# 2009 Publications Resulting from the Use of NERSC Resources

On their Allocation Year 2010 ERCAP Request Forms Principal Investigators reported 1,407 refereed publications (published or in press) - as well as 239 publications submitted to refereed journals - for the preceding 12 months, based on using, at least in part, NERSC resources.

## A** **

**PI Paul Adams **

H. Liu, K. Sale, B. Holmes, B. A. Simmons and S. Singh, “Understanding the polousef saccharide chain in ionic liquid: A molecular dynamics study”, submitted to J. Phys. Chem. B.

H. Liu, K.Sale, J. H. Pereira, P. D. Adams, B. A. Simmons and R. Sapra, "Computational Modeling Provides New Insight into Role of Accessory IG-like Domain of Cel9A", submitted to Angew. Chem.

**PI Deborah Agarwal **

A Data Centered Collaboration Portal to Support Global Carbon-Flux Analysis, D. Agarwal, M. Humphrey, and N. Beekwilder, Microsoft e-Science Meeting, Indianapolis, IN, December 8-9, 2008.

Synthesis of Hydrologic Data Reveals Rainfall-Runoff Relationships and Examines Watershed-Scale Changes, J. Hunt, D. Agarwal, and C. van Ingen, Computational Methods in Water Resources, Ecoinformatics Session, San Francisco, CA, July 2008.

**PI Mowfak Al-Jassim **

Lixin Zhang, Yanfa Yan, and Su-Huai Wei, Enhancing dopant solubility via epitaxial surfactant growth Phys. Rev B 80, 073305 (2009)

Aron Walsh, Juarez L. F. Da Silva, Yanfa Yan, M. M. Al-Jassim, and Su-Huai Wei Origin of electronic and optical trends in ternary In2O3(ZnO)n transparent conducting oxides (n=1,3,5): Hybrid density functional theory calculations Phys. Rev. B 79, 073105 (2009)

**PI Greg Aldering **

D. Rubin, E.V. Linder, M. Kowalski, G. Aldering, R. Amanullah, K. Barbary, N.V. Connolly, K.S. Dawson, L. Faccioli, V. Fadeyev, G. Goldhaber, A. Goobar, I. Hook, C. Lidman, J. Meyers, S. Nobili, P.E. Nugent, R. Pain, S. Perlmutter, P. Ruiz-Lapuente, A.L. Spadafora, M. Strovink, N. Suzuki, H. Swift, Looking Beyond Lambda with the Union Supernova Compilation, Astrophys. J., 692, 67, 2009.

K.S. Dawson, G. Aldering, R. Amanullah, K. Barbary, L. F. Barrientos, M. Brodwin, N. Connolly, A. Dey, M. Doi, M. Donahue, P. Eisenhardt, E. Ellingson, L. Faccioli, V. Fadeyev, H. K. Fakhouri, A. S. Fruchter, D. G. Gilbank, M. D. Gladders, G. Goldhaber, A. H. Gonzalez, A. Goobar, A. Gude, T. Hattori, H. Hoekstra, X. Huang, Y. Ihara, B. T. Jannuzi, D. Johnston, K. Kashikawa, B. Koester, K. Konishi, M. Kowalski, C. Lidman, E. V. Linder, L. Lubin, J. Meyers, T. Morokuma, F. Munshi, C. Mullis, T. Oda, N. Panagia, S. Perlmutter, M. Postman, T. Pritchard, J. Rhodes, P. Rosati, D. Rubin, D. J. Schlegel, A. Spadafora, S. A. Stanford, V. Stanishev, D. Stern, M. Strovink, N. Suzuki, N. Takanashi, K. Tokita, M. Wagner, L. Wang, N. Yasuda, H. K. C. Yee, An Intensive HST Survey for z>1 Supernovae by Targeting Galaxy Clusters, Astronomical J., in press.

S. Nobili, V. Fadeyev, G. Aldering, R. Amanullah, K. Barbary, M. S. Burns, K. S. Dawson, S. E. Deustua, L. Faccioli, A. S. Fruchter, G. Goldhaber, A. Goobar, I. Hook, D. A. Howell, A. G. Kim, R. A. Knop, C. Lidman, J. Meyers, P. E. Nugent, R. Pain, N. Panagia, S. Perlmutter, D. Rubin, A. L. Spadafora, M. Strovink, N. Suzuki, H. Swift, Constraining dust and color variations of high-z SNe using NICMOS on Hubble Space Telescope, Astrophys. J., 700, 1415, 2009

**PI Yoram Alhassid **

Heavy Deformed Nuclei in the Shell Model Monte Carlo Method, Y. Alhassid, L. Fang and H. Nakada, Phys. Rev. Lett. 101, 082501 (2008).

Mesoscopic Competition of Superconductivity and Ferromagnetism: Conductance Peak Statistics in Metallic Grains, S. Schmidt and Y. Alhassid, Phys. Rev. Lett. 101, 207003 (2008).

**PI Loan Andricioaei **

C.V. Kelly, P. R. Leroueil, E.K. Nett, J. M. Wereszczynski, J.R. Baker, B. G. Orr, M.M. Banaszak Holl and I. Andricioaei, "Poly(amidoamine) Dendrimers on Lipid Bilayers I: Free Energy and Conformation of Binding," J. Phys. Chem. B 112, 9337-9345 (2008).

C.V. Kelly, P. R. Leroueil, B. G. Orr, M.M. Banaszak Holl and I. Andricioaei, "Poly(amidoamine) Dendrimers on Lipid Bilayers II: Effects of Bilayer Phase and Dendrimer Termination," J. Phys. Chem. B 112, 9346-9353 (2008).

E. Dethoff, A. Hansen, C. Musselman, E. Watt, I. Andricioaei, and H.M. Al-Hashimi, "Characterizing Complex Dynamics in the TAR Apical Loop and Motional Correlations with the Bulge by NMR, MD and Mutagenesis," Biophys. J. 95, 3906-3915 (2008).

J. Nummela and I. Andricioaei, "Energy landscape for DNA rotation and sliding through a phage portal," Biophys.J. (Letter) 96, L29-L31 (2008).

A.T. Frank, A.C. Stelzer, H.M. Al-Hashimi and I. Andricioaei, "Constructing RNA dynamical ensembles by combining MD and motionally decoupled NMR RDCs: New insights into RNA dynamics and adaptive ligand recognition," Nucleic Acids Res. 37, 3670-3679 (2009).

A.C. Stelzer, A.T. Frank, M. Bailor, H.M. Al-Hashimi,and I. Andricioaei, "Constructing Atomic- Resolution RNA Structural Ensembles Using MD and Motionally Decoupled NMR RDCs," Methods, (2009, in press).

C. Musselman, Q. Zhang, H.M. Al-Hashimi and I. Andricioaei, "A referencing strategy for the direct comparison of NMR and MD motional parameters in RNA," J. Phys. Chem. B (2009, accepted)

J. Wereszczynski and I. Andricioaei, "Conformational and Solvent Entropy Contributions to Thermoswitching in Nucleic Acid-Based Nanothermometers" J. Phys. Chem. B (2009, submitted)

**PI Marco Arienti **

"Towards an Efficient, High-Fidelity Methodology for Liquid Jet Atomization Computations," by X. Li , M. Arienti , M. Soteriou and M. Sussman, AIAA 2010-92407, submitted.

**PI Jonathan Arons **

Giannios, D. & Spitkovsky, A. 2009, "Signatures of a Thermal Component in Shock-Accelerated Electrons in GRBs," MNRAS, submitted, arxiv:0905.1970

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", submitted to ApJL, arXiv:0908.3193

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

**PI Alan Aspuru-Guzik **

Roel S. Sanchez-Carrera, Sule Atahan-Evrenk, Joshua Schrier, and Alan Aspuru-Guzik Theoretical Characterization of the Air-stable, High-performance Dinaphto[2,3-b]thieno[3,2-b]-thiophene Organic Semiconductor. In preparation. To be submitted to Advanced Materials.

A. V. Subhas and J. Schrier, "Rapid estimation of organic thin-film transistor carrier type using density functional theory" (in preparation)

J. McClain and J. Schrier, "Multiple exciton generation in graphene nanostructures" (in preparation)

**PI Tom Autrey **

Experimental and computational studies on collective hydrogen dynamics in ammonia borane: Incoherent inelastic neutron scattering, Shawn M. Kathmann,Vencislav Parvanov, Gregory K. Schenter, Ashley C. Stowe, Luc L. Daemen, Monika Hartl, John Linehan, Nancy J. Hess, Abhi Karkamkar, and Tom Autrey THE JOURNAL OF CHEMICAL PHYSICS 130, 024507 (2009)

Thermodynamic and Structural Investigations of Ammonium Borohydride, a Solid with a Highest Content of Thermodynamically and Kinetically Accessible Hydrogen, Abhijeet Karkamkar, Shawn M. Kathmann, Gregory K. Schenter, David J. Heldebrant, Nancy Hess, Maciej Gutowski, and Tom Autrey, Chem. Mater. 2009, 21, 4356-4358

## B

**PI Dmitri Babikov **

Y. Gu and D. Babikov, "On the role of vibrational anharmonicities in a two-qubit system", J. Chem. Phys. 131, 034306 (11 pages), 2009.

L. Jiang and D. Babikov, "A reduced dimensionality model of ozone: Semi-classical treatment of van der Waals states", Chem. Phys. Lett. 474, pp. 273-277, 2009.

**PI Scott Baden **

Pietro Cicotti and Xiaoye S. Li and Scott B. Baden. Performance Modeling Tools for Parallel Sparse Linear Algebra Computations. Proceedings of the International Conference on Parallel Computing (ParCo), September 2009, Lyon, France

**PI Zhaojun Bai **

C. N. Varney, C.-R. Lee, Z. Bai, S. Chiesa, M. Jarrell and R. T. Scalettar, Quantum Monte Carlo study of the two-dimensional fermion Hubbard model. Phy. Rev. B, 80, 975116, 2009

I. Yamazaki, Z. Bai, W. Chen and R. Scalettar, A high-quality preconditioning technique for multi-length-scale symmetric positive definite linear systems. Numer. Math. Theor. Meth. Appl. Vol.2, No.4, pp.469-484, 2009

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 . submitted to Phy. Rev. E., 2009

**PI David Bailey **

David H. Bailey, Jonathan M. Borwein and Richard E. Crandall, "Advances in the Theory of Box Integrals," Mathematics of Computation, to appear, Jun 2009; LBNL-2161E.

David H. Bailey and Jonathan M. Borwein, "Experimental Computation with Oscillatory Integrals," manuscript, May 2009; LBNL-2158E.

David H. Bailey, "Can An Evolutionary Process Generate English Text?", Biological Theory, to appear, Oct 2009; LBNL-2159E.

Catherine Mills Olschanowsky, Mustafa M. Tikir, Laura Carrington, Allan Snavely, "PSnAP: Accurate Synthetic Address Streams Through Memory Profiles", 22nd International Workshop on Languages and Compilers for Parallel Computing, University of Delaware, Oct 2009.

Lin-Wang Wang, Byounghak Lee, Hongzhang Shan, Zhengji Zhao, Juan Meza, Erich Strohmaier and David Bailey, "Linearly Scaling 3D Fragment Method for Large-Scale Electronic Structure Calculations", SC08, Austin, TX, USA, Nov 2008. Recipient of the 2008 ACM Gordon Bell Prize in the special category for "algorithmic innovation".

S. Williams, J. Carter, L. Oliker, J. Shalf, K. Yelick, "Resource-Efficient, Hierarchical Auto-Tuning of a Hybrid Lattice Boltzmann Computation on the Cray XT4", 51st Cray User Group Conference (CUG2009), Atlanta, GA, May 2009.

Xingfu Wu, Benchun Duan and Valerie Taylor, "An OpenMP Approach to Modeling Dynamic Earthquake Rupture Along Geometrically Complex Faults on CMP Systems", ICPP2009 SMECS Workshop, Sep 2009, Vienna, Austria.

Xingfu Wu, Valerie Taylor, Charles Lively and Sameh Sharkawi, "Performance Analysis and Optimization of Parallel Scientific Applications on CMP Clusters", Scalable Computing: Practice and Experience, vol. 10, no. 1, 2009.

Xingfu Wu and Valerie Taylor, "Using Processor Partitioning to Evaluate the Performance of MPI, OpenMP and Hybrid Parallel Applications on Dual- and Quad-core Cray XT4 Systems", 51st Cray User Group Conference (CUG2009), Atlanta, GA, May 2009.

**PI V. Balaji **

M. Zhao and I. M. Held and S-J Lin and G. A. Vecchi, "Simulations of global hurricane climatology, interannual variability, and response to global warming using a 50km resolution GCM", Journal of climate, 2009, volume 22 number 24, 6653-6678

M. Zhao and I. M. Held G. A. Vecchi, "Retrospective forecasts of the hurricane season using a global atmospheric model assuming persistence of SST anomalies", submitted to Monthly Weather Review.

**PI Krishnan Balasubramanian **

Z. Cao, K. Balasubramanian, M. Calvert and H. Nitsche, "Solvation Effects on Isomeric Preferences of Curium (III) Complexes with Multidentate Acid Ligands: CmH2PPA2+ and CmHPPA+ Complexes" Inorganic Chemistry, ic-2009-01054h.R2, 2009, in press

M. Benavides and K. Balasubramanian, "Structural Insights into the Toxicity of Uranyl: Interaction with Human Serum Protein Apotransferrin-Structure and Spectra",Chemical Research in Toxicology, 2009, in press

Z. Cao, K. Balasubramanian,"Spectroscopic Properties and Potential Energy Surfaces for Curium Hydrides: CmH2, CmH2+, CmH and CmH+.", Journal of Physical Chemistry, 2009, in press

Z. Cao, K. Balasubramanian,, Theoretical studies of UO2(OH)(H2O)n+, UO2(OH)2(H2O)n, NpO2(OH)(H2O)n, and PuO2(OH)(H2O)n+ (n ) complexes in aqueous solution", Journal of Chemical Physics, in press, (2009)

T. Simeon, K. Balasubramanian, J. Leszynski, " New Insights Into the Chemical and Electronic Properties of C69M [M = In-, Tl-, Sb+, Bi+] Species", J. Phys. Chem. A, 2008, 112 (47), pp 12179 - 12186

Balasubramanian, K.; Cao, Z., " Geometries and energy separations of electronic states of In3N, InN3, and their ions", Journal of Theoretical and Computational Chemistry, Journal of Theoretical and Computational Chemistry, Vol. 7, No. 4 (2008) 751 - 765

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 January 2009 , pages 797 - 807 (2009)

**PI Perla Balbuena **

Pussana Hirunsit and Perla B. Balbuena, "Effects of water and electric field on atomic oxygen adsorption on PtCo alloys," Surf. Sci., in press.

Julibeth M. Martinez De La Hoz, Rafael Callejas-Tovar and Perla B. Balbuena, "Size effect on the stability of Cu-Ag nanoalloys," Mol. Sim., 35, 785-794, (2009).

Gustavo Ramirez-Caballero and Perla B. Balbuena, "Effect of confinement on oxygen adsorbed between Pt(111) surfaces," J. Phys. Chem. C, 113, 7851-7856, (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).

Yuguang Ma and Perla B. Balbuena, "Kinetic model of surface segregation in Pt-based alloys," J. Chem. Theory and Comp., 4, 1991-1995, (2008).

Rafael Callejas-Tovar and Perla B. Balbuena, "Oxygen adsorption and surface segregation in (211) surfaces of Pt(shell)/M(core) and Pt3M (M=Co, Ir) alloys," Surf. Science, 602, 3531-3539, (2008).

Yuguang Ma and P. B. Balbuena, "Surface properties and dissolution trends of Pt3M alloys in the presence of adsorbates," J. Phys. Chem. C, 112, 14520-14528, (2008).

G. E. Ramirez-Caballero and P. B. Balbuena, "Surface segregation of core atoms in core-shell structures," Chem. Phys. Lett., 456, 64-67, (2008).

F. Tarazona-Vasquez and P. B. Balbuena, "Pt(II) uptake by dendrimer outer pockets: 2. Solvent-mediated complexation," J. Phys. Chem. B., 112, 4182-4193, (2008).

F. Tarazona-Vasquez and P. B. Balbuena, "Pt(II) uptake by dendrimer outer pockets: 1. Solventless ligand exchange reaction," J. Phys. Chem. B., 112, 4172-4181, (2008).

Z. Gu and P. B. Balbuena, "Atomic oxygen absorption into Pt-based alloy subsurfaces," J. Phys. Chem. C, 112, 5057-5065, (2008).

Y. Ma and P. B. Balbuena, "Pt-surface segregation in bimetallic Pt3M alloys: A density functional theory study," Surf. Sci., 602, 107-113, (2008).

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., in press.

Gustavo E. Ramirez-Caballero, Juan C. Burgos, and Perla B. Balbuena, "Growth of carbon structures on stepped (211) cobalt surfaces," J. Phys. Chem. C,113, 15658-15666, (2009). Highlighted in journal cover.

Diego A. Gomez-Gualdron and Perla B. Balbuena, "Growth of chiral single-walled carbon nanotubes in the presence of a cobalt cluster," Nanotechnology, 20, 215601, (2009).

Diego A. Gomez-Gualdron 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).

Diego A. Gomez-Gualdron and Perla B. Balbuena, "The role of cap chirality on the mechanism of growth of single-wall carbon nanotubes," Nanotechnology, 19, 485604 (2008). Highlighted article: http://nanotechweb.org/cws/article/lab/36963

Jin Zhao and P. B. Balbuena, "Effect of nanotube cap on the aromaticity of single-wall carbon nanotubes," J. Phys. Chem. C, 112, 13175-13180, (2008).

J. Zhao and P. B. Balbuena, "Effect of nanotube length on the aromaticity of single-wall carbon nanotubes," J. Phys. Chem. C, 112, 3482-3488, (2008).

**PI Arun Bansil **

D. Hsieh, Y. Xia, D. Qian, L. Wray, J. H. Dil, F. Meier, J. Osterwalder, L. Patthey, J. G. Checkelsky, N. P. Ong, A. V. Fedorov, H. Lin, A. Bansil, D. Grauer, Y. S. Hor, R. J. Cava and M. Z. Hasan, (A tunable topological insulator in the spin helical Dirac transport regime), Nature 460, 1101 (2009).

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

J. Nieminen, H. Lin, R. S. Markiewicz, and A. Bansil, (Origin of the Electron-Hole Asymmetry in the Scanning Tunneling Spectrum of the High-Temperature Bi[sub 2]Sr[sub 2]CaCu[sub 2]O[sub 8 + delta] Superconductor), Physical Review Letters 102, 037001 (2009).

B. Barbiellini, A. Koizumi, P. E. Mijnarends, W. Al-Sawai, Hsin Lin, T. Nagao, K. Hirota, M. Itou, Y. Sakurai, and A. Bansil, (Role of Oxygen Electrons in the Metal-Insulator Transition in the Magnetoresistive Oxide La[sub 2-2x]Sr[sub 1 + 2x]Mn[sub 2][bold O][sub 7] Probed by Compton Scattering), Physical Review Letters 102, 206402 (2009).

V. Arpiainen, A. Bansil, and M. Lindroos, (Circular Dichroism in the Angle-Resolved Photoemission Spectrum of the High-Temperature Bi[sub 2]Sr[sub 2]CaCu[sub 2][bold O][sub 8 + delta] Superconductor: Can These Measurements Be Interpreted as Evidence for Time-Reversal Symmetry Breaking?), Physical Review Letters 103, 067005 (2009).

B. Barbiellini and T. Jarlborg, (Importance of Local Band Effects for Ferromagnetism in Hole-Doped La[sub 2]CuO[sub 4] Cuprate Superconductors), Physical Review Letters 101, 157002 (2008).

S. Basak, T. Das, H. Lin, J. Nieminen, M. Lindroos, R. S. Markiewicz, and A. Bansil, (Origin of the high-energy kink or the waterfall effect in the photoemission spectrum of the ${\rm Bi_2Sr_2CaCu_2O_8}$ high-temperature superconductor), Submitted to Physical Review Letters ArXiv e-prints 0904, 1749 (2009)

S. W. H. Eijt, P. E. Mijnarends, L. C. van Schaarenburg, A. J. Houtepen, D. Vanmaekelbergh, B. Barbiellini, and A. Bansil, (Electronic coupling of colloidal CdSe nanocrystals monitored by thin-film positron-electron momentum density methods), Applied Physics Letters 94, 091908 (2009).

D. Nissenbaum, L. Spanu, C. Attaccalite, B. Barbiellini, and A. Bansil, (Resonating-valence-bond ground state of lithium nanoclusters), Physical Review B 79, 035416 (2009).

B. Barbiellini, C. Bellin, G. Loupias, T. Buslaps, and A. Shukla, (How the hydrogen bond in NH[sub 4]F is revealed with Compton scattering), Physical Review B 79, 155115 (2009).

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

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 LaO1-xF(x)FeAs), Journal of Superconductivity and Novel Magnetism 22, 569 (2009).

**PI Michael Barad **

Barad, M.F. and O.B. Fringer, Simulations of shear instabilities in interfacial internal gravity waves, In press at the Journal of Fluid Mechanics.

Barad, M.F., Colella, P. and Schladow, S.G., An adaptive cut-cell method for environmental fluid mechanics, International Journal for Numerical Methods in Fluids, 2009, Vol. 60, pp 473-514, doi 10.1002/fld.1893.

**PI Edward Baron **

S. Knop, P. Hauschildt, E. Baron, A New Formal Solution of the Radiative Transfer in Arbitrary Velocity Fields, A&A, (2009), 496, 295--298.

P. H. Hauschildt, E. Baron, A 3D Radiative Transfer Framework: IV. Spherical & Cylindrical Coordinate Systems, A&A, (2009) 498, 981--985.

E. Baron, P. H. Hauschildt, B. Chen, A 3D Radiative Transfer Framework: V. Homologous Flows, A&A, (2009) 498, 987--992.

D. Jack, P. H. Hauschildt, E. Baron, Time-dependent Radiative Transfer with PHOENIX A&A, (2009), 502, 1043--1049.

Soma De, E. Baron, P. H. Hauschildt, On the Hydrogen Recombination Time in Type II Supernova Atmospheres, MNRAS, (2009), submitted.

S. Knop, P. H. Hauschildt, E. Baron, Comoving frame radiative transfer in arbitrary velocity fields II. Large-scale applications., A&A, (2009) 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, currently in review.

D. Batchelor, G. Abla, E. D'Azevedo, G. Bateman, D. E. Bernholdt, L. Berry, P. Bonoli, R. Bramley, J. Breslau, M. Chance, J. Chen, M. Choi, W. Elwasif, S. Foley, G. Fu, R. Harvey, E. Jaeger, S. Jardin, T. Jenkins, D. Keyes, S. Klasky, S. Kruger, L. Ku, V. Lynch, D. McCune, J. Ramos, D. Schissel, D. Schnack, and J. Wright, "Advances in simulation of wave interactions with extended MHD phenomena", Journal of Physics: Conference Series 180 (SciDAC 2009), 012054 (2009).

D. L. Green, E. F. Jaeger, L. A. Berry, and the RF-SciDAC Team, Journal of Physics Conference Series 180, 012058 (2009), "Exploration of finite ion orbit effects in the ion cyclotron range of frequencies"

**PI Victor Batista **

J. Am. Chem. Soc. 130:14329-14338, 2008 Acetylacetonate anchors for robust functionalization of TiO2 nanoparticles with Mn(II)-terpyridine complexes, William R. McNamara,Robert C. Snoeberger III, Gonghu Li, James M. Schleicher, Clyde W. Cady, Macarena Poyatos, Charles A. Schmuttenmaer, Robert H. Crabtree, Gary W. Brudvig and Victor S. Batista.

Proc. SPIE 7034, 70340R, 2008 Characterization of Siloxane Adsorbates Covalently Attached to TiO2, Nobuhito Iguchi, Clyde Cady, Robert C. Snoeberger III, Bryan M. Hunter, Eduardo M. Sproviero, Charles A. Schmuttenmaer, Robert H. Crabtree, Gary W. Brudvig and Victor S. Batista.

Energy & Environ. Sci. 2:230-238 2009 Deposition of an Oxomanganese Water Oxidation Catalyst on TiO2 Nanoparticles: Computational Modeling, Assembly and Characterization, Gonghu Li, Eduardo M. Sproviero, Robert C. Snoeberger III, Nobuhito Iguchi, James D. Blakemore, Robert H. Crabtree, Gary W. Brudvig and Victor S. Batista.

Ann. Rev. Phys. Chem. 60:293-320, 2009 Coherent Control of Quantum Dynamics with Sequences of Unitary Phase-Kick Pulses, Luis G.C. Rego, Lea F. Santos and Victor S. Batista.

Israel J. Chem. 49: 187-197, 2009 Quantum Dynamics of the Excited State Intramolecular Proton Transfer in 2-(2'-hydroxyphenyl)-benzothiazole, by Justin Kim, Yinghua Wu, Jean-Luc Bredas and Victor S. Batista.

Energy & Environ. Sci. (in press) 2009 Hydroxamate Anchors for Functionalization of Semiconductor Surfaces, 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. Am. Chem. Soc. (submitted) 2009 Single molecule electron transfer dynamics in interfacial donor-bridge-nanoparticle acceptor complexes, Shengye Jin, Robert C. Snoeberger III, Abey Issac, Victor S. Batista and Tianquan Lian.

J. Phys. Chem. A (in press) 2009 Interfacial electron transfer in TiO2 surfaces sensitized with Ru(II)-polypyridine complexes, Elena Jakubikova, Robert C. Snoeberger III, Victor S. Batista and Enrique R. Batista.

Phil. Trans. R. Soc. London B 363:1149-1156, 2008 QM/MM computational studies of substrate water binding to the oxygen evolving complex of Photosystem II, by Eduardo M. Sproviero, Katherine Shinopoulos, Jose A. Gascon, James P. McEvoy, Gary W. Brudvig and Victor S. Batista.

Coord. Chem. Rev. 252:395-415, 2008 Computational studies of the O2-evolving complex of photosystem II and biomimetic oxomanganese complexes, by Eduardo M. Sproviero, Jose A. Gascon, James P. McEvoy, Gary W. Brudvig and Victor S. Batista.

J. Am. Chem. Soc. 130: 3428-3442, 2008 QM/MM Study of the Catalytic Cycle of Water Splitting in Photosystem II, by Eduardo M. Sproviero, Jose A. Gascon, James P. McEvoy, Gary W. Brudvig and Victor S. Batista.

Photosynth. Res. 97:91-114, 2008 Computational insights into the O2-evolving complex of photosystem II, by Eduardo M. Sproviero, James P. McEvoy, Jose A. Gascon, Gary W. Brudvig and Victor S. Batista.

J. Am. Chem. Soc., 130: 6728-6730, 2008 supporting information A Model of the Oxygen Evolving Center of Photosystem II Predicted by Structural Refinement Based on EXAFS Simulations, by Eduardo M. Sproviero, James P. McEvoy, Jose A. Gascon, Gary W. Brudvig and Victor S. Batista.

Photosynth. Res. (in press) 2009 The MoD-QM/MM Methodology for Structural Refinement of Photosystem II and Other Biological Macromolecules, by Eduardo M. Sproviero, Michael B. Newcomer, Jose A. Gascon, Enrique R. Batista, Gary W. Brudvig and Victor S. Batista.

**PI Pat Behling **

Lee D., Z. Liu and Y. Liu, 2008: Beyond thermo interaction between ocean and atmosphere: on the extratropical climate variability due to wind-induced SST. J. Climate, 21, 2001-2018

Notaro, M., Y. Wang, Z. Liu, R. Gallimore and S. Levis, 2008: Combined statistical and dynamical assessment of the simulated negative vegetation feedback on North African annual precipitation during the mid-Holocene. Global Change Biology, 14, 347-368, doi:10.111/j.1365-2486.2007.01495.x.

Notaro M. and Z. Liu, 2008: Joint statistical and dynamical assessment of vegetation feedbacks on climate over boreal forest. Climate Dynamics, 31, 691-712.

Zhong Y., Z. Liu and R. Jacob, 2008: The origin of Pacific Decadal Variability in the NCAR-CCSM3. J. Climate, 21, 114-133.

Zhong Y. F. and Z. Liu, 2008: A joint statistical and dynamical assessment of atmospheric response to North Pacific oceanic variability in CCSM3. J. Clim., 21, 6044-6051

Zhong Y. F. and Z. Liu, 2009: On the Mechanism of Pacific Multidecadal Climate Variability in CCSM3: The Role of Subpolar North Pacific Ocean. J. Phys. Oceanogr., in press

**PI John Bell **

M. M. Scase, A. J. Aspden, and C. P. Caulfield, "The effect of sudden source buoyancy flux increases on turbulent plumes", Journal of Fluid Mechanics, 635 pp. 137-169, Sept 2009.

M. Day, J. Bell, P.-T. Bremer, V. Pascucci, V. Beckner, M. Lijewski, "Turbulence effects on cellular burning structures in lean premixed hydrogen flames", Combustion and Flame 156 1035-1045 (2009).

G. S. H. Pau, A. S. Almgren, J. B. Bell, and M. J. Lijewski, "A Parallel Second-Order Adaptive Mesh Algorithm for Incompressible Flow in Porous Media", Phil. Trans. R. Soc. A, 2009.

M. Zingale, A. S. Almgren, J. B. Bell, A. Nonaka, and S. E. Woosley, "Low Mach Number Modeling of Type Ia Supernovae. IV. White Dwarf Convection", Astrophysical Journal, 2009.

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,'' submitted for publication.

