wu, C. Li, T. L. Einstein, H. H. Weitering and Z. Y. Zhang "Strong Quantum Size Effects in Pb(111) Thin Films Mediated by Anomalous Friedel Oscillations." Physical Review Letters 105(6).

Khajetoorians, A. A., W. G. Zhu, J. Kim, S. Y. Qin, H. Eisele, Z. Y. Zhang and C. K. Shih (2009). "Adsorbate-induced restructuring of Pb mesas grown on vicinal Si(111) in the quantum regime."  Physical Review B 80(24).

Kim, H. J., S. Oh, K. S. Kim, Z. Y. Zhang and J. H. Cho "Length- and parity-dependent electronic states
in one-dimensional carbon atomic chains on C(111)." Physical Review B 82(4).

Lee, J. Y., J. H. Cho and Z. Y. Zhang (2009). "Quantum size effects in competing charge and spin orderings of dangling bond wires on Si(001)." Physical Review B 80(15).

Li, S. F., H. S. Li, X. L. Xue, Y. Jia, Z. X. Guo, Z. Y. Zhang and X. G. Gong "hcp metal nanoclusters with hexagonal A-A bilayer stacking stabilized by enhanced covalent bonding." Physical Review B 82(3).

Li, X. G., Z. Y. Zhang and D. Xiao "Pseudospin valve in bilayer graphene nanoribbons." Physical Review B 81(19).

Ozer, M. M., C. Z. Wang, Z. Y. Zhang and H. H. Weitering (2009). "Quantum Size Effects in the Growth, Coarsening, and Properties of Ultra-thin Metal Films and Related Nanostructures." Journal of Low Temperature Physics 157(3-4): 221-251.

Pan, H., B. H. Gu, G. Eres and Z. Y. Zhang "Ab initio study on noncompensated CrO codoping of GaN for enhanced solar energy conversion." Journal of Chemical Physics 132(10).

Pan, H., B. H. Gu and Z. Y. Zhang (2009). "Phase-Dependent Photocatalytic Ability of TiO2: A First-Principles Study." Journal of Chemical Theory and Computation 5(11): 3074-3078.

Pan, H., X. F. Qiu, I. N. Ivanovc, H. M. Meyer, W. Wang, W. G. Zhu, M. P. Paranthaman, Z. Y. Zhang, G.Eres and B. H. Gu (2009). "Fabrication and characterization of brookite-rich, visible light-active TiO2
films for water splitting." Applied Catalysis B-Environmental 93(1-2): 90-95.

Troparevsky, M. C., K. Zhao, D. Xiao, A. G. Eguiluz and Z. Y. Zhang "Molecular orbital view of the electronic coupling between two metal nanoparticles." Physical Review B 82(4).

Troparevsky, M. C., K. Zhao, D. Xiao, Z. Y. Zhang and A. G. Eguiluz (2009). "Tuning the Electronic Coupling and Magnetic Moment of a Metal Nanoparticle Dimer in the Nonlinear Dielectric-Response Regime." Nano Letters 9(12): 4452-4455.

Wang, W., Z. P. Li, B. H. Gu, Z. Y. Zhang and H. X. Xu (2009). "Ag@SiO2 Core-Shell Nanoparticles for Probing Spatial Distribution of Electromagnetic Field Enhancement via Surface-Enhanced Raman Scattering.?" Acs Nano 3(11): 3493-3496.

Xiao, D., Y. Yao, W. Feng, J. Weng, W. Zhu, X. Chen, G. M. Stocks, Z. Zhang, "Half-Heusler Compounds as a New Class of Three-Dimensional Topological Insulators," Physical Review Letters 105 (096404) 2010.

PI Alberto Striolo

D. Argyris, P.D. Ashby, A. Striolo, Assessing the Structure of Interfacial Water via AFM: Insights from Simulations, Nano Letters (2010) to be submitted.

N.R. Tummala, B.H. Morrow, D.E. Resasco, A. Striolo, Stabilization of Aqueous Carbon Nanotube Dispersions using Surfactants: Insights from Molecular Dynamics Simulations, ACS Nano (2010) submitted.

T.A. Ho, D. Argyris, D.V. Papavassiliou, A. Striolo, L.L. Lee, D.R. Cole, Interfacial Water on Crystalline Silica: A Comparative Molecular Dynamics Simulation Study, Molecular Simulation (2010) in press.

N.R. Tummala, B.P. Grady, and A. Striolo, Lateral Confinement Effects on the Structural Properties of Surfactant Aggregates: SDS on Graphene, Physical Chemistry Chemical Physics (2010) in press.

D. Argyris, D.R. Cole, and A. Striolo, Ion-Specific Effects Under Confinement: The Role of Interfacial Water, ACS Nano 4 (2010) 2035-2042.

L. Shi, N.R. Tummala, and A. Striolo, A Molecular Dynamics Study for C12E6 and SDS Surfactants at the Water-Vacuum Interface, Langmuir 26 (2010) 5462-5474.

D. Argyris, D.R. Cole, and A. Striolo, Dynamic Behavior of Interfacial Water at the Silica Surface, Journal of Physical Chemistry C, 113 (2009) 19591-19600.

N.R. Tummala and A. Striolo, Curvature Effects on the Adsorption of Aqueous SDS Surfactants on Carbonaceous Substrates: Structural Features and Counterion Dynamics, Physical Review E 80 (2009) 021408.

B.H. Morrow, D.E. Resasco, A. Striolo, M. Buongiorno Nardelli, CO Adsorption on Noble Metal Clusters: Local-Environment Effects, Journal of Physical Chemistry C (2010) submitted.

B.H. Morrow and A. Striolo, Supported Bimetallic Pt-Au Nanoparticles: Structural Features Predicted by Molecular Dynamics Simulations, Physical Review B 81 (2010) 155437.

B.H. Morrow and A. Striolo, Assessing How Metal-Carbon Interactions Affect the Structure of Supported Platinum Nanoparticles, Molecular Simulation 35 (2009) 795-803.

D. Konatham, K. Bui, D.V. Papavassiliou, A. Striolo, Thermally Conductive Graphene-Based Nanocomposites Nanocomposites, Molecular Physics (2010) submitted.

D. Konatham and A. Striolo, Thermal Boundary Resistance at the Graphene-Oil Interface, Applied Physics Letters 95 (2009) 163105.


T

PI Jason Tillett

Large-scale propagation of ultrasound in a 3-D breast model based on high-resolution MRI: G. S. Salahura, J. C. Tillett, L. A. Metlay, and R. C. Waag. IEEE Trans. Biomed. Eng., 57(6):1273-1284 ('10).

PI Doug Toussaint

"Full nonperturbative QCD simulations with 2+1 flavors of improved staggered quarks", A. Bazavov, C. Bernard, C. DeTar, Steven Gottlieb, U.M. Heller, J.E. Hetrick, J. Laiho, L. Levkova, P.B. Mackenzie, M.B. Oktay, R. Sugar, D. Toussaint, R.S. Van de Water, arXiv:0903.3598, Rev. Mod. Phys. 82, 1349-1417 (2010).

"The strange quark condensate in the nucleon in 2+1 flavor QCD", D. Toussaint and W. Freeman (for the MILC Collaboration), arXiv:0905.2432, Phys. Rev. Lett. 103, 2009, 122002.

"Equation of state and QCD transition at finite temperature", A. Bazavov, T. Bhattacharya, M. Cheng, N.H. Christ, C. DeTar, S. Ejiri, Steven Gottlieb, R. Gupta, U.M. Heller, K. Huebner, C. Jung, F. Karsch, E. Laermann, L. Levkova, C. Miao, R.D. Mawhinney, P. Petreczky, C. Schmidt, R.A. Soltz, W. Soeldner, R. Sugar, D. Toussaint, P. Vranas, arXiv:0903.4379, Phys. Rev. D 80, 104504 (2009).

"Topological susceptibility with the asqtad action", MILC collaboration: A. Bazavov, C. Bernard, B. Billeter, C. DeTar, Steven Gottlieb, U. M. Heller, J. E. Hetrick, J. Laiho, L. Levkova, B. Oktay, J. Osborn, R. L. Sugar, D. Toussaint, R. S. Van de Water, arXiv:1003.5695, Phys. Rev. D 82, 114501 (2010).

"QCD thermodynamics with nonzero chemical potential at $N_t=6$ and effects from heavy quarks", C. DeTar, L. Levkova, Steven Gottlieb, U.M. Heller, J.E. Hetrick, R. Sugar, D. Toussaint, arXiv:1003.5682, Phys. Rev. D 81, 114504 (2010).

Scaling studies of QCD with the dynamical HISQ action, MILC collaboration: A. Bazavov, C. Bernard, C. DeTar, W. Freeman, Steven Gottlieb, U. M. Heller, J. E. Hetrick, J. Laiho, L. Levkova, M. Oktay, J. Osborn, R.L. Sugar, D. Toussaint, R.S. Van de Water [arXiv:1004.0342], to be published in Phys. Rev. D.

Tuning Fermilab Heavy Quarks in 2+1 Flavor Lattice QCD with Application to Hyperfine Splittings, C. Bernard, C. DeTar, M. Di Pierro, A.X. El-Khadra, R.T. Evans, E.D. Freeland, E. G??miz, Steven Gottlieb, U.M. Heller, J.E. Hetrick, A.S. Kronfeld, J. Laiho, L. Levkova, P.B. Mackenzie, J.N. Simone, R. Sugar, D. Toussaint, R.S. Van de Water, (the Fermilab Lattice Collaboration and the MILC Collaboration) arXiv:1003.1937, submitted to Phys. Rev. D.

PI Trevor Tyson

T. A. Tyson, T. Wu, K. H. Ahn, S.-B. Kim and S.-W Cheong, "Local spin-coupled distortions in multiferroic hexagonal HoMnO3", Phys. Rev. B: Condens. Matter Mater. Phys. 81, 054101 (2010).

P. Gao, Z. Chen, T. A. Tyson, Z. Liu, J. Hu, C. Zhang, S.-B. Kim and S.-W. Cheong, "Pressure Dependence of Structural Stability of Multiferroic Hexagonal RMnO3", submitted to Phys. Rev. B.