S.E. Woosley, A.S. Almgren, A.J. Aspden, J.B. Bell, D. Kasen, A.R. Kerstein, H. Ma, A. Nonaka and M. Zingale, "Type Ia Supernovae: Advances in Large Scale Simulation ", SciDAC 2009, J. of Physics: Conference Series, 180, July 2009.

M. Day, J. Bell, P.-T. Bremer, V. Pascucci, V. Beckner, M. Lijewski, "Turbulence effects on cellular burning structures in lean premixed hydrogen flames", Combustion and Flame156 1035-1045 (2009).

M.S.Day, J.B. Bell, R.K. Cheng, S. Tachibana, V.E. Beckner and M.J. Lijewski, "Cellular burning in lean premixed turbulent hydrogen-air flames: coupling experimental and computational analysis at the laboratory scale", SciDAC 2009, J. of Physics: Conference Series, San Diego, California, July 2009.

**PI Roy Benedek **

Phase stability of cation-doped LiMnO2 within the GGA+U approximationi; Shukla, NN; Shukla, S; Prasad, R, et al.; MODELLING AND SIMULATION IN MATERIALS SCIENCE AND ENGINEERING, Volume: 16, Issue: 5 (Article Number: 055008, Published: 2008)

Free energy for protonation reaction in lithium-ion battery cathode materials; Benedek, R; Thackeray, MM; van de Walle, A; CHEMISTRY OF MATERIALS, Volume: 20, Issue: 17 (Pages: 5485-5490, Published: 2008)

Free energies for acid attack reactions of lithium cobaltate; Benedek, R; van de Walle, A; JOURNAL OF THE ELECTROCHEMICAL SOCIETY, Volume: 155, Issue: 10 (Pages: A711-A715, Published: 2008)

Pourbaix-like phase diagram for lithium manganese spinels in acid; Benedek, R; Thackeray, MM; van de Walle, A; Journal of Materials Chemistry (submitted July, 2009)

**PI Bernd Berg **

B.A. Berg, Fortran MPI Checkerboard Code for SU(3) Lattice Gauge Theory I, arxiv:0904.0642, submitted to Comp. Phys. Commun.

B.A. Berg and Hao Wu, Fortran MPI Checkerboard Code for SU(3) Lattice Gauge Theory II, arxiv:0904.1179, submitted to Comp. Phys. Commun.

B.A. Berg, A. Bazavov, and Hao Wu, Deconfining Phase Transition on a Double Layered Torus, arxiv:0909.3077, submitted to Proc. Science.

**PI Dan Bergmann **

Reidmiller, D. R., A. M. Fiore, D. A. Jaffe, D. Bergmann, K. Cuvelier, F. J. Dentener, B. N. Duncan, G. Folberth, M. Gauss, S. Gong, P. Hess, J. E. Jonson, T. Keating, A. Lupu, E. Marmer, R. Park, M. G. Schultz, D. T. Shindell, S. Szopa, M. G. Vivanco, O. Wild, and A. Zuber., 2009 The influence of foreign vs. North American emissions on surface ozone in the U.S. S Atmospheric Chemistry and Physics, V9, 5027-5042

Casper-Anenberg,S., J.J. West, A.M. Fiore, D.A. Jaffe, M.J. Prather, D. Bergmann, C. Cuvelier, F.J. Dentener, B.N. Duncan, M. Gauss, P. Hess, J.E. Jonson, A. Lupu, I.A. MacKenzie, R.J. Park, M. Sanderson, M. Schultz, D.T. Shindell, S. Szopa, M.G. Vivanco, O. Wild, G. Zeng, 2009: Intercontinental impacts of ozone pollution on human mortality. Environmental Science and Technology. 2009, 43 (17), 6482-6487

**PI Zvi Bern **

C.F. Berger et al., "Precise Predictions for W+3 Jet Production at Hadron Colliders", Phys. Rev. Lett. 102: 222001,2009.

C.F. Berger, et al., "Next-to-Leading Order QCD Predictions for W+3-Jet Distributions at Hadron Colliders", e-Print: arXiv:0907.1984 [hep-ph] (to appear in Physical Review D)

**PI Wes Bethel **

Shoaib Kamil, Cy Chan, Sam Williams, Leonid Oliker, John Shalf, Mark Howison, E. Wes Bethel, Prabhat. "A Generalized Framework for Auto-tuning Stencil Computations." In CUG 2009, May 4-7, 2009, Atlanta GA, USA. Best Paper Award winner. (LBNL-2078E).

E. Wes Bethel. "High Performance, Three-dimensional Bilateral Filtering." Lawrence Berkeley National Laboratory, Tech Report LBNL-1601E, 2009.

Extreme Scaling of Production Visualization Software on Diverse Architectures", Childs, Pugmire, Ahern, Whitlock, Howison, Prabhat, Weber, and Bethel, submitted to a special issue of Computer Graphics and Applications on large data visualization

Dave Pugmire, Hank Childs, Christoph Garth, Sean Ahern, Gunther Weber. "Scalable Computation of Streamlines on Very Large Datasets" In Proceedings of Supercomputing 2009

G. Weber and P.-T. Bremer and J. Bell and M. Day and V. Pascucci, Feature Tracking Using {R}eeb graphs, Mathematics and Visualization, Springer, to appear 2010.

M. Day and J. Bell and P.-T. Bremer and V. Pascucci and V. Beckner and M. Lijewski, Turbulence effects on cellular burning structures in lean premixed hydrogen flames, Combustion and Flame, 156,pp. 1035-1045.

P.-T. Bremer and G. Weber and V. Pascucci and M. Day and J. Bell, Analyzing and Tracking Burning Structures in Lean Premixed Hydrogen Flames, IEEE Transactions on Visualization and Computer Graphics, 2009, to appear.

P.-T. Bremer and G. H. Weber and J. Tierny and V. Pascucci and M. Day and J. B. Bell, A Topological Framework for the Interactive Exploration of Large Scale Turbulent Combustion, Proc. {IEEE} International Conference on e-Science, 2009, to appear.

**PI Amitava Bhattacharjee **

A. Bhattacharjee, Yi-Min Huang, H. Yang, B. Rogers "Fast Reconnection in High-Lundquist-Number Plasmas Due to Secondary Tearing Instabilities", submitted to Phys. Plasmas. Preprint available in arXiv:0906.5599.

Rasera, Y., and Chandran, B., "Numerical Simulations of Buoyancy Instabilities in Galaxy Cluster Plasmas with Cosmic Rays and Anisotropic Thermal Conduction," The Astrophysical Journal, Volume 685, Issue 1, pp. 105-117 (2008)

P. Zhu, J. Raeder, K. Germaschewski, and C. C. Hegna Initiation of ballooning instability in the near-Earth plasma sheet prior to the 23 March 2007 THEMIS substorm expansion onset, Ann. Geophys., 27, 1129-1138, 2009

P. Zhu, C.C. Hegna, C.R. Sovinec, A. Bhattacharjee, and K. Germaschewski, Intermediate nonlinear regimes of line-tied g mode and ballooning instability, Nucl. Fusion 49, 095009 (2009).

**PI Erik Boman **

Advances in Parallel Partitioning, Load Balancing, and Matrix Ordering, E.G. Boman, U.V. Catalyurek, C. Chevalier, K.D. Devine, I. Safro, M.M. Wolf, J. of Physics: Conference Series, vol. 180 (SciDAC09 Conference, San Diego, June 2009).

**PI Paul Bonoli **

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

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

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

"Exploration of finite ion orbit effects in the ion cyclotron range of frequencies", D. L. Green, E. F. Jaeger, L. A. Berry, and the RF-SciDAC Team, Journal of Physics Conference Series 180, 012058 (2009).

"Advances in simulation of wave interactions with extended MHD phenomena", D. Batchelor, G. Abla, E. D'Azevedo, G. Bateman, D. E. Bernholdt, L. Berry, P. Bonoli, R. Bramley, J. Breslau, M. Chance, J. Chen, M. Choi, W. Elwasif, S. Foley, G. Fu, R. Harvey, E. Jaeger, S. Jardin, T. Jenkins, D. Keyes, S. Klasky, S. Kruger, L. Ku, V. Lynch, D. McCune, J. Ramos, D. Schissel, D. Schnack and J. Wright, Journal of Physics Conference Series 180, 012054 (2009).

**PI Julian Borrill **

"MADmap: A Massively Parallel Maximum-Likelihood Cosmic Microwave Background Map-Maker", C.M.Cantalupo et al, submitted to Astrophysical Journal Supplement. http://arxiv.org/abs/0906.1775

"Residual noise covariance for Planck low-resolution data analysis", R. Keskitalo et al, submitted to Astronomy and Astrophysics. http://arxiv.org/abs/0906.0175

"PReBeaM for Planck: A Polarized Regularized Beam Deconvolution Map-Making Method", Charmaine Armitage-Caplan et al, submitted to Astrophysical Journal Supplement. http://arxiv.org/abs/0807.4179

"Sub-Degree Sunyaev-Zel'dovich Signal from Multi-Frequency BOOMERanG observations", M. Veneziani et al, submitted to Astrophysical Journal Letters. http://arxiv.org/abs/0904.4313

"BOOMERanG Constraints on Primordial Non-Gaussianity from Analytical Minkowski Functionals", P. Natoli et al, submitted to Monthly Notices of the Royal Astronomical Society. http://arxiv.org/abs/0905.4301

"Properties of Galactic cirrus clouds observed by BOOMERanG", M. Veneziani et al, submitted to Astrophysical Journal. http://arxiv.org/abs/0907.5012

**PI Joel Bowman **

A. R. Sharma, B. J. Braams, S. Carter, B. C. Shepler, and J. M. Bowman: Full-dimensional ab initio potential energy surface and vibrational configuration interaction calculations for vinyl. J. Chem. Phys. 130, #174301, 2009.

C. Chen, B. C. Shepler, B. J. Braams, and J. M. Bowman: Quasiclassical trajectory calculations of the HO2 + NO reaction on a global potential energy surface. Phys. Chem. Chem. Phys. 11, 4722, 2009

R. Warmbier, R. Schneider, A. R. Sharma, B .J. Braams, J. M. Bowman, and P. H. Hauschildt: Ab initio modeling of molecular IR spectra of astrophysical interest: Application to CH4. Astron. Astrophys. 495, p655, 2009.

Y. Wang, B. C. Shepler, B. J. Braams and J. M. Bowman: Full-dimensional, ab initio potential energy and dipole moment surfaces for water. J. Chem. Phys., in press.

A. R. Sharma, B. J. Braams, S. Carter, B. C. Shepler, and J. M. Bowman: Full-dimensional ab initio potential energy surface and vibrational configuration interaction calculations for vinyl. J. Chem. Phys. 130, #174301, 2009.

C. Chen, B. C. Shepler, B. J. Braams, and J. M. Bowman: Quasiclassical trajectory calculations of the HO2 + NO reaction on a global potential energy surface. Phys. Chem. Chem. Phys. 11, 4722, 2009

R. Warmbier, R. Schneider, A. R. Sharma, B .J. Braams, J. M. Bowman, and P. H. Hauschildt: Ab initio modeling of molecular IR spectra of astrophysical interest: Application to CH4. Astron. Astrophys. 495, p655, 2009.

G. Czako, B. C. Shepler, B. J. Braams, and J. M. Bowman: Accurate ab initio potential energy surface, dynamics , and thermochemistry of the F + CH4 HF + CH3 reaction. J. Chem. Phys. 130, #084301, 2009.

B. C. Shepler, B. J. Braams, and J. M. Bowman: "Roaming" dynamics in CH3CHO photodissociation revealed on a global potential energy surface. J. Phys. Chem. A 112, p9344, 2008.

**PI Marcia Branstetter **

Ganguly, Auroop R., K. Steinhaeuser, D.J. Erickson III, M. Branstetter, E.S. Parish, N. Singh, J.B. Drake, and L. Buja, "Higher trends but larger uncertainty and geographic variability in 21st century temperature and heat waves," Proceedings of the National Academy of Sciences, vol. 106, no. 37, September 15, 2009.

**PI Dylan Brennan **

R. Takahashi, D.P. Brennan, and C.C. Kim, "Kinetic Effects of Energetic Particles on Resistive MHD Stability", Phys. Rev. Lett 102, 135001 (2009).

R. Takahashi, D.P. Brennan, and C.C. Kim, "A detailed study of kinetic effects of energetic particles on resistive MHD linear stability," Nucl. Fusion 49, 065032 (2009).

**PI Linda Broadbelt **

Konstantinov, I. and Broadbelt, L.J. "Reaction Free Energies in Organic Solvents: Comparing Different Quantum Mechanical Methods", submitted to Molecular Simulation, 2009.

**PI David Bruhwiler **

A.V. Sobol, D.L. Bruhwiler, G.I. Bell, A. Fedotov and V. Litvinenko, "Numerical calculation of dynamical friction in future electron cooling systems, including magnetic field perturbations and finite time effects," submitted to New J. Physics.

## C

**PI Philip Cameron-Smith **

"TransCom model simulations of hourly atmospheric CO2: Analysis of synoptic-scale variations for the period 2002-2003", P. K. Patra, and 37 other authors, including P. J. Cameron-Smith and D. J. Bergmann, Global Biogeo. Cycles, 22, GB4013, doi:10.1029/2007GB003081, 2008.

**PI Roberto Car**

Xifan Wu, Annabella Selloni, and Roberto Car, Order N implementation of exact exchange in extended insulating system," Physical Review B 79, 085102 (2009)

Xifan Wu, Eric J. Walter, Andrew M. Rappe, Roberto Car and Annabella Selloni, Hybrid density functional calculations of the band gap of GaxIn1-xN," Physical Review B 80, 115201 (2009).

Wei Chen, Xifan Wu, Roberto Car, "X-ray absorption signatures of the molecular environment in water and ice", submitted to Physical Review Lettes, http://arxiv.org/abs/0909.3752v1

**PI Joseph Carlson **

A. M. Shirokov, A. I. Mazur, J. P. Vary and E. A. Mazur, "Inverse scattering J- matrix approach to nucleon-nucleus scattering and the shell model," Phys. Rev. C. 79, 014610 (2009), arXiv 0806.4018.

P. Maris, J.P. Vary and A. M. Shirokov, "Ab Initio no-core full configuration calculations of light nuclei," Phys. Rev. C. 79, 014308(2009), DOI: 10.1103/Phys.RevC.79.014308, arXiv 0808.3420.

A. M. Shirokov, A. I. Mazur, E. A. Mazur, and J. P. Vary, "No-Core Shell Model and Continuum Spectrum States of Light Nuclei," Applied Mathematics and Information Science, 2008, to appear.

J.C. Pei, W. Nazarewicz, and M. Stoitsov; "Coordinate-Space Hartree-Fock-Bogoliubov Description of Superfluid Fermi Systems", accepted by Eur. Phys. J. A (2009); arXiv:0901.0545.

J.C. Pei, W. Nazarewicz, J.A. Sheikh and A.K. Kerman, "Fission barriers of compound superheavy nuclei", Phys. Rev. Lett. 102, 192501 (2009).

G. Bertsch, J. Dobaczewski, W. Nazarewicz, and J. Pei, "Hartree-Fock-Bogoliubov Theory of Polarized Fermi Systems", Phys. Rev. A 79, 043602 (2009).

W. Satula, J. Dobaczewski, W. Nazarewicz, and M. Rafalski, "Isospin mixing in nuclei within the nuclear density functional theory", Phys. Rev. Lett. 103, 012502 (2009).

M. Stoitsov, W. Nazarewicz, and N. Schunck, "Large-Scale Mass Table Calculations", Journal of Modern Physics E 18, 816 (2009).

A. Staszczak, A. Baran, J. Dobaczewski, W. Nazarewicz, "Microscopic description of complex nuclear decay: multimodal fission", Phys. Rev. C 80, 014309 (2009).

G.F. Bertsch, C.A. Bertulani, W. Nazarewicz, N. Schunck, M.V. Stoitsov, "Odd-even mass differences from self-consistent mean-field theory" , Phys. Rev. C 79, 034306 (2009).

J. Dobaczewski, W. Satula, B.G. Carlsson, J. Engel, P. Olbratowski, P. Powalowski, M. Sadziak, J. Sarich, N. Schunck, A. Staszczak, M. Stoitsov, M. Zalewski and H. Zdunczuk, "Solution of the Skyrme- Hartree-Fock-Bogolyubov equations in the Cartesian deformed harmonic-oscillator basis - HFODD (v2.38j): a new version of the program", Aceepted to Comp. Phys. Comm. (2009), arXiv:0903.1020.

J.A. Sheikh, W. Nazarewicz, J.C. Pei, "Systematic Study of Fission Barriers of Excited Superheavy Nuclei", Phys. Rev. C 80, 011302(R) (2009).

J. C. Pei, M. V. Stoitsov, G. I. Fann, W. Nazarewicz, N. Schunck and F. R. Xu, "Deformed Coordinate- Space Hartree-Fock-Bogoliubov Approach to Weakly Bound Nuclei and Large Deformations", Phys. Rev. C 78, 064306 (2008).

Alexandros Gezerlis, S. Gandolfi, K. E. Schmidt and J. Carlson, "Heavy-Light Fermion Mixtures at Unitarity" , Physical Review Letters 103:060403 (2009).

J. Terasaki, J. Engel, and G. F. Bertsch, "Systematics of the First 2+ Excitation in Spherical Nuclei with the Skryme Qasiparticle Random-Phase Approximation". Phys. Rev. C 78, 044311 (2008).

J. Terasaki, Genshikaku Kenkyu, "Nuclear Density Functional Theory", (Nuclear Study) 52, 64 (2008).

A. Bulgac, J.E. Drut, and P. Magierski, Quantum Monte Carlo Simulations of the BCS-BEC Crossover at Finite Temperature, Phys. Rev. A 78, 023625 (2008).

**PI Alfredo Caro **

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

A. Stukowski, B. Sadigh, P. Erhart, and A. Caro "Efficient implementation of the concentration-dependent embedded atom method for molecular dynamics and Monte-Carlo simulations", Modelling Simul. Mater. Sci. Eng. 17, 075005 (2009)

B. Sadigh, P. Erhart, A. Stukowski, and A. Caro "Composition-Dependent Interatomic Potentials: A systematic approach to modelling multicomponent alloys", Phil. Mag., in print

B. Sadigh, P. Erhart, A. Stukowski, E. Martinez, and A. Caro "A massively-parallel algorithm for atomic scale modelling of multi-component systems", submitted to Modelling Simul. Mater. Sci. Eng.

G. Kimminau, P. Erhart, E. Bringa, B. Remington, and Justin S. Wark "The Plasticity Mechanism exhibited in Molecular Dynamics Simulations of Uniaxially Compressed face-centred-cubic Metals", submitted to Phys. Rev. Lett.

**PI Paul Cassak **

P. A. Cassak and M. A. Shay, "The Scaling of Asymmetric Hall Reconnection," Geophys. Res. Lett., 35, L19102, 2008.

P. A. Cassak and M. A. Shay, "Structure of the Dissipation Region in Fluid Simulations of Asymmetric Magnetic Reconnection," Phys. Plasmas, 16, 055704, 2009.

T. N. Parashar, M. A. Shay, P. A. Cassak, and W. H. Matthaeus, "Kinetic dissipation and anisotropic heating in a turbulent collisionless plasma," Phys. Plasmas, 16, 032310, 2009.

K. Malakit, P. A. Cassak, M. A. Shay, and J. F. Drake, "The Hall effect in magnetic reconnction: Hybrid vs. Hall-less hybrid simulations," Geophys. Res. Lett., 36, L07107, 2009.

J. F. Drake, M. Swisdak, T. D. Phan, P. A. Cassak, M. A. Shay, S. 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.

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," Ap. J. Lett., 700, L16, 2009.

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

P. A. Cassak, M. A. Shay, and J. F. Drake, "Scaling of Sweet-Parker Reconnection with Secondary Islands," submitted to Physics of Plasmas, September 2009.

**PI Paola Cessi **

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

Wolfe, C. L., and P. Cessi, 2009: Overturning circulation in an eddy-resolving model: The effect of the pole-to-pole temperature gradient. Journal of Physical Oceanography, 39, 125-142.

Wolfe, C. L., P. Cessi, J. L. McClean, and M. E. Maltrud, 2008: Vertical heat transport in eddying ocean models. Geophysical Research Letters, 35, L23605.

**PI Yuen-Dat Chan **

A Generic Surface Sampler for Monte Carlo Simulations, J. A. Detwiler, R. Henning, R. A. Johnson, M. G. Marino. IEEE Trans. Nucl .Sci. 55 (2008) 2329

Evaluation of radioactive background rejection in 76Ge neutrino-less double-beta decay experiments using a highly segmented HPGe detector, Campbell et al, Nuclear Instr. and Methods A 587 (2008) 60

An independent measurement of the total active 8B solar neutrino flux using an array of 3He proportional counters at the Sudbury Neutrino Observatory, B. Aharmim et al. (SNO collaboration), Phys. Rev. Lett. 101, 111301 (2008), arXiv:0806.0989 (2008)

Measurement of the Cosmic Ray and Neutrino-Induced Muon Flux at the Sudbury Neutrino Observatory, B. Aharmim et al. (SNO collaboration) Phys. Rev. D (2009) arXiv:0902.2776 (2009)

**PI Choong-Seock Chang **

M. Adams, S. Ku, P. Worley, D'Azevedo, J. Cummings, C.S. Chang, "Scaling to 150K cores: recent algorithm and performance engineering developments enabling XGC1 to run at scale," Journal of Physics: Conference Series 180 (2009) 012036

C. S. Chang,, S. Ku, P. H. Diamond, Z. Lin, S. Parker, T. S. Hahm and N. Samatova, "Compressed ion temperature gradient turbulence in diverted tokamak edge," Phys. Plasmas 16, 056108 (2009)

C.S. Chang, S. Ku, et al, "Whole Volume Integrated Simulation of Plasma Turbulence in Realistic Diverted-Tokamak Geometry," Journal of Physics: Conference Series 180 (2009) 012057.

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," Nucl. Fusion, accepted.

X. Q. Xu, E. Belli, K. Bodi, J. Candy, C. S. Chang, et al, "Dynamics of kinetic Geodesic-Acoustic modes and the radial electric _eld in tokamak neoclassical plasmas," Nuclear Fusion, 49 065023 (2009).

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 (2009) 055025.

E.M. Hollmann, P.S. Krstic, R.P. Doerner, D. Nishijima, A.Yu. Pigarov, C.O. Reinhold, and S.J. Stuart, "Measurement and modeling of hydrogen molecule ro-vibrational accommodation on graphite," Plasma Phys. Control. Fusion 50, 102001 (2008).

P.S. Krstic, C.O. Reinhold, and S.J. Stuart, "Energy and Angle Spectra of Sputtered Particles for Low-Energy Deuterium Impact of Carbon," J. Appl. Phys. 104, 103308 (2008).

J.A. Ludlow, S.D. Loch, M.S. Pindzola, C.P. Ballance, D.C. Griffin, M.E. Bannister,M. Fogle, "Electron-impact ionization of C+ in both ground and metastable states," Phys. Rev. A 78, 052708 (2008).

P.S. Krstic, C.O. Reinhold, and S.J. Stuart, "Plasma-surface interactions of hydrogenated carbon," Nucl. Instr. Meth. B 267, 704 (2009).

S.D. Loch, C.P. Ballance, M.S. Pindzola, and D.P. Stotler, "The role of excited state ionization data on H and He generalized collisional"radiative coefficients," Plasma Physics and Controlled Fusion 51, 105006 (2009).

C.O. Reinhold, P.S. Krstic, and S.J. Stuart, "Hydrogen reflection in low-energy collisions with amorphous carbon," Nucl. Instr. Meth. B 267, 691 (2009).

P.S. Krstic, E.M. Hollmann, C.O. Reinhold, S.J. Stuart, R.P. Doerner, D. Nishijima, and A.Yu. Pigarov, "Transfer of Rovibrational Energies in Hydrogen Plasma-Carbon Surface Interactions," J. Nuclear Materials 390-391, 88 (2009).

S.J. Stuart, M. Fallet, P.S. Krstic, and C.O. Reinhold, Evolution of carbon surfaces under simulated bombardment by deuterium," Submitted to J. Phys. Conf. (2009).

P.S. Krstic and C.O. Reinhold, "Burning Plasma " Wall Interactions," Submitted to AIP Conference Proceedings.

C.P. Ballance, J.A. Ludlow, M.S. Pindzola, and S.D. Loch, "Electron-impact ionization of ground and metastable neon," J. Phys. B 42, 175202 (2009).

J.A. Ludlow, C.P. Ballance, S.D. Loch, M.S. Pindzola, and D.C. Griffin, "Electron-impact single ionization of Mg and Al+," Phys. Rev. A 79, 032715 (2009)

**PI James Chelikowsky **

M.M.G. Alemany, X. Huang, M.L. Tiago, L.J. Gallego, and J.R. Chelikowsky, "Ab initio calculations for p-type doped bulk indium phosphide," Solid State Commun., 146: 245 (2008).

N. Sai, M.L. Tiago, J.R. Chelikowsky, and F.A. Reboredo, "Optical spectra and exchange correlation effects in molecular crystals," Phys. Rev. B, 77: 161306 (2008).

A.T. Zayak, P. Entel, and J.R. Chelikowsky, "Minority spin polarization and surface magnetic enhancement in Heusler clusters," Phys. Rev. B, 77: 212401 (2008).

H. Kwak, M.L. Tiago, T.-L. Chan and J.R. Chelikowsky, "Hyperfine splitting of partially ionized Li donors in ZnO nanocrystals," Chem. Phys. Lett., 454: 337 (2008).

A. Natan, A. Mor, D. Naveh, L. Kronik, M.L. Tiago, S.P. Beckman and J.R. Chelikowsky, "Real space pseudopotential method for first principles calculations of general periodic and partially periodic systems," Phys. Rev. B, 78: 075109 (2008).

H. Kwak, M.L. Tiago, T.-L. Chan, and J.R. Chelikowsky, "The Role of Quantum Confinement and Hyperfine Splitting in Li Doped ZnO Nanocrystals," Phys. Rev. B, 78: 195324 (2008).

J. Han, M.L. Tiago, T.-L. Chan, and J.R. Chelikowsky, "Real-Space First-Principles Method for the Electronic Structure of One Dimensional Periodic Systems," J. Chem. Phys., 129: 144109 (2008).

M.M.G. Alemany, L. Tortajada, X. Huang, M.L. Tiago, L.J. Gallego, and J.R. Chelikowsky, "The role of dimensionality and quantum confinement in p-type semiconductor indium phosphide nanomaterials," Phys. Rev. B, 78: 233101 (2008).

T.-L. Chan, A.T. Zayak, G.M. Dalpian, and J.R. Chelikowsky, "Size effects on diffusion barriers in semiconductor nanocrystals," Phys. Rev. Lett., 102: 025901 (2009).

J.R. Chelikowsky, A.T. Zayak, T.-L. Chan, M.L. Tiago, Y. Zhou, and Y. Saad, "Algorithms for the Electronic and Vibrational Properties of Nanocrystals," J. Phys. Cond. Matter, 21: 064207 (2009).

J.R. Chelikowsky, Y. Saad, T.-L Chan, M.L. Tiago, A.T. Zayak, and Y. Zhou "Pseudopotentials on Grids: Application to the Electronic, Optical, and Vibrational Properties of Silicon Nanocrystals," Journal of Computational and Theoretical Nanoscience, 6: 1247 (2009).

T.-L. Chan, C.Z. Wang, K.M. Ho, and J.R. Chelikowsky, "Efficient first-principles simulation of non-contact atomic force microscopy for structural analysis," Phys. Rev. Lett., 102: 176101 (2009).

M.L. Tiago, J.C. Idrobo, S. Ogut, J. Jellinek, and J.R. Chelikowsky, "Electronic and optical excitations in Agn clusters (n=1-8): Comparison of density-functional and many-body theories," Phys. Rev. B, 79: 155419 (2009).

K.H. Khoo and J.R. Chelikowsky, "Electron transport across carbon nanotube junctions decorated with Au nanoparticles: Density functional calculations," Phys. Rev. B, 79: 205422 (2009).

I. Vasiliev, M. Lopez del Puerto, M. Jain, A. Lugo-Solis, and J.R. Chelikowsky, "Application of time-dependent density-functional theory to molecules and nanostructures," Theochem (special issue entitled "TD-DFT for molecules and molecular solids"), in press.

T.-L. Chan and J.R. Chelikowsky, "Controlling diffusion in semiconductor nanostructures by size and dimensionality," Phys. Rev. Lett. (submitted).

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

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 (submitted).

**PI Jackie Chen **

E.S. Richardson, J.H. Chen et al., "Effects of equivalence ratio variation on lean, stratified methane-air laminar counterflow flames," 6th Mediterranean Combustion Symposium, Ajaccio, France 2009 (also submitted to Combustion Science and Technology).

**PI Liu Chen **

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

Yong Xiao and Zhihong Lin, Turbulent transport of trapped electron modes in collisionless plasmas, Phys. Rev. Lett. 103, 085004 (2009).

Y. Nishimura, Z. Lin and L. Chen, Full Torus Electromagnetic Gyrokinetic Particle Simulations with Kinetic Electrons,Commun. Comput. Phys. 5, 183-194 (2009).

X. Y. Wang, Y. Lin, L. Chen, and Z. Lin, A particle simulation of current sheet instabilities under finite guide field, Phys. Plasmas 15, 072103 (2008).

H. Qu, Z. Lin, and L. Chen, Nonlinear Saturation of Mirror Instability, Geophy. Res. Lett. 35, L10108 (2008).

H. Qu and Z. Lin, Gyrokinetic Particle Simulation of Compressional Electromagnetic Modes, Commun. Comput. Phys. 4, 519-536 (2008).

W. Zhang, Z. Lin, P. H. Yoon, and X. Wang, Two-Fluid Formulation of Lower-Hybrid Drift Instabilities in Current-Sheet Equilibrium with a Guide Field, Commun. Comput. Phys. 4, 719-728 (2008).

Wenlu Zhang, Zhihong Lin, and Liu Chen, Transport of Energetic Particles by Microturbulence in Magnetized Plasmas, Phys. Rev. Lett. 101, 095001 (2008).

I. Holod and Z. Lin, Gyrokinetic particle simulations of toroidal momentum transport, Phys. Plasmas 15, 092302 (2008).

**PI Yang Chen **

C-S Chang et. al., ``Whole-volume integrated gyrokinetic simulation of plasma turbulence in realistic diverted-tokamak geometry,'' Journal of Physics: Conference Series, Vol. 180, 012057 (2009).

Y. Chen and S. E. Parker, ``Particle-in-Cell simulation with Vlasov ions and drift-kinetic electrons,'' Phys. Plasmas 16, 052305 (2009)

D.R. Ernst, J. Lang, W. Nevins, M. Hoffman, {\bf Y. Chen}, W. Dorland and S. Parker, ``Role of zonal flows in TEM turbulence through nonlinear gyrokinetic particle and continuum simulation,'' Phys. Plasmas 16, 055906 (2009); doi:10.1063/1.3116282

**PI Hai-Ping Cheng **

Atomistic origins of molecular memristors, Luis A. Agapito, Sabri Alkis, Jeffrey L. Krause, and Hai- Ping Cheng, accepted (JPC, C 2009)

Nonequilibrium Green's function study of Pd-4-cluster-functionalized carbon nanotubes as hydrogen sensors, C. Cao, A.F. Kemper, L. Agapito, Hai-Ping Cheng et al. Phys. Rev. B79, 75127 (2009).

Insensitivity of d-wave pairing to disorder in the high-temperature cuprate superconductors, Kemper, AF; Doluweera, DGSP; Maier, TA, et al., PHYSICAL REVIEW B, Volume: 79, Issue: 10, Article Number: 104502, Published: 2009

Molecular Dynamics Simulations of Au Penetration through Alkanethiol Monolayers on the Au(111) Surface, Alkis, S; Cao, C; Cheng, HP, et al., JOURNAL OF PHYSICAL CHEMISTRY C, Volume: 113, Issue: 16, Pages: 6360-6366, Published: 2009

Dynamics of Ag clusters on complex surfaces: Molecular dynamics simulations, Alkis, S; Krause, JL; Fry, JN, et al., PHYSICAL REVIEW B, Volume: 79, Issue: 12, Article Number: 121402, Published: 2009

Effects of cobalt doping and three-dimensionality in BaFe2As2 A.F. Kemper, C. Cao, P.J. Hirschfeld, and H-P. Cheng, (PRB, in press 2009).

First-Principles Calculations of Fe-doped monolayer C60 on h-BN/Ni(111) Surface I: Electronic and Magnetic Structures, Lan Li, Yuning Wu, and Hai-Ping Cheng (submitted to JCP)

Multi-scale multi-center simulation based on MPI-2 protocol: OPAL, Chao Cao, Erik Deumens, and Hai-Ping Cheng (submitted to J. Compt. Phys.).

**PI Wai-Yim Ching **

S.K. Arora, H. C. Wu, H. Yao, and W.Y. Ching, I.V. Shvets, O.N. Mryasov, "Magnetic Properties of Ultra-thin Magnetite Films Grown by Molecular Beam Epitaxy", IEEE Transactions on Magnetics, 44(11) 2628-2631 (2008).

Altaf Hussain, S. Aryal, P. Rulis, M.S. Choudhry and W.Y. Ching, "Density functional calculations of the electronic structure and optical properties of ternary carbides: Al4SiC4 and Al4Si2C5", Phys. Rev. B. 78,195102-1-9 (2008).

W.Y. Ching and Paul. Rulis, "XANES/ELNES calculation using the supercell OLCAO method", J. Physics: Conden. Matter, 21,104202-1-16 (2009).

W.Y. Ching, Paul Rulis, Lizhi Ouyang, Anil Misra, "Ab initio tensile experiment on a model of intergranular glassy film in beta-Si3N4 with prismatic surfaces", Appl. Phys. Lett. 94(6), 051907-1-3, (2009).

A.N. Caruso, K.I. Pokhodnya, W.W. Shum, W.Y. Ching, B. Anderson, M.T. Bremer, E. Vescovo, P. Rulis, A.J. Epstein and J.S. Miller, "Spin polarization from organic-based magnet [FeII(TCNE)(NCMe)2][FeIIICl4]", Physical Review B: 79(19), 195202/1-195202/5 (2009).

W.Y. Ching, Paul Rulis1 and A. Misra, "Ab initio elastic properties and tensile strength in hydroxyapatite crystal", Acta Biomaterialia, 6, 3067-3075 (2009).

Paul Rulis, Liaoyuan Wang and W.Y, Ching, "Prediction of the XANES/ELNES spectra of gamma-B28 and comparison with alpha-B12", Phys. Status Solidi RRL 3, 133-135 (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, (in press, 2009).

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. (Accepted, 2009)

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, (accepted, 2009).

Lei Liang, Paul Rulis, Bart Kahr, W.Y. Ching, "Origin of giant optical anisotropy in herapathite", submitted to Phys. Rev. Lett.

A. Misra, L. Ouyang, J. Chen, W.Y. Ching, "Role of Intergranular Glassy Films in the Failure of Ceramics: Insights from Ab initio Theoretical Experiments", submitted to Phil. Mag..

A. Altay, C.B. Carter, P. Rulis, W.Y. Ching, I. Arslan and M.A. Gulgun, "Structural investigation of CA2 and CA6 by energy-loss near-edge spectrometry and ab initio calculations", submitted to J. Solid State Chemistry.

Sitaram Arayal, Liaoyuan Wang, Lizhi Ouyang, Paul Rulis, and W.Y, Ching, "Ab initio calculations of the elastic, thermodynamic, electronic and spectroscopic properties of alpha-B12, B4C and B6O crystals", submitted to Phys. Rev. B.

**PI Mei-Yin Chou **

"Size- and Strain-Dependent Electronic Structures in H-Passivated Si [112] Nanowires," L. Huang, N. Lu, J. A. Yan, M. Y. Chou, C. Z. Wang, and K. M. Ho, J. Phys. Chem. C 112, 15680-15683 (2008).

"Electron-Phonon Interactions for Optical Phonon Modes in Few-Layer Graphene," J.-A. Yan, W. Y. Ruan, and M. Y. Chou, Phys. Rev. B 79, 115443/1-6 (2009).

"Path to Wigner Localization in Circular Quantum Dots," L. Zeng, W. Geist, W.Y. Ruan, C.J. Umrigar, and M.Y. Chou, Phys. Rev. B 79, 235334/1-5 (2009).

"Structural and Electronic Properties of Oxidized Graphene," Jia-An Yan, Lede Xian, and M. Y. Chou, Phys. Rev. Lett. 103, 086802/1-4 (2009).

"Low-Energy Ordered Structures of Li2Mg(NH)2," Z. Ma and M. Y. Chou, J. Appl. Phys. 104, 093619/1-6 (2008).

"First-Principles Investigation of Sodium and Lithium Alloyed Alanates," Z. Ma and M. Y. Chou, J. Alloys Compd. 479, 679-683 (2009).

**PI Alok Choudhary **

Kui Gao, Wei-keng Liao, Alok Choudhary, Robert Ross, and Robert Latham. Combining I/O Operations for Multiple Array Variables in Parallel NetCDF. In the Proceedings of the Workshop on Interfaces and Architectures for Scientific Data Storage, held in conjunction with the the IEEE Cluster Conference, New Orleans, Louisiana, September 2009.

Kui Gao, Wei-keng Liao, Arifa Nisar, Alok Choudhary, Robert Ross, Robert Latham. Using Subfiling to Improve Programming Flexibility and Performance of Parallel Shared-file I/O. In the proceeding of the International Conference on Parallel Processing, Vienna, Austria, September 2009.

**PI Daryl Chrzan **

E. Ertekin, D. C. Chrzan and M. S. Daw. 2009. Topological description of the Stone-Wales defect formation energy in carbon nanotubes and graphene. Physical Review B 79, 155421/1-17.

**PI Catherine Chuang **

Fiore, A.M., F. J. Dentener, O. Wild, C. Cuvelier, M. G. Schultz, P. Hess, C. Textor, M. Schulz, R. M. Doherty, L. W. Horowitz, I. A. MacKenzie, M. G. Sanderson, D. T. Shindell, D. S. Stevenson, S. Szopa, R. Van Dingenen, G. Zeng, C. Atherton, D. Bergmann, and 27 coauthors, 2009: Multimodel estimates of intercontinental source-receptor relationships for ozone pollution. J. Geophys. Res., 114, D04301, doi:10.1029/2008JD010816.

Sanderson, M.G., F.J. Dentener, A. M. Fiore, C. Cuvelier, T. J. Keating, A. Zuber, C. S. Atherton, D. J. Bergmann, and 21 coauthors, 2008: A multi-model study of the hemispheric transport and deposition of oxidised nitrogen. Geophys. Res. Lett., 35, L17815, doi:10.1029/2008GL035389.

**PI Bruce Cohen **

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," Nucl. Fusion 48, 165023 (2008).

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," Phys. Plasmas 16, 055906 (2009).

D.R. Hatch, P.W. Terry, W.M. Nevins, W. Dorland, "Role of stable eigenmodes in gyrokinetic models of ion temperature gradient turbulence," Phys. Plasmas 16, 022311 (2009).

X.Q. Xu, "Neoclassical simulation of tokamak plasmas using the continuum gyrokinetic code TEMPEST," Physical Review 78, 016406 (2008).

X.Q. Xu, Z. Xiong, Z. Gao, W.M. Nevins, and G.R. McKee, "TEMPEST Simulations of Collisionless Damping of the Geodesic-Acoustic Mode in Edge-Plasma Pedestals," Physical Review Letters 100, 215001 (2008).

X.Q. Xu, M.V. Umansky, B. Dudson and P.B. Snyder, "Boundary Plasma Turbulence Simulations for Tokamaks," Communications in Computational Physics 4, 949 (2008).

J. Lang, Y. Chen and S.E. Parker, ``Nonlinear saturation of collisionless trapped electron mode turbulence: zonal flows and zonal density,'' Phys. Plasmas 15, 055907 (2008).

D.R. Ernst, J. Lang, W. Nevins, M. Hoffman, Y. Chen, W. Dorland and S. Parker, ``Role of zonal flows in TEM turbulence through nonlinear gyrokinetic particle and continuum simulation,'' Phys. Plasmas 16, 055906 (2009);

T. Tatsuno, W. Dorland, A. A. Schekochihin, G. G. Plunk, M. Barnes, S. C. Cowley, and G. G. Howes, Nonlinear Phase Mixing and Phase-Space Cascade of Entropyin Gyrokinetic Plasma Turbulence, Phys. Rev. Lett. 103,015003 (2009).

D. R. Mikkelsen and W. Dorland, "The Dimits Shift in Realistic Gyrokinetic Plasma Turbulence Simulations", Phys. Rev. Letters 101 (2008) 135003.

D. A. Gates, et al., "Overview of Results from the National Spherical Torus Experiment (NSTX)", Nucl. Fusion 49 (2009) 104016.

J. E. Kinsey, G. M. Staebler, and R. E. Waltz, The first transport code simulations using the trapped gyro- Landau-fluid model Phys. Plasmas 15 055908 (2008)

B. I. Cohen, E. A. Williams, R. L. Berger, D. Pesme, and C. Riconda, "Stimulated Brillouin Backscattering and Ion Acoustic Wave Secondary Instability," Phys. Plasmas 16, 032701 (2009) (LLNL-JRNL-407238); "Erratum: "Stimulated Brillouin Backscattering and Ion Acoustic Wave Secondary Instability," [Phys. Plasmas 16, 032701 (2009)], Phys. Plasmas 16, 089902 (2009).

S. C. Wilks, B. I. Cohen, J. F. Latkowski, and E. A. Williams, "Evaluation of Several Issues Concerning Laser Beam Propagation through the Laser Inertial Confinement Fusion-Fission Energy Engine (LIFE) Target Chamber," 18th Topical Meeting on the Technolodgy of Fusion Energy, San Francisco, CA, September 28 " October 2, 2008 (refeered proceedings) LLNL-CONF-409597.

B. I. Cohen, A. J. Kemp, and L. Divol, "Hybrid Simulation of Laser-Plasma Interactions in Inhomogeneous Plasmas," submitted to J. Comput. Phys., May, 2009 (LLNL-JRNL-413523)

X. Xu, Z. Xiong, M. Dorr, J. Hittinger, K. Bodi, J. Candy, B. Cohen, R. Cohen, P. Colella, G. Kerbel, S. Krasheninnikov, W. Nevins, H. Qin, T. Rognlien, P. Snyder and M. Umansky, "Edge gyrokinetic theory and continuum simulations", Nuclear Fusion 47, 809 (2007).

B.I. Cohen, C.A. Romero-Talamas, E.B. Hooper, L.L. LoDestro, D. Ryutov, H.S. McLean, T.L. Stewart, and R.D. Wood, "The Role of the n=1 Column Mode in Spheromak Formation," Phys. Plasmas 16, 042501 (2009).

E.B. Hooper, C.A. Romero-Talamas, L.L. LoDestro, R.D. Wood, and H.S. McLean, "Aspect-ratio effects in the driven, flux-core spheromak," Phys. Plasmas 16, 052506 (19 May 2009); DOI:10.1063/1.3134064.

E.B. Hooper, B.I. Cohen, H.S. McLean, R.D. Wood, and C.A. Romero-Talamas, "Nimrod resistive magnetohydrodynamic simulations of spheromak physics," Phys. Plasmas 15, 032502 (2008).

**PI Marvin Cohen **

Li Yang, Marvin L. Cohen, and Steven G. Louie, "Magnetic Edge-State Excitons in Zigzag Graphene Nanoribbons", Phys. Rev. Lett. 101, 186401 (2008)

Hoonkyung Lee, Jisoon Ihm, Marvin L. Cohen, and Steven G. Louie, "Ca-decorated Carbon Nanotubes for High-Capacity Hydrogen Storage", accepted to Physical Review B.

Brad D. Malone, Steven G. Louie, and Marvin L. Cohen, "Ab Initio study of the optical properties of bct-Si", (submitted to Phys. Rev. B)

Brad D. Malone, Jay D. Sau, and Marvin L. Cohen, "Ab Initio study of the optical properties of Si-XII", Phys. Rev. B 78, 161202(R) (2008)

C.-H. Park, F. Giustino, M.L. Cohen, and S.G. Louie, "Electron-phonon Interactions in Graphene, Bilayer Graphene, and Graphite", Nano Lett. 8, 4229 (2008). [Erratum: Nano Lett. 9), 1731 (2009)]

W. Luo, M.L. Cohen, J.W. Morris, Jr., "On the possibility of cleavage in Nb", Phil. Mag. Lett. 89, 23 (2009).

C.-H. Park, F. Giustino, C.D. Spataru, M.L. Cohen, and S.G. Louie, "First-Principles Study of Electron Linewidths in Graphene", Phys. Rev. Lett. 102, 076803 (2009). [Erratum: Phys. Rev. Lett. 102, 189904(E) (2009)]

H.J. Choi, S.G. Louie, and M.L. Cohen, "Anisotropic Eliashberg Theory for Superconductivity in Compressed and Doped MgB2", Phys. Rev B 79, 094518 (2009).

C.O. Girit, J.C. Meyer, R. Erni, M.D. Rossell, C. Kisielowski, Li Yang, C.-H. Park, M.F. Crommie, M.L. Cohen, S.G. Louie, and A. Zettl, "Graphene at the Edge: Stability And Dynamics", Science 323, 1705 (2009).

J. Noffsinger, F. Giustino, S.G. Louie, and M.L. Cohen, "Origin of Superconductivity in Boron-Doped Silicon Carbide from First Principles", Phys. Rev B 79, 104511 (2009).

S.R. Leslie, J. Guzman, M. Vengalattore, J.D. Sau, M.L. Cohen, and D.M. Stamper-Kurn, "Amplification of fluctuations in a spinor Bose-Einstein condensate", Phys. Rev. A 79, 043631 (2009).

J. Noffsinger, S.G. Louie, F. Giustino, and M.L. Cohen, "Role of Fluorine in the Iron Pnictides: Phonon Softening and Effective Hole Doping", Phys. Rev. Lett. 102, 147003 (2009).

C.-H. Park, Y.-W. Son, L. Yang, M.L. Cohen, and S.G. Louie, "Landau Levels and Quantum Hall Effect in Graphene Superlattices", Phys. Rev. Lett. 103, 046808 (2009).

H.J. Choi, S.G. Louie, and M.L. Cohen, "Prediction of Superconducting Properties of CaB2 Using Anisotropic Eliashberg Theory", Phys. Rev. B 80, 064503 (2009).

R. Vijay, J.D. Sau, M.L. Cohen, and I. Siddiqi, "Optimizing anharmonicity in nanoscale weak link Josephson junction oscillators", Phys. Rev. Lett. 103, 087003 (2009).

**PI Phil Collela **

B.V. Straalen, J. Shalf, T. Ligocki, N. Keen, and W. Yang "Scalability Challenges for Massively Parallel AMR Application", 23rd IEEE International Symposium on Parallel and Distributed Processing, 2009.

D. Trebotich, B.V. Straalen, D. Graves and P. Colella "Performance of embedded boundary methods for CFD with complex geometry" , 2008 J. Phys.: Conf. Ser. 125 012083

**PI William Collins **

Qian, Y., S.J. Ghan, and L.R. Leung, 2009: Downscaling hydroclimatic changes over the western U.S. based on CAM-subgrid scheme and WRF regional climate simulations. Int. J. Climatol., doi:10.1002/joc.1928.

Salathe, E.P., L.R. Leung, Y. Qian, and Y. Zhang, 2009: Regional climate model projections for the state of Washington. Climatic Change, submitted.

Zhang, Y., Y. Qian, V. Duliere, E.P. Salathe, and L.R. Leung, 2009: ENSO anomalies over the western United States: Present and future patterns in global and regional climate models simulations. Climatic Change, submitted.

Cooley, HS, WJ Riley, MS Torn, and Y He, (2005) Effect of harvest on regional climate and soil moisture and temperature, 110, D03113, doi:10.1029/2004JD005160, JGR Atmospheres. (LBNL-56063)

**PI Gil Compo **

Bronnimann, S., T. Ewen, and J. Luterbacher, 2009: Variability of the global atmospheric circulation during the past 100 years. Meteorologische Zeitschrift, 18, 365-368, doi: 10.1127/0941-2948/2009/0392.

Giese B.S., G.P. Compo, N.C. Slowey, P.D. Sardeshmukh, J.A. Carton, S. Ray, and J.S. Whitaker, 2009: The 1918/1919 El Nino. Bulletin of the American Meteorological Society: In Press, doi: 10.1175/2009BAMS2903.1.

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. Monthly Weather Review, 137, 1991-1999, DOI: 10.1175/2008MWR2781.1.

Wood, K.R., and J.E. Overland, 2009: Early 20th century Arctic warming in retrospect. International Journal of Climatology, in press, doi:10.1002/joc.1973.

**PI Jennifer Comstock **

Fan, J., M. Ovtchinnikov, J. M. Comstock, S. A. McFarlane, and A. Khain (2009), Ice formation in Arctic mixed-phase clouds: Insights from a 3-D cloud-resolving model with size-resolved aerosol and cloud microphysics, J. Geophys. Res., 114, D04205, doi:10.1029/2008JD010782.

Fan, J., T. Yuan, J. M. Comstock, S. Ghan, A. Khain, L. R. Leung, Z. Li, V. J. Martins, and M. Ovchinnikov (2009), Dominant role by vertical wind shear in regulating aerosol effects on deep convective clouds, J. Geophys. Res., 114, D22206, doi:10.1029/2009JD012352.

**PI Valentino Cooper **

D. E. Jiang, V. R. Cooper and S. Dai "Porous gaphene as the ultimate membrane for gas separation" Nano Letters (2009) (published on the web: DOI: 10.1021/nl9021946).

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

V. R. Cooper "Van der Waals density functional: an appropriate exchange functional" (under review: Phys Rev. Lett. 2009; arXiv:0910.1250).

**PI Curtis Covey **

Wang, W., X. Liu, S. Xie, J. Boyle, and S. McFarlane, 2009: Testing ice microphysics parameterizations in the NCAR Community Atmospheric Model Version 3 using Tropical Warm Pool-International Cloud Experiment data, J. Geophys. Res., 114, D14107, doi:10.1029/2008JD011220

**PI Peter Cummings **

Christina M. Payne, Xiongce Zhao and Peter T. Cummings, Electrophoresis of ss-DNA through nanoelectrode gaps from molecular dynamics: Impact of gap width and chain length, Journal of Physical Chemistry B, 112 12851-12858 (2008).

Pu, Q., Leng, Y., and Cummings, P. T., Rate-Dependent Energy Release Mechanism of Gold Nanowires under Elongation, Journal of the American Chemical Society, 130, 17907-17912 (2008).

O. A. Mazyar, G. Pan and C. McCabe, Comparison of the Molecular and Atomic Stress Tensors in the Prediction of the Viscosity of n-Decane at Experimentally Accessible Shear Rates with the Transient Time Correlation Function Method, Molecular Physics, 107 (14) 1423-1429 (2009).

A. M. Cione, O. A. Mazyar, B. D. Booth, C. McCabe, and G. K. Jennings, Deposition and Wettability of [bmim] [triflate] on Self-Assembled Monolayers, Journal of Physical Chemistry C, 113, 2384-2392 (2009).

Mamontov, E., Vlcek, L., Wesolowski, D. J., Cummings, P. T., Rosenqvist, J., Wang, W., Cole, D. R., Anovitz, L. M., and Gasparovic, G., Suppression of the dynamic transition in surface water at low hydration levels: A study of water on rutile, Physical Review E 79 (2009) Art. No. 051504

O. A. Mazyar, G. K. Jennings, and C. McCabe, Frictional Dynamics of Alkylsilane Monolayers on SiO2: Effect of 1-n-butyl-3-methylimidazolium Nitrate as a Lubricant, Langmuir, 25 (9), 5103-5110 (2009).

Redmill, P. S., Capps, S. L., Cummings, P. T., and McCabe, C., A molecular dynamics study of the Gibbs free energy of solvation of fullerene particles in octanol and water, Carbon 47 (2009) 2865-2874.

P. S. Redmill and C. McCabe, A Molecular Dynamics Study of the Behavior of Selected Nanoscale Building Blocks in a Lipid Bilayer, Journal of Physical Chemistry B, submitted (2009).

Rosenqvist, J., Machesky, M. L., Lukas Vlcek, Peter T. Cummings and David J. Wesolowski, Charging Properties of Cassiterite ( -SnO2) Surfaces in NaCl and RbCl Ionic Media, Langmuir, 25 (2009) 10852-10862.

P. J. Dyer, H. Docherty and P. T. Cummings, The importance of polarizability in the modeling of solubility: Quantifying the effect of charged co-solutes on the solubility of small non-polar solutes, Journal of Chemical Physics, submitted (2009).

H. Docherty and P. T. Cummings, Direct evidence for fluid-solid transition of nanoconfined fluids, Nano Letters, submitted (2009).

## D

**PI Valerie Daggett **

Van der Kamp, M.W., Schaeffer, R.D., Jonsson, A.L., Scouras, A.D., Simms, A., Toofanny, R.D., Benson, N.C., Anderson, P.C., Bromley, D.N., Merkley, E.D., Rysavy, S., Beck, D.A.C., Daggett, V. Dynameomics: A comprehensive database of protein dynamics and unfolding simulations. Structure, Submitted, 2009.

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, In Press, 2009.

Toofany, R. D., Daggett, V. A Comprehensive One-Dimensional Reaction Coordinate for Protein Unfolding/Folding. Biophysical Journal, Submitted, 2009.

Anderson P.C. and Daggett V. The R46Q, R131Q and R154H Polymorphs of Human DNA Glycosylase/- Lyase hOgg1 Severely Distort the Active Site and DNA Recognition Site but do not Cause Unfolding. Journal of the American Chemical Society 131: 9506-9515, 2009.

Rutherford K. and Daggett V. A Hotspot of Inactivation: The A22S and V108M Polymorphisms Individually Destabilize the Active Site Structure of Catechol O-Methyltransferase. Biochemistry 48: 6450-6460, 2009.

Benson N. and Daggett V. Dynameomics: Large-Scale Assessment of Native Protein Flexibility. Protein Science 17: 2038-2050, 2009.

**PI Ronald Davidson **

"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, submitted for publication (2009).

"Generalized Kapchinskij-Vladimirskij Distribution and Envelope Equation for High-Intensity Beams in a Coupled Transverse Focusing Lattice", H. Qin, M. Chung and R. C. Davidson, Physical Review Special Topic on Accelerators and Beams, submitted for publication (2009).

"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, Physical Review Special Topic on Accelerators and Beams, submitted for publication (2009).

"Adiabatic Formation of a Matched-Beam Distribution for an Alternating-Gradient Quadrupole Lattice'", M. A. Dorf, R. C. Davidson, E. A. Startsev and H. Qin, submitted for publication (2009).

"Two-Stream Stability Properties of the Return-Current Layer for Intense Ion Beam Propagation Through Background Plasma", E. A. Startsev, R. C. Davidson and M. Dorf, submitted for publication (2009).

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

"Enhanced Self-Focusing of an Ion Beam Propagating through a Background Plasma along a Solenoidal Magnetic Field", M. Dorf, I. D. Kaganovich, E. A. Startsev and R. C. Davidson, Physical Review Letters 103, 075003 (2009).

"Simulations and Experiments of Intense Ion Beam Current density in Space and Time", A. B. Sefkow, R. C. Davidson, E. P. Gilson, I. D. Kaganovich, A. Anders, J. Coleman, M. Letner, S. M. Lidia, P. K. Roy, P. A. Seidl, P. L. Waldron, S. S. Yu and D. R. Welch, Physics of Plasmas 16, 056701 (2009).

"Generalized Courant-Snyder Theory for Coupled Transverse Dynamics of Charged Particles in Electromagnetic Focusing Lattices", H. Qin and R. C. Davidson, Physical Review Special Topics in Accelerators and Beams 12, 064001 (2009).

"A Physical Parameterization of Coupled Transverse Dynamics Based on Generalized Courant-Snyder Theory and its Applications, H. Qin and R. C. Davidson, Physics of Plasmas 16, 050705 (2009).

"Experimental Investigation of Random Noise-Induced Beam Degradation in High-Intensity Accelerators Using a Linear Paul Trap", M. Chung, E. P. Gilson, R. C. Davidson, P. C Efthimion, and R. Majeski, Physical Review Special Topics on Accelerators and Beams 12, 054203 (2009).

"Use of a Linear Paul Trap to Study Random Noise-Induced Beam Degradation in High-Intensity Accelerators", M. Chung, E. P. Gilsom, R. C. Davidson, P. C Efthimion, and R. Majeski, Physical Review Letters 102, 145003 (2009).

"Survey of Collective Instabilities and Beam-Plasma Interactions in Intense Heavy Ion Beams", R. C. Davidson, M. A. Dorf, I. D. Kaganovich, H. Qin, A. B. Sefkow, E. A. Startsev, D. R. Welch, D. V. Rose, and S. M. Lund, Nuclear Instruments and Methods in Physics Research A 606, 11 (2009).

E. V. Belova and R. C. Davidson, Simulation studies of field-reversed configurations with rotating magnetic field current drive, Proceedings of the 22th Int. Conf. Geneva, 2008, paper IAEA-IC/P4-3 (International Atomic Energy Agency, Vienna, 2008).

S. P. Gerhardt, E. V. Belova, M. Yamada, et al., New inductive field-reversed configuration formation scheme utilizing a spheromak and solenoid induction, Physics of Plasmas 15, 032503 (2008).

S. P. Gerhardt, E. V. Belova, M. Yamada, et al., Inductive sustainment of oblate FRCs with the assistance of magnetic diffusion, shaping, and finite-Larmor radius stabilization, Physics of Plasmas 15, 022503 (2008).

S. P. Gerhardt, E. V. Belova, M. Yamada, H. Ji, M. Inomoto, Y. Ren, and B. McGeeham, New method for inductively forming an oblate field reversed configuration from a spheromak, Nuclear Fusion 48, 032001 (2008).

**PI Murray Daw **

Xing Gao and Murray S. Daw, "First-principles super-cell investigation of the rattling effect in Li-doped KCl", J. Phys.: Condens. Matter, v21 a045401 (2009)

**PI Wibe De Jong **

P.J. Nichols, N. Govind, E.J. Bylaska, and W.A. de Jong, "Gaussian Basis Set and Planewave Relativistic Spin-Orbit Methods in NWChem", J. Chem. Theory Comp. 5, 491 (2009)

Bylaska EJ, KL Tsemekhman, N Govind, and M Valiev. 2009. "Large Scale Plane Wave Based 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. (submitted).

Windus TL, EJ Bylaska, K Tsemekhman, J Andzelm, N Govind, Computational Nanoscience with NWChem, J. Comput. Theor. Nanosci. 6, 1297-1304 (2009)

E.J. Bylaska, K. Glass, D. Baxter, S.B. Baden, J. H. Weare, "Hard scaling challenges for ab initio molecular dynamics capabilities in NWChem: Using 100,000 CPUs per second", Journal of Physics: Conference Series, published on line September 2009, (http://www.iop.org/EJ/toc/1742-6596/180/1)

**PI Viktor Decyk **

V. I. Sotnikov, V. Ivanov, R. Presura, J. N. Leboeuf, O. G. Onishchenko, B. V. Oliver, B. Jones, T. A. Mehlhorn, and C. Deeney, "Investigation of Compressible Electromagnetic Flute Mode Instability in Finite Beta Plasma in Support of Z-pinch and Laboratory Astrophysics Experiments", Commun. Comput. Phys. 4 (2008), pp. 611-623. Published Online at http://www.global-sci.com/: April 17, 2008.