P. Gao, Z. Liu, T. A. Tyson, and S. W. Cheong, "Low Temperature Phonon Properties of Orthorhombic REMnO3???, ", Presented at the APS 2010 March Meeting (Portland), March 15-19, abstract #D24.001. (Oral)

T. A. Tyson, T. Wu, H. Chen, and S. W. Cheong, "Local Structure of Hexagonal HoMnO3 at High Temperature", Presented at the APS 2010 March Meeting (Portland), March 15-19, abstract #D24.005. (Oral)

T. Wu, L. Wang, T. A. Tyson, H. Chen, S. Kim and S. W. Cheong, "High pressure structure of Orthorhombic Multiferroic Systems", Presented at the APS 2010 March Meeting (Portland), March 15-19, abstract #D24.002. (Oral)



V

PI Goerge Vahala

Yepez, J., G. Vahala, L. Vahala, and M. Soe, Phys. Rev. Lett. 103, 084501 (2009), URL http://link.aps. org/abstract/PRL/v103/e084501 ; Phys. Rev. Lett. 105, 129402 (2010)

G. Vahala, J. Yepez, L. Vahala, M. Soe and S. Ziegeler, SPIE 7702, 770207 (2010)

G. Vahala, J. Yepez, L. Vahala, M. Soe and S. Ziegeler, IEEE Computer Society (accepted for publication)

PI Chris Van de Walle

"Interactions between hydrogen impurities and vacancies in Mg and Al: a comparative analysis based on density functional theory:, Ismer L., Park, M.S., Janotti, A. and Van de Walle, C.G., Phys. Rev. B 80, 184110 (2009).

"Hydrogen-related defects and the role of metal additives in the kinetics of complex hydrides: a first-principles study", Hoang, K., and Van de Walle C.G., Phys. Rev. B 80, 214109 (2009).

"First-principles study of the formation and migration of native defects in NaAlH4", Wilson-Short, G.B., Janotti, A., Hoang, K., Peles, A., and Van de Walle, C. G., Phys. Rev. B. 80, 224102 (2009).

"First-principles investigations of F and Cl impurities in NaAlH4", Wilson-Short, G.B., Janotti, A., Peles, A., Van de Walle, C.G., J. Alloys Compd. 484, 347 (2009).

"Mechanisms for the decomposition and hydrogenation of Li amide/imide", Hoang, K, Janotti A., and Van de Walle C. G., submitted to Phys. Rev. B

"Stability and mobility of native point defects in AlH3", Ismer, L., Janotti, A., Van de Walle, C.G., submitted to J. Alloys Compd. (Supplement Issue: MH2010).

"Point-defect-mediated dehydrogenation of AlH3", Ismer, L., Janotti, A., Van de Walle, C.G., submitted to Appl. Phys. Lett.

PI Kalman Varga

Varga, K "Biexciton in magnetic fields," FEW-BODY SYSTEMS Volume: 47 Issue: 1-2 Pages: 65-71 Published: 2010

Title: Multidomain decomposition approach to large-scale electronic structure calculations
Author(s): Varga, K
Source: PHYSICAL REVIEW B Volume: 81 Issue: 4
Published: 2010

Title: Origin of Colossal Ionic Conductivity in Oxide Multilayers: Interface Induced Sublattice Disorder
Author(s): Pennycook, TJ; Beck, MJ; Varga, K; et al.
Source: PHYSICAL REVIEW LETTERS Volume: 104 Issue: 11
Published: 2010

Title: Convergence in quantum transport calculations: Localized atomic orbitals versus nonlocalized basis sets
Author(s): Driscoll, JA; Varga, K
Source: PHYSICAL REVIEW B Volume: 81 Issue: 11
Published: 2010

Title: Boron induced charge traps near the interface of Si/SiO2 probed by second harmonic generation
Author(s): Park, H; Qi, JB; Xu, Y; et al.
Source: PHYSICA STATUS SOLIDI B-BASIC SOLID STATE PHYSICS Volume: 247 Issue: 8
Pages: 1997-2001
Published: 2010
Conference Title: 8th International Conference on Optics of Surfaces and Interfaces (OSI-VIII) Conference Date: SEP 07-11, 2009
Conference Location: Ischia, ITALY

Title: Configuration and conductance evolution of benzene-dithiol molecular junctions under elongation
Author(s): Sergueev, N; Tsetseris, L; Varga, K; et al.
Source: PHYSICAL REVIEW B Volume: 82 Issue: 7
Published: 2010

Title: First-principles calculations of electron mobilities in silicon: Phonon and Coulomb scattering
Author(s): Restrepo, OD; Varga, K; Pantelides, ST
Source: APPLIED PHYSICS LETTERS Volume: 94 Issue: 21
Published: 2009

Title: Quantum transport calculations using complex absorbing potentials
Author(s): Varga, K
Source: PHYSICA STATUS SOLIDI B-BASIC SOLID STATE PHYSICS Volume: 246 Issue: 7
Pages: 1407-1412
Published: 2009

Title: Characterization of boron charge traps at the interface of Si/SiO2 using second harmonic generation
Author(s): Park, H; Qi, J; Xu, Y; et al.
Source: APPLIED PHYSICS LETTERS Volume: 95 Issue: 6
Published: 2009

Title: R-matrix calculation of Bloch states for scattering and transport problems
Author(s): Varga, K
Source: PHYSICAL REVIEW B Volume: 80 Issue: 8
Published: 2009

Positron Scattering and Annihilation from the Hydrogen Molecule at Zero Energy
Author(s): Zhang, JY; Mitroy, J; Varga, K
Source: PHYSICAL REVIEW LETTERS Volume: 103 Issue: 22
Published: 2009

Title: The Role of Atomic Displacements in Ion-Induced Dielectric Breakdown
Author(s): Beck, MJ; Puzyrev, YS; Sergueev, N; et al.
Source: IEEE TRANSACTIONS ON NUCLEAR SCIENCE Volume: 56 Issue: 6 Pages: 3210-3217
Published: 2009
Conference Title: 46th Annual IEEE International Nuclear and Space Radiation Effects Conference Conference Date: JUL 20-24, 2009
Conference Location: Quebec City, CANADA


Title: Time-dependent density-functional study of field emission from tipped
carbon nanotubes
Author(s): Driscoll, JA; Varga, K
Source: PHYSICAL REVIEW B Volume: 80 Issue: 24
Published: 2009

Title: Conductance of kinked nanowires
Author(s): B. G. Cook and K. Varga
Source: Submitted to Physical Review Letters, August 2010

PI James Vary

P. Maris, M. Sosonkina, J. P. Vary, E. G. Ng and C. Yang, "Scaling of ab-initio nuclear physics calculations on multicore computer architectures," International Conference on Computer Science, ICCS 2010, Procedia Computer Science 1, 97 (2010).

P. Maris, A. M. Shirokov and J. P. Vary, "Ab initio nuclear structure simulations: the speculative 14F nucleus," Phys. Rev. C 81, 021301(R) (2010).

A.G. Negoita, J. P. Vary and S. Stoica, "No core shell model for A=47 and A=49," J. Phys. G: Nucl. Part. Phys. 37 (2010) 055109.; arXiv:nucl-th/0612022

J. P. Vary, H. Honkanen, Jun Li, P. Maris, S. J. Brodsky, A. Harindranath, G. F. de Teramond, P. Sternberg, E. G. Ng, C. Yang, "Hamiltonian light-front field theory in a basis function approach", Phys. Rev. C 81, 035205 (2010); arXiv nucl-th 0905.1411; DOI: 10.1103/PhysRevC.81.035205

 J. P. Vary, H. Honkanen, Jun Li, P. Maris, S. J. Brodsky, A. Harindranath, G. F. de Teramond, P. Sternberg, E. G. Ng, C. Yang, "Hamiltonian light-front field theory within an AdS/QCD basis", Nucl. Phys. B199, 64 (2010) DOI: 10.1016/j.nuclphysbps.2010.02.008.

A. M. Shirokov, V. A. Kulikov, A. I. Mazur, E. A. Mazur, P. Maris and J. P. Vary, ???Further development of realistic JISP16 NN interaction," Izvestia Rossiskoj Academii Nauk, Ser. Fiz. 74, 571 (2010) "[English translation was published in Bul. Rus. Acad. Sci.: Phys. 74, 538 (2010)].

Gianina Alina Negoita, "Ab initio Nuclear Structure Theory," (Doctoral dissertation, Iowa State University, 2010) ProQuest.com UMI 11359.

A. M. Shirokov, V. A. Kulikov, P. Maris, A. I. Mazur, E. A. Mazur, J. P. Vary, "NN Interaction JISP16: Current Status and Prospect", EPJ Web of Conf. 3, 05015 (2010), proceedings of the 19th Conference on Few-Body Problems in Physics, Bonn, Germany, Sept. 2009, DOI 10.1051/epjconf/20100305015, arXiv nucl-th 0912.2967.

T. Luu, M. Savage, A. Schwenk and J. P. Vary, "Nucleon-Nucleon Scattering in a harmonic potential," accepted for publication in Phys. Rev. C, arXiv nucl-th 1006.0427.


W

PI Ronald Waltz

M.S. Chu and M. Okabayashi, "Stabilization of the External Kink and the Resistive Wall Mode," Plasma Phys. Control. Fusion to be published, 2010.

N.M. Ferraro, S.C. Jardin, and P.B. Snyder, "Ideal and Resistive Edge Stability Calculations with M3D-C1," to be submitted to Phys. Plasmas, 2010.

V.A. Izzo, and P.B. Parks, "Plasma Current Spikes Due to Internal Reconnection During Tokamak Disruptions," submitted to Nucl. Fusion; General Atomics Report GA-A26637 (2010).

A.D. Turnbull, E.A. Lazarus, M. Choi, L.L. Lao, "A new view of the sawtooth instability and its relation to the internal kink mode," submitted to Phys. Plasmas, 2010.

R.E. Waltz, "Nonlinear Subcritical MHD Beta Limit," submitted to Phys. Plasmas; General Atomics Report GA-A26625 (2010) Phys. Plasmas 17, 072501 (2010)
2009

E.A. Belli and J. Candy, "An Eulerian Method for Solution of the Multispecies Drift-Kinetic Equation," Plasmas Phys. Control. Fusion 51, 075018 (2009).