P. W. Terry, M. Greenwald, J.-N. Leboeuf, G. R. McKee, D. R. Mikkelsen, W. M. Nevins, D. E. Newman, and D. P. Stotler, "Validation in Fusion Research: Towards Guidelines and Best Practices", Phys. Plasmas 15, 062503 (2008).

P.-A. Gourdain, and J.-N. Leboeuf, "Unity beta dual equilibrium in a finite aspect ratio tokamak", Physics Letters A 372 (2008) 6097 - 6100. http://www.sciencedirect.com/science/journal/03759601

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. Y. Neches, S. C. Cowley, P. A. Gourdain, and J. N. Leboeuf, "The convergence of analytic high-b equilibrium in a finite aspect ratio tokamak", Phys. Plasmas 15,122504(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).

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, Submitted for Publication, August 6, 2009.

**PI James Demmel **

Christof Voemel and Stanimire Z. Tomov and Osni Marques, "Bulk based preconditioning for quantum dot computations", in SAC '09: Proceedings of the 2009 ACM symposium on Applied Computing, 2009, pp. 961--965.

Marghoob Mohiyuddin, Mark Hoemmen, James Demmel, and Kathy Yelick, "Minimizing Communication in Sparse Matrix Solvers", in Proc. of SC09, November 2009.

Grey Ballard, James Demmel, Olga Holtz and Oded Schwartz, "Communication-optimal Parallel and Sequential Cholesky decomposition", in Proc. of SPAA, August 2009.

James Demmel, Mark Hoemmen, Yozo Hida, and E. Jason Riedy, "Non-negative diagonals and high performance on low-profile matrices from Householder QR", SIAM Journal on Scientific Computing, Volume 31, Issue 4, pp. 2832-2841, July 2009.

**PI William Detmold **

Bottom hadron mass splittings in the static limit from 2+1 flavour lattice QCD. William Detmold, C.-J.David Lin, Matthew Wingate, Nucl.Phys.B818:17-27,2009.

**PI Thomas Devereaux **

W. L. Yang, A. P. Sorini, C-C. Chen, B. Moritz, W.-S. Lee, F. Vernay, P. Olalde-Velasco, J. D. Denlinger, B. Delley, J.-H. Chu, J. G. Analytis, I. R. Fisher, Z. A. Ren, J. Yang, W. Lu, Z. X. Zhao, J. van den Brink, Z. Hussain, Z.-X. Shen, and T. P. Devereaux, "Evidence for weak electronic correlations in iron pnictides," Physical Review B 80, 014508 (2009) [Highlighted in Viewpoint commentary Physics 2, 60 (2009)]

B. Moritz, F. Schmitt, W. Meevasana, S. Johnston, E. M. Motoyama, M. Greven, D.H. Lu, C. Kim, R. T. Scalettar, Z.-X. Shen, and T. P. Devereaux, "Effect of strong correlations on the high energy anomaly in hole- and electron-doped high T_c superconductors," New J. Phys. 11, 093020 (2009)

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," arXiv:0908.0800v1 [cond-mat.str-el](submitted to Physical Review Letters)

**PI Pat Diamond **

Transport of Parallel Momentum by Collisionless Drift Wave Turbulence, P.H. Diamond, C.J. McDevitt, O.D. Gurcan, T.S. Hahm and V. Naulin, Phys. Plasmas 15, 012303, 2008.

Turbulent Equipartition Theory of Toroidal Momentum Pinch, T.S. Hahm, P.H. Diamond, O.D. Gurcan and G. Rewoldt, "Turbulent Equipartition Theory of Toroidal Momentum Pinch", Phys. Plasmas 15, 055902, 2008.

Disparate Scale Nonlinear Interactions in Edge Turbulence, M. Yagi, S.-I. Itoh, K. Itoh and P.H. Diamond, Contrib. Plasma Phys. 48 (No. 1-3), 13-22, 2008.

Turbulent Equipartition and Homogenization of Plasma Angular Momentum, O.D. Gurcan and P.H. Diamond, Phys. Rev. Lett. 100, 135001, 2008.

On Cross-Phase and the Quenching of the Turbulent Diffusion of Magnetic Fields in Two Dimensions, Shane R. Keating, L.J. Silvers and P.H. Diamond, The Astrophy. J. Lett. 678(2), L137, 2008.

Momentum Theorems and the Structure of Atmospheric Jets and Zonal Flows in Plasmas, P.H. Diamond, O.D. Gurcan, T.S. Hahm, K. Miki, Y. Kosuga and X. Garbet, Plasma Phys. Control. Fusion 50(12), 124018, 2008.

Transport of parallel momentum by collisionless drift wave turbulence, P. H. Diamond, C. J. McDevitt, O. D. Gurcan. T. S. Hahm and V. Naulin, Phys. Plasmas 15, 012303, 2008.

Compressed Ion Temperature Gradient Turbulence in Diverted Tokamak Edge, C.S. Chang, C.S., S. Ku, P.H. Diamond, Z. Lin, S. Parker, T.S. Hahm, W.W. Lee and N. Samatova, Phys. Plasmas 16, 056108, 2009.

A Novel Mechanism for Exciting Intrinsic Toroidal Rotation, C.J. McDevitt, P.H. Diamond, O.D. Gurcan and T.S. Hahm, Phys. Plasmas 16, 052302, 2009.

Physics of Non-Diffusive Turbulent Transport of Momentum and the Origins of Spontaneous Rotation in Tokamaks, P.H. Diamond, C.J. McDevitt, O.D. Gurcan, T.S. Hahm, W.X. Wang, E.S. Yoon, I. Holod, Z. Lin, V. Naulin and R. Singh, Nuclear Fusion 49, 045002, 2009.

Wave-Number Spectrum of Drift Wave Turbulence, O.D. Gurcan, X. Garbet, P. Hennequin, P.H. Diamond, A. Casati, and G.L. Falchetto, Phys. Rev. Lett. 102, 255002, 2009

Transport of Parallel Momentum by Drift-Alfven Turbulence, C.J. McDevitt and P.H. Diamond, Phys. of Plasmas 16, 012301, 2009

Guiding center orbit studies in a tokamak edge geometry employing Boozer and Cartesian coordinates, Y. Nishimura, Y. Xiao, and Z. Lin, Contributions Plasma Phys. 48, 224-228 (2008).

A particle simulation of current sheet instabilities under finite guide field, X. Y. Wang, Y. Lin, L. Chen, and Z. Lin, Phys. Plasmas 15, 072103 (2008).

Gyrokinetic Particle Simulation of Compressional Electromagnetic Modes, H. Qu and Z. Lin, Commun. Comput. Phys. 4, 519-536 (2008).

Two-Fluid Formulation of Lower-Hybrid Drift Instabilities in Current-Sheet Equilibrium with a Guide Field, W. Zhang, Z. Lin, P. H. Yoon, and X. Wang, Commun. Comput. Phys. 4, 719-728 (2008).

Transport of Energetic Particles by Microturbulence in Magnetized Plasmas, Wenlu Zhang, Zhihong Lin, and Liu Chen, Phys. Rev. Lett. 101, 095001 (2008).

Gyrokinetic particle simulations of toroidal momentum transport, I. Holod and Z. Lin, Phys. Plasmas 15, 092302 (2008).

Turbulent transport of trapped electron modes in collisionless plasmas, Y. Xiao and Z. Lin, Phys. Rev. Lett. 103, 085004 (2009).

Full Torus Electromagnetic Gyrokinetic Particle Simulations with Kinetic Electrons, Y. Nishimura, Z. Lin and L. Chen, Commun. Comput. Phys. 5, 183-194 (2009).

**PI Dimitre Dimitrov**

D. A. Dimitrov, R. Busby, J. R. Cary, I. Ben-Zvi, X. Chang, J. Keister, E. Muller, T. Rao, J. Smedley, and Q. Wu, Investigation of Charge Gain in Diamond Electron Beam Amplifiers via 3D Simulations, in the Proceedings of the PAC09 Particle Accelerator Conference, IEEE (2009).

R. Busby, D. A. Dimitrov, J. R. Cary, I. Ben-Zvi, X. Chang, J. Keister, E. Muller, T. Rao, J. Smedley, and Q. Wu, 3D Simulations of Secondary Electron Generation and Transport in a Diamond Electron Beam Amplifier, in the Proceedings of the PAC09 Particle Accelerator Conference, IEEE (2009).

**PI William Dorland **

T. Tatsuno, W. Dorland, A. A. Schekochihin, G. G. Plunk, M. Barnes, S. C. Cowley, and G. G. Howes, Nonlinear phase mixing and phase-space cascade of entropy in gyrokinetic plasma turbulence, Phys. Rev. Lett. 103, 015003 (2009).

G. G. Howes, W. Dorland, S. C. Cowley, et al., Kinetic simulations of magnetized turbulence in astrophysical plasmas, Phys. Rev. Lett. 100, 065004, 2008.

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

J. Egedal, W. Daughton, J. F. Drake, N. Katz and A. Le, Formation of a localized acceleration potential during magnetic reconnection with a guide field, Phys. Plasmas 16, 050701, 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. 700, L16, 2009.

R. Fermo, J. F. Drake and M. Swisdak, A statistical model of magnetic islands in a current layer, Phys. Rev. Lett., submitted, 2009.

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

Loss of confinement at the density limit due to the suppression of stabilizing zonal flows by magnetic turbulence, R.G. Kleva and P.N. Guzdar, Phys. Plasmas 15, 082307 (2008).

**PI Michel Dupuis **

1. R. Devanathan, "Recent developments in proton exchange membranes for fuel cells", ENERGY & ENVIRONMENTAL SCIENCE 1(1) (2008) 101-119.

## E

**PI Charlotte Elster **

C. Elster, T. Lin, W. N. Polyzou and W. Gloeckle, ``Poincare Invariant Three-Body Scattering,'' Few Body Syst. 45, 157 (2009)

W. Polyzou. T. Lin, Ch. Elster, W. Gloeckle, ``A Poincare invariant treatment of the three-nucleon problem,'' PoS LC2008, 039 (2008) [arXiv:0812.2204 [nucl-th].

H. Kamada, W. Gloeckle, H. Witala, J. Golak, R. Skibinski, W. Polyzou and C. Elster, %``Lorentz Boosted Nucleon-Nucleon T-matrix and the Triton Binding Energy,'' Mod. Phys. Lett. A 24, 804 (2009)

C. Elster, T. Lin, W. Gloeckle and S. Jeschonnek, ``Faddeev and Glauber Calculations at Intermediate Energies in a Model for n+d Scattering,'' Phys. Rev. 78, 034002 (2008)

T. Lin, C. Elster, W. N. Polyzou, H. Witala and W. Gloeckle, ``Poincare Invariant Three-Body Scattering at Intermediate Energies,'' Phys. Rev. bf 78, 024002 (2008)

W. N. Polyzou, T. Lin, C. Elster and W. Gloeckle, ``Three-body scattering in Poincare invariant quantum mechanics,'' Few Body Syst. 44, 287 (2008)

T. Lin, C. Elster, W. N. Polyzou and W. Gloeckle, ``Relativistic Effects in Exclusive pd Breakup Scattering at Intermediate Energies,'' Phys. Lett. 660, 345 (2008)

## F

**PI Roland Faller **

Ian G. Elliott, Dennis E. Mulder, Petra T. Troskelin, John R. Ell, Timothy E. Patten, Tonya L. Kuhl, and Roland Faller: Simulations and Neutron Scattering in Confined Polymer Systems Soft Matter in press

Petra Troskelin, Tonya L. Kuhl, and Roland Faller: Molecular dynamics simulations of polystyrene melts and brushes under confinement submitted

John Ell, Dennis Mulder, Roland Faller, Timothy Patten, Tonya L. Kuhl: Structural Determination of High Density, ATRP Grown Polystyrene Brushes by Neutron Surface Reflectivity submitted

**PI Alexey Fedorov **

Fedorov, A., C. Brierley, and K. Emanuel (2010). Tropical cyclones, and the permanent El Niño of the early Pliocene. Nature, in press.

**PI Andrew Felmy **

Stuart Bogatko, John Weare, and Eric Bylaska (2009) First principles simulation of the bonding, vibrational, and electronic properties of the hydration shells of the high spin Fe3+ ion in aqueous solution, Journal of Physical Chemistry (submitted)

Eric J. Bylaska, John H. Weare, and Michael Holst (2009), An Adaptive Finite Element Method for Solving the Exact Kohn-Sham Equation of Density Functional Theory, Journal of Chemical Theory and Computation, vol. 5(4), pp 937-948.

E.J. Bylaska, K. Glass, D. Baxter, S.B. Baden, J. H. Weare, Hard scaling challenges for ab initio molecular dynamics capabilities in NWChem: Using 100,000 CPUs per second, Journal of Physics: Conference Series (in press).

E.J. Bylaska et al. (2009) 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. (submitted).

E.J. Bylaska et al. (2009) Parallel Implementation of Pseudopotential Plane-Wave DFT with Exact Exchange, Journal of Computational Chemistry (submitted)

Emilie Cauet, et al. (2009) Structure and Dynamics of the Hydration Shells of the Zn2+ Ion from ab initio Molecular Dynamics and Combined ab initio and Classical Molecular Dynamics Simulations, Journal of Chemical Physics (submitted)

Nichols P , Govind N, Bylaska EJ, de Jong WA (2009) Gaussian Basis Set and Planewave Relativistic Spin- Orbit Methods in NWChem, JOURNAL OF CHEMICAL THEORY AND COMPUTATION, Vol. 5, 491-499

Windus TL, Bylaska EJ, Tsemekhman K, Andzelm J, Govind N (2009) Computational Nanoscience with NWChem, JOURNAL OF COMPUTATIONAL AND THEORETICAL NANOSCIENCE, Vol. 6, 1297-1304

**PI Graham Fleming **

EL Read, GS Schlau-Cohen, GS Engel, T Georgiou, MZ Papiz, GR Fleming, Pigment Organization and Energy Level Structure in Light-Harvesting Complex 4: Insights from Two-Dimensional Electronic Spectroscopy, J. Phys. Chem. B 113, 6495 (2009).

EL Read, H Lee, GR Fleming, Photon echo studies of photosynthetic light harvesting, Photosynthesis Research (2009).

Y-C Cheng, GR Fleming, Dynamics of Light Harvesting in Photosynthesis, Annual Review of Physical Chemistry 60, 241 (2009).

NS Ginsberg, Y-C Cheng, GR Fleming, Two-Dimensional Electronic Spectroscopy of Molecular Aggregates, Accounts of Chemical Research 42, 1352 (2009).

GS Schlau-Cohen, TR Calhoun, NS Ginsberg, EL Read, M. Ballottari, R. Bassi, GR Fleming, The Pathways of Energy Flow in LHCII from Two-Dimensional Electronic Spectroscopy, J. Phys. Chem. B 113, 15352.

**PI Michael Fox-Rabinovitz **

V. Krasnopolsky , 2008: "Neural Network Applications to Developing Hybrid Atmospheric and Oceanic Numerical Models ", a book chapter in "Artificial Intelligence in Environmental Sciences", ed. by S.E. Haupt, A. Pasini, and C. Marzban, Springer, 375 pp.

**PI Alberto Franceschetti **

J.W. Luo, A. Franceschetti, and A. Zunger, "Carrier multiplication in semiconductor nanocrystals: Theoretical screening of candidate materials based on band-structure effects", Nano Letters 8, 3174 (2008).

A. Franceschetti, S. Lany, and G. Bester, "Quantum-dot intermediate-band solar cells with inverted band alignment", Physica E 41, 15 (2008).

V. Mlinar, A. Franceschetti, and A. Zunger, "Rules of peak multiplicity and peak alignment in multiexcitonic spectra of (In,Ga)As quantum dots", Phys. Rev. B 79, 121307(R) (2009).

A. Franceschetti and M.C. Troparevsky, "Pseudopotential theory of electronic excitations in semiconductor nanostructures", Journal of Computational and Theoretical Nanoscience, 6, 1272 (2009).

J.W. Luo, A. Franceschetti, and A. Zunger, "Nonmonotonic size dependence of the dark/bright exciton splitting in GaAs nanocrystals", Phys. Rev. B 79, 201301(R) (2009).

A. Franceschetti et al., "Origin of one-photon and two-photon optical transitions in PbSe nanocrystals", Phys. Rev. B 79, 241311(R) (2009).

J.W. Luo, A. Franceschetti, and A. Zunger, "Direct-bandgap InAs quantum-dots have long-range electron-hole exchange whereas indirect gap Si dots have short-range exchange", Nano Letters 9, 2648 (2009).

S.L. Sewall, A. Franceschetti, R.R. Cooney, A. Zunger, and P. Kambhampati, "Direct observation of the structure of band-edge biexcitons in colloidal semiconductor CdSe quantum dots", Phys. Rev. B 80, 081310 (2009).

**PI Stuart Freedman **

S.Abe et al. [KamLAND Collaboration], "Study of the Production of Radioactive Isotopes through Cosmic Muon Spallation in KamLAND", submitted to Physical Review C.

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

S.Abe et al. [KamLAND Collaboration], "Precision Measurement of Neutrino Oscillation Parameters with KamLAND,'' Phys. Rev. Lett. 100, 221803 (2008).

C. Arnaboldi et al. [CUORICINO Collaboration], "Results from a search for the nu beta beta-decay of {130}Te," Phys. Rev. C 78, 035502 (2008).

**PI Arthur Freeman **

M. S. Park, J.-H. Song, and A. J. Freeman,Charge imbalance and magnetic properties at the Fe3O4/BaTiO3 interface, Phys. Rev. B 79, 024420 (2009).

M. D. Irwin, D. B. Buchholz, B. J. Leever, J. Liu, J. Emery, M. Zhang, J.-H. Song, A. J. Freeman, M. J. Bedzyk, M. C. Hersam, R. P. H. Chang, and T. J. Marks, Microstructure, Electronic Structure, and Function of NiO Anode Overlayers in High-Efficiency P3HT:PCBM Bulk-Heterojunction Organic Photovoltaic Devices, submitted to J. Am. Chem. Soc.

G. Trimarchi, A. J. Freeman, and A. Zunger, Predicting stable stoichiometries of compounds via evolutionary global space-group optimization,Phys. Rev. B 80, 092101 (2009)

I. Todorov, D. Y. Chung, C. D. Malliakas, Q. Li, T. Bakas, A. Douvalis, G. Trimarchi, K. Gray, J. F. Mitchell, A. J. Freeman, and M. G. Kanatzidis, CaFe4As3: A Metallic Iron Arsenide with Anisotropic Magnetic and Charge-Transport Properties, J. Am. Chem. Soc., 131 (15), 5405, (2009)

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

J-H. Lee, A. J. Freeman, and M. Weinert, Magnetically driven structural transformation of iron, submitted to Phys. Rev. Lett.

**PI James Freericks **

B. Moritz, T. P. Devereaux, and J. K. Freericks, "Time-resolved photoemission of strongly correlated electrons driven out of equilibrium," arXiv:0908.1807 [cond-mat.str-el] (Submitted to Physical Review Letters)

**PI Alex Friedman **

J.-L. Vay, "Application of the Reduction of Scale Range in a Lorentz Boosted Frame to the Numerical Simulation of Particle Acceleration Devices," to be published in the Proceedings of the 2009 Particle Accelerator Conference, Vancouver, Canada, 4-8 May 2009.

J.-L. Vay, C. M. Celata, M. Furman, M. Venturini, and K. G. Sonnad, "Update on Electron-Cloud Simulations Using the Package WARP-POSINST," to be published in the Proceedings of the 2009 Particle Accelerator Conference, Vancouver, Canada, 4-8 May 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).

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).

A. Friedman, J. J. Barnard, R. J. Briggs, M. Dorf, D. P. Grote, E. Henestroza, I. D. Kaganovich, M. Leitner, E. P. Lee, B. G. Logan, A. B. Sefkow, W. M. Sharp, W. L. Waldron, D. R. Welch, and S. S. Yu, "Toward 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).

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

J.-L. Vay, "Simulation of Beams or Plasmas Crossing at Relativistic Velocity," Physics of Plasmas 15, 056701 (2008).

C. M. Celata, M. A. Furman, J.-L. Vay, and J. W. Wu, "Electron Cloud Cyclotron Resonances in the Presence of a Short-Bunch Relativistic Beam," Phys. Rev. ST Accel. Beams 11, 091002 (2008).

**PI Guoyong Fu **

G. Y. Fu, "Energetic-Particle-Induced Geodesic Acoustic Mode", Phys. Rev. Lett. 101, 185002 (2008).

J. Lang, Y. Chen, S.E. Parker, and G.Y. Fu, "Gyrokinetic delta_f particle simulations of toroidicity-induced Alfven eigenmode", submitted to Physics of Plasmas, August 2009.

**PI Inez Fung **

Lee, JE, Johnson, K Fung, I (2009). Precipitation over South America during the Last Glacial Maximum: An analysis of the "amount effect" with a water isotope-enabled general circulation model. GEOPHYSICAL RESEARCH LETTERS 36 DOI: 10.1029/2009GL039265

Lee, JE Fung, I DePaolo, DJ Otto-Bliesner, B (2008). Water isotopes during the Last Glacial Maximum: New general circulation model calculations. JOURNAL OF GEOPHYSICAL RESEARCH-ATMOSPHERES 113 D19 DOI: 10.1029/2008JD009859

**PI Miguel Furman **

CONTINUING STUDY ON ELECTRON-CLOUD CLEARING TECHNIQUES IN HIGH INTENSITY POSITRON RING: MITIGATION BY USING GROOVE SURFACE IN VERTICAL MAGNETIC FIELD Y. Suetsugu, H. Fukuma, M. Pivi, L. Wang Nuclear Inst. and Methods in Physics Research, A, 604 (3), p.449-456, (2009) Nuclear Inst. and Methods in Physics Research, A, 598 (2), p.372-378, (2009.)

DEMONSTRATION OF ELECTRON CLEARING EFFECT BY MEANS OF A CLEARING ELECTRODE IN HIGH-INTENSITY POSITRON RING Y. Suetsugu, H. Fukuma, L. Wang, M. Pivi, A. Morishige, Y. Suzuki, M.Tsukamoto, M. Tsuchiya Nuclear Inst. and Methods in Physics Research, A, 598 (2), p.372-378, (2009).

SHARP REDUCTION OF THE SECONDARY ELECTRON EMISSION YIELD FROM GROOVED SURFACE M. Pivi, F. K. King, R. E. Kirby, T. O. Raubenheimer, G. Stupakov and F. Le Pimpec Journal of Applied Physics 104, 104904 (2008).

## G

**PI Giulia Galli **

The nature and strength of inter-layer binding in graphite, L.Spanu, S.Sorella and G.Galli (submitted to Phys. Rev. Lett. 2009).

High energy excitations of silicon nanoparticles, A.Gali, D.Rocca, G.Zimany and G.Galli (submitted to Nanolett. 2009).

Solution of the Bethe-Salpeter equation within density matrix perturbation theory: ab-initio calculations of absorption spectra, D.Rocca, D.Lu and G.Galli (submitted to Phys. Rev. Lett. 2009).

Emerging Photoluminescence in Monolayer MoS2, A. Splendiani, Y. Zhang, T. Li, J. Kim, C-Y. Chim, G. Galli, and F. Wang (submitted to Phys. Rev. Lett. 2009 ).

The 1,4-Phenylenediisocyande Dimer: Gas-phase properties and insights into organic self-assembled monolayers , Ryan P. Steele,Robert A. DiStasio Jr., Martin Head-Gordon, Yan Li and Giulia Galli (submitted to PCCP 2009).

Surface Induced Crystallization in Supercooled Tetrahedral Liquids, T.Li, D.Donadio, L.Ghiringhelli and G.Galli, Nature Materials 8, 726 (2009).

Ab initio calculation of van der Waals bonded molecular crystals, D. Lu, Y. Li, D. Rocca and G. Galli, Phys. Rev. Lett. 102, 206411 (2009).

Calculation of Quasi-Particle Energies of Aromatic Self-Assembled Monolayers on Au(111), Y. Li, D. Lu and G. Galli, JCTC, 5, 881 (2009).

Electronic Structure of Thiol-Covered Gold Nanoparticles: Au102(MBA)44, Y.Li, G.Galli and F.Gygi, ACS Nano, 2, 1896 (2008).

**PI Bruce Garrett **

SS Xantheas, "Dances with Hydrogen Cations" Nature 457, 673 (2009). Invited News & Views article

SS Xantheas, GA Voth, "Aqueous Solutions and their Interfaces", Journal of Physical Chemistry B 113, 3997 (2009)

CD Wick and SS Xantheas, "Computational Investigation of the First Solvation Shell Structure of Interfacial and Bulk Aqueous Chloride and Iodide Ions", Special Issue on Aqueous solutions and their Interfaces (invited), Journal of Physical Chemistry B 113, 4141 (2009). Journal cover

S Yoo, MV Kirov and SS Xantheas, "Lowest energy networks of the T-cage (H2O)24 cluster and their use in constructing unit cells of the structure I hydrate lattice", Communication to the Editor, Journal of the American Chemical Society 131, 7564 (2009). Highlighted in the "Science Concentrates" section, Chemical & Engineering News, June 1st (2009). Selected for DOE National Impact feature article

S Yoo, XC Zeng and SS Xantheas, "On the phase diagram of water with density functional potentials: the melting temperature of ice Ih with the Perdew-Burke-Ernzerhof and Becke-Lee-Yang-Parr functionals", Communication to the Editor, Journal of Chemical Physics 130, 221102 (2009). Featured in the Virtual Journal of Biological Physics Research. 3rd most downloaded paper in July 2009

X-B Wang, J Werhahn, L-S Wang, K Kowalski, A Laubereau and SS Xantheas, "Observation of a remarkable temperature effect in the hydrogen bonding structure and dynamics of the CN-(H2O) cluster", Letter to the Editor, Journal of Physical Chemistry A 113, 9579 (2009). Journal cover

M Valiev, R D'Auria, DJ Tobias, BC Garrett, "Interactions of Cl- and OH radical in aqueous solution", J. Phys. Chem. A 113, 8823 (2009)

N Govind, PV Sushko, WP Hess, M Valiev, K Kowalski, "Excitons in potassium bromide: A study using embedded time-dependent density functional theory and equation-of-motion coupled cluster methods", Chem. Phys. Lett. 470, 353 (2009)

KA Maerzke, G Murdachaew, CJ Mundy, GK Schenter, JI Siepmann, " Self-Consistent Polarization Density Functional Theory: Application to Argon" J. Phys. Chem. A 113, 2075 (2009)

SM Kathmann, GK Schenter, BC Garrett, B Chen, JI Siepmann, "Thermodynamics and Kinetics of Nanoclusters Controlling Gas-to-Particle Nucleation", J. Phys. Chem. C 113, 10354 (2009)

N Hontama, Y Inokuchi, T Ebata, C Dedonder-Lardeux, C Jouvet, and SS Xantheas, "The structure of the Calix[4]arene-(H2O) cluster, world's smallest cup of water", Journal of Physical Chemistry A, ASAP article: DOI:10.1021/jp902967q (2009). Journal cover

F Paesani, SS Xantheas and GA 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, ASAP article: DOI: 10.1021/jp907648y (2009)

X Sun, S Yoo, SS Xantheas, LX Dang, "The reorientation mechanism of hydroxide ions in water: A molecular dynamics study", Frontiers article (invited), Chemical Physics Letters, ASAP article: DOI: 10.1016/j.cplett.2009.09.004 (2009). Journal cover

E Apra, RJ Harrison, WA deJong, AP Rendell, V Tipparaju, SS Xantheas, "Liquid Water: Obtaining the right answer for the right reasons", SC'09: Proceedings of the 2009 ACM/IEEE conference on Supercomputing (accepted, May 2009). Considered in the final round for the Gordon-Bell price

S Yoo, SS Xantheas, XC Zeng, "The melting temperature of Bulk Silicon from Ab initio Molecular Dynamics Simulations" Chemical Physics Letters (accepted, 09/21/2009)

**PI Silvina Gatica **

Ordering transition of gases adsorbed on a C_60 surface: Monte Carlo simulations and lattice-gas models, Silvina M. Gatica, Milen K. Kostov, and Milton W. Cole, Phys. Rev. B 78, 205417 (2008)

**PI Cameron Geddes **

C.G.R. Geddes, E. Cormier-Michel, E.H. Esarey, C.B. Schroeder, J-L. Vay, W.P. Leemans, and the LOASIS team, LBNL; D.L. Bruhwiler, J.R. Cary, B. Cowan, M. Durant, P. Hamill, P. Messmer, P. Mullowney, C. Nieter, K. Paul, S. Shasharina, S. Veitzer, and the VORPAL development team, Tech-X; G. Weber, O. Rubel, D. Ushizima, Prabhat, and E.W. Bethel, VACET; and J. Wu, SciDAC Scientific Data Management Center, "Laser Plasma Particle Accelerators: Large Fields for Smaller Facility Sources," SciDAC Review 13, pp. 13 (2009). LBNL-2299E. (Journal cover)

C. Huang, W. An, V.K. Decyk, W. Lu, W.B. Mori, F. S. Tsung, M. Tzoufras, S. Morshed, T. Antonsen, B. Feng, T Katsouleas, R.A. Fonseca, S.F. Martins, J. Vieira, L.O Silva, E. Esarey, C. G. R. Geddes, W. P. Leemans, E. Cormier-Michel, J.-L. Vay, D. L. Bruhwiler, B. Cowan, J. R.Cary, K. Paul "Recent results and future challenges for large scale Particle-In-Cell simulations of plasma-based accelerator concepts," In Journal of Physics Conference Series, Proceedings of SciDAC 2009. LBNL-2202E.