J. Candy, "A Unified Method for Operator Evaluation in Local Grad-Shafranov Plasma Equilibria," Plasmas Phys. Control. Fusion 51, 105009 (2009).

J. Candy, C. Holland, R.E. Waltz, M.R. Fahey, and E. Belli, "Tokamak Profile Prediction Using Direct Gyrokinetic and Neoclassical Simulation," Phys. Plasmas 16, 060704 (2009).

M. Choi, V.S. Chan, L.A. Berry, E.F. Jaeger, D. Green, P. Bonoli, J. Wright, and RF SciDAC Team, "Comparison of Monte-Carlo Ion Cyclotron Heating Model with Full-Wave Linear Absorption Model," Phys. Plasmas 16, 052513 (2009).

M. Choi, V.S. Chan, D. Green, W.W. Heidbrink, E.F. Jaeger, L.A. Berry, and the RF SciDAC Team, "Simulation of the DIII-D Beam Ion Heating Experiment Using a Monte-Carlo Particle Code Combined with a Full Wave Code," Proc. 18th Topical Conf. on Radio Frequency Power in Plasmas, June 24-26, 2009, Gent, Belgium; General Atomics Report GA-A26493 (2009).

M.S. Chu and M. Okabayashi, "Stabilization of the External Kink and Resistive Wall Mode," submitted to Plasmas Phys. Control. Fusion, 2009.

N.M. Ferraro and S.C. Jardin, "Calculations of Two-Fluid Magnetohydrodynamic Axisymmetric Steady-States," J. Comp. Phys. 228, 7742 (2009).

V.A. Izzo, P.B. Parks, and L.L. Lao, "DIII-D and ITER Rapid Shutdown with Radially Uniform Deuterium Delivery," Plasmas Phys. Control. Fusion 51, 105004 (2009).

P.B. Parks, T. Lu, and R. Samulyak, "Charging and ExB Rotation of Ablation Clouds Surrounding Refueling Pellets," Phys Plasmas 16, 060705 (2009)

P.B. Snyder, N. Aiba, M. Beurskens, R.J. Groebner, L.D. Horton, A.E. Hubbard, J.W. Hughes, G.T.A. Huysmans, Y. Kamada, A. Kirk, C. Konz, A.W. Leonard, J. Lonnroth, C.F. Maggi, R. Maingi, T.H. Osborne, N. Oyama, A. Pankin, S. Saarelma, G. Saibene, J.L. Terry, H. Urano, and H.R. Wilson "Pedestal Stability Comparison and ITER Pedestal Prediction," Nucl. Fusion 49, 085035 (2009).

P.B. Snyder, R.J. Groebner, A.W. Leonard, T.H. Osborne, and H.R. Wilson, "Development and Validation of a Predictive Model for the Pedestal Height," Phys. Plasmas 16, 056118 (2009).

R.E. Waltz, A. Casati, and G. Staebler, "Gyrokinetic Simulation Tests of Quasilinear and Tracer Transport," Phys. Plasmas 16, 072303 (2009).

S.K. Wong and V.S. Chan, "Self-Consistent Poloidal Electric Field and Neoclassical Angular Momentum Flux," Phys. Plasmas, 16 122507 (2009)

PI Cai-Zhuang Wang

"Prediction of cooling rate dependent ordering in metallic glass transition using a two-state model", S. G. Hao, C. Z. Wang, Maozhi Li, R. E. Napolitano, M. I. Mendelev and K. M. Ho, Comp. Mat. Sci. (accepted).

"Energetics of local clusters in Cu64.5Zr35.5 metallic liquid and glass", S. Q. Wu, C. Z. Wang, S. G. Hao, Z. Z. Zhu, and K. M. Ho, Appl. Phys. Lett., 97, 021901 (2010).

"Thermodynamic limits of crystallization and the prediction of glass formation tendency", Y. X. Yao, R. Napolitano, C. Z. Wang, and K. M. Ho, Phys. Rev. B 81, 212202 (2010).

"Short- and Medium-Range Order in Amorphous Zr2Ni Metallic Alloys", Li Huang, C.Z. Wang, S.G. Hao, M.J. Kramer, and K.M. Ho, Phys. Rev. B 81, 094118 (2010).

"Structural and dynamical heterogeneity in molten Si-rich oxides", S. Q. Wu, C. Z. Wang, Z. Z. Zhu, and K. M. Ho, Appl. Phys. Lett. 96, 043121 (2010).

"Structure of Zr1-xCux Metallic Liquids and Origin of Slow Diffusion at the Good-Glass-Forming Composition Range", Shaogang Hao, C. Z. Wang, Maozhi Li, M. J. Kramer, and Kai-Ming Ho, J. Appl. Phys. 107, 053511 (2010).

"Atomic Size and Chemical Effects on the Local Order of Zr2M (M= Co, Ni, Cu, Ag) Binary Liquids", Li Huang, C.Z. Wang, S.G. Hao, M.J. Kramer, and K.M. Ho, Phys. Rev. B 81, 014108 (2010).

"Effect of local structures and atomic packing on glass forming ability in CuxZr100-x metallic glasses", H. L. Peng, M. Z. Li, W. H. Wang, C.-Z. Wang, and K. M. Ho, Appl. Phys. Lett., 96, 021901 (2010).

"Structural Heterogeneity and Medium-Range Order in ZrxCu1-x Metallic Glasses", M. Li, C. Z. Wang, S. G. Hao, M. J. Kramer, and K. M. Ho, Phys. Rev. B, 80, 184201 (2009).

"Development of Medium-Range Order in Metallic Cu64.??5Zr35.5 Liquid and Glass", X. W. Fang, C. Z. Wang, S. G. Hao, M. J. Kramer, Y. X. Yao, M. I. Mendelev, Z. J. Ding, R. Napolitano, and K. M. Ho, PNAS, submitted.

"Competition between FCC and icosahedral short range orders in pure and Sm doped Al liquids", X. W. Fang, C. Z. Wang, Y. X. Yao, Z. J. Ding, and K. M. Ho, Appl. Phys. Lett., Submitted.

"Atomistic cluster alignment method for local order mining in liquids and glasses", X. W. Fang, C. Z. Wang, Y. X. Yao, Z. J. Ding, and K. M. Ho, Phys. Rev. B, Submitted.

"Dynamic arrest and glass formation induced by self-aggregation of icosahedral clusters in Zr1-xCux alloys", S. G. Hao, C. Z. Wang, M. Z. Li, R. E. Napolitano, and K. M. Ho, Phys. Rev. Lett. Submitted.

"Fluctuation between icosahedral and BCC short range orders in undercooled Zr liquid", S. Wu, X. W. Fang, S. Y. Wang, C. Z. Wang, Y. X. Yao, K. M. Ho, Z. J. Ding and L. Y. Chen, Appl. Phys. Lett. Submitted.

PI Guofeng Wang

"Modelling surface segregation phenomena in the (111) surface of ordered Pt3Ti crystal", Zhiyao Duan, Jun Zhong, and Guofeng Wang, The Journal of Chemical Physics, 133, 114701 (2010).

"Density functional theory study on the Platinum surface segregation in ternary alloy Pt3NiM (111) surface", Yuhua Zhang, Zhiyao Duan, Chan Xiao, and Guofeng Wang, submitted to The Journal of Physical Chemistry C.

PI Haobin Wang

H. Wang and M. Thoss, ``From coherent motion to localization. II. Dynamics of the spin-boson model with sub-Ohmic spectral density at zero temperature'', Chem. Phys., 370, 78 (2010).

F. Ding, S. Chen, and H. Wang, ``Computational Study of Ferrocene-Based Molecular Frameworks with 2,5-Diethynylpyridine as a Chemical Bridge'', Materials, 3, 2668 (2010).

F. Ding, H. Wang, Q. Wu, T. Van Voorhis, S. Chen, and J. P. Konopelski, ``Computational Study of Bridge-Assisted Intervalence Electron Transfer'', J. Phys. Chem. A, 114, 6039 (2010).

K. A. Velizhanin, M. Thoss, and H. Wang, ``Meir-Wingreen formula for heat transport in a spin-boson nanojunction model'', J. Chem. Phys., 133, 084593 (2010).

J. Li, I. Kondov, H. Wang, and M. Thoss, ``Theoretical Study of Photoinduced Electron Transfer Processes in the Dye-Semiconductor System Alizarin-TiO2'', J. Phys. Chem. C, in press.

PI Jianwei Wang

Jianwei Wang, Fuxiang Zhang, Jie Lian, Rodney C. Ewing, and Udo Becker. Energetics and concentration of defect in Gd2Ti2O7 andGd2Zr2O7 pyrochlore at high pressure. (Submitted)

PI Lin-Wang Wang

N. Vukmirovic, L.W. Wang, "Charge carrier motion in disordered conjugated polymers: a multiscale ab-initio study", Nano Lett. 9, 3996 (2009).

S. Dag, L.W. Wang, "Packing structure of Poly(3-hexylthiophene) crystal: ab initio and molecular dynamics studies", J. Phys. Chem. B, 114, 5997 (2010).

M.G. Vargniory, C. Yang, A. Garcia-Lekue, L.W. Wang, "Complex band structure under plane-wave nonlocal pseudopotential Hamiltonian of metallic wires and electrodes", Comp. Mat. Sci. 48, 544 (2010).

S.Z. Wang, L.W. Wang, "Atomic and electronic structures of GaN:ZnO Alloys", Phys. Rev. Lett. 104, 065501 (2010).

Y. Luo and L.W. Wang, "Electronic structures of CdSe/CdS core shell nanorods", ACS Nano. 4, 91 (2010).

M.T. Sheldon, P.E. Trudeau, T. Mokari, L.W. Wang, A.P. Alivisatos, "Enhanced semiconductor nanocrystal conductance via solution grown contacts", Nano Lett. 9, 3676 (2009).

X.W. Jiang, H.X. Deng, S.S. Li, J.W. Luo, L.W. Wang, "Quantum mechanical simulation of nanosized metal-oxide-semiconductor field effect transistor using empirical pseudopotentials: A comparison for charge density occupation methods", J. Appl. Phys. 106, 084510 (2009).

Z. Zhao, J.C. Meza, B. Lee, H. Shan, E. Strohmaier, D.H. Bailey, L.W. Wang, J. Phys: Conf. Series, 180, 012079 (2009).

B. Lee, L.W. Wang, "Electronic structure of ZnTe:O and its usability for intermediate band solar cell", Appl. Phys. Lett. 96, 071903 (2010).

F. Tao, S. Dag, L.W. Wang, Z. Liu, D.R. Butcher, H. Bluhm, M. Salmeron, G.A. Somorjai, "Break-up of stepped Pt catalyst surfaces by high CO coverage", Science, 327 850 (2010).

L.W. Wang, "Novel computational methods for nanostructure electronic structure calculations", Ann. Rev. Phys. Chem. 61, 19, (2010).

N. Vukmirovic, L.W. Wang, "Quantum Dots: Theory", Book Chapter (in press).

N. Vukmirovic, L.W. Wang, "Carrier heating in disordered conjugated polymers in electric field", Phys. Rev. B 81, 035210 (2010).

D.H. Bailey, L.W. Wang, Z. Zhao, J. Meza, E. Strohmaier, B. Lee, "Tuning an electronic structure code". Book Chapter, in "Performance Science", Ed. D.H. Bailey, R. Lucas, 2010.

A. Canning, J. Shalf, L.W. Wang, H. Wasserman, M. Gajbe, "A comparison of different communication structures for scalable parallel three dimensional FFTs in first principle codes", Proceed. Parco09, Lyon France (2009).

I. Yamazaki, Z. Bai, H. Simon, L.W. Wang, K. Wu, "Adaptive projection subspace dimension for the thick-restart Lanczos method", Trans. Math. Soft. Vol. 31, Number 3 (2010).

A. Garcia-Lekue, L.W. Wang, "Plane-wave-based electron tunneling through Au nanojunctions", Phys. Rev. B 82, 035410 (2010).

L.W. Wang, "On the relationship between random phase approximation and the GW calculations", Phys. Rev. B 82, 115111 (2010).

N. Vukmirovic and L.-W. Wang, "Carrier hopping in disordered semiconducting polymers: How accurate is the Miller-Abrahams model?", Appl. Phys. Lett. 97, 043305 (2010).

PI Yi Wang (Pennsylvania State University)

Y. Wang, S. L. Shang, L. Q. Chen and Z. K. Liu, "Magnetic Excitation and Thermodynamics of BaFe2As2", Int J. Quantum Chem. (accepted, May 2010)

Y. Wang, J. E. Saal, J. J. Wang, A. Saengdeejing, S. L. Shang, L. Q. Chen, and Z. K. Liu, "Broken symmetry, strong correlation, and splitting between longitudinal and transverse optical phonons of MnO and NiO from firstprinciples", Phys. Rev. B (Rapid Communication) 82, 081104 (2010) http://link.aps.org/doi/10.1103/PhysRevB.82.081104.

Y. Wang, S. L. Shang, H. Zhang, L. -Q. Chen, and Z. -K. Liu, "Thermodynamic Fluctuations in Magnetic States: Fe3Pt as a Prototype", Phil. Mag. Lett. http://dx.doi.org/10.1080/09500839.2010.508446.

Y. Wang, S. L. Shang, X. D. Hui, L. Q. Chen, and Z. K. Liu, "Effects of Spin Structures on Phonons in BaFe2As2", Appl. Phys. Lett. 97, 022504 (2010), http://dx.doi.org/10.1063/1.3464166

Y. Wang, J. J. Wang, H. Zhang, V. R. Manga, S. L. Shang, L. Q. Chen, and Z. K. Liu, ???A First-principles Approach to Elasticity at Finite Temperatures???, J. Phys. Cond. Mat. 22 (2010) 225404, http://dx.doi.org/10.1088/0953-8984/22/22/225404

Y. Wang, J. J. Wang, W. Y. Wang, Z. G. Mei, S. L. Shang, L. Q. Chen, and Z. K. Liu, ???A Mixed-space Scheme to the Direct Method for Phonons in Polar Materials???, J. Phys. Cond. Mat. (Fast Track Communication) 22 (2010) 202201, http://dx.doi.org/10.1088/0953-8984/22/20/202201 (This work is highly scored by Journal of Physics: condensed Matters and highlighted in IOP news web site http://iopscience.iop.org/0953-8984/labtalk-article/42532)

7. Y. Wang, L. Q. Chen, Z. K. Liu, and S. N. Mathaudhu, ???First-principles Calculations of Twin-boundary and Stacking-fault Energies in Magnesium???, Scr. Mater. 62 (2010) 646???649, http://dx.doi.org/10.1016/j.scriptamat.2010.01.014

Y. Wang, S. L. Shang, X. D. Hui, L. Q. Chen, and Z. K. Liu, " Effects of Spin Structures on Fermi Surface Topologies in BaFe2As2", Solid State Communication (submitted, review comments is back, need revising).

Y. Wang, J. J. Wang, J. E. Saal, S. L. Shang, L. -Q. Chen, and Z. -K. Liu, ???Phonon Dispersions for Sr2RuO4: A First-principles Cumulative Force Constant Approach???, PRB (Revised manuscript resubmitted on August 7)

Y. Wang, Z. G. Mei, J. J. Wang, J. E. Saal, S. L. Shang, Z. K. Liu, and L. Q. Chen, ???Translating Phonons from Low into High Symmetry Structures: A First-principles Calculation of Tetragonal and Cubic SrTiO3??? APL (Submitted on July 30, under review Sep 2nd).

PI Yi Wang (University of Sussex)

Wang, Y, C. N. Long, J. H. Mather, and X. Liu (2010) Convective signals from surface measurements at DOE ACRF Tropical Western Pacific site: Manus, Climate Dynamics, online first, DOI : 10.1007/s00382-009-0736-z, 2010.

Wang, Y, N. T. Roulet, S. Frolking, and L. A. Mysak (2009) The Importance of Northern Peatlands in Global Carbon Systems During the Holocene, Climate of the Past, 5, 683-693, 2009.

Wang, Y, C. N. Long, L. R. Leung, J. Dudhia, S. A. McFarlane, J. H. Mather, S. J. Ghan, and X. Liu (2009) Evaluating regional cloud-permitting simulations of the WRF model for the TWP-ICE (Darwin, 2006), Journal of Geophysical Research-Atmospheres, 114, D21203, doi: 10.1029/2009JD012729, 2009.

PI Warren Washington

Meehl, G.A. and J. Arblaster, 2010: Climate change over the 21st Century using the CCSM4. To be submitted to J. Climate, in 4Q2010.

Teng, H., G. Branstator, and G.A. Meehl, 2010: Predictability of Atlantic overturning circulation and associated surface patterns in two CCSM3 large ensemble experiments. To be submitted to Clim. Dyn. in October 2010.

Teng, H. and G. Branstator, 2010: Initial value predictability in prominent modes of north Pacific subsurface temperature in a coupled GCM. Climate Dynamics, DOI: 1007/s00382-010-0749-7

Branstator, G. and H. Teng, 2010: Two limits of initial-value decadal predictability in a CGCM. J. Climate, in press.

PI William Weber

J. Yu, R. Devanathan, and W. J. Weber, First-Principles Study of Defects and Phase Transition in UO2, J. Phys.: Condens. Matter 21 [43]: 435401 (2009).

R. Devanathan and W. J. Weber, Simulation of Collision Cascades and Thermal Spikes in Ceramics, Nucl. Instrum. and Methods in Physics Res. B 268 [19]: 2857-2862 (2010).

PI Suhuai Wei

J. Kang, S.-H. Wei, and Y.-H. Kim, "Microscopic theory of hysteretic hydrogen adsorption in nanoporous materials", J. Am. Chem. Soc. 132, 1510 (2010).

Y. Zhao, Q. Xu, L. J. Simpson, and A. C. Dillon, "Prediction of Diamond-like, Metallic Boron Structures", Chem. Phys. Lett. 496, 280 (2010).

W. I. Choi, S.-H. Jhi, K. Kim, and Y.-H. Kim, "Divacancy-Nitrogen-Assisted Transition Metal Dispersion and Hydrogen Adsorption in Defective Graphenes: a First-Principles Study", Phys. Rev. B 81, 085441 (2010).

S.-H. Wei and Y. Yan, "Overcome bipolar doping difficulty in wide gap semiconductors", Chapter X in Electronic Structure Method for the Study of Defects, edited by Peter Deak and Vera Palmer, (Wiley, New York, 2010).

L. Zhang, X.-F. Zhou, H.-T. Wang, J.-J. Xu, J. Li, E. G. Wang, and S.-H. Wei, "Origin of the insulating behavior of the p-type LaAlO3/SrTiO3 interface: Polarization-induced asymmetric distribution of oxygen vacancies", Phys. Rev. B 82, 125412 (2010).

H.-X. Deng, J. Li, S.-S. Li, J.-B. Xia, A. Walsh, and S.-H. Wei, "Origin of antiferromagnetism in CoO: A density functional study", Appl. Phys. Lett. 96, 162508 (2010).

H. J. Xiang, S.-H. Wei, and X. G. Gong, "Structure of [Ag7(SR)4]- and [Ag7(DMSA)4]", J. Am. Chem. Soc. 132, 7355 (2010).

J. Zhu, F. Liu, G. B. Stringfellow, and S.-H. Wei, "Strain-Enhanced Doping in Semiconductors: Effects of Dopant Size and Charge State", submitted to Phys. Rev. Lett.

Y. Zhao, C. Ban, Q. Xu, S.-H. Wei, and A. C. Dillon, "Prediction of Charge-Driven Transformation of Boron Layers in Magnesium Borides: Valence Versatility and Application as a Mg-Boron Battery", submitted to Phys. Rev. Lett.

Y.-H. Kim, J. Kang, and S.-H. Wei, "Origin of enhanced dihydrogen-metal interaction in carboxylate bridged Cu2-paddle-wheel frameworks", submitted to Phys. Rev. Lett.

PI Harold Weitzner

R. Schmitt "Perturbation theory approach to stellarator coil optimization" by R.F. Schmitt Fusion Science and Technology, Vol. 57, Feb. 2010, pp. 152-161

R. Maingi, S.M. Kaye, R.E. Bell, T.M. Biewer, C.S. Chang, D.A. et al, "Overview of L-H power threshold studies, in NSTX," Nucl. Fusion 50, 064010 (2010)

G.Y. Park, C.S. Chang, I. Joseph, and R. Moyer, "Plasma transport in stochastic magnetic field caused by vacumm resonant magnetic perturbations at diverted tokamak edge," Physics of Plasmas, accepted for publication.