J.-L. Vay, D. L. Bruhwiler, C. G. R. Geddes, W. M. Fawley, S. F. Martins, J. R. Cary, E. Cormier-Michel, B. Cowan, R. A. Fonseca, M. A. Furman, W. Lu, W. B. Mori, L. O. Silva "Simulating relativistic beam and plasma systems using an optimal boosting frame," In Journal of Physics Conference Series, Proceedings of SciDAC 2009. LBNL-2201E. [Vay, Geddes etal, Boosted Frame Simulation JCP 2009.pdf]

E. W. Bethel, C. Johnson, S. Ahern, J. Bell, P.-T. Bremer, H. Childs, E. Cormier-Michel, M. Day, E. Deines, T. Fogal, C. Garth, C. G. R. Geddes, H. Hagen, B. Hamann, C. Hansen, J. Jacobsen, K. Joy, J. Kruger, J. Meredith, P. Messmer, G. Ostrouchov, V. Pascucci, K. Potter, Prabhat, D. Pugmire, O. Rubel, A. Sanderson, C. Silva, D. Ushizima, G. Weber, B. Whitlock, K. Wu. "Occam's Razor and Petascale Visual Data Analysis." In Journal of Physics Conference Series, Proceedings of SciDAC 2009.

K. Wu, S. Ahern, E. W. Bethel, J. Chen, H. Childs, E. Cormier-Michel, C. Geddes, J. Gu, H. Hagen, B. Hamann, W. Koegler, J. Lauret, J. Meredith, P. Messmer, E. Otoo, V. Perevoztchikov, A. Poskanzer, Prabhat, O. Rubel, A. Shoshani, A. Sim, K. Stockinger, G. Weber, W.-M. Zhang. "FastBit: Interactively Searching Massive Data." In Journal of Physics Conference Series, Proceedings of SciDAC 2009. LBNL- 2164E.

K. Wu, A. Shoshani, and E. Otoo "FastBit: A Lightning-Fast Index Drives Massive Data Analysis." SciDAC Review 2009.

**PI Phillip Geissler **

Gin BC, Garrahan JP, Geissler PL. The Limited Role of Nonnative Contacts in the Folding Pathways of a Lattice Protein. Journal of Molecular Biology 392 (2009) pp. 1303-1314

**PI Alexandros Gezerlis **

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

**PI Stephen Gray **

Rayleigh anomaly-surface plasmon polariton resonances in palladium and gold subwavelength hole arrays H. Gao, J. M. McMahon, M. H. Lee, J. Henzie, S. K. Gray, G. C. Schatz, and T. W. Odom, Optics Express 17, 2334-2340 (2009).

Confining standing waves in optical corrals Y. Babayan, J. M. McMahon, S. Li, S. K. Gray, G. C. Schatz, and T. W. Odom, ACS Nano 3, 615-620 (2009).

SERS enhancements via periodic arrays of gold nanoparticles on silver film structures J. M. Montgomery, A. Imre, U. Welp, V. Vlasko-Vlasov, and S. K. Gray, Optics Express 17, 8669-8675 (2009).

Model plasmonic crystals for detecting and spatially imaging surface bound species by surface- enhanced Raman scattering A. J. Baca, T. T. Truong, L. R. Cambrea, J. M. Montgomery, S. K. Gray,D. Abdula, T. R. Banks, J. Yao, R. G. Nuzzo, and J. A. Rogers, Appl. Phys. Lett. 94, 243109 (2009).

High fidelity nano-hole enhanced Raman spectroscopy J. T. Bahns, Q. Guo, J. M. Montgomery, S. K. Gray, H. M. Jaeger, and L. Chen, J. Phys. Chem. C 113, 11190-11197 (2009).

**PI Chris Greene **

N. Douguet, J. Blandon, and V. Kokoouline "Correlation diagrams in a process of collision of three identical particles" J. Phys. B: At. Mol. Opt. Phys. 41, 045202 (2008).

N. Douguet, V. Kokoouline, and C.H. Greene, "Theoretical rate of dissociative recombination of HCO+ and DCO+ ions" Phys. Rev. A 77 064703 (4pp) (2008).

L. Pagani, C. Vastel, E. Hugo, V. Kokoouline, C. H. Greene, A. Bacmann, E. Bayet, C. Ceccarelli, R. Peng, and S. Schlemmer, "Chemical modeling of L183 (=L134N): an estimate of the ortho/para H2 ratio" A&A 494, 623(14pp) (2009).

J. Glosik, I. Korolov, R. Plasil, O. Novotny, T. Kotrik, P. Hlavenka, J. Varju, I.A. Mikhailov, V. Kokoouline, and Chris H. Greene, "Recombination of H3+ Ions in the Afterglow of a He-Ar-H2 Plasma" J. Phys. B: At. Mol. Opt. Phys. 41, 191001 (6pp) (2008).

J. Blandon and V. Kokoouline "Geometrical phase driven predissociation: Lifetimes of 2^2A' levels of H3" Phys. Rev. Lett. 102, 143002 (4pp) (2009).

J. Glosik, R. Plasil, I. Korolov, T. Kotrik, P. Dohnal, O. Novotny, P. Hlavenka, J. Varju, V. Kokoouline, C.H. Greene "Temperature dependence of binary and ternary recombination of H3+ ions with electrons" Phys. Rev. A 79, 052707 (2009)

N. Douguet, V. Kokoouline, and C.H. Greene "Theory of dissociative recombination of a linear triatomic ion with permanent electric dipole moment: Study of HCO+" Submitted (2009)

J. Glosik, I. Korolov, R. Plasil, T. Kotrik, P. Dohnal, O. Novotny, J. Varju, C.H. Greene, V. Kokoouline "Binary and ternary recombination of D3+ ions with electrons in He-D2 plasma" Phys. Rev. A Accepted (2009)

**PI Jeffrey Grossman **

G. E. Begtrup, W. Gannett, J. C. Meyer, T. D. Yuzvinsky, B. M. Kessler, E. Ertekin, J. C. Grossman, A. Zettl, Phys. Rev. B 79, 205409 (2009).

E. Ertekin, M. S. Daw, D. C. Chrzan, Phys. Rev. B 79, 155421 (2009).

J.-H. Lee, G. A. Galli and J. C. Grossman, Nano Lett. 8, 3750 (2008).

J.-H. Lee and J. C. Grossman, Appl. Phys. Phys. 95, 013136 (2009).

**PI Hua Guo **

M. Jorfi, P. Honvault, P. Halvick, S.Y. Lin, and H. Guo, Chem. Phys. Lett., 462, 53 (2008), Quasiclassical trajectory scattering calculations for the OH + O --> H + O2 reaction: cross sections and rate constants

S. Y. Lin, and H. Guo, J. Chem. Phys., 129, 124311 (2008), Energy dependence of the differential and integral cross section for the O(1D) + H2 --> OH + H reaction.

W. Lai, S. Y. Lin, D. Xie, and H. Guo, J. Chem. Phys., 129, 154311 (2008), Full-dimensional quantum dynamics of A-state photodissociation of ammonia. Absorption spectra.

S. Lin, D. Xie, and H. Guo, J. Chem. Phys., 129, 154313 (2008), Ab initio potential energy surfaces for both the ground (X1A') and excited (A1A") electronic states of HGeCl and the absorption and emission spectra of HGeCl/DGeCl.

Z. Sun, D. Zhang, C. Xu, S. Zhou, D. Xie, G. Lendvay, S.-Y. Lee, S. Y. Lin, and H. Guo, J. Am. Chem. Soc. (communication), 130, 14962 (2008), State-to-state dynamics of H + O2 reaction, evidence for non-statistical behaviors.

S. Y. Lin and H. Guo, J. Phys. Chem. A (Schatz Festschrift), 113, 4285 (2009), Adiabatic and non-adiabatic state-to-state quantum dynamics for O + H2 --> OH + H reaction.

Z. Sun, S.-Y. Lee, H. Guo, D. H. Zhang, J. Chem. Phys., 130, 174102 (2009), Comparison of second-order split operator and Chebyshev propagator in wave packet based state-to-state reactive scattering calculations. (One of ten most download articles from J. Chem. Phys., May 2009)

S. Zhou, Z. Li, D. Xie, S. Y. Lin, and H. Guo, J. Chem. Phys., 130, 184307 (2009), An ab initio global potential-energy surface for NH2(A2A') and vibrational spectrum of the Renner-Teller A2A'- X2A" system.

S. Y. Lin, H. Guo, G. Lendvay, and D. Xie, Phys. Chem. Chem. Phys. (Special Issue on Electronic Structures and Reaction Dynamics of Open-shell Species), 11, 4715 (2009), Effects of reactant rotational excitation on H + O2 --> OH + O reaction rate constant: quantum wave packet, quasi-classical trajectory, and phase space theory calculations.

S. Lin, D. Xie, and H. Guo, J. Phys. Chem. A (Gerber Festschrift), 113, 7314 (2009), Ab initio potential energy surfaces for the ground and excited electronic states of HGeBr and the absorption and emission spectra of HGeBr/DGeBr.

**PI William Gutowski **

JM Prusa, PK Smolarkiewicz, and AA Wyszogrodzki, 2008, "EULAG, a computational model for multiscale flows", Computers & Fluids V37, 1193-1207.

BJ Abiodun, JM Prusa, and WJ Gutowski, 2008a, "Implementation of a non-hydrostatic, adaptive-grid dynamics core in CAM3. Part I: comparison of dynamics cores in aqua-planet simulations", Clim Dyn V31, 795-810.

BJ Abiodun, WJ Gutowski, and JM Prusa, 2008b, "Implementation of a non-hydrostatic, adaptive-grid dynamics core in CAM3. Part II: dynamical influences on ITCZ behavior and tropical precipitation", Clim Dyn V31, 811-822.

## H

**PI Stephan Haas **

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

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

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

Electron-phonon bound states and impurity band formation in quantum wells B.P.W. de Oliveira and S. Haas, Phys. Rev. B {\bf 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 {\bf 79}, 104510 (2009).

Quantum fluctuations in small lasers}\\ K. Roy-Choudhury, S. Haas, and A.F.J. Levi, Phys. Rev. Lett. {\bf 102}, 053902 (2009).

Subarea law of entanglement in nodal fermionic systems}\\ L. Ding, N. Bray-Ali, R. Yu, and S. Haas, Phys. Rev. Lett. {\bf 100}, 215701 (2008).

Entanglement, fidelity, and topological entropy in a quantum phase transition to topological order A. Hamma, W. Zhang, S. Haas, and D. A. Lidar, Phys. Rev. B {\bf 77}, 155111 (2008).

Scaling Analysis and Application: Phase Diagram of Magnetic Nanorings and Elliptical Particles W. Zhang, R. Singh, N. Bray-Ali, and S. Haas, Phys. Rev. B {\bf 77}, 144428 (2008).

Entanglement entropy in the two-dimensional random transverse field Ising model}\\ R. Yu, H. Saleur, and S. Haas, Phys. Rev. B {\bf 77}, 140402 (2008).

Optimal control of electromagnetic field using metallic nanoclusters I. Grigorenko, S. Haas, A.V. Balatsky, and A.F.J. Levi, New J. Phys. {\bf 10}, 043017 (2008).

Field induced disordered-local-moment phase in site-diluted spin-gap antiferromagnets R. Yu, T. Roscilde, and S. Haas, New J. Phys. {\bf 10}, 013034 (2008).

**PI 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," submitted to Phys. Rev. Lett. (Sept 2009).

**PI Bruce Harmon **

Feng-Chuan Chuang, Chia-Hsiu Hsu, C. Z. Wang, and K. M. Ho, Atomic and electronic structures of Ag/Si(111)-c(12x2) surface: A first-principles study, Phys. Rev. B 78, 245418 (2008).

M. Li, C. Z. Wang, J. W. Evans, M. Hupalo, M. C. Tringides, and K. M. Ho, Competition Netween Area and Height Evolution of Pb Islands on Si(111) Surface, Phys. Rev. B 79, 113404 (2009).

T. L. Chan, C. Z. Wang, K. M. Ho, J. Chelikowsky, Efficient first-principles simulation of non-contact atomic force microscopy for structural analysis Phys. Rev. Lett. 102, 176101 (2009).

Wei Zhang, Wen-Cai Lu, Qing-Jun Zang, C. Z. Wang, and K. M. Ho, Bulklike Structures for Medium-sized Aln (n=31-40) Clusters, J. Chem. Phys. 130, 144701 (2009).

Wei Ren, C. Z. Wang, K. M. Ho, C.T. Chan, Transport in a metallic nanotube at finite temperature, Phys. Rev. B. 79, 161404(R) (2009)..

Xiao-Ping Li, W. C. Lu, Q. J. Zang, Guangju Chen, C. Z. Wang, K. M. Ho, Structures and Stabilities of Pbn (n < 20) Clusters, J. Phys. Chem. A 113, 6217 (2009).

Y. X. Yao, C. Z. Wang, G. P. Zhang, M. Ji and K. M. Ho, A first-principles divide-and-conquer approach for electronic structure of big systems and its application to graphene nanoribbons, J. Phys. Condens Matters, 21, 235501 (2009).

G. Vantarakis, C. Mathioudakis, G. Kopidakis, C. Z. Wang, K. M. Ho, and P. C. Kelires, Interfacial disorder and optoelectronic properties of diamond nanocrystals, Phys. Rev. B 80, 045307 (2009).

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

A planar four-port channel drop filter in the 3-d woodpile photonic crystal, D. Stiehler, A. Barsic, R. Biswas. G. Tuttle. K.-M. Ho, Optics Express 17, 6128-6133 (2009).

Waveguide bends and circuits in three-dimensional photonic crystals, R. Biswas, C. Christensen, J. Muehlmeier, G. Tuttle, K-M. Ho, Photonics and Nanostructures 6, 208 (2008) doi:10.1016/j.photonics.2008.03.002

Sharp thermal emission and absorption from conformally coated metallic photonic crystal with triangular lattice, R. Biswas, D. Zhou, I. Puscasu, E. Johnson, A. Taylor and W. Zhao, Applied Physics Letters 93, 063307 (2008). Virtual J of Nanoscale Science & Technology 18 (September 2008.

Simulation of plasmonic crystal enhancement of absoprtion in thin film solar cells, R. Biswas, D. Zhou, L. Garcia, MRS Symposium Proceedings 1153, Symp A (2009).

R. Biswas, W. Zhao, I. Puscasu, E. Johnson, "Angular variation of absorption and thermal emission from photonic crystals," J Opt Soc. of America B 26, Iss. 9, pp. 1808"1817 (2009).

**PI Charles Harris **

J.F. Cahoon, M.F. Kling, K.R. Sawyer, L.K. Andersen, C.B. Harris, "DFT and Time-resolved IR Investigation of Electron Transfer between Photogenerated 17- and 19-electron organometallic radicals", J. Mol. Struct., 890, 328-338 (2008).

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, C.B. Harris, "Time-resolved IR studies on the mechanism for the functionalization of primary C-H bonds by tungsten-boryl complexes.", J. Am. Chem. Soc., submitted.

**PI Martin Head-Gordon **

Maximoff S, Head-Gordon M. "Chemistry of fast electrons", PNAS, 106, 2009.

Casanova D, Rhee YM, Head-Gordon M. "Quasidegenerate scaled opposite spin second order perturbation corrections to single excitation configuration interaction", JOURNAL OF CHEMICAL PHYSICS, 128(16), 2008.

Tkatchenko A, DiStasio RA, Head-Gordon M, et al. "Dispersion-corrected Moller-Plesset second-order perturbation theory", JOURNAL OF CHEMICAL PHYSICS, 131(9), 2009.

Lochan RC, Khaliullin RZ, Head-Gordon M. "Interaction of molecular hydrogen with open transition metal centers for enhanced binding in metal-organic frameworks: A computational study", INORGANIC CHEMISTRY, 47(10), 2008.

Saravanan C, Markovic NM, Head-Gordon M, et al. "Multi-Scale Modeling of CO Oxidation on Pt-Based Electrocatalysts", DEVICE AND MATERIALS MODELING IN PEM FUEL CELLS, 113, 2009.

Lawler KV, Parkhill JA, Head-Gordon M. "Penalty functions for combining coupled-cluster and perturbation amplitudes in local correlation methods with optimized orbitals", MOLECULAR PHYSICS, 106(19), 2008.

Thom AJW, Head-Gordon M. "Locating Multiple Self-Consistent Field Solutions: An Approach Inspired by Metadynamics", PHYSICAL REVIEW LETTERS, 101(19), 2008.

Khaliullin RZ, Bell AT, Head-Gordon M. "Electron Donation in the Water-Water Hydrogen Bond", CHEMISTRY-A EUROPEAN JOURNAL, 15(4), 2009.

Casanova D, Slipchenko LV, Krylov AI, et al. "Double spin-flip approach within equation-of-motion coupled cluster and configuration interaction formalisms: Theory, implementation, and examples", JOURNAL OF CHEMICAL PHYSICS, 130(4), 2009.

Tkatchenko A, DiStasio RA, Head-Gordon M, et al. "Dispersion-corrected Moller-Plesset second-order perturbation theory", JOURNAL OF CHEMICAL PHYSICS, 131(9), 2009.

Steele RP, DiStasio RA, Head-Gordon M. "Non-Covalent Interactions with Dual-Basis Methods: Pairings for Augmented Basis Sets", JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 5(6), 2009.

Willard AP and Chandler D. "Coarse-grained modeling of the interface between water and heterogeneous surfaces," Faraday Discuss. 141, 209-220 (2009).

Willard, A.P., S.K. Reed, P.A. Madden, and D. Chandler, "Water at an electrochemical interface--a simulation study," Faraday Discuss. 141, 423-441 (2009).

**PI Teresa Head-Gordon **

J. Z. Ruscio, N. Lux Fawzi & T. Head-Gordon (2009). How hot? Systematic convergence of the replica exchange method using multiple reservoirs. J. Comp. Chem. Published online (http://www3.interscience.wiley.com /cgi-bin/fulltext/122465268.)

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

J. E. Kohn, P. Afonine, J. Z. Ruscio, P. D. Adams, T. Head-Gordon (2009). Validation of molecular dynamics models using x-ray crystallographic data. 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. (http://pubs.acs.org/doi/full/10.1021/ja905396s ).

A. Sodt and T. Head-Gordon (2009). An implicit solvent coarse-grained lipid model for transmembrane protein oligomerization. Submitted to Biophys. J.

M. E Johnson, C. Malardier-Jugroot, and T. Head-Gordon (2009). Effects of co-solvents on peptide hydration water structure and dynamics. Submitted to Phys. Chem. Chem. Phys.

N. Lux Fawzi, E.-H. Yap, Y. Okabe, K. Kohlstedt, S. P. Brown & T. Head-Gordon (2008). Contrasting disease and non-disease protein aggregation. Acc. Chem. Research 41, 1037-1047.

N. Lux Fawzi, A. Phillips, J. Z. Ruscio, M. Doucleff, D. E. Wemmer & T. Head-Gordon (2008). Structure and dynamics of the Alzheimer"s A 21-30 peptide from the interplay of NMR experiments and simulation. J. Am. Chem. Soc. 130, 6145-6158.

M. S. Lin and T. Head-Gordon (2008). Improved energy selection of native loops from loop decoys. J. Chem. Theory Comput, 4, 515-521 (Cover article).

T. Head-Gordon and R. M. Lynden-Bell (2008). Hydrophobic solvation of Gay-Berne particles in modified water models. J. Chem. Phys. 128, 104506-104512.

N. Lux Fawzi, K. Kohlstedt, Y. Okabe & T. Head-Gordon (2008). Protofibril assemblies of the Arctic, Dutch and Flemish mutants of the Alzheimer"s Ab1-40 peptide. Biophys. J. 94, 2007-2016.

R. K. Murakra and T. Head-Gordon (2008). Dielectric relaxation of aqueous solutions of hydrophobic and hydrophilic peptides. J. Phys. Chem. B 112, 179-186.

E.-H. Yap, N. Lux Fawzi & T. Head-Gordon (2008). A coarse-grained carbon protein model with anisotropic hydrogen-bonding. Proteins, Struct. Func.. Bioinf. 70, 626-638.

**PI Ian Hinchliffe **

The ATLAS Experiment at the CERN Large Hadron Collider. By ATLAS Collaboration (G. Aad et al.). 2008. 437pp. Published in JINST 3:S08003,2008.

**PI Kai-Ming Ho **

Y. Han and D.J. Liu, Quantum size effects in metal nanofilms: comparison of an electron-gas model and density functional theory calculations Phys. Rev. B, in press (2009)

Rajesh Sathiyanarayanan, T.L. Einstein , Ab-initio calculations of interactions between Cu adatoms on Cu(1 1 0): Sensitivity of strong multi-site interactions to adatom relaxations Surface Science 603 (2009) 2387-2392

Ajmi BH Hamouda T J Stasevich, Alberto Pimpinelli and T L Einstein Effects of impurities on surface morphology: some examples J. Phys.: Condens. Matter 21 (2009) 084215 (10pp)

Rajesh Sathiyanarayanan, T.J. Stasevich, and T L Einstein, Sensitivity of Short-Range Trio Interactions to Lateral Relaxation of Adatoms: Challenges for Detailed Lattice-Gas Modeling, Surface Sci. 602, 1243-1249 (2008)

A. B. Pang, K. L. Man, M. S. Altman, T. J. Stasevich, F. Szalma, and T. L. Einstein, Step line tension and step morphological evolution on the Si(111) (1x1) surface, Phys. Rev. B 77, 115424 (2008).

Yoon M, Yang SY, Zhang ZY, Interaction between hydrogen molecules and metallofullerenes, JOURNAL OF CHEMICAL PHYSICS Volume: 131 Issue: 6 Article Number: 064707 Published: AUG 14 2009

Chen H, Zhu WG, Kaxiras E, et al. Optimization of Mn doping in group-IV-based dilute magnetic semiconductors by electronic codopants, PHYSICAL REVIEW B Volume: 79 Issue: 23 Article Number: 235202 Published: JUN 2009

Li MZ, Yao YG, Wu BA, et al. Strain effect on the instability of island formation in submonolayer heteroepitaxy EPL Volume: 86 Issue: 1 Article Number: 16001 Published: APR 2009

Zhao K, Troparevsky MC, Xiao D, et al. Electronic Coupling and Optimal Gap Size between Two Metal Nanoparticles PHYSICAL REVIEW LETTERS Volume: 102 Issue: 18 Article Number: 186804 Published: MAY 8 2009

Song YL, Zhao K, Jia Y, et al. Finite size effects on the electromagnetic field enhancement from low-dimensional silver nanoshell dimer arrays JOURNAL OF CHEMICAL PHYSICS Volume: 129 Issue: 20 Article Number: 204506 Published: NOV 28 2008

Guo Y, Qu ZH, Braiman Y, et al. Nanotribology and Nanoscale Friction SMOOTH SLIDING THROUGH FEEDBACK CONTROL IEEE CONTROL SYSTEMS MAGAZINE Volume: 28 Issue: 6 Pages: 92-100 Published: DEC 2008

Mo YN, Zhu WG, Kaxiras E, et al. Electronic Nature of Step-Edge Barriers against Adatom Descent on Transition-Metal Surfaces PHYSICAL REVIEW LETTERS Volume: 101 Issue: 21 Article Number: 216101 Published: NOV 21 2008

Shegai T, Li ZP, Dadosh T, et al. Managing light polarization via plasmon-molecule interactions within an asymmetric metal nanoparticle trimer PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA Volume: 105 Issue: 43 Pages: 16448-16453 Published: OCT 28 2008

Yang SY, Yoon MN, Wang E, et al. Energetics and kinetics of Ti clustering on neutral and charged C-60 surfaces JOURNAL OF CHEMICAL PHYSICS Volume: 129 Issue: 13 Article Number: 134707 Published: OCT 7 2008

Yang SY, Yoon M, Hicke C, et al. Electron transfer and localization in endohedral metallofullerenes: Ab initio density functional theory calculations PHYSICAL REVIEW B Volume: 78 Issue: 11 Article Number: 115435 Published: SEP 2008

M. Li, C. Z. Wang, J. W. Evans, M. Hupalo, M. C. Tringides, and K. M. Ho, Competition Netween Area and Height Evolution of Pb Islands on Si(111) Surface Phys. Rev. B 79, 113404 (2009)

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

Ji Young Lee and Jun-Hyung Cho, Zhenyu Zhang, Quantum Size Effects in Competing Charge and Spin Orderings of Dangling-Bond Wires on Si(001) Phys. Rev. Lett. Submitted

## I

**PI Hong Im **

Lu T.F., Yoo C.S., Chen J.H., and Law C.K., "Three-dimensional direct numerical simulation of turbulent lifted hydrogen jet flame in heated coflow: A chemical explosive mode analysis," Journal of Fluid Mechanics, submitted.

Narayanan, P. and Trouve, A. (2009), "Radiation-driven flame weakening effects in sooting turbulent diffusion flames," Proceedings of the Combustion Institute, 32, 1481-1489.

Lu T. F., Law C.K., Yoo C.S., and Chen J.H., "Dynamic Stiffness Removal for Direct Numerical Simulations," Combustion and Flame, 156(8) 1542-1551, 2009.

Lignell D.O., Chen J.H., Smith P.J., Lu T.F., and Law C.K., "The Effect of Flame Structure on Soot Formation and Transport in Turbulent Nonpremixed Flames Using Direct Numerical Simulation," Combustion and Flame, 151(1-2) 2, 28, 2007. (Feature issue article)

Wang, Y. and Rutland, C. J. (2007), "Direct numerical simulation of ignition in turbulent n-heptane liquid fuel spray jets," Combustion and Flame, 149, 353-365.

Yoo, C. S. and Im, H. G. (2007), "Characteristic boundary conditions for simulations of compressible reacting flows with multi-dimensional, viscous, and reaction effects," Combustion Theory and Modelling, 11:259-286.

Cook, D. J., Pitsch, H., Chen, J. H., and Hawkes, E. R. (2007), "Flamelet-based modeling of H2/Air Auto-ignition with thermal inhomogeneities," Proceedings of the Combustion Institute, 31, 2903-2911.

Hawkes, E. R., Sankaran, R., Sutherland, J., and Chen, J. H. (2007), "Scalar mixing in direct numerical simulations of temporally-evolving plane jet flames with detailed CO/H2 kinetics," Proceedings of the Combustion Institute, 31, 1633-1640.

Sankaran, R., Hawkes, E. R., Chen, J. H., Lu, T., and Law, C. K. (2007), "Structure of a spatially-developing lean methane-air turbulent bunsen flame," Proceedings of the Combustion Institute, 31, 1291-1298.

Yoo, C. S. and Im, H. G. (2007), "Transient soot dynamics in turbulent nonpremixed ethylene-air counterflow flames," Proceedings of the Combustion Institute, 31, 701-708.

**PI Valerie Izzo **

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, currently in review.

D. Batchelor, G. Abla, E. D'Azevedo, G. Bateman, D. E. Bernholdt, L. Berry, P. Bonoli, R. Bramley, J. Breslau, M. Chance, J. Chen, M. Choi, W. Elwasif, S. Foley, G. Fu, R. Harvey, E. Jaeger, S. Jardin, T. Jenkins, D. Keyes, S. Klasky, S. Kruger, L. Ku, V. Lynch, D. McCune, J. Ramos, D. Schissel, D. Schnack, and J. Wright, "Advances in simulation of wave interactions with extended MHD phenomena", Journal of Physics: Conference Series 180 (SciDAC 2009), 012054 (2009).

V.A. Izzo, P.B. Parks, and L.L. Lao, "DIII-D and ITER rapid shutdown with radially uniform deuterium delivery" Plasma Phys. Control. Fusion 51 (2009) 105004.

R. Takahashi, D.P. Brennan, and C.C. Kim, "Kinetic Effects of Energetic Particles on Resistive MHD Stability", Phys. Rev. Lett 102, 135001 (2009).

R. Takahashi, D.P. Brennan, and C.C. Kim, Nucl. Fusion 49, 065032 (2009).

## J

**PI Stephen Jardin **

L.P. Ku and A. H. Boozer, "Nonaxisymmetric Shaping of Tokamaks Preserving Quasiaxisymmetry," Physics of Plasmas 16, 082506 (2009).

L. Bromberg, et al., "Shaping in Stellarators Using High Temperature Superconducting Monoliths," 36th International conference on Plasma Science and 23rd symposium on fusion Engineering, San Diego, CA, May 31-June 5 (2009).

J. Breslau, N. Ferraro, and S. Jardin, "Some properties of the M3D-C1 form of the 3D magnetohydrodynamics equations," Phys. Plasmas 16, 092503 (2009).

R. Paccagnella, H.R. Strauss, and J. Breslau, "3D MHD VDE and disruptions simulations of tokamaks plasmas including some ITER scenarios," Nucl. Fus. 49 (2009).

L. E. Sugiyama and the M3D Team, "Magnetic X-points, stochasticity, and Edge Localized Modes," J. Phys: Conf. Series 180 (2009) 012060

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

R. Samtaney, N. F. Loureiro, A. A. Schekochihin, D. Uzdensky, S. C. Cowley, Formation of plasmoid chains in magnetic reconnection, Physical Review Letters, 103, 105004 2009.