Seung-Hoon Park and C.S. Chang, "Numerical study of the plasma wall-bias effect on the ion flux through acceleration grid hole," Phys. Plasmas 17, 073505 (2010)

G. Dif-Pradalier* and P. H. Diamond, V. Grandgirard, Y. Sarazin, J. Abiteboul, X. Garbet, Ph. Ghendrih, and A. Strugarek, S. Ku and C. S. Chang, "On the validity of the local diffusive paradigm in turbulent plasma transport," PHYSICAL REVIEW E 82, 025401(R) (2010)

S.H. Park, Suk Jae Yoo, Choong-Seock Chang, "Molecular dynamics simulation of hyperthermal neutrals generated by energetic ion impact on a metal plate," Appl. Phys. Lett. 107, 13304 (2009)

PI Gerhard Wellein

C. Feichtinger, J. Habich, H. Koestler, G. Hager, U. Ruede, G. Wellein: A flexible patch-based lattice Boltzmann parallelization approach for heterogeneous GPU-CPU clusters. Submitted to Parallel Computing, Elsevier. Special Issue: Emerging Programming Paradigms for Large-Scale Scientific Computing.

J. Habich, T. Zeiser, G. Hager, G. Wellein: Performance analysis and optimization strategies for a D3Q19 Lattice Boltzmann Kernel on nVIDIA GPUs using CUDA. Submitted to Advances in Engineering Software and Computers & Structures.

J. Habich, C. Feichtinger, G. Hager, G. Wellein: Parallelizing lattice Boltzmann simulations on heterogeneous GPU-CPU clusters. Accepted as poster at SC2010.

PI Jeff Wereszczynski

J. Wereszczynski and J.A. McCammon. "Using Selectively Applied Accelerated Molecular Dynamics to Enhance Free Energy Calculations." J. Chem. Theory Comput. in press (2010)

J. Wereszczynski and I. Andricioaei, ???Free Energy Calculations Reveal Rotating-Ratchet Mechanism for DNA Supercoil Relaxation by Topoisomerase IB and its Inhibition??? Biophys J., 99, 869 (2010)

J. Wereszczynski and I. Andricioaei, ???Conformational and Solvent Entropy Contributions to the Thermal Response of Nucleic Acid-Based Nanothermometers??? J. Phys. Chem. B, 114, 2076 (2010)

PI Dan Werthimer

New SETI Sky Surveys For Radio Pulses
Siemion, et al
Acta Astronautica, 2010

The Precision Array for Probing the Epoch of Re-ionization
Parsons, et al,
The Astronomical Journal, 2010

The Allen Telescope Array: The First Widefield, Panchromatic, Snapshot Radio Camera for Radio Astronomy and SETI
Welch, et al
Proceedings of the IEEE, 2009

PI Myung Whangbo

E. J. Kan, H. J. Xiang, J. L. Yang and M.-H. Whangbo, "Magnetism of Semiconductor-based Magnetic Tunnel Junctions Under Electric Field from First Principles", Appl. Phys. Lett. 94, 252102 (2009).

J. Kang, C. Lee, R. K. Kremer and M.-H. Whangbo, "Consequences of the intrachain dimer-monomer spin frustration and the interchain dimer-monomer spin exchange in the diamond-chain compound Azurite Cu3(CO3)2(OH)2", J. Phys.:
Condens. Matter, 21, 392201 (2009).

E. J. Kan, H. J. Xiang, Y. Zhang, C. Lee and M.-H. Whangbo, "Density functional analysis of the spin exchange and the ferroelectric polarization in AgCrO2", Phys. Rev. B, 80, 104417 (2009).

H.-J. Koo, H. J. Xiang, C. Lee, and M.-H. Whangbo, "Effect of Magnetic Dipole-Dipole Interactions on the Spin Orientation and Magnetic Ordering of the Spin Ladder Compound Sr3Fe2O5", Inorg. Chem. 48, 9051 (2009).

C. Tian, C. Lee, H. J. Xiang, Y. Zhang, C. Payen, S. Jobic,M.-H. Whangbo, "Magnetic structure and ferroelectric polarization of MnWO4 investigated by density functional calculations and classical spin analysis", Phys. Rev. B, 80,
104426 (2009).

J. L. Musfeldt, L. I. Vergara, T. V. Brinzari, C. Lee, L. C. Tung, J. Kang, Y. J. Wang, J. A. Schlueter, J. L. Manson and M.-H. Whangbo, "Magnetoelastic interactions in a two-dimensional quantum antiferromagnet", Phys. Rev. Lett.
103, 157301 (2009).

O. Mentrr, E. Janod, P. Rabu, M. Hennion, F.Leclercq-Hugeux, J. Kang, C. Lee, M.-H. Whangbo and S. Petit, "BiCu2PO6: Frustration driven incommensurate dispersion in a gapped quantum spin ladder", Phys. Rev. B 80, 180413 (2009).

C. Lee, M.-H. Whangbo and J. Kohler, "Analysis of electronic structures and chemical bonding of metal-rich compounds. 2. Presence of dimer (T-T)4- and isolated T2- anions in the polar intermetallic Cr5B3-type compounds AE5T3 (AE =
Ca, Sr; T = Au, Ag, Hg, Cd, Zn)", Z. Anorg. Allge. Chem. 636, 36 (2010).

E. J. Kan, H. J. Xiang, C. Lee, F. Wu, J. L. Yang and M.-H. Whangbo, "Origin of the ferroelectricity in pervoskites with s0 A-site cations: Toward Near-Room-Temperature Multiferroics", Angew. Chem. Int. Ed. 49, 1603 (2010).

F. Wu, E. J. Kan and M.-H. Whangbo, "On the Importance of the Interplaquette Spin Exchanges in Na3RuO4: Density Functional Theory Analysis of the Spin Exchange and Magnetic Properties", Inorg. Chem. 49, 3025 (2010).

E. J. Kan, H. J. Xiang, F. Wu, C. Lee, J. L. Yang, and M.-H. Whangbo, "Ferrimagnetism in zigzag graphene nanoribbons induced by main-group adatoms", Appl. Phys. Lett. 96, 162503 (2010).

C. Tian, E. J. Kan, C. Lee, and M.-H. Whangbo, "Back-Donation Effect of the Cyanide Ligands on the Electron Correlation and Charge Transfer in Prussian Blue RbMn[Fe(CN)6]", Inorg. Chem. 49, 3086 (2010).

S. Ji, E. J. Kan, M.-H. Whangbo, J.-H. Kim, Y. Qiu, M. Matsuda, H. Yoshida, Z. Hiroi, M. A. Green, T. Ziman, and S.-H. Lee, "Orbital order and partial electronic delocalization in a triangular magnetic metal Ag2MnO2", Phys. Rev. B,
81, 094421 (2010).

E. Dorolti, L. Cario, B. Corraze, E. Janod, C. Vaju, H.-J. Koo, E. J. Kan and M.-H. Whangbo, "Half-metallic ferromagnetism and large negative magnetoresistance in the new lacunar spinel GaTi3VS8", J. Am. Chem. Soc. 132,
5704 (2010).

F. Wu, E. J. Kan, C. Tian and M.-H. Whangbo, "Theoretical analysis of the spin exchange and magnetic dipole-dipole nteractions leading to the magnetic structure of Ni3TeO6", Inorg. Chem. 49, 7545 (2010).

PI Martin White

Seo, Hee-Jong, Eckel, Jonathan, Eisenstein, Daniel J., Mehta, Kushal, Metchnik, Marc, Padmanabhan, Nikhil, Pinto, Phillip, Takahashi, Ryuichi, White, Martin, and Xu, Xiaoying, High-precision Predictions for the Acoustic Scale in the Nonlinear Regime, The Astrophysical Journal, 720, 1667, 2010

White, Martin, Cohn, J. D., and Smit, Renske, Cluster galaxy dynamics and the effects of large-scale environment, Monthly Notices of the Royal Astronomical Society, 2010

Xu, X., White, M., Padmanabhan, N., Eisenstein, D. J., Eckel, J., Mehta, K., Metchnik, M., Pinto, P., and Seo, H.-J., A New Statistic for Analyzing Baryon Acoustic Oscillations, The Astrophysical Journal, 718, 1234, 2010

White, Martin, Pope, Adrian, Carlson, Jordan, Heitmann, Katrin, Habib, Salman, Fasel, Patricia, Daniel, David, and Lukic, Zarija, Particle Mesh Simulations of the Lyα Forest and the Signature of Baryon Acoustic Oscillations in the Intergalactic Medium, The Astrophysical Journal, 713, 393, 2010

Carlson, Jordan and White, Martin, Embedding realistic surveys in simulations through volume remapping, ApJS in press, 2010

Noh, Yookyung, White, Martin, and Padmanabhan, Nikhil, Reconstructing baryon oscillations, Physical Review D, 80, 2009

Slosar, An&zcaron;e, Ho, Shirley, White, Martin, and Louis, Thibaut, The acoustic peak in the Lyman alpha forest, Journal of Cosmology and Astro-Particle Physics, 10, 2009

Padmanabhan, Nikhil and White, Martin, Calibrating the baryon oscillation ruler for matter and halos, Physical Review D, 80, 2009

Carlson, Jordan, White, Martin, and Padmanabhan, Nikhil, Critical look at cosmological perturbation theory techniques, Physical Review D, 80, 2009

Padmanabhan, Nikhil, White, Martin, Norberg, Peder, and Porciani, Cristiano, The real-space clustering of luminous red galaxies around z < 0.6 quasars in the Sloan Digital Sky Survey, Monthly Notices of the Royal Astronomical Society, 397, 1875, 2009

White, Martin, Song, Yong-Seon, and Percival, Will J., Forecasting cosmological constraints from redshift surveys, Monthly Notices of the Royal Astronomical Society, 397, 1354, 2009

White, Martin and Padmanabhan, Nikhil, Breaking halo occupation degeneracies with marked statistics, Monthly Notices of the Royal Astronomical Society, 395, 2384, 2009

PI John Wilkins

Kevin P. Driver, R. E. Cohen, Z. Wu and B. Militzer, P. Lopez Rios, M. D. Towler, R. J. Needs, and J. W. Wilkins, Quantum Monte Carlo computations of phase stability, equations of state, and elasticity of high-pressure silica, Proc. Natl. Acad. Sci. U S A 107, 9519-9524 (2010) - (Plus supplement online).

Michael R. Fellinger, Hyoungki Park, and John W. Wilkins, Force-matched embedded-atom method potential for niobium, Phys. Rev. B 81, 144119 (2010).

Jeremy W Nicklas and J W Wilkins, Accurate ab-initio prediction of III-IV direct-indirect gap crossovers, Appl. Phys. Lett. 97, 091902 (2010) - (Plus supplement online

Amita Wadehra, Jeremy W Nicklas, and John W Wilkins, Band offsets of semiconductor heterostructures: A hybrid density functional study, Appl. Phys. Lett. 97, 092119 (2010) - (Plus supplement online).

R. G. Hennig, A. Wadehra, K. P. Driver, W. D. Parker, C. J. Umrigar, and J. W. Wilkins, Phase transformation in Si from semiconducting diamond to metallic beta-Sn phase in QMC and DFT under hydrostatic and anisotropic stress, Phys. Rev. B. 82, 014101 (2010).

Hyoungki Park and, J.W. Wilkins, Relativity stability of extended interstitials in silicon, Phys. Rev. B 79, 241203(R) (2009).

William D. Parker, John W. Wilkins, and Richard G. Hennig, Accuracy of Quantum Monte Carlo Methods for Point Defects in Solids, Phys. Status Solidi B, published online 16 August 2010.

PI Hugh Wilson

Hugh F Wilson and Burkhard Militzer, "Sequestration of Noble Gases in Giant Planet Interiors", Phys. Rev. Lett 104 (2010).

Burkhard Militzer and Hugh F. Wilson, "New phases of water ice predicted at megabar pressures", submitted to Phys. Rev. Lett.

PI Peter Winsor

Condron, A. and Winsor, P, 2010, A subtropical fate awaited freshwater discharged from glacial Lake Agassiz, submitted to Nature.

PI Brian Wirth

C. Hin and B.D. Wirth, ???Formation of Y2O3 nanoclusters in nano-structured ferritic alloys: Modeling of precipitation kinetics and yield strength???, Journal of Nuclear Materials 402 (2010) 30-37.

C. Hin, B.D. Wirth, and J.B. Neaton, ???Formation of Y2O3 nanoclusters in nanostructured ferritic alloys during isothermal and anisothermal heat treatment: A kinetic Monte Carlo study???, Phys. Rev. B 80 (2009) 134118.

PI Stan Woosley

Aspden, Andrew; Bell, John; Woosley, Stan "Distributed flames and Damk"ohler `small-scale turbulence' in type Ia supernovae" 2010, ApJ, 720, 694.

Nordhaus, J.; Burrows, A.; Almgren, A.; Bell, J. "Dimension as a Key to the Neutrino Mechanism of Core-collapse Supernova Explosions," 2010, ApJ, 720, 694.

Almgren, A.; Bell, J.; Kasen, D.; Lijewski, M.; Nonaka, A.; Nugent, P.; Rendleman, C.; Thomas, R.; Zingale, M. "MAESTRO, CASTRO, and SEDONA -- Petascale Codes for Astrophysical Applications," 2010, ApJS, 188, 358.

Nonaka, A.; Almgren, A. S.; Bell, J. B.; Lijewski, M. J.; Malone, C. M.; Zingale, M. "MAESTRO: An Adaptive Low Mach Number Hydrodynamics Algorithm for Stellar Flows," 2010, ApJ, 715, 1221.

Almgren, A. S.; Beckner, V. E.; Bell, J. B.; Day, M. S.; Howell, L. H.; Joggerst, C. C.; Lijewski, M. J.; Nonaka, A.; Singer, M.; Zingale, M. "CASTRO: A New Compressible Astrophysical Solver. I. Hydrodynamics and Self-gravity" 2010, ApJ, 709, 11.

Nonaka, Andrew; Almgren, A. S.; Bell, J. B.; Malone, C. M.; Zingale, M. MAESTRO: An Adaptive Low Mach Number Hydrodynamics Algorithm for Stellar Flows," 2010, ApJ. Suppl. 188, 358.

Ma, H., Zingale, M., Woosley, S. E., Aspden, A. J., Bell, J. B., Almgren, A. S., Nonaka, A. and Dong, S. "Type Ia Supernovae: Advances in Large Scale Simulation", Proceedings SciDAC PI Conference, Chatanooga, TN, July, 2010 (refereed).

Bell, J.; Almgren, A.; Kasen, D.; Lijewski, M.; Nonaka, A.; Nugent, P.; Rendleman, C.; Thomas, R.; Zingale, M. MAESTRO, CASTRO, and SEDONA -- Petascale Codes for Astrophysical Applications" Proceedings SciDAC PI Conference, Chatanooga, TN, July, 2010 (refereed).

Kasen, D. 2010, "Seeing the Collision of a Supernova with its Companion Star," ApJ 708, 1025.

Kasen, D., Ropke, F., and Woosley, S.E. 2009, "The Diversity of Type~Ia Supernovae from Broken Symmetries," Nature, 460, 869 (2009).

Malone, Christopher M.; Almgren, A. S.; Bell, J. B.; Cumming, A.; Nonaka, A.; Woosley, S. E.; Zingale, M. Convection from Burning Preceding a Type I X-ray Burst, 2010, submitted to ApJ.

PI Jianzhong Wu

X. Xu, D. Cao and J. Wu,???Density functional theory for predicting polymeric forces against surface fouling???, Soft Matter, in press, 2010 (invited).

J. Wu, ''Density functional theory for liquid structure and thermodynamics,'' pp1-74, in Molecular Thermodynamics of Complex Systems, Series: Structure and Bonding , Vol. 131, Lu, Xiaohua and Hu, Ying (Eds.), Springer, 2009

"Entropic forces of single-chain confinement in spherical cavities", Z. Jin, S. Zhao and J. Wu, Physical Review E, submitted, 2010.

H. Y. Shin and J. Wu, "Equation of state for the phase behavior of polymers in carbon dioxide", Industrial and Engineering Chemical Research, 49 (16), 7678-7684, 2010.

L. Wang, H. Liang, C. Wu and J. Wu, "Electrostatic origins of polyelectrolyte adsorption: Theory and Monte Carlo Simulations", Journal of Chemical Physics, 133(4), 044906(13 pages), 2010

L. Wang, T. Wu, F. Zuo, X. Z., X. Bu, J. Wu, and P. Feng, "Self-Similarity in Metal Chalcogenide Nanocluster Chemistry: Assembly of Supertetrahedral T5 Copper-Indium Chalcogenide Clusters into Super-Supertetrahedron of Infinite Order", Journal of the American Chemical Society, 132(10), 3283-3285, 2010

L. Cao, A. K. Jones, V. K. Sikka, J. Wu, and D. Gao, "Anti-Icing Superhydrophobic Coatings", Langmuir, 25 (21), 12444-12448, 2009.

J. Jin, J. Wu, A. L. Frischknecht, "Modeling microscopic morphology and mechanical properties of block copolymer/nanoparticle composites", Macromolecules, 42 (19), 7537-7544, 2009.

J. Wu, "Solvation of a spherical cavity in simple liquids: Stretching the limits", The Journal of Physical Chemistry B, 113 (219), 6813-6818, 2009.

T. Jiang and J. Wu, "Cluster formation and bulk phase behavior of colloidal dispersions", Physical Review E, 80, 021401 (2009).

T. Jiang, Z. G. Wang and J. Wu, "Electrostatic regulation of genome packaging in human hepatitis B virus", Biophysical Journal, 96, 3065-3073, 2009.

Z. Li and J. Wu, "Formation of lamellar structures from spherical particles", Journal of Chemical Physics, 130(16), 165102, 2009.

PI Ruqian Wu

A. Shinde, J.X. Cao, W.J. Ouyang, R.Q. Wu and R. Ragan, "Determination of preferential rare earth adatom adsorption geometries on Si(001)", Phys. Lett. A, 373, 3459 (2009).

Jian-Ge Zhou, Quinton L. Williams,1 and R.Q. Wu, "Thioglycolic acid on the gold (111) surface and Raman vibrational spectra", J. Chem. Phys. 132, 064702 (2010).

A. Shinde, R.Q. Wu and R. Ragan, "Thermodynamic Driving Forces Governing Assembly of Disilicide Nanowires", Surf. Sci. 604, 1481 (2010).

 X.F. Yang, J. Hu, R.Q. Wu, and B.E. Koel, "Formation of Pd Monomers and Dimers on a Single-Crystal Pd3Fe(111) Surface", J. Phys. Chem. Lett., 1, 2493 (2010).

Z.X. Yang , Z.M. Fu, Y.N. Zhang and Ruqian Wu, "The direct CO oxidation by lattice oxygen on Zr-doped ceria surfaces", Cata. Lett. in press.

W.J. Ouyang, A. Shinde, R. Ragan and R.Q. Wu, ??? Electronic Structure and Chemical Activity of Au Rare Earth Disilicide Core-Shell Nanowires???, ACS Nano, submitted.

Y. Zhu, W. X. Ying, Z. Q. Yang, J. X. Cao, and R. Q. Wu, "Phase transition and electronic structure of Zn1-xMnxSe (x=0, 0.25) under high pressure", Eur. Phys. J. B 72, 367 (2009).

R. D. Gann, J.X. Cao, J.S. Wen, Z.J. Xu, G. D. Gu, R. Q. Wu, and J. A. Yarmoff, "Adsorption of Iodine and Potassium on Bi2Sr2CaCu2O8+", Phys. Rev. B 81, 035418 (2010).

J. Hu, D.D. Li, J.G. Lu and R.Q. Wu, "Effects on electronic properties of molecule adsorption on CuO surface and nanowire", J. Phys. Chem. C, Oct. 14, 2010.

L Zeng, J.X. Cao, E. Helgren, J. Karel, E. Arenholz, L. Ouyang, D.J. Smith, R.Q. Wu, F. Hellman, "Distinct Local Electronic Structure and Magnetism for Mn in Amorphous Si and Ge", Phys. Rev. B, submitted.