D. R. Reynolds, R. Samtaney, C. S. Woodward, Operator-base preconditioning of stiff hyperbolic systems, SIAM J. Sci. Comput, to appear, 2009.

V. Wheatley, R. Samtaney, D. I. Pullin, The Richtmyer-Meshkov instability in MHD. Phys. Fluids, 21, 082102, 2009.

**PI Julius Jellinek **

ATOMISTIC DIPOLE MOMENTS AND POLARIZABILITIES OF Na_N Clusters, N= 2-20 K. Jackson, L. Ma, M. Yang, and J. Jellinek J. Chem. Phys. 128, 144309(1-10), (2008)

ATOMISTIC DESCRIPTION OF ELECTRIC DIPOLE POLARIZABILITY IN Si_nH_m S. Srinivas, M. Yang, K. A. Jackson, and J. Jellinek In "Computational Methods in Science and Engineering", Vol. 1, G. Maroulis and T. E. Simos, Eds., AIP Conference Proceedings, 2009, pp. 71-81

ELECTRONIC AND OPTICAL EXCITATIONS IN Agn CLUSTERS (n=1-8): COMPARISON OF DENSITY- FUNCTIONAL AND MANY-BODY THEORIES M. L. Tiago, J. C. Idrobo, S. Ogut, J. Jellinek, and J. R. Chelikowsky Phys. Rev. B 79, 155419 (1-14) (2009)

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

THERMAL BEHAVIOR OF 13-MOLECULE HYDROGEN CLUSTER UNDER PRESSURE R. Santamaria, J. Soullard, and J. Jellinek J. Chem. Phys. (submitted)

**PI Puru Jena **

S. Li and P. Jena Origin of the anatase to rutile conversion of metal-doped TiO2 Phys. Rev. B (Rapid Comm.) 79, 201204 (2009)

Yanwen Wang, Lizhi Zhang, Sa Li, and Puru Jena Polyol-Mediated Synthesis of Ultrafine TiO2 Nanocrystals and Tailored Physiochemical Properties by Ni Doping J. Phys. Chem. C 113, 9210 (2009)

Oleksandr Dolotko, Haiqiao Zhang, Sa Li, Puru Jena, and Vitalij Pecharsky Mechanochemically driven nonequilibrium processes in MNH2-CaH2 systems(M = Li or Na). J. Phys. Chem. C (Submitted in Sep. 2009)

**PI Chueng Ryong Ji **

C. R. Ji, W. Melnitchouk and A. W. Thomas, ``Equivalence of pion loops in equal-time and light-front dynamics,'' Phys. Rev. D, in press (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. D80, 054016 (2009), arXiv:0903.0455 [hep-ph].

M. Blasone, A. Capolupo, C. R. Ji and G. Vitiello, ``On flavor violation for massive and mixed neutrinos,'' Nucl. Phys. Proc. Suppl. 188, 37 (2009), [arXiv:0812.2133 [hep-ph]].

**PI De-en Jiang **

Jiang, D. E.*; Cooper, V. R.; Dai, S. "Porous Graphene as the Ultimate Membrane for Gas Separation." Submitted.

Jiang, D. E.*; Du, M. H.; Dai, S. "First principles study of the graphene/Ru(0001) interface." J. Chem. Phys., 130, 074705 (2009).

Jiang, D. E.*; Dai, S. "Diffusion of the linear CH3S-Au-SCH3 complex on Au(111) from first principles." J. Phys. Chem. C,113, 3763 (2009).

Jiang, D. E.*; Dai, S. "Cis-trans Conversion of the CH3S-Au-SCH3 complex on Au(111)." Phys. Chem. Chem. Phys., in press.

**PI Donald Johnson **

Pierce, R. B., J. A. Al-Saadi, C. Kittaka, T. Schaack, A. Lenzen, K. Bowman, J. Szykman, A. Soja, T. Ryerson, A. Thompson, P. Bhartia (2009), Impacts of background ozone production on Houston and Dallas, Texas, air quality during the Second Texas Air Quality Study field mission, J. Geophys. Res., 114, D00F09, doi:10.1029/2008JD011337.

**K**

**PI Andrey Kalinichev **

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.

R.T.Cygan, J.A.Greathouse, H.Heinz, A.G.Kalinichev (2009) Molecular models and simulations of layered materials. (Invited). Journal of Materials Chemistry, 19, 2470-2481.

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.

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, in print (http://dx.doi.org/10.1039/b907859b).

A.G.Kalinichev, P.Kumar, R.J.Kirkpatrick (2009) Effects of hydrogen bonding on the properties of layered double hydroxides intercalated with organic acids: Molecular dynamics computer simulations. (Invited). Philosophical Magazine, accepted.

**PI Martin Karplus **

S. F. Chekmarev, A. Y. Palyanov, and M. Karplus. Hydrodynamics of Protein Folding, Phys. Rev. Lett. 100, 18107-1-18107-4 (2008),

Q. Cui and M. Karplus. Allostery and Cooperativity Revisited, Protein Science 17, 1295-1307 (2008).

M. Cecchini, A. Houdusse, and M. Karplus. Allosteric Communication in Myosin V: From Small Conformational Changes to Large Directed Movements, PLoS Computational Biology 4, e1000129:1-19 (2008).

S. Krivov, S. Muff, A. Caflisch, and M. Karplus. One-Dimensional Barrier Preserving Free-Energy Projections of a beta-sheet Miniprotein: New Insights into the Folding Process, J. Phys. Chem. B 112, 8701-8714 (2008).

S. Krivov and M. Karplus. Diffusive Reaction Dynamics on Invariant Free Energy, Proc. Natl. Acad. Sci. USA 105, 13841-13846 (2008).

A. S. Khalil, D. C. Appleyard, A. K. Labno, A. Georges, M. Karplus, A. M. Belcher, W. Hwang, M. J. Lang. Kinesin's Cover-Neck Bundle Folds Forward to Generate Force, Proc. Natl. Acad. Sci. USA 105, 19246-19251 (2008).

Y. Kong and M. Karplus. Signaling Pathways of the PDZ2 Domain: A Molecular Dynamics Interaction Correlation Analysis, Proteins: Structure, Function & Genetics 74, 145-154 (2009).

M. Spichty. A. Taly, F. Hagn, H. Kessler, N. Winssinger, and M. Karplus.The HSP90 Binding Mode of a Radicicol-Like E-oxime From Docking, Binding Free Energy Estimations, and NMR 15N Chemical Shift, Biophysical Chem. 143, 111-123 (2009).

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

**PI Paul Kent **

"Dynamics of locking of peptides onto growing amyloid fibrils", G. Reddy, et al., Proc. Natl. Acad. Sci. 106, 11948 (2009)

"Influence of Preformed Asp23-Lys28 Salt Bridge on the Conformational Fluctuations of Monomers and Dimers of A beta Peptides with Implications for Rates of Fibril Formation", G. Reddy et al. J. Phys. Chem. B 113, 1162-1172 (2009).

"Water-mediated interactions between hydrophobic and ionic species in cylindrical nanopores", S. Vaitheeswaran, G. Reddy, D. Thirumalai, J. Chem. Phys. 130, 094502 (2009)

"Nanoscale van der Waals Interactions" M. W. Cole, D. Velegol, Hye-Young Kim, and A. A. Lucas, Molecular Simulation, 35, 849-866 (2009); special invited issue, Frontiers of Molecular Simulation

"van der Waals forces: Accurate calculation and assessment of approximate methods in dielectric nanocolloids upto 16nm" Hye-Young Kim and P. R. C. Kent, Accepted in J. Chem. Phys. (17 September 2009)

"Prediction of Surface Oxygen Vacancy Concentrations of (La1-xSrx)MnO3" Y.-L. Lee and D. Morgan, "ECS Transactions - Vienna, Austria" Volume 25, "Solid Oxide Fuel Cells 11 (SOFC-XI)", to be published in September, 2009.

"Hydrogen bonds and vibrations of water on (110) rutile" N. Kumar, S. Neogi, J. O. Sofo, P. R. C. Kent, A. V. Bandura and J. Kubicki, Geochim. Cosmochim. Acta 73, A705 (2009)

"Hydrogen Bonds and Vibrations of Water on (110) Rutile" N. Kumar, S. Neogi, P. R. C. Kent, A. V. Bandura, J. Kubicki, D. R. Cole, D. J. Wesolowski and J. O. Sofo, J. Phys. Chem. C 113, 13732 - 13740 (2009)

"Thermochemistry of propane activation on cluster models of the M1 phase of Mo-V-Te-Nb-O mixed oxide", Agalya Govindasamy, Muthukumar Kaliappan, Junjun Yu, Ye Xu, and Vadim Guliants, submitted to JPC-C (2009)

"Partial and total reduction of O2 by hydrogen on transition metal surfaces", D. Ford et al. submitted to JACS (2009)

"Electronic properties of metal-modified DNA base pairs", G. Brancolini and R. Di Felice, J. Phys. Chem. B 112, 14281 (2008).

"First principles effective electronic couplings for hole transfer in natural and size-expanded DNA", S. Migliore et al. J. Phys. Chem. B 113, 9402 (2009).

"Ab initio study of the structural, tautomeric, pairing and electronic properties of seleno-derivatives of Thymine." Alvaro Vazquez-Mayagoitia et al. Accepted in the J. of Phys. Chem. B (2009)

"Theoretical study on the intermolecular interactions of potentially primordial base pair analogues" Judit E, Sponer, Alvaro Vazque-Mayagoitia, et al. Accepted in Chemistry: a European Journal (2009)

"Atomistic origins of molecular memristors",Luis A. Agapito et al., accepted (JPC, C 2009)

"Nonequilibrium Green's function study of Pd-4-cluster-functionalized carbon nanotubes as hydrogen sensors", C. Cao, A.F. Kemper et al. Phys. Rev. B 79, 75127 (2009).

"Insensitivity of d-wave pairing to disorder in the high-temperature cuprate superconductors" A. F. Kemper et al. Phys. Rev. B 79 104502 (2009)

"Molecular Dynamics Simulations of Au Penetration through Alkanethiol Monolayers on the Au(111) Surface" S. Alkis et al., J. PHYS.L CHEM. C 113 6360 (2009)

"Dynamics of Ag clusters on complex surfaces: Molecular dynamics simulations" S. Alkis et al. Phys. Rev. B 79 121402 (2009)

"The origin of nanoscale phase stability reversals in titanium oxide polymorphs". D. R. Hummer et al. J. Phys. Chem. C 113 4240 (2009)

"Structure of YSi2 nanowires from scanning tunneling spectroscopy and first-principles". V. Iancu et al. Accepted in Applied Physics Letters (2009)

**PI Kwiseon Kim **

Chang, C.H. and K. Kim (2009) Density Functional Theory Calculation of Bonding and Charge Parameters for Molecular Dynamics Studies on [FeFe] Hydrogenases. J. Chem. Theory Comput. 5(4): 1137-45

**PI Joanna Kiryluk **

R. Abbassi et al., "The IceCube Data Acquisition System: Signal Capture, Digitization, and Timestamping", Nuclear Instruments & Methods A601, 294 (2009).

R. Abbassi et al., "Limits on a Muon Flux from Neutralino Annihilations in the Sun with the IceCube 22- String Detector", Phys. Rev. Lett. 102, 201302 (2009).

R. Abbassi et al., "Determination of the atmospheric neutrino flux and searches for new physics with AMANDA- II", Phys. Rev. D79, 102005 (2009).

R. Abassi et al., "Solar Energetic Particle Spectrum on 13 December 2006 Determined by IceTop", Astrophysical J. Lett. 689, L65 (2008).

R. Abassi et al., "Search for Point Sources of High Energy Neutrinos with Final Data from AMANDA-II", Rev. D79, 062001 (2009).

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

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

**PI Richard Klein **

Offner, S.S.R. and Krumholz, M.R. 2009, ApJ, 693, 914

Offner, S.S.R., Klein, R.I., McKee, C.F., and Krumholz, M.R. 2009, ApJ, 703, 131

**PI Kwok Ko **

"Simulations of beam-beam and beam-wire interactions in RHIC", Phys. Rev. ST Accel. Beams 12, 031001 (2009)

Volkan Akcelik, Lie-Quan Lee, Zenghai Li, Cho Ng. Liling Xiao and Kwok Ko, Large Scale Shape Optimization for Accelerator Cavities, SciDAC 2009 Conference, San Diego, June 14-18, 2009

Arno Candel, Andrews Kabel, Lie-Quan Lee, Zenghai Li, Cho Ng, Greg Schussman, Kwok Ko, State of the art in Electromagnetic Modeling for Compact Linear Collider, SciDAC 2009 Conference, San Diego, June 14-18, 2009

CONTINUING STUDY ON ELECTRON-CLOUD CLEARING TECHNIQUES IN HIGH INTENSITY POSITRON RING: MITIGATION BY USING GROOVE SURFACE IN VERTICAL MAGNETIC FIELD Y. Suetsugu, H. Fukuma, M. Pivi, L. Wang Nuclear Inst. and Methods in Physics Research, A, 604 (3), p.449-456, (2009)

Ben-Shan Liao, Zhaojun Bai, Lie-Quan Lee, and Kwok Ko, Nonlinear Rayleigh-Ritz Iterative Method for Solving Large-Scale Nonlinear Eigenvalue Problems, to be appeared, Taiwan Journal of Mathematics on matrix eigenvalue computation and applications, 2009

Xiao-Juan Luo, Mark S. Shephard, Lie-Quan Lee, Lixin Ge, and Cho Ng, Moving Curved Mesh Adaptation for Higher Order Finite Element Simulations, to be appeared, Journal of Engineering with Computers, 2009

**PI Joel Koplik **

Y. Yan and J. Koplik, Transport and sedimentation of suspended particles in inertial pressure-driven flow, Phys. Fluids 21, 013301 (2009).

**PI Henry Krakauer **

Daniel L. Pechkis and Eric J. Walter and Henry Krakauer, "High sensitivity of [sup 17]O NMR to p-d hybridization in transition metal perovskites: First principles calculations of large anisotropic chemical shielding", The Journal of Chemical Physics, 2009, vol 131, 18

**PI Petr Kral **

S. R. Stoyanov and P. Kral, Multifunctional metal-doped carbon nanocapsules, J. Chem. Phys. 129, 234702 (2008).

K. Sint, B. Wang and P. Kral, Selective Ion Passage through Functionalized Graphene Nanopores, JACS (Communication) 130, 16448 (2008).

B. Wang and P. Kral, Dragging of Polarizable Nanodroplets by Distantly Solvated Ions, Phys. Rev. Let. 101, 046103 (2008).

L. Vukovic and P. Kral, Coulombically Driven Rolling of Nanorods on Water, (submitted).

N. Patra, B. Wang and P. Kral, Nanodroplet Activated and Guided Folding of Graphene Nanostructures, (submitted).

**PI Arnold Kritz **

J. Cummings, A. Pankin, N. Podhorszki et al. (2008) Plasma edge kinetic-MHD modeling in tokamaks using Kepler workflow for code coupling, data management and visualization, Commun. Comput. Phys. 4, 675-702.

**PI Scott Kruger **

S. Shasharina, J. R. Cary, A. Hakim, G. R. Werner, S. Kruger, and A. Pletzer, "Facets: A physics driven parallel component framework," in 2008 compFrame/HPC-GECO workshop on Component based high performance computing, 2008.

## L

**PI Andrew Lacis **

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. submitted.

Yu. I. Baranov, W. J. Lafferty, Q. Ma and R. H. Tipping, Water-Vapor Continuum Absorption in the 800 cm-1 to 1250 cm-1 Spectral Region at Temperatures from 311 to 363 K. J. Q. S. R. T. 109, 2291-2302 (2008).

V. B. Podobedov, D. F. Plusquellic, K. E. Siegrist, G. T. Fraser, Q. Ma, and R. H. Tipping, Continuum and Magnetic Dipole Absorption of Water Vapor-Oxygen Mixture in the Region 0.3-3.6 THz, J. Mol. Spec. 251, 203-209 (2008).

Q. Ma, R. H. Tipping, and C. Leforestier, Temperature Dependence of Mechanisms Responsible for the Water-Vapor Continuum Absorption: I Far Wings of Allowed Lines. J. Chem. Phys. 128, 124313 (2008).

V. B. Podobedov, D. F. Plusquellic, K. E. Siegrist, G. T. Fraser, Q. Ma, and R. H. Tipping, New Measurements of the Water Vapor Continuum in the Region from 0.3 to 2.7 THz. J.Q.S.R.T, 109, 458 (2008).

**PI Uzi Landman **

"Nanojets, Electrospray, and Ion Field Evaporation: Molecular Dynamics Simulations and Laboratory Experiments", W. D. Luedtke, Uzi Landman, Y.-H. Chiu, D. J. Levandier, R. A. Dressler, S. Sok, and M. S. Gordon, J. Phys. Chem. A 112, 9628 (2008).

"Control and Manipulation of Au nanocatalysts: effects of metal oxide support thickness and composition", C. Harding, V. Habibpour, S. Kunz, A. N.-S. Farnbacher, U. Heiz, B. Yoon, U. Landman, J. Am. Chem. Soc. 131, 538 (2009).

"Hydrogen Promoted Oxygen Activation by Free Gold Cluster Cations", S. M. Lang, T. M. Bernhardt, R. N. Barnett, B. Yoon and U. Landman , J. Amer. Chem. Soc. 131, 8939 (2009).

**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.

F. N. Abu-Khzam, H. Fernau and M. A. Langston, "A Bounded Search Tree Algorithm for Parameterized Face Cover," Journal of Discrete Algorithms, accepted for publication.

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, accepted for publication.

A. D. Perkins and M. A. Langston, "Threshold Selection in Gene Co-Expression Networks Using Spectral Graph Theory Techniques," BMC Bioinformatics, accepted for publication.

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, accepted for publication.

**PI Stephan Lany **

"Semiconductor thermochemistry in density functional calculations", S. Lany, Phys. Rev. B 78, 245207 (2008)

"Energetics of quaternary III-V alloys described by incorporation and clustering of impurities", K. Biswas, S. Lany, Phys. Rev. B 80, 115206 (2009).

**PI Jean-Noel Leboeuf **

P. W. Terry, M. Greenwald, J.-N. Leboeuf, G. R. McKee, D. R. Mikkelsen, W. M. Nevins, D. E. Newman, and D. P. Stotler, "Validation in Fusion Research: Towards Guidelines and Best Practices", Phys. Plasmas 15, 062503 (2008).

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).

**PI Frank Lee **

Magnetic moments of vector, axial, and tensor mesons in lattice QCD F.X. Lee, S. Moerschbacher, W. Wilcox, Phys. Rev. D 78, 094502 (2008).

N to Delta transition amplitudes from QCD sum rules Lai Wang, F.X. Lee, Phys. Rev. D 80, 034003 (2009).

Classical Limits of Scalar and Tensor Gauge Operators Based on the Overlap Dirac Matrix, A. Alexandru, I. Horvath and K.F. Liu, Phys. Rev. D 78, 085002 (2008).

**PI T. S. Harry Lee **

Dynamical coupled-channels analysis of 1H(e,e'pi)N reactions, B. Julia-Diaz, H. Kamano, T.-S.H. Lee, A. Matsuyama, T. Sato, N. Suzuki, JLAB-THY-09-966 Phys. Rev. C 80, 025207 (2009) arXiv:0904.1918

Dynamical models of the excitations of nucleon resonances, T. Sato, T.-S.H. Lee, JLAB-THY-09-946 J. Phys. G 36, 073001 (2009) arXiv:0902.3653

Dynamical coupled-channels study of pi N --> pi pi N reactions, H. Kamano, B. Julia-Diaz, T.-S.H. Lee, A. Matsuyama, T. Sato, JLAB-THY-08-855 Phys. Rev. C 79, 025206 (2009) arXiv:0807.2273

Extraction of resonances from meson-nucleon reactions, N. Suzuki, T.-S.H. Lee, T. Sato, JLAB-THY-08-825 Phys. Rev. C 79, 025205 (2009) arXiv:0806.2043

Coupled-channels study of the pion- p --> eta n process, J. Durand, B. Julia-Diaz, T.-S.H. Lee, B. Saghai, T. Sato, JLAB-THY-08-812 Phys. Rev. C 78, 025204 (2008) arXiv:0804.0347

Dynamical coupled-channels effects in pion photoproduction, B. Julia-Diaz, T.-S.H. Lee, A. Matsuyama, T. Sato, and L.C. Smith, JLAB-THY-07-765 Phys. Rev. C 77, 045205 (2008) arXiv:0712.2283

Structure and dynamical evolution of low lying nucleon resonances, N. Suzuki, B. Julia-Diaz, H. Kamano, T.-S.H. Lee, A. Matsuyama, T. Sato, JLAB-THY-09-1063 Submitted to PRL arXiv:0909.1356

Double and single pion photoproduction within a dynamical coupled-channels model, H. Kamano, B. Julia-Diaz, T.-S.H. Lee, A. Matsuyama, T. Sato, JLAB-THY-09-1064 Submitted to PRC arXiv:0909.1129

**PI Wei-li Lee **

"Gyrokinetic Studies on Turbulence-Driven and Neoclassical Nondiffusive Toroidal-Momentum Transport and the Effect of Residual Fluctuations in Strong E x B Shear," W. X. Wang, T. S. Hahm, S. Ethier, G. Rewoldt, W. W. Lee, W. M. Tang,S. M. Kaye, and P. H. Diamond, Phys. Rev. Lett. 102, 035005 (2009)

"Study of turbulent fuctuations driven by the electron temperature gradient in the National Spherical Torus Experiment," E. Mazzucato, R.E. Bell, S. Ethier, J.C. Hosea, S.M. Kaye, B. P. LeBlanc, W.W. Lee, P.M. Ryan, D.R. Smith, W.X. Wang, J.R.Wilson and H. Yuh, Nucl. Fusion 49, 055001 (2009)

"Physics of non-diffusive turbulent transport of momentum and the origins of spontaneous rotation in tokamaks", P.H. Diamond, C.J. McDevitt, O.D. Gurcan, T.S. Hahm, W. X. Wang,E. S. Yoon, I. Holod, Z. Lin, V. Naulin and R. Singh, Nucl. Fusion 49, 045002 (2009)

"On higher order corrections to gyrokinetic Vlasov-Poisson equations in the long wavelength limit," W. W. Lee, R. A. Kolesnikov, Phys. Plasmas 16, 044506 (2009)

"Momentum-Transport Studies in High ExB Shear Plasmas in the National Spherical Torus Experiment", W. M. Solomon, S. M. Kaye, R. E. Bell, B. P. LeBlanc, J. E. Menard, G. Rewoldt, and W. Wang, Phys. Rev. Lett. 101, 065004 (2008)

"Momentum transport in electron-dominated NSTX spherical torus plasmas", S.M. Kaye, W. Solomon, R.E. Bell, B.P. LeBlanc, F. Levinton, J. Menard, G.Rewoldt, S.Sabbagh, W.Wang and H.Yuh, Nucl. Fusion 49 045010 (2009)

"Nonlinear turbulence transport in magnetic fusion plasmas," W. W. Lee, S. Ethier, R. Kolesnikov, W. X. Wang, and W. M. Tang , Comp. Sci. & Disc. 1, 015010 (2008)

"Multiscale turbulence simulation and steady state transport," W. W. Lee, S. Ethier, R. Ganesh, R. Kolesnikov, and W. X. Wang, Invited talk, Joint Varenna-Lausanne International Workshop on Theory of Fusion Plasmas, Varenna, Italy, AIP Conf. Proc. 1069, 144 (2008)

"Electromagnetic High Frequency Gyrokinetic Oarticle-in-Cell Simulation," R. A. Kolesnikov, W. W. Lee and H. Qin, Comm. Comp. Phys. 4, 575 (2008)

**PI Xuhui Lee **

Huang J, X Lee, EG Patton (2008) A modeling study of flux imbalance and the influence of entrainment in the convective boundary layer. Boundary-Layer Meteorology, 127: 273-292.

Huang J, X Lee, EG Patton (2009) Dissimilarity of scalar transport in the convective boundary layer in inhomogeneous landscapes. Boundary-Layer Meteorology, 130: 327-345.

Huang J, X Lee, EG Patton (2009) Entrainment and budget analysis of heat, water vapor and carbon dioxide in the convective boundary layer driven by time-varying solar radiation. In preparation for submission to Journal of Geophysical Research Atmospheres

**PI Sanjiva Lele **

J. Larsson, "Effect of shock-capturing errors on turbulence statistics", AIAA J., under review.

J. Larsson and S. K. Lele, "Direct numerical simulation of canonical shock/turbulence interaction, Phys. Fluids, revised version submitted.

E. Johnsen, J. Larsson, A. V. Bhagatwala, W. H. Cabot, P. Moin, B. J. Olson, 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", J. Comput. Phys., revised version submitted.

A. Mani, J. Larsson, and P. Moin, "Suitability of artificial bulk viscosity for large-eddy simulation of turbulent flows with shocks", J. Comput. Phys. 228, 7368--7374, 2009.

J. Larsson, "Blending technique for compressible inflow turbulence: algorithm localization and accuracy assessment", J. Comput. Phys. 228, 933--937, 2009.

J. Larsson and B. Gustafsson, "Stability criteria for hybrid difference methods", J. Comput. Phys. 227, 2886--2898, 2008.

**PI Yongsheng Leng **

Pu, Q., Leng, Y. S., Cummings, P. T, "Rate-dependent energy release mechanism of gold nanowires under elongation," Journal of the American Chemical Society 130, 17907 (2008).

Xu, D. Y., Leng, Y. S., Chen, Y. F., and Li, D. Y. "Water structure near charged (100) and (111) silicon surfaces," Appl. Phys. Lett. 94, 1 (2009).

Leng, Y. S., Lei, Y. J., Cumming, P. T., "Comparative studies of the structure and dynamics of aqueous and nonpolar liquid films under nanoconfinement", Modeling and Simulation in Materials Science and Engineering (invited) (2009).

**PI William Lester **

"Quantitative Characteristics of Qualitative Localized Bonding Patterns", Zubarev, Dmitry; Domin, Dominik; Lester, William; Accepted to J. Phys. Chem. A

"Local Electronic Structure and Stability of Pentacene Oxyradicals", Zubarev, Dmitry; Robertson, Neil; Domin, Dominik; McClean, Jarrod; Wang, Jinhua; Lester, William; Whitesides, Russell; You, Xiaoqing; Frenklach, Michael; Under consideration in J. Phys. Chem A

"Quantum Monte Carlo for atoms, molecules and solids", William A. Lester Jr., Lubos Mitas, Brian Hammond; Chemical Physics Letters, Volume 478, Pages 1-10

"Quantum Monte Carlo for Electronic Structure", William A. Lester Jr., "Practical Aspects of Computational Chemistry: Methods, Concepts and Applications", Leszczynski, Jerzy; Shukla, Manoj K. (Eds.); Springer, 2009

**PI Guang Lin **

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.

G. Lin , C.-H. Su and G.E. Karniadakis, Stochastic modeling of random roughness in shock scattering problems: Theory and simulations, Comput. Methods Appl. Math. Eng., Volume 197, Issues 43-44, 1 August 2008, Pages 3420-3434.

G. Lin and G.E. Karniadakis, Stochastic Simulations and Sensitivity Analysis of Plasma Flow, International Journal for Numerical Methods in Engineering, in press.

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, in press.

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, in press.

**PI Yu Lin **

Wang, X. Y., Y. Lin, L. Chen, and Z. Lin, A Particle Simulation of Current Sheet Instabilities Under Finite Guide Field, Physics of Plasmas, 15, 072103, 2008.

Yoon, P., Y. Lin, X. Y. Wang, and A. T. Y. Lui, Drift instabilities for current sheet equilibrium with guide field, Physics of Plasmas, 15, 112103, 2008.

Wang, X. Y., Y. Lin, and S.-W. Chang, Hybrid Simulation of Foreshock Waves and Ion Spectra and Their Linkage to Cusp Energetic Ions, Journal of Geophysical Research, 114, A06203, doi:10.1029/2008JA013745, 2009.

**PI Zhihong Lin **

G. Vlad et al, Particle simulation of energetic particle driven Alfven modes in NBI heated DIII-D experiments, Nuclear Fusion 49, 075024 (2009).

Y. Nishimura, Excitation of low-n toroidicity induced Alfven eigenmodes by energetic particles in global gyrokinetic tokamak plasmas, Phys. Plasmas 16, 030702 (2009).

Y. Nishimura, Z. Lin and L. Chen, Full Torus Electromagnetic Gyrokinetic Particle Simulations with Kinetic Electrons, Commun. Comput. Phys. 5, 183 (2009).

Yong Xiao and Zhihong Lin, Turbulent transport of trapped electron modes in collisionless plasmas, Phys. Rev. Lett. 103, 085004 (2009).

P. H. Diamond, C.J. McDevitt, O. D. Gurcan, T. S. Hahm, W. X. Wang, E. S. Yoon, I. Holod, Z. Lin, V. Naulin and R. Singh, Physics of non-diffusive turbulent transport of momentum and the origins of spontaneous rotation in tokamaks, Nuclear Fusion 49, 045002 (2009).

C. S. Chang, S. Ku, P. H. Diamond, Z. Lin, S. Parker, T. S. Hahm, and N. Samatova, Compressed ITG turbulence in diverted tokamak edge, Phys. Plasmas 16, 056108 (2009).

A. Bierwage and L. Chen, A linear gyrokinetic delta f particle-in-cell simulation code for the study of Alfvenic instabilities in high-beta tokamak plasmas, Commun. Comput. Phys. 4, 457 (2008).

Wenlu Zhang, Zhihong Lin, and Liu Chen, Transport of energetic particles by microturbulence in magnetized plasmas, Phys. Rev. Lett. 101, 095001 (2008).

I. Holod and Z. Lin, Gyrokinetic particle simulations of toroidal momentum transport, Phys. Plasmas 15, 092302 (2008).

**PI Da-Jiang Liu **

"The effects of chemical adsorbates on coarsening of nanoislands on metal surfaces," M. Shen, et al., Surf. Sci., 603, 1486 (2009) special issue in honor of Ertl's Nobel Prize.

"Coarsening of two-dimensional nanosclusters on metal surfaces," P. A. Thiel, M. Shen, D.-J. Liu, and J. W. Evans, J. Phys. Chem. C 113, 5047 (2009) Centennial feature article.

"The effect of chemical adsorbates 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, 1486-1491 (2009) (Special issue in honor of Ertl's Nobel Prize).

"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, submitted to Phys. Rev. B.

"Shell structure and phase relation in electronic properties of metal nanowires from an electron gas model," Y. Han and D.-J. Liu, submitted to Phys. Rev. B.

"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 , in press.

"DFT analysis of key energetics in metal homoepitaxy: quantum size effects in periodic slab calculations," D.-J. Liu, submitted to Phys. Rev. B.

**PI Feng Liu **

Y.Y. Li, M. Liu, D.Y. Ma, D.C. Yu, X. Chen, X.C. Ma, Q.K. Xue, K.W. Xu, J.F. Jia, F. Liu Bistability of Nanoscale Ag Islands on a Si(111)-(4X1)-In Surface Induced by Anisotropic Stress Physical Review Letters vol.103 (2009) 076102

D. Yu, Y Zhang, F. Liu First Principles study of electronic properties of biaxially strained silicon: Effects on charge carrier mobility Physical Review B vol. 78 (2008) 245204

J.Y. Zhu, F. Liu, G.B. Stringfellow Dual Surfactant Effect to Enhance p-Type Doping in III-V Semiconductor Thin Films Physical Review Letters vol. 101 (2008) 196103

**PI Keh-Fei Liu **

K.F. Liu, `Neutron Electric Dipole Moment at Fixed Topology', Mod. Phys. Lett. A24, 1971 (2009), [arXiv:0807.1365].

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].

H. Iida, T. Doi, N. Ishii, H. Suganuma, K. Tsumura, `Survival of charmonia above T(c) in anisotropic lattice QCD', Prog. Theor. Phys. Suppl. 174, 238 (2008), [arXiv:0806.0126 [hep-lat]].

H.Y. Cheng, H.N. Li, and K.F. Liu, `Pseudoscalar Glueball Mass from the $\eta-\eta'$-G Mixing', Phys. Rev. D79, 014024 (2009), [arXiv:0811.2577].

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', Submitted to Phys. Rev. Lett., [arXiv:0903.3232 [hep-ph]].

**PI Ping Liu **

Y. Choi, P. Liu, "Mechanism of ethanol synthesis from syngas on Rh(111)", Journal of the American Chemical Society 131 (2009) 13054-13061.

P. Liu, Y. Choi, Y. Yang, M.G. White, "Methanol synthesis from H2 and CO2 on a Mo6S8 cluster: a density functional study", Journal of Physical Chemistry A, submitted.

**PI Charles Long **

Evaluating regional cloud-permitting simulations of the WRF model for the Tropical Warm Pool International Cloud Experiment (TWP-ICE, Darwin 2006), Yi Wang, CN Long, LR Leung, J Dudhia, SA McFarlane, JH Mather, SJ Ghan, and X Liu, J. Geophys. Res., 114, D21203

"The importance of Northern Peatlands in global carbon systems during the Holocene", Y. Wang, N. T. Roulet, S. Frolking, and L. A. Mysak, Clim. Past, 5, 683-693, 2009, www.clim-past.net/5/683/2009/

**PI Steven Louie **

L.Yang, M.L.Cohen, and S.G.Louie, "Magnetic Edge-State Excitons in Zigzag Graphene Nanoribbons," Phys. Rev. Lett. 101, 186401 (2008).

C.-H.Park, F.Giustino, M.L.Cohen, and S.G.Louie, "Electron-phonon Interactions in Graphene, Bilayer Graphene, and Graphite," Nano Lett. 8, 4229 (2008). [Erratum: Nano Lett. 9, 1731 (2009)]

C.-H.Park, F.Giustino, C.D.Spataru, M.L.Cohen, and S.G.Louie, "First-Principles Study of Electron Linewidths in Graphene," Phys. Rev. Lett. 102, 076803 (2009). [Erratum: Phys. Rev. Lett. 102, 189904(E) (2009)]

H.J.Choi, S.G.Louie, and M.L.Cohen, "Anisotropic Eliashberg Theory for Superconductivity in Compressed and Doped MgB2," Phys. Rev B 79, 094518 (2009).

C.O.Girit, J.C.Meyer, R.Erni, M.D.Rossell, C.Kisielowski, L.Yang, C.-H.Park, M.F.Crommie, M.L.Cohen, S.G.Louie, and A.Zettl, "Graphene at the Edge: Stability And Dynamics," Science 323, 1705 (2009).

J.Noffsinger, F.Giustino, S.G.Louie, and M.L.Cohen," Origin of Superconductivity in Boron-Doped Silicon Carbide from First Principles," Phys. Rev B 79, 104511 (2009).

J.Deslippe, M.Dipoppa, D.Prendergast, M.V.O.Moutinho, R.B.Capaz, and S.G.Louie, "Electron-Hole Interaction in Carbon Nanotubes: Novel Screening and Exciton Excitation Spectra," Nano Lett. 9, 1330 (2009).

J.Noffsinger, S.G.Louie, F.Giustino, and M.L.Cohen, "Role of Fluorine in the Iron Pnictides: Phonon Softening and Effective Hole Doping," Phys. Rev. Lett. 102, 147003 (2009).

C.D.Spataru, M.S.Hybertsen, S.G.Louie, and A.J.Millis, "GW Approach to Anderson Model Out of Equilibrium: Coulomb Blockade and False Hysteresis in the I-V Characteristics," Phys. Rev. B 79, 155110 (2009).

S.Y.Quek, M.Kamenetska, M.L.Steigerwald, H.J.Choi, S.G.Louie, M.S.Hybertsen, J.B.Neaton, and L.Venkataraman, "Mechanically Controlled Binary Conductance Switching of a Single-Molecule Junction," Nature Nanotechnology 4, 230 (2009).

C.-H.Park and S.G.Louie, "Making Massless Dirac Fermions from a Patterned Two-Dimensional Electron Gas," Nano Lett. 9, 1793 (2009).

C.-H.Park, Y.-W.Son, L.Yang, M.L.Cohen, and S.G.Louie, "Landau Levels and Quantum Hall Effect in Graphene Superlattices," Phys. Rev. Lett. 103, 046808 (2009).

H.J.Choi, S.G.Louie, and M.L.Cohen, "Prediction of Superconducting Properties of CaB2 Using Anisotropic Eliashberg Theory," Phys. Rev. B 80, 064503 (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," arXiv:0906.0969 (submitted to Phys. Rev. Lett.).

L.Z.Tan, C.-H.Park, and S.G.Louie, "Graphene Dirac Fermions in Inhomogenous Fields: Transforming Magnetic to Electric Field," arXiv:0906.4975 (submitted to Phys. Rev. Lett.).

S.Choi, D.-H.Lee, S.G.Louie, and J.Clarke, "Localization of Metal-Induced Gap States at the Metal-Insulator Interface: Origin of Flux Noise in SQUIDs and Superconducting Qubits," arXiv:0907.3904 (submitted to Phys. Rev. Lett.).

M.J.Comstock, D.A.Strubbe, L.Berbil-Bautista, N.Levy, J.Cho, D.Poulsen, J.M.J.Frechet, S.G.Louie, and M.F.Crommie, "Determination of molecular photoswitching dynamics through single-molecule chiral mapping" (submitted to Phys. Rev. Lett.)

D.Prendergast and S.G.Louie, "Shirley interpolation - optimal basis sets for detailed Brillouin zone integrations revisited," arXiv:0908.3876 (Submitted to Phys. Rev. B).

**PI Walter Loveland **

Gulzari L Malli"Dramatic antibinding effects of relativity for atomization energy of molecules of superheavy elements: atomization energy of tetravalent Eka-lead tetrachloride UuqCl4 ", Phys.Rev.A,Submitted.

Gulzari L Malli "Relativistic and electron correlation effects for molecules of superheavy elements: All-electron all-virtual spinor space (AVSS) relativistic and nonrelativistic coupled-cluster calculations for the superheravy eka-lead tetrahydride UuqH4 " , Journal of Chemical Theory and Computation, Submitted.

G.L.Malli,M.Siegert and D.P.Turner," All-Electron All-Virtual Spinor Space Relativistic Coupled-Cluster Calculations for Molecules of Heavy Elements using Contracted Basis set: Prediction of Atomization Energy of PbH4",Int.J.Quantum Chem,108,2299(2008).

G.L.Malli," Thirty years of relativistic self-consistent field theory for molecules:relativistic and electron correlation effects for atomic and molecular systems of transactinide superheavy elements up to ekaplutonium E126 with g-atomic spinors in the ground state configuration", Theor Chem Account. 118, 473(2007).

## M

**PI Chung-Pei Ma **

J. DeBuhr, E. Quataert, C.-P. Ma, and P. Hopkins (2009) Monthly Notices of the Royal Astronomical Society, submitted. Self-Regulated Black Hole Growth via Momentum Deposition in Galaxy Merger Simulations

**PI Angus Macnab **

A. I. D. Macnab and Simon Woodruff, "Extended MHD Simulations of the Compression and Stability of Spheromaks for Current Drive", Journal of Fusion Energy, Volume 28, Number 2, June 2009.

**PI Kyoko Makino **

High-Order Description of the Dynamics in FFAG and Related Accelerators K. Makino and M. Berz and P. Snopok and C. Johnstone, in print (2009)

On the Estimation of Topological Entropy on Surfaces S. Newhouse, M. Berz, J. Grote and K. Makino, Contemporary Mathematics 469 (2008) 243-270

Taylor Model-based Enclosure of Invariant Manifolds for Planar Diffeomorphisms and Applications J. Grote, M. Berz, K. Makino and S. Newhouse, Proc. Applied Mathematics and Mechanics 7 (2008) 1022907

Conceptual Design of a Superconducting Quadrupole with Elliptical Acceptance and Tunable Higher Order Multipoles S. Manikonda, J. Nolen, M. Berz and K. Makino, Int. Journal Modern Physics A 24,5 (2008) 923-940

**PI Lev Manovich **

Jeremy Douglass. "Computer Visions of Computer Games: analysis and visualization of play recordings." Workshop on Media Arts, Science, and Technology (MAST) 2009: The Future of Interactive Media. UC Santa Barbara, January 2009.

Jeremy Douglass. "Playpower: Radically Affordable Computer-Aided Learning with $12 TV-Computers." co-authored with Derek Lomas and Daniel Rehn. Meaningful Play 2008. Michigan State U., October 2008.

**PI Steven Manson **

"Photoionization of Doubly-Charged Scandium Ions," A. M. Sossah, H.-L. Zhou, S. T. Manson, Phys. Rev. A 78, 053405 (2008).

"Photoionization of the Be Isoelectronic Sequence: Total Cross Sections," W.-C. Chu, H.-L. Zhou, A. Hibbert and S. T. Manson, J. Phys. B (in press).

**PI Angelo Mascarenhas **

Y. Zhang, A. Mascarenhas, S.-H. Wei, and L.-W. Wang, Comparison of atomistic simulations and statistical theories for variable degree of long-range order in semiconductor alloys, Phys. Rev. B 80 045206 (2009).

X.F. Lu, D.A. Beaton, R.B. Lewis, T. Tiedje1, and Y. Zhang, Composition Dependence of Photoluminescence of GaAs1-xBix Alloys, Appl. Phys. Lett. 95, 041903 (2009).

Y. Zhang, C.-S. Jiang, D. J. Friedman, J. F. Geisz, and A. Mascarenhas, Tailoring the electronic properties of GaxIn1-xP beyond simply varying alloy composition, Appl. Phys. Lett. 94, 091113(2009).

Y. Zhang, A. Mascarenhas, and L.-W. Wang, Interplay of alloying and ordering on the electronic structure of GaxIn1-xP alloys, Phys. Rev. B 78, 235202 (2008).

**PI Artem Masunov **

Mikhailov, I. A., Bondar, M. A., Belfied, K. D., Masunov, A. E., "Electronic properties of a new two-photon absorbing fluorene derivative: The role of DFT functionals in quantum-chemical design of improved nonlinear chromophore". J. Phys. Chem. A (2009) submitted.

Belfield, K. D., Bondar, M. V., Hernandez, F. E., Masunov, A. E., Mikhailov, I. A., Morales, A. R., Przhonska, O. V., Yao, S., "Two-Photon Absorption Properties of New Fluorene-Based Singlet Oxygen Photosensitizers". J. Phys. Chem. C 113 (2009) 4706-4711.

Patel, P. D., Masunov, A. E. Theoretical Study of Photochromic Compounds: 1. Bond Lengths Alternation and Absorption Spectra for the Open and Closed Forms of 29 Diarylethene Derivatives. J. Phys. Chem. A 113 (2009) 8409-8414.

Patel, P. D., Mikhailov, I. M., Belfield, K. D., Masunov, A. E. Theoretical Study of Photochromic Compounds: 2. Thermal Mechanism for Byproduct Formation and Fatigue-Resistance of Diarylethenes Used as Data Storage Materials. Int. J. Quantum Chem 109 (2009) accepted.

Mikhailov, I. A., Belfield, K. D., Masunov, A. E. DFT-Based Methods in the Design of Two-Photon Operated Molecular Switches. J. Phys. Chem. A 113 (2009) 7080-7089.

Hernandez, F., Toro, C., Boni, L. D., Yao, S., Ritchie, J. P., Masunov, A. E., Belfield, K. D. Linear and nonlinear optical characterization of a monomeric symmetric squaraine-based dye in solution. J. Chem. Phys. (2009) accepted.

Iordanov, T. D., Davis, J. L., Masunov, A. E., Levenson, A., Przhonska, O. V., Kachkovski, A. D. Symmetry breaking in cationic polymethine dyes: 1. Ground state potential energy surfaces and solvent effects on electronic spectra of streptocyanines. Int. J. Quantum Chem (2009) submitted.

Vincent, A., Babu, S., Heckert, E, Dowding, J., Hirst, S., Inerbaev, T. A., Self, W., Reilly,

C. Masunov, A. E., Seal,* S. Protonated nanoparticle surface governing ligand tethering and cellular targeting. ACS Nano.; 3, (5), 1203-1211, 2009.

Babu, S., Thanneeru, R., Inerbaev, T. A., Day, R., Masunov, A. E, Schulte, A. and Seal,* S. Dopant mediated oxygen vacancy tuning in ceria nanoparticle. Nanotechnology. 20(8); 085713, 2009.

Vincent, A.; Inerbaev, T. M.; Babu, S.; Karakoti, A. S.; Self, W. T.; Masunov*, A. E.; Seal,* S. Ion Exchange on Hydrated Tunable Nanoceria Surface: Implications in Biomedical and Chemical Mechanical Polishing. Small. Submitted, 2009.

Hirsch-Kuchma,* M.; Komanski, C. B.; Colon, J.; Teblum, A.; Masunov, A. E.; Seal, S.; Alvarado, B.; Summy, J.; Baker, C. H. Phosphate ester hydrolysis by cerium oxide nanoparticles. J. Inorg. Biochem. Submitted

Gangopadhayay, S., Inerbaev, T., Masunov,* A.E., Orlovskaya, N.S. Structural characterization combined with the first principles simulations of barium/strontium ferrate/cobaltate as a promising material for sofc. ACS Applied Materials & Interfaces.1 (7), 1512-1519, 2009.

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.; Submitted, 2009

Gangopadhyay, S., Masunov, A.E., Poalelungi, E.;,Leuenberger, M.N. "Prediction of exchange coupling constant for Mn12 molecular magnet using DFT+U", Proceedings of the 9th International Conference on Computational Science (ICCS), LNCS 5545, pp. 151, Springer: 2009.

Thanneeru, R. K., Patil, S., Babu, S., Seal,* S., Guo, Y., Schulte, A., Day, R., Inerbaev, T., Masunov, A. E. Positive and negative lattice modulation in nanoceria: An insight into tuning defects and surface chemistry in nanoparticles. Appl. Phys. Lett.; Submitted, 2009.

Inerbaev, T., Masunov,* A. E., Khondaker, S., Dobrinescu, A., Plamado, A.-V., Kawazoe,Y. Quantum chemistry of quantum dots: effects of ligands and oxidation. J. Chem. Phys.; Submitted, 2009.

Suponitsky, K. Yu., Liao,* Y., Masunov,* A. E., electronic Electronic hyperpolarizabilities for donor-acceptor molecules with long conjugated bridges: calculations vs. Experiment. J. Phys. Chem. A., Submitted, 2009.

**PI Manos Mavrikakis **

A. A. Gokhale, J. A. Dumesic, and M. Mavrikakis, "On the Mechanism of Low-Temperature Water Gas Shift Reaction on Copper", Journal of American Chemical Society, 130, 1402 (2008).

N. Schumacher, K. Andersson, L.C. Grabow, M. Mavrikakis, J. Nerlov, I. Chorkendorff, "Interaction of carbon dioxide with Cu overlayers on Pt(111)", Surface Science, 602, 702 (2008).

L. C. Grabow, A. A. Gokhale, S. Evans, J. A. Dumesic, and M. Mavrikakis, "Mechanism of the water gas shift reaction on Pt: First-principles, experiments, and microkinetic modeling", Journal of Physical Chemistry C 112, 4608 (2008).

S. Alayoglu, A.U. Nilekar, M. Mavrikakis, and B. Eichhorn "Ru-Pt core-shell nanoparticles for preferential oxidation of carbon monoxide in hydrogen", Nature Materials, 7, 333 (2008).

A.U. Nilekar and M. Mavrikakis, "Improved oxygen reduction reactivity of platinum monolayers on transition metal surfaces", Surface Science, 602, L89 (2008).

P. Ferrin, A. U. Nilekar, J. Greeley, J. Rossmeisl, and M. Mavrikakis, "Reactivity Descriptors for Direct Methanol Fuel Cell Anode Catalysts", Surface Science, 602, 3424 (2008).

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. Lagsgaard, 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 (in press).

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 (in press).

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", (submitted).

**PI William McCurdy **

D. A. Horner, C. W. McCurdy and T. N. Rescigno, "Triple Differential Cross sections and Nuclear Recoil in Two-Photon Double Ionization of Helium", Phys. Rev. A 78, 043416 (2008).

A. Horner, S. Miyabe, T. N. Rescigno, C. W. McCurdy, F. Morales and F. Martin, "Classical two-slit interference effects in double photoionization of molecular hydrogen at high energies", Phys. Rev. Lett. 101, 183002 (2008).

D. J. Haxton, T. N. Rescigno and C. W. McCurdy, "Three-body breakup in dissociative electron attachment to the water molecule", Phys. Rev. A 78, 040702(R) (2008).

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).

Liang Tao, C. W.McCurdy and T. N. Rescigno, "Grid-based methods for diatomic quantum scattering problems: a finite-element, discrete variable representation in prolate spheroidal coordinates", Phys. Rev. A 79, 012719 (2009).

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).

F. Morales, F. Martin, D. A. Horner, T. N. Rescigno and C. W. McCurdy,"Two-photon double ionization of H2 at 30 eV using Exterior Complex Scaling", J. Phys. B 42, 134013 (2009).

S. Miyabe, C. W. McCurdy, A. E. Orel and T. N. Rescigno, "Theoretical study of asymmetric molecular-frame photoelectron angular distributions for C 1s photoejection from CO2", Phys. Rev. A 79, 053401 (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, 013402 (2009).

H. Adaniya, B. Rudek, T. Osipov, D. J. Haxton, T. Weber, C. W. McCurdy and A. Belkacem, "Imaging the dynamics of dissociative electron attachment to water", Phys. Rev. Lett. (submitted).

Two-electron time-delay interference in atomic double ionization by attosecond pulses (with A. Palacios and C. W. McCurdy), Phys. Rev. Letters (submitted).

Liang Tao, W. Vanroose, B. Reps, T.N. Rescigno, 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 (submitted).

**PI Julia Medvedeva **

J.E. Medvedeva, Combining optical transparency with electrical conductivity: challenges and prospects, in "Transparent Electronics: From Synthesis to Applications", Eds. A. Facchetti and T. Marks, John Wiley & Sons (in production)

J.E. Medvedeva and C.L. Hettiarachchi, Complex transparent conducting oxides with tunable properties: role of crystal symmetry, chemical composition and carrier generation, submitted for publication to Physical Review B

**PI Donghai Mei **

Kwak, J. H., J. Z. Hu, et al. (2009). "Co-ordinatively unsaturated Al3+ centers as binding sites for active catalyst phases on Al2O3 " Science, in press.

Mei, D. H., L. J. Xu, et al. (2009). "Potential Energy Surface of Methanol Decomposition on Cu(110)." Journal of Physical Chemistry C 113(11): 4522-4537.

Mei, D. (2009). "Density Functional Theory Study of Surface Carbonate Formation on BaO(001) " Journal of Physical Chemistry C, submitted.

Mei, D., J. H. Kwak, et al. (2009). "Size and Morphological Effects on the Interaction of NO2 with BaO-Al2O3 Materials " Catalysis Today, submitted.

Mei, D. H., Q. F. Ge, et al. (2009). "Characterization of surface and bulk nitrates of gamma-Al2O3- supported alkaline earth oxides using density functional theory." Physical Chemistry Chemical Physics 11(18): 3380-3389.

Mei, D., Q. F. Ge, et al. (2009). "First-Principles Analysis of NOx Adsorption on Anhydrous gamma- Al2O3 Surfaces." Journal of Physical Chemistry C 113(18): 7779-7789.

Kwak, J. H., D. H. Mei, et al. (2009). "Understanding the nature of surface nitrates in BaO/gamma- Al2O3 NOx storage materials: A combined experimental and theoretical study." Journal of Catalysis 261(1): 17-22.

Kim, Y. K., Z. Dohnalek, et al. (2009). "Competitive Oxidation and Reduction of Aliphatic Alcohols over (WO3)(3) Clusters." Journal of Physical Chemistry C 113(22): 9721-9730.

She, X., R. Rousseau, et al. (2009). "Kinetics and Mechanism of Double-bond isomerization of n- butenes over tungsten oxide supported on mesoporous silica SBA-15." J. Phys. Chem. C, submitted.

Rousseau, R., G. K. Schenter, et al. (2009). "Defining Active Catalyst Structure and Reaction Pathways from ab Initio Molecular Dynamics and Operando XAFS: Dehydrogenation of Dimethylaminoborane by Rhodium Clusters." Journal of the American Chemical Society 131(30): 10516-10524.

Mei, D., R. Rousseau, et al. (2009). "Ethanol synthesis from syngas over Rh-based/SiO2 catalysts: A combined experimental and theoretical modeling study." J. Catal., submitted.

Deskins, N. A. (2009). "Ti 3p electrons: Core or valence?" Chemical Physics Letters 471(1-3): 75- 79.

Deskins, N. A. and M. Dupuis (2009). "Intrinsic Hole Migration Rates in TiO2 from Density Functional Theory." Journal of Physical Chemistry C 113(1): 346-358.

Deskins, N. A., R. Rousseau, et al. (2009). "Localized Electronic States from Surface Hydroxyls and Polarons in TiO2(110)." Journal of Physical Chemistry C 113(33): 14583-14586.

Deskins, N. A., R. Rousseau, et al. (2009). "The universal role of excess electrons in the surface chemistry of TiO2." Journal of Physical Chemistry C, submitted.

Du, Y., N. A. Deskins, et al. (2009). "Two Pathways for Water Interaction with Oxygen Adatoms on TiO2(110)." Physical Review Letters 102(9).

Du, Y. G., N. A. Deskins, et al. (2009). "Imaging Consecutive Steps of O-2 Reaction with Hydroxylated TiO2(110): Identification of HO2 and Terminal OH Intermediates." Journal of Physical Chemistry C 113(2): 666-671.

Lyubinetsky, I., N. A. Deskins, et al. (2009). "Adsorption States and Mobility of TMAA Molecules on the Reduced TiO2(110) Surface." Physical Chemistry Chemical Physics, submitted.

Glezakou, V. A. and L. X. Dang (2009). "Spontaneous Activation of CO2 and Possible Corrosion Pathways on the Low-Index Iron Surface Fe(100)." Journal of Physical Chemistry C 113(9): 3691-3696.

**PI David Mikkelsen **

D. R. Mikkelsen and W. Dorland, "The Dimits Shift in Realistic Gyrokinetic Plasma Turbulence Simulations", Phys. Rev. Letters 101 (2008) 135003.

P. Xanthopoulos, D.R. Mikkelsen, et al, "Verification and application of numerically generated magnetic coordinate systems in gyrokinetics", Phys. Plasmas 15 (2008) 122108.

D. A. Gates, et al., "Overview of Results from the National Spherical Torus Experiment (NSTX)", Nucl. Fusion 49 (2009) 104016.

A. Casati, T. Gerbaud, P. Hennequin, C. Bourdelle, et al., "Turbulence in the TORE SUPRA Tokamak: Measurements and Validation of Nonlinear Simulations", Phys. Rev. Letters 102 (2009) 165005.

A. Casati, C. Bourdelle, X. Garbet, et al., "Validating a quasi-linear transport model versus nonlinear simulations", Nucl. Fusion 49 (2009) 085012 .

**PI Burkhard Militzer **

B. Militzer, "Correlations in Hot Dense Helium", J Phys. A 42 (2009) 214001.

S. A. Khairallah and B. Militzer, "First-Principles Studies of the Metallization and the Equation of State of Solid Helium", Phys. Rev. Lett. 101 (2008) 106407.

J. J. Fortney, S. H. Glenzer, M. Koenig, B. Militzer, D. Saumon, and D. Valencia, "Frontiers of the Physics of Dense Plasmas and Planetary Interiors: Experiment, Theory, Applications", accepted for publication in Physics of Plasmas (2009).

B. Militzer, "Path Integral Monte Carlo and Density Functional Molecular Dynamics Simulations of Hot, Dense Helium", Phys. Rev. B 79 (2009) 155105.

**PI Doug Miller **

Keighton, S., L. Lee, B. Holloway, D. Hotz, S. Zubrick, J. Hovis, G. Votaw, L. B. Perry, G. Lackmann, S. E. Yuter, C. Konrad, D. Miller, and B. Etherton, 2009: A collaborative approach to study northwest flow snow in the southern Appalachians. Bull. Amer. Meteor. Soc., 90, 979- 991.

**PI Thomas Miller **

T. F. Miller, III, J. Chem. Phys., 129, 194502 (2008).

**PI William Miller **

Guohua Tao, William H. Miller, "Gaussian Approximation for the Structure Function in Semiclassical Forward-Backward Initial Value Representations of Time Correlation Functions", Journal of Chemical Physics, submitted

Jian Liu, William H. Miller, 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, William H. Miller, Francesco Paesani, Wei Zhang, Greg Voth and David Case, "Quantum dynamical effects in liquid water: A semiclassical study on the diffusion and the infrared absorption spectrum", Journal of Chemical Physics, (submitted)

Jian Liu and William H. Miller, "A simple model for the treatment of imaginary frequencies in chemical reaction rates and molecular liquids", Journal of Chemical Physics, 131, 074113 (2009)

**PI Warren Mori **

S. F. Martins R. A. Fonseca, W. B. Mori, L. O. Silva, Exploring the future of laser wakefield acceleration using particle-in-cell simulations in Lorentz boosted frames, submitted to Nature Physics (2009).

S. F. Martins R. A. Fonseca, W. B. Mori, L. O. Silva, Numerical Simulations of Laser Wakefield Accelerators in Optimal Lorentz Frames, submitted to Computer Physics Communications (2009). C. K. Huang et al, Recent Results and Future Challenges for Large Scale Particle-In-Cell Simulations of Plasma-Based Accelerator Concepts, sumitted to Jour. of Phys. (2009).

M. Tzoufras, W. Lu, F. S. Tsung, C. Huang, W. B. Mori, T. Katsouleas, J. Vieira, R. A. Fonseca, and L. O. Silva, Beam Loading by Electrons in Nonlinear Plasma Waves, Phys. Plas., 16, 056705 (2009).

S. Kneip, S. R. Nagel, S. F. Martins et al., Near-GeV Acceleration of Electrons by a Nonlinear Plasma Wave Driven by a Self-Guided Laser Pulse, Phys. Rev. Lett. 103, 035002 (2009).

S. F. Martins, R. A. Fonseca, W. B. Mori, L. O. Silva, Ion dynamics and acceleration in relativistic shocks, Astrophysical Journal Letters 695, L189-L193 (2009).

N. Kirby, S. F. Martins, et al., Transverse emittance and current of multi-GeV trapped electrons in a plasma wakefield accelerator, Physical Review Special Topics: Accelerators and Beams, 12, 051302 (2009).

F. Fiuza, S. F. Martins, R. A. Fonseca, and L. O. Silva, Short, wavelength magnetic structures from the plasma magnetic mode and their applications, submitted for publication in the proceedings of SPIE (2009).

L. O. Silva, et al., Laser electron acceleration with 10 PW lasers, C. R. Physique 10 (2009). R. A. Fonseca, S. F. Martins, L. O. Silva, J. W. Tonge, F. S. Tsung, and W. B. Mori, One-to-one direct modeling of experiments and astrophysical scenarios: pushing the envelope on kinetic plasma simulations, Plasma Physics and Controlled Fusion 50, 124034 (2008).