J. X. Cao, J. Lindner, A. Ney and R. Q. Wu, "Determination of distribution of Co in (ZnCo)O through the Co K-edge x-ray magnetic circular dichroism", Phys. Rev. Lett., submitted.

Y. Jiang, Y. N. Zhang, J.X. Cao, R. Q. Wu and W. Ho, "Real-space imaging of Kondo screening in a two-dimensional Kondo lattice", Science, submitted.

PI Donald Wuebbles

K. O. Patten and D. J. Wuebbles, Atmospheric lifetimes and Ozone Depletion Potentials of trans-1-chloro-3,3,3-trifluoropropylene and trans-1,2-dichloroethylene in a three-dimensional model, Atmos. Chem. Phys., under review (2010) (available at http://www.atmos-chem-phys-discuss.net/10/16637/2010/)

A. M. Stoner, K. Hayhoe, and D. Wuebbles, Assessing General Circulation Model Simulations of Atmospheric Teleconnection Patterns, J. Climate 22, 4348-4372 (2009)

D. J. Wuebbles, P. Forster, H. Rogers, and R. Herman, Issues and uncertainties affecting metrics for aviation impacts on climate, Bull. Amer. Met. Soc. 91, 491-496 (2010)

D. J. Wuebbles and K. O. Patten, Three-Dimensional Modeling of HCFC-123 in the Atmosphere: Assessing Its Potential Environmental Impacts and Rationale for Continued Use, Environ. Sci. Technol. 43, 3208-3213 (2009)

D. J. Wuebbles, K. O. Patten, D. Wang, D. Youn, M. Martinez-Aviles, and J. S. Francisco, Three-dimensional model evaluation of the Ozone Depletion Potentials for n-propyl bromide, trichloroethylene and perchloroethylene, Atmos. Chem. Phys., under review (2010) (available at http://www.atmos-chem-phys-discuss.net/10/17889/2010)

D. Youn, K. O. Patten, J.-T. Lin, and D. J. Wuebbles, Explicit calculation of indirect global warming potentials for halons using atmospheric models, Atmos. Chem. Phys. 9, 8719-8733 (2009) (available at http://www.atmos-chem-phys.net/9/8719/2009/)

D. Youn, K. O. Patten, D. J. Wuebbles, H. Lee, and C.-W. So, Potential impact of iodinated replacement compounds CF3I and CH3I on atmospheric ozone: A three-dimensional modeling study, Atmos. Chem. Phys., under review (2010) (manuscript available at http://www.atmos-chem-phys-discuss.net/10/16659/2010/


Y

PI Chao Yan

L. Lin, C. Yang, J. C. Meza, J. Lu, L. Ying and W. E. SelInv - An Algorithm for Selected Inversion of a Sparse Symmetric Matrix , LBNL-2746E , 2009, accepted by ACM Trans on Mathematical Software

L. Lin, C. Yang, J. Lu, L. Ying and W. E. A Fast Parallel Algorithm for Selected Inversion of Structured Sparse Matrix with Application to 2D Electronic Structure Calculations , LBNL-2677E , 2009, submitted to SIAM J. Sci. Comp.

C. Yang and J. Meza, Total Energy Minimization for Periodic Systems, accepted by Linear Alg and Its Applications, 2010.

F. Maia, C. Yang and S. Marchesini, Compressive auto-indexing in Femtosecond nanocrystallography. accepted Ultramicroscopy, 2010

5. C. Yang, Z. Wang and S. Marchesini, Orientation Determination for 3D Single Molecule Diffraction Imaging, Proceedings SPIE Conference, San Diego, 2010

6. J. Chung, P. Sternberg and C. Yang, High Performance Three-dimensional Image REconstruction for Molecular Structure Determination, International Journal on High Performance Computing Applications, 2009.

PI Lin Yang

L. H. Yang, Ken-ichi Nomura, Rajiv Kalia, Aiichiro Nakano, and Priya Vashishta, "Dynamic Fracture in Silica
Glass: Micro-second Molecular Dynamics Simulations," in preparation.

K. Nomura , R. Seymour, W. Wang, H. Dursun, R. K. Kalia , A. Nakano , P. Vashishta, F. Shimojo and L. H.
Yang, "A Metascalable Computing Framework for Large Spatiotemporal-Scale Atomistic Simulations," in
preparation.

L.H. Yang, Randy Hood, and John Moriarty, "First-principles DFT calculations on water-silica surface
interaction," in preparation.

PI Weiming Yao

Search for Technicolor Particles Produced in Association with a W Boson at CDF.  T. Aaltonen et al., The CDF Collaboration, Phys. Rev. Lett. 104, 111802 (2010). arXiv: 0912.2059.

Combination of Tevatron Searches for the Standard Model Higgs Boson in the W+W- Decay Mode T. Aaltonen et al., The CDF Collaboration, submitted to Phys. Rev. Lett. January 25, 2010. Fermilab-Pub-10-017-E. arXiv: 1001.4162.

Search for a Standard Model Higgs Boson in WH --> l nu bb-bar in p anti-p Collisions at s**(1/2) .96 TeV Phys. Rev. Lett. 103, 101802 (2009). arXiv: 0906.5613.

PI Katherine Yelick

Krste Asanovic, Rastislav Bodik, James Demmel, Tony Keaveny, Kurt Keutzer, John Kubiatowicz, Nelson Morgan, David Patterson, Koushik Sen, John Wawrzynek, David Wessel, and Katherine Yelick, "A View of the Parallel Computing Landscape," Communications of the ACM, November 2009.

Amir Kamil and Katherine Yelick, "Enforcing Textual Alignment of Collectives Using Dynamic Checks," 22nd International Workshop on Languages and Compilers for Parallel Computing (LCPC), October 2009. To appear in Springer-Verlag Lecture Notes in Computer Science.

J. Mellor-Crummey, L. Adhianto, and W. Scherer III. "A New Vision for Coarray Fortran." The 3rd Conference on Partitioned Global Address Space Programming Models, Ashburn, VA. October 5-8 2009.

William N. Scherer III, Laksono Adhianto, Guohua Jin, John Mellor-Crummey, and Chaoran Yang. Hiding Latency in Coarray Fortran 2.0. The 4th Conference on Partitioned Global Address Space Programming Models, New York, NY. October 12-15, 2010. To appear.

Hybrid PGAS Runtime Support for Multicore Nodes, Filip Blagojevic, Paul Hargrove, Costin Iancu, Katherine Yelick. Conference on Partitioned Global Address Space languages. October 12-14, 2010, New York, NY. To appear.

PI Hua-Gen Yu

H.-G. Yu, A general rigorous quantum dynamics algorithm to calculate vibrational energy levels of pentaatomic molecules, J. Mol. Spectrosc. 256, 287 (2009).

H.-G. Yu, Product branching ratios of the reaction of CO with H3+ and H2D+, Astrophys. J. Lett. 706, L52 (2009).

J.S. Francisco, J.T. Muckerman and H.-G. Yu, HOCO radical chemistry, Acc. Chem. Res. (Accepted, 2010).

H.-G. Yu, A direct ab initio molecular dynamics study of the roaming mechanism of the H2 + HOC+ reaction, Phys. Script A, (submitted, 2010).


Z

PI Nicholas Zabaras

Xiang Ma and N. Zabaras, "Kernel Principal Component Analysis for Stochastic Input Model Reduction", Journal of Computational Physics, submitted.

Xiang Ma and N. Zabaras, "A stochastic mixed finite element heterogeneous multiscale method for flow in porous media", Journal of Computational Physics, submitted.

PI Bin Zhang

Bin Zhang
Kinetic equilibration from a radiative transport
Proceedings of 25th winter workshop on nuclear dynamics, pp 1-6.

Bin Zhang
Thermalization through parton transport
Nuclear Physics A 834, 279c-281c (2010)

Bin Zhang and Warner A. Wortman
Parton radiative processes and pressure isotropization in relativistic heavy ion collisions
Phys. Lett. B 693, 24-27 (2010)

Bin Zhang and Warner A Wortman
Chemical and kinetic equilibrations via radiative parton transport
submitted to the Proceedings of the International Nuclear Physics Conference 2010

PI Guoping Zhang

M. S. Si and G. P. Zhang, Resolving photon-shortage mystery in femtosecond magnetism, J. Phys.: Condensed Matter {\bf 22}, 076005 (2010).

G. P. Zhang, Yihua Bai and T. F. George, An energy- and crystal momentum-resolved study of laser-induced femtosecond magnetism, Physical Review B {\bf 80}, 214415 (2009).

Georgios Lefkidis, G. P. Zhang, and W. Hubner, Angular momentum conservation for coherently manipulated spin
polarization in photoexcited NiO: An ab initio calculation, Physical Review Letters {\bf 103}, 217401 (2009).

G. P. Zhang and Thomas F. George, Laser-Induced Femtosecond Magnetism, Computational studies of new materials, (World Scientific), edited by T. F. George, D. Jelski, R. Leftfullin and G. P. Zhang, (in press, 2010).

G. P. Zhang and Thomas F. George, Exciting Infrared Normal Modes in $\rm C_{60}$ by an Ultrafast Laser, Computational studies of new materials, (World Scientific), edited by T. F. George, D. Jelski, R. Leftfullin and G. P. Zhang, (in press, 2010).

PI Zhenyu Zhang

Chen, H., W. G. Zhu and Z. Y. Zhang, "Contrasting Behavior of Carbon Nucleation in the Initial Stages of Graphene Epitaxial Growth on Stepped Metal Surface", Physical Review Letters 104(18), 186101 (2010).

Jia, Y., S. Y. Wang, W. G. Chen, Q. Sun, H. H. Weitering and Z. Y. Zhang "First-principles study of quantum size effects in ultrathin Pb-Bi metal alloy films", Physical Review B 81(24), 245425.

Jia, Y., B. A. Wu, C. Li, T. L. Einstein, H. H. Weitering and Z. Y. Zhang "Strong Quantum Size Effects in Pb(111) Thin Films Mediated by Anomalous Friedel Oscillations", Physical Review Letters 105(6) (2010).

Khajetoorians, A. A., W. G. Zhu, J. Kim, S. Y. Qin, H. Eisele, Z. Y. Zhang and C. K. Shih (2009). "Adsorbate-induced restructuring of Pb mesas grown on vicinal Si(111) in the quantum regime", Physical Review B 80(24), 245426.