J. F. Vieira, S. F. Martins, et al., Three-dimensional structure of the laser wakefield accelerator in the blowout regime, IEEE Transactions on Plasma Science 36 (4), 1124-1125 Part 1 (2008).

X. Kong, J. Park, C. Ren, Z. M. Sheng, J. W. Tonge, "Evolution of a relativistic electron beam-plasma return current system," Physics of Plasmas 16, 032107 (2009)

J. Tonge, J. May, W. B. Mori, F. Fiuza, S. F. Martina, R. A. Fonseca, L. O. Silva, and C. Ren, "A simulation study of fast ignition with ultrahigh intensity lasers," Physics of Plasmas 16, 056311 (2009)

**PI James Morris **

M.K. Miller, C.L. Fu, M. Krcmar, D.T. Hoelzer, and C.T. Liu, "Vacancies as a constitutive element for the design of nanocluster-strengthened ferritic steels," Frontiers of Materials Science in China 3(1), 9-14 (2009) (Shanghai Metals 30 (4), 1-6 2008, in Chinese).

T. Kawakami, Y. Tsujimoto, H. Kageyamo, X.Q. Chen, C.L. Fu, C. Tassel, A. Kitada, S. Suto, K. Hirama, Y. Sekiya, Y. Makino, T. Okada, T. Yagi, N. Hayashi, K. Yoshimura, S. Nasu, R. Podloucky, and M. Takano, "Spin Transition in a four-coordinate oxide compound," Nature Chemistry 1, 371 (2009).

F.W. Averill, J. R. Morris, V. R. Cooper, "Calculated Properties of Fully Hydrogenated Single Layers of BN, BC2N, and Graphene: Graphane and Its BN-Containing Analogues," submitted to Phys. Rev. B.

Xing-Qiu Chen ,C. L. Fu, and J. R. Morris, "The electronic, elastic, and structural properties of Ti-Pd intermetallics from first-principles calculation," submitted to Intermetallics.

**PI Adam Moule **

David M. Huang, Roland Faller, Khanh Do, and Adam J. Moule, "Coarse-grained computer simulations of polymer/fullerene bulk heterojunctions for organic photovoltaic applications", submitted.

**PI Alfred Msezane **

G. P. Gupta and A. Z. Msezane, "Oscillator Strengths and Lifetimes in Ge XXI", Phys. Scr 77, 035303 (2008).

Z. Felfli, A.Z. Msezane, and D. Sokolovski, "Simple Method for Electron Affinity Determination: Results for Ca, Sr and Ce", J. Phys. B 41, 041001 (2008) (FAST TRACK)

A.Z. Msezane, Z. Felfli, and D. Sokolovski, "Dramatic Resonances in Low- Energy Electron Scattering from Rb, Cs and Fr", Chem. Phys. Lett. 456, 96 (2008)

A.Z. Msezane, Z. Felfli and D. Sokolovski, "Near-Threshold Resonances in Electron Elastic Scattering Cross Sections for Au and Pt Atoms", , J. Phys. B 41,105201 (2008)

.Z. Msezane, Z. Felfli and D. Sokolovski, "Near-Threshold Electron Attachment as Regge Resonances: Cross Sections for K, Rb and Cs Atoms", A J. Phys. Chem. A 112, 10, 199 (2008)

Z. Felfli, A.Z. Msezane and D. Sokolovski,"Strong resonances in low-energy electron elastic total and differential cross sections for Hf and Lu atoms", Phys. Rev. A 78, 030703 (R) (2008)

Z. Felfli, A.Z. Msezane and D. Sokolovski,"Low-Energy Electron Elastic Scattering from Complex Atoms: Nd, Eu and Tm", Can. J. Phys. 87, 321 (2009)

V.R. Shaginyan, A.Z. Msezane. K.G. Popov and V.A. Stephanovich, "Main Universal Features of the 3He Experimental Temperature"Density Phase Diagram", Phys. Rev. Lett. 100, 096406 (2008)

Z. Felfli, A.Z. Msezane and D. Sokolovski,"Resonances in Low-Energy Electron Elastic Cross Sections for Lanthanide Atoms", Phys. Rev. A 79, 012714 (2009)

V.R. Shaginyan, M. Ya. Amusia, A.Z. Msezane, K.G. Popov and V.A. Stephanovich,"Energy Scales and Magnetoresistance at a Quantum Critical Point", Physics Letters A 373, 986 (2009)

N. C. Deb, A. H. Hibbert, Z. Felfli and A. Z. Msezane, "[Ti II] lines observed in Carinae Sr-"lament and lifetimes of the metastable states of Ti+", J. Phys. B 42, 015701 (2009)

A. S. Baltenkov, V. K. Dolmatov, S. T. Manson, and A. Z. Msezane, "Fast charged-particle impact ionization of endohedral atoms: e + He@C60", Phys. Rev. A 79, 043201 (2009)

Z. Felfli, A.Z. Msezane and D. Sokolovski, "Differential Cross Sections for Low-Energy Electron Elastic Scattering by Lanthanide Atoms: La, Ce, Pr, Nd, Eu, Gd, Dy and Tm", Phys. Rev. A 79, 062709 (2009)

Zhifan Chen and Alfred Z. Msezane, "Photoionization of Ce3+ and Ce3+ @C60", J. Phys. B 42, 165206 (2009).

Zhifan Chen and Alfred Z. Msezane, "Photoionization of I+ Ion", J. Phys. B 42, At Press (2009).

V.R. Shaginyan, A.Z. Msezane, K.G. Popov and V.A. Stephanovich, "Magnetic-Field-induced Reentrance of Fermi-Liquid Behavior and Spin-Lattice Relaxation Rates in YbCu5Aux", Physics Letters A, At Press (2009)

S. Bhattacharya, K.B. Choudhury, N.C. Deb, C. Sinha, K. Roy and A.Z. Msezane, "Ionization of Sodium by the Impact of Alpha Particles", Eur. Phys. J. D 47, 335 (2008)

G. P. Gupta and A. Z. Msezane, "Oscillator Strengths and Lifetimes in Ge XXI", Phys. Scr 77, 035303 (2008)

**PI James Muckerman **

Yu, H.-G.; Poggi, G.; Francisco, J.S.; Muckerman, J. T., "Energetics and molecular dynamics of the reaction of HOCO with HO2 radicals," J. Chem. Phys. 2008, 129, 214307.

Shen, X.; Allen, P. B.; Hybertsen, M. S.; Muckerman, J. T., "Water adsorption on the GaN (10-10) nonpolar surface," J. Phys. Chem. C 2009, 113, 3365-3368.

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.

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.

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. 2009, in press.

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. 2009, submitted.

**PI Patric Muggli **

Enhancing parallel quasi-static particle-in-cell simulations with a pipelining algorithm, B. Feng , C. Huang, V. Decyk, W.B. Mori, c, P. Muggli and T. Katsouleas, Journal of Computational Physics, 228(15), 5340 (2009).

Optimization of Positron Trapping and Acceleration in an Electron-beam-driven Plasma Wakefield Accelerator, X. Wang, P. Muggli, T. Katsouleas, C. Joshi, W. B. Mori, R. Ischebeck, M. J. Hogan, Phys. Rev. ST Accel. Beams 12, 051303 (2009).

Review of High-energy Plasma Wakefield Experiments, Patric Muggli and Mark J. Hogan, Comptes Rendus Physique, 10(2-3), 116 (2009).

Positron Injection and Acceleration on the Wake Driven by an Electron Beam in a Foil and Gas Plasma, X. Wang, R.Ischebeck, P. Muggli, T. Katsouleas, C. Joshi, W. B. Mori, M. J. Hogan., Phys. Rev. Lett. 101, 124801 (2008) edit Mundy, Christopher

**PI Christopher Mundy **

C.J. Mundy, I.-F. Kuo, M.E. Tuckerman, H-S. Lee, D.J. Tobias, "Hydroxide anion at the air water interface," Chemical Physics Letters, Frontiers Article doi:10.1016/j.cplett.2009.09.003

"Thermodynamic and Structural Investigations of Ammonium Borohydride, a Solid with a Highest Content of Thermodynamically and Kinetically Accesible Hydrogen" Abhijeet Karkamkar, Shawn M. Kathmann, Gregory K. Schenter, David J. Heldebrant, Nancy Hess, Maciej Gutowski and Tom Autrey, Chemistry of Materials Communication, in press (2009).

"Hydrated Structure of Ag(I) Ion from Symmetry-Dependent, K- and L-edge XAFS Multiple Scattering and Molecular Dynamics Simulations, John L. Fulton, Shawn M. Kathmann, Gregory K. Schenter, and Mahalingam Balasubramanian, Journal of Physical Chemistry A, in press (2009).

"Self-consistent polarization density functional theory: Application to water," G. Murdachaew, C.J. Mundy, and G.K. Schenter, Journal of Chemical Physics, submitted

Z. Zhang, R. Rousseau, J. Gong, B. D. Kay, and Z. Dohnlek, J. Am. Chem. Soc, submitted Imaging Hindered Rotations of Alkoxy Species on TiO2(110)

## N

**PI Jeffret Neaton **

S. Y. Quek, H. J. Choi, S. G. Louie, and J. B. Neaton, "Length Dependence of Conductance in Aromatic Single-Molecule Junctions", Nano Lett. (in press)

K. Phoa, J. B. Neaton, and V. Subramanian, "First-Principles Studies of the Dynamics of [2]rotaxane Molecular Switches", Nano Lett., in press (2009)

Z. Wu, J. B. Neaton, and J. C. Grossman, "Charge Separation via Strain in Silicon Nanowires", Nano Lett. 9, 2418 (2009)

B. Chandra, J. Bhattacharjee, Y. W. Son, M. Purewal, Y. Wu, M. Huang, T. Heinz, P. Kim, J. B. Neaton, and J. Hone, "Molecular-Scale Quantum Dots from Carbon Nanotube Heterojunctions", Nano Lett. 9, 1544 (2009)

S. Y. Quek, M. Kamenetska, M. L. Steigerwald, H. J. Choi, S. G. Louie, M. S. Hybertsen, J. B. Neaton, and L. Venkataraman, "Mechanically-Controlled Binary Conductance Switching of a Single-Molecule Junction", Nature Nanotechnology 4, 230 (2009)

R. Jasti, J. Bhattacharjee, J. B. Neaton, and C. R. Bertozzi, "Synthesis, Characterization, and Theory of [9]-, [12]-, and [18] Cycloparaphenylene: Carbon Nanohoop Structures", J. Am. Chem. Soc. 130, 17646 (2008)

J. B. Neaton, D. Prendergast, S. Whitelam, and S. G. Louie, "Understanding Nanoscale Systems at the Molecular Foundry", SciDAC Review 10, 22 (2008)

David Prendergast and Steven G. Louie, "Shirley interpolation - optimal basis sets for detailed Brillouin Zone sampling revisited", Phys Rev B (submitted).

**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].

Constantia Alexandrou, Giannis Koutsou, "A Study of Hadron Deformation in Lattice QCD", Phys. Rev. D78, 094506 (2008).

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]

**PI Gregory Newman **

Commer M. and Newman G. A., 2009, Three-dimensional controlled-source electromagnetic and magnetotelluric joint inversion: Geophysical Journal International, Vol 178, No. 3, 1305-1316.

Newman G. A., Commer M. and Carazzone J. J., 2009, Imaging CSEM data in the presence of electrical anisotropy: Geophysics In Press.

**PI Cheuk-Yiu Ng **

Y.-C. Chang, C.-S. Lam, B. Reed, K.-C. Lau, H. T. Liou, and C. Y. Ng "Rovibronically Selected and Resolved Two-Color Laser Photoionization and Photoelectron Study of the Iron Carbide Cation" J. Phys. Chem. A 2009, 113, 4242 (2009).

Xi Xing, Beth Reed, Mi-Kyung Bahng, S. J. Baek, Peng Wang, and C. Y. Ng, "Infrared-vacuum ultraviolet pulsed field ionization-photoelectron study of CH3I+ using a high-resolution infrared laser", J. Chem. Phys. 128, 104306 (2008).

Xi Xing, Beth Reed, Mi-Kyung Bahng, and C. Y. Ng, "Infrared-vacuum ultraviolet pulsed field ionization-photoelectron study of C2H4+ using a high-resolution infrared laser", J. Phys. Chem. A 112, 2572-2578 (2008).

Xi Xing, Peng Wang, Beth Reed, S. J. Baek, and C. Y. Ng, "Infrared-vacuum ultraviolet pulsed field ionization-photoelectron study of CH3Br+", J. Phys. Chem. A, 112, 9277 (2008).

Y. Hou, H.-K. Woo, P. Wang, X. Xing, C. Y. Ng, and K.-C. Lau, "Vacuum ultraviolet pulsed field ionization-photoelectron and infrared-photoinduced Rydberg ionization study of 1,3-butadiene", J. Chem. Phys., 129, 124305 (2008).

**PI Esmond Ng **

X. S. Li, "Evaluation of sparse factorization and triangular solution on multicore architectures", Proceedings in VECPAR'08 8th International Meeting High Performance Computing for Computational Science, June 24-27, 2008, Toulouse, France. (LBNL-571E)

X. S. Li, "Evaluation of SuperLU on multicore architectures", Proceedings of SciDAC 2008, Journal of Physics: Conference Series 125 (2008) 012079. Institute of Physics Publishing. Proceedings of SciDAC 2008, July 13-17, 2008, Seattle.

P. Cicotti, X.S. Li, and S. Baden, "LUsim: A framework for simulation-based performance modeling and prediction of parallel sparse LU factorization", Technical Report, LBNL- 196E, April 2008.

X. S. Li and Meiyue Shao, "A Supernodal Approach to Incomplete LU factorization", In preparation, 2009.

Philip Sternberg, Esmond G. Ng, Chao Yang, Pieter Maris, James P. Vary, Masha Sosonkina, and Hung Viet Le, "Accelerating Configuration Interaction Calculations for Nuclear Structure", Proc. SC08, November 15-21, 2008. IEEE/ACM.

J.P. Vary, H. Honkanen, Jun Li, P. Maris, S.J. Brodsky, P. Sternberg, E.G., Ng, and C. Yang, "Recent Progress in Hamiltonian Light-front QCD", Proc. LIGHT CONE 2008 Relativistic Nuclear and Particle Physics, July 7-11, 2008, Mulhouse, France.

**PI Peter Nugent **

"Exploring the Optical Transient Sky with the Palomar Transient Factory", Rau et al., Publications of the Astronomical Society of the Pacific, 2009

"The Palomar Transient Factory: System Overview, Performance and First Results", Law et al., Instrumentation and Methods for Astrophysics, 2009.** **

## O

**PI Grazyna Odyniec **

B. Abelev et al. [STAR Collaboration], Pion Interferometry in Au+Au and Cu+Cu Collisions at RHIC, Phys. Rev. C 80 (2009) 24905

B. Abelev et al. [STAR Collaboration], K/pi Fluctuations at Relativistic Energies, Phys. Rev. Lett. 103 (2009) 92301

B. Abelev et al. [STAR Collaboration], Measurement of D* Mesons in Jets from p+p Collisions at sqrt(s) = 200 GeV, Phys. Rev. D 79 (2009) 112006

B. Abelev et al. [STAR Collaboration], Observation of Two-source Interference in the Photoproduction Reaction Au Au - Au Au rho^0, Phys. Rev. Lett. 102 (2009) 112301

B. Abelev et al. [STAR Collaboration], Energy and system size dependence of \phi meson production in Cu+Cu and Au+Au collisions, Phys. Lett. B 673 (2009) 183

B. Abelev et al. [STAR Collaboration], Measurements of phi meson production in relativistic heavy-ion collisions at RHIC, Phys. Rev. C 79 (2009) 64903

B. Abelev et al. [STAR Collaboration], Systematic Measurements of Identified Particle Spectra in pp, d+Au and Au+Au Collisions from STAR, Phys. Rev. C 79 (2009) 34909

B. Abelev et al. [STAR Collaboration], Beam-Energy and System-Size Dependence of Dynamical Net Charge , Phys. Rev. C 79 (2009) 24906

B. Abelev et al. [STAR Collaboration], Indications of Conical Emission of Charged Hadrons at RHIC, Phys. Rev. Lett. 102 (2009) 52302

B.I. Abelev [STAR Collaboration] Neutral Pion Production in Au+Au Collisions at s(NN)**(1/2) = 200-GeV. Phys.Rev.C80:024905,2009.

Jean-Yves Ollitrault, Arthur M. Poskanzer, and Sergei A. Voloshin, Effect of flow fluctuations and nonflow on elliptic flow methods, Phys. Rev. C. 80, 014904 (2009)

Anthony J. Baltz, Yuri Gorbunov, Spencer R. Klein, Joakim Nystrand, . Two-Photon Interactions with Nuclear Breakup in Relativistic Heavy Ion Collisions, Accepted for publication Phys. Rev. C. Jul 2009. 17pp. e-Print: *arXiv:0907.1214* [nucl-ex]

B.I. Abelev [STAR Collaboration] Azimuthal Charged-Particle Correlations and Possible Local Strong Parity Violation. Submitted Phys. Rev. Lett. Sep 2009. e-Print: arXiv:0909.1739

B.I. Abelev [STAR Collaboration] Growth of Long Range Forward-Backward Multiplicity Correlations with Centrality in Au+Au Collisions at s(NN)**(1/2) = 200-GeV. Submitted Phys. Rev. Lett. May 2009 e-Print: arXiv:0905.0237

B.I. Abelev [STAR Collaboration] J/psi production at high transverse momentum in p+p and Cu+Cu collisions at s(NN)**1/2 = 200GeV. Submitted Phys. Rev. Lett. Apr 2009. e-Print: arXiv:0904.0439

B.I. Abelev [STAR Collaboration] Observation of charge-dependent azimuthal correlations and possible local strong parity violation in heavy ion collisions. Submitted Phys. Rev C Sep 2009. e-Print: arXiv:0909.1717

B.I. Abelev [STAR Collaboration] Long range rapidity correlations and jet production in high energy nuclear collisions. Submitted Phys. Rev. C Sep 2009. e-Print: arXiv:0909.0191 [nucl-ex]

B.I. Abelev [STAR Collaboration] Yields and elliptic flow of $d(\bar{d})$ and $^{3}He(\bar{^{3}He})$ in Au+Au collisions at $\sqrt{s_{_{NN}}} =$ 200 GeV. Sumitted Phys. Lett. B Sep 2009. e-Print: arXiv:0909.0566

B.I. Abelev [STAR Collaboration] System size dependence of associated yields in hadron-triggered jets. Submitted Phys. Lett. B Apr 2009. e-Print: arXiv:0904.1722

**PI Joseph Oefelein **

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, 2009. Submitted.

J. C. Oefelein and R. Sankaran. Large eddy simulation of turbulence-chemistry interactions in reacting flows: Experiences on the Cray-XT platforms. Proceedings of the 21st International Conference on Parallel Computational Fluid Dynamics, May 18-22 2009. Moffett Field, California.

J. H. Frank, S. A. Kaiser, and J. C. Oefelein. Coupling imaging measurements and LES of dissipation structures in turbulent nonreacting jets and nonpremixed jet flames. Proceedings of the 6th Joint Meeting of the US Sections of the Combustion Institute, Paper 32D1, May 17-20 2009a. Ann Arbor, Michigan.

J. H. Frank, S. A. Kaiser, and J. C. Oefelein. Coupling imaging diagnostics and large eddy simulation in turbulent nonreacting jets and nonpremixed jet flames. Proceedings of the 4th European Combustion Meeting, April 14-17 2009b. Vienna, Austria.

V. Sankaran, T. G. Drozda, and J. C. Oefelein. A tabulated closure for turbulent nonpremixed combustion based on the linear eddy model. Proceedings of the Combustion Institute, 32:In Press, 2009.

T. G. Drozda, G.-H. Wang, V. Sankaran, J. R. Mayo, J. C. Oefelein, and R. S. Barlow. Scalar filtered mass density functions in non-premixed turbulent jet flames. Combustion and Flame, 155:54-69, 2008.

J. H. Chen, C. S. Yoo, R. Sankaran, and J. C. Oefelein. High-fidelity simulations for clean and efficient combustion of alternative fuels. Journal of Physics, 125:1-6, 2008. DOI 10.1088/1742-6596/125/1/012028.

**PI Serdar Ogut **

M. L. Tiago, J. C. Idrobo, S. Ogut, J. Jellinek, and J. R. Chelikowsky, "Electronic and optical excitations in Ag_n (n = 1-8): Comparison of density-functional and many-body theories", Phys. Rev. B 79, 155419 (2009).

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", submitted to Phys. Rev. B (August 2009).

**PI Leonid Oliker **

J. Borrill, L. Oliker. J. Shalf, H. Shan, A. Uselton, "HPC Global File System Performance Analysis Using A Scientific-Application Derived Benchmark", Parallel Computing Journal, 2009

M. Wehner, L. Oliker, J. Shalf, "Green Flash: Designing an energy efficient climate supercomputer", IEEE Spectrum, in press

S. Williams, J. Carter, L. Oliker, J. Shalf, K. Yelick, "Resource-Efficient, Hierarchical Auto-Tuning of a Hybrid Lattice Boltzmann Computation on the Cray XT4", Cray Users Group Workshop (CUG), 2009.

"An Auto-Parallelizing and Auto-Tuning Framework for Multicore Stencil Computations" Cy Chan , Shoaib Kamil, Leonid Oliker, John Shalf, Samuel Williams, submitted to SC09

**PI Kostas Orginos **

Magnetic Moments of Delta and Omega Baryons with Dynamical Clover Fermions, C. Aubin, K. Orginos, V. Pascalutsa, and M. Vanderhaeghen, Phys. Rev. D79, 051502(R) (2009), 0811-2440.

Computing and deflating eigenvalues while solving multiple right hand side linear systems in quantum chromodynamics, Andreas Stathopoulos, Kostas Orginos, e-Print: arXiv:0707.0131 accepted SIAM Journal of Numerical Analysis.

## P

**PI Bahram Parvin **

Kurpinski K, Jang DJ, Bhattacharya S, Rydberg B, Chu J, So J, Wyrobek A, Li S,Wang D.Differential Effects of X-Rays and High-Energy (56)Fe Ions on Human Mesenchymal Stem Cells. Int J Radiat Oncol Biol Phys. 2008 Dec 18. [Epub ahead of print] PMID: 19101095

Chin, L, Gray, JW. Translating insights from the cancer genome into clinical practice. Nature 452:553-63 (2008)

Groesser, T., Cooper, B., and Rydberg, B. Lack of Bystander Effects from High-LET Radiation for Early Cytogenetic End Points. Radiat. Res. 170, 794-802 (2008).

Lowe, X. R., Bhattacharya, S., Marchetti, F. and Wyrobek, A. J. Early Brain Response to Low-Dose Radiation Exposure Involves Molecular Networks and Pathways Associated with Cognitive Functions, Advanced Aging and Alzheimer's Disease. Radiat. Res. 171, 53"65 (2009).

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, in press.

C. Maxwell, M.C. Fleisch, S.V. Coastes, A.C. Erickson, A. Boissiere, R. Gupta, S.A. Ravani, B. Parvin, and M.H. Barcellos-Hoff, "Targeted and nontargeted effects of ionizing radiation that impact genomic instability," Cancer research, V. 69, 2009.

**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, Bound.-Lay. Meteorol., In press.

Finnigan, J. J., R. H. Shaw, E. Patton: 2009, Turbulence structure above a vegetation canopy, J. Fluid Mech., In press.

Huang, J., X. Lee, E. G. Patton: 2009, Dissimilarity of scalar transport in the convective boundary layer in inhomogeneous landscapes, Bound.-Lay. Meteorol., 130, pp. 327-345, DOI: 10.1007/s10546-009- 9356-8.

Huang, J., X. Lee, E. G. Patton: 2008, A modeling study of flux imbalance and the influence of entrainment in the convective boundary layer, Bound.-Lay. Meteorol., 127, pp. 273-292, DOI: 10.1007/s10546-007-9254-x.

**PI Joyce Penner **

Lee, S. S., J.E. Penner, and S.M. Saleeby, 2009: Aerosol effects on liquid-water path of thin stratocumulus clouds, J. Geophys. Res., 114, D07204, doi:10.1029/2008JD010513.

Lee, S.S., J.E. Penner, and M. Wang, Comparison of a global-climate model simulation to a cloud- system resolving model simulation for long-term thin stratocumulus clouds, submitted, Atmos. Chem. Phys., submitted, 2009.

Lee, S.S. and J.E. Penner, 2009: 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., submitted.

Lee, S.S. and J.E. Penner, 2009: Factors determining the effect of aerosols on cloud mass and their dependence on liquid-water path, Atmos. Chem. Phys., submitted.

C. Jablonowski, R. C. Oehmke, Q. F. Stout, Block-Structured Adaptive Meshes and Reduced Grids for Atmospheric General Circulation Models, Phil. Trans. Roy. Soc., in press, 2009.

Oehmke,R and Stout, Q.F. 2008, "A parallel adaptive block library supporting multiple topologies", Computer Physics Communications, submitted 2009.

**PI Stephen Pennycook **

Weidong Luo, Stephen J. Pennycook, and Sokrates T. Pantelides, "Magnetic dead layer at a complex oxide interface", Physical Review Letters 101, 247204 (Dec. 2008).

Weidong Luo, Maria Varela, Jing Tao, Stephen J. Pennycook, and Sokrates T. Pantelides, "Electronic and crystal-field effects in the fine structure of electron energy-loss spectra of manganites", Physical Review B 79, 052405 (2009).

M. Varela, M. P. Oxley, W. Luo, J. Tao, M. Watanabe, A. R. Lupini, S. T. Pantelides, and S. J. Pennycook, "Atomic resolution imaging of oxidation states in manganites", Physical Review B 79, 085117 (2009).

J.C. Idrobo, A. Halabica, R.H. Magruder III, R.F. Haglund Jr., S.J. Pennycook, and S.T. Pantelides, "Universal response of Si-Si bonds and its evolution from nanoparticles to bulk", Physical Review B 79, 125322 (2009).

S. J. Pennycook, M. F. Chisholm, A. R. Lupini, M. Varela, A. Y. Borisevich, M. P. Oxley, W. Luo, K. van Benthem, S-H. Oh, D. L. Sales, S. I. Molina, J. Garcia-Barriocanal, C. Leon, J. Santamaria, S. N. Rashkeev, and S. T. Pantelides, "Aberration-corrected scanning transmission electron microscopy: from atomic imaging and analysis to solving energy problems", Phil. Trans. R. Soc. A 367, 3709 (2009).

J.C. Idrobo, M.P. Oxley, W. Walkosz, R.F. Klie, S. Ogut, B. Mikijelj, S.J. Pennycook, and S.T. Pantelides, "Identification and lattice location of oxygen impurities in Si3N4" Applied Physics Letters, in print September (2009).

T.J. Pennycook, M.J. Beck, K. Varga, M. Varela, S.J. Pennycook, S.T. Pantelides, "Origin of Colossal Ionic Conductivity in Oxide Multilayers: Interface Induced Sublattice Disorder," under review Phys. Rev. Lett. September (2009).

Matthew F. Chisholm, Weidong Luo, Ho Nyung Lee, and Sokrates T. Pantelides, "Atomic-scale compensation phenomena at polar interfaces", submitted to Nature September (2009).

**PI Saul Perlmutter **

Prieto, Eric; Ealet, Anne; Milliard, Bruno; Aumeunier, Marie-Helene; Bonissent, Alain; Cerna, Cedric; Crouzet, Pierre-Elie; Karst, Pierre; Kneib, Jean-Paul; Malina, Roger; Pamplona, Tony; Rossin, Christelle; Smadja, Gerard; Vives, Sebastien, An integral field spectrograph for SNAP, Space Telescopes and Instrumentation 2008: Optical, Infrared, and Millimeter. Edited by Oschmann, Jacobus M., Jr.; de Graauw, Mattheus W. M.; MacEwen, Howard A. Proceedings of the SPIE, Volume 7010, pp. 701019- 701019-8 (2008).

Dahlen, Tomas; Mobasher, Bahram; Jouvel, Stephanie; Kneib, Jean-Paul; Ilbert, Olivier; Arnouts, Stephane; Bernstein, Gary; Rhodes, Jason, Supernova Acceleration Probe: Investigating Photometric Redshift Optimization, The Astronomical Journal, Volume 136, Issue 3, pp. 1361-1371 (2008)

Carlson, Jordan, White, Martin, & Padmanabhan, Nikhil, Critical look at cosmological perturbation theory techniques, Physical Review D, 80, 043531 (2009)

Padmanabhan, Nikhil, et al., 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, 1862 (2009)

White, Martin, Song, Yong-Seon, & Percival, Will J., Forecasting cosmological constraints from redshift surveys, Monthly Notices of the Royal Astronomical Society, 397, 1348 (2009)

White, Martin & Padmanabhan, Nikhil, Breaking halo occupation degeneracies with marked statistics, Monthly Notices of the Royal Astronomical Society, 395, 2381 (2009)

Slosar, Anze, et al., The Acoustic Peak in the Lyman Alpha Forest, JCAP, in press (2009)

Padmanabhan, Nikhil & White, Martin, Calibrating the Baryon Oscillation Ruler for Matter and Halos, Phys.Rev.D80 063508 (2009)

Cohn, J. D. & White, Martin, Issues in joint SZ and optical cluster finding, Monthly Notices of the Royal Astronomical Society, 393, 393 (2009)

Percival, Will J. & White, Martin, Testing cosmological structure formation using redshift-space distortions, Monthly Notices of the Royal Astronomical Society, 393, 297 (2009)

Heitmann, Katrin, et al., The Coyote Universe II: Cosmological Models and Precision Emulation of the Nonlinear Matter Power Spectrum, ArXiv