Kim, H. J., S. Oh, K. S. Kim, Z. Y. Zhang and J. H. Cho, "Length- and parity-dependent electronic states in one-dimensional carbon atomic chains on C(111)",.Physical Review B 82(4), 041401.

Lee, J. Y., J. H. Cho and Z. Y. Zhang. "Quantum size effects in competing charge and spin orderings of dangling bond wires on Si(001)", Physical Review B 80(15), 2009.

Li, S. F., H. S. Li, X. L. Xue, Y. Jia, Z. X. Guo, Z. Y. Zhang and X. G. Gong ???hcp metal nanoclusters with hexagonal A-A bilayer stacking stabilized by enhanced covalent bonding.??? Physical Review B 82(3).

Pan, H., B. H. Gu, G. Eres and Z. Y. Zhang, "Ab initio study on noncompensated CrO codoping of GaN for enhanced solar energy conversion", Journal of Chemical Physics 132(10).

Pan, H., B. H. Gu and Z. Y. Zhang, "Phase-Dependent Photocatalytic Ability of TiO2: A First-Principles Study, "Journal of Chemical Theory and Computation 5(11): 3074-3078 (2009).

Pan, H., X. F. Qiu, I. N. Ivanovc, H. M. Meyer, W. Wang, W. G. Zhu, M. P. Paranthaman, Z. Y. Zhang, G. Eres and B. H. Gu, "Fabrication and characterization of brookite-rich, visible light-active TiO2 films for water splitting", Applied Catalysis B-Environmental 93(1-2): 90-95 (2009).

Troparevsky, M. C., K. Zhao, D. Xiao, A. G. Eguiluz and Z. Y. Zhang, "Molecular orbital view of the electronic coupling between two metal nanoparticles", Physical Review B 82(4).

Troparevsky, M. C., K. Zhao, D. Xiao, Z. Y. Zhang and A. G. Eguiluz, "Tuning the Electronic Coupling and Magnetic Moment of a Metal Nanoparticle Dimer in the Nonlinear Dielectric-Response Regime", Nano Letters 9(12): 4452-4455 (2009).

Xiao, D., Y. Yao, W. Feng, J. Weng, W. Zhu, X. Chen, G. M. Stocks, Z. Zhang, "Half-Heusler Compounds as a New Class of Three-Dimensional Topological Insulators", Physical Review Letters 105, 096404 (2010).

Zheng, S., W. G. Zhu, Y. F. Gao, G. M. Stocks and Z. Y. Zhang, "Kinetic Monte Carlo simulations of nanocolumn formation in two-component epitaxial growth", Applied Physics Letters 96(7).

Yoon, M., Weitering, H.H., Zhang, Z. Y. "Hydrogen Affinity to Pristine and Metal-doped ultrathin Mg films", submitted (Phys. Rev. B).

PI Linjin Zheng

A. Y. Aydemir, "An intrinsic source of radial electric field and edge flows in tokamaks", Nucl. Fusion
49 (6), 065001 (2009).

R. Fitzpatrick, and F. L. Waelbroeck, "Effect of flow damping on drift-tearing magnetic islands in
tokamak plasmas", Phys. Plasmas 16, 072507 (2009).

R. Fitzpatrick, and F. L. Waelbroeck, "Locked magnetic island chains in toroidally flow damped
tokamak plasmas", Plasma Phys. Control. Fusion 52, 055006 (2010).

R. Fitzpatrick and F. L. Waelbroeck, "A drift-magnetohydrodynamical fluid model of helical
magnetic island equilibria in the pedestals of H-mode tokamak plasmas", to appear in Physics of
Plasmas (2010).

M. Furukawa and L.-J. Zheng, "Suppression of error-field-induced magnetic islands by Alfven
resonance effect in rotating plasmas", Nucl. Fusion 49, 075018 (2009).

M. Furukawa, S. Tokuda, and L. J. Zheng, "A numerical matching technique for linear resistive
magnetohydrodynamics modes", Phys. Plasmas 17, 052502 (2010).

W. Horton, C. Correa, G. D. Chagelishvili, V. S. Avsarkisov, J. G. Lominadze, J. C. Perez, J.-H. Perez,
and T. A. Carter, "On generation of Alfvenic-like fluctuations by drift wave-zonal flow system in large
plasma device experiments", Phys. Plasmas 16, 092102 (2009).

W. Horton, T. Ditmire, and Yu. P. Zakharov, "Laser experiments to simulate coronal mass ejection
driven magnetospheres and astrophysical plasma winds on compact magnetized stars", High Energy
Density Physics 6, 190-193 (2010).

W. Horton, J.-H. Kim, G. D. Chagelishvili, et al, "Angular redistribution of nonlinear perturbations: A
universal feature of nonuniform flows", Phys Rev. E, accepted May 24, 2010.

O. Yamagishi, H. Sugama and W. Horton, "Interaction of Zonal Flow and Drift Wave Turbulence
from Classic DW Models", Transport Task Force Meeting and submitted for publication in Phys of
Plasmas (2010).

W. Horton, X. Fu, A. Ivanov, and A. Beklemishev, "Parameter Optimization Studies for a Tandem
Mirror Neutron Source", Journal of Fusion Engineering, accepted for publication (2010).

M. Kotschenreuther, P. Valanju, S. Mahajan, L. J. Zheng, L. D. Pearlstein, R. H. Bulmer, J. Canik, and
R. Maingi, "The super X divertor (SXD) and a compact fusion neutron source (CFNS)", Nucl. Fusion 50
(3), 035003 (2010).

F. Millitello and F. L. Waelbroeck, "Error field penetration in the presence of diamagnetic effects",
Nucl. Fusion 49, 065018 (2009).

M. Nakata, T.-H. Watanabe, H. Sugama, and W. Horton, "Formation of coherent vortex streets and
transport reduction in electron temperature gradient driven turbulence", Phys. Plasmas 17, 042306
(2010).

P. M. Valanju, M. Kotschenreuther, and S. M. Mahajan, "Super X divertors for solving heat and
neutron flux problems of fusion devices", Fusion Engineering and Design 85 (1), 46-52 (2010).

F. L. Waelbroeck, "Theory and observations of magnetic islands", Nucl. Fusion 49, 104025, (2009).

L. J. Zheng and M. Furukawa, "Current-interchange tearing modes: Conversion of interchange-type
modes to tearing modes", Phys. Plasmas 17, 052508 (2010).

L. J. Zheng, M. T. Kotschenreuther, and J. W. Van Dam, "Kinetic analysis of the resistive wall modes
in the ITER advanced tokamak scenario", Nucl. Fusion 49 (7), 075021 (2009).

L. J. Zheng, M. T. Kotschenreuther, and J. W. Van Dam, "Rotational stabilization of resistive wall
modes in ITER advanced tokamak scenarios", Phys. Plasmas 17, 056104 (2009).

L. J. Zheng, M. T. Kotschenreuther, and J. W. Van Dam, "AEGIS-K code for linear kinetic analysis of
toroidally axisymmetric plasma stability", J. Comp. Phys. 229,3605 (2010)

PI Xiaolin Zhong

Rawat, P.S., and Zhong, X., On High-Order Shock-Fitting and Front-Tracking Schemes for Numerical Simulation of Shock-Disturbance Interactions. Journal of Computational Physics, 229 (19) 2010, p. 6744-6780.

PI Ping Zhu

J. Raeder, P. Zhu, Y. Ge, and G. Siscoe, Tail Force Imbalance and Ballooning Instability Preceding Substorm Onset, submitted to J. Geophys. Res. (2010).

B.J. Burke, S.E. Kruger, C.C. Hegna, P. Zhu, P.B. Snyder, C.R. Sovinec, and E.C. Howell, Edge localized linear ideal magnetohydrodynamic instability studies in an extended-magnetohydrodynamic code, Phys. of Plasmas 17, 32103 (2010).

PI Alex Zunger

J.W. Luo and A. Zunger
Design Principles and Coupling Mechanisms in the 2D Quantum-Well Topological Insulator HgTe/CdTe
Phys. Rev. Lett. In press (2010).

L. Zhang, J.W. Luo, A. Zunger, N. Akopian, V. Zwiller, and J.C. Harmand
Wide InP Nanowires with Wurtzite/Zincblende Superlattice Segments Are Type-II whereas Narrower Nanowires Become Type-I: An Atomistic Pseudopotential Calculation
Nano Letters (ASAP) (2010).

Voicu Popescu, Gabriel Bester, and Alex Zunger
Coexistence and coupling of zero-dimensional, two-dimensional, and continuum resonances in nanostructures
Phys. Rev. B 80, 045327 (2009).

V. Popescu, G. Bester, and A. Zunger
Strain-induced localized states within the matrix continuum of self-assembled quantum dots
Appl. Phys. Lett. 95, 023108 (2009).

A. Franceschetti, J.W. Luo, J.M. An, and A. Zunger
Origin of one-photon and two-photon optical transitions in PbSe nanocrystals
Phys. Rev. B. (Rapid Comm.) 79, 241311(R) (2009).

J. A. Chan, J. Z. Liu, and Alex Zunger
Bridging the gap between atomic microstructure and electronic properties of alloys: The case of (In,Ga)N
Phys. Rev. B 82, 045112 (2010).

Voicu Popescu and Alex Zunger
Effective Band Structure of Random Alloys
Phys. Rev. Lett. 104, 236403 (2010)

K. Biswas, S. Lany, A. Zunger, "The electronic consequences of multivalent elements in inorganic solar absorbers: Multivalency of Sn in Cu2ZnSnS4", Appl. Phys. Lett. 96, 201902 (2010).

S. Lany, A. Zunger, "Generalized Koopmans density functional calculations reveal the deep acceptor state of NO in ZnO", Phys. Rev. B 81, 205209 (2010).

S. Lany, A. Zunger, "Dual nature of acceptors in GaN and ZnO: The curious case of the shallow MgGa deep state", Appl. Phys. Lett. 96, 142114 (2010).

PI Piotr Zyla

 O.Kamaev et al, Physics Letters B693 236 (2010)

K. Nakamura et al. (Particle Data Group), J. Phys. G 37, 075021 (2010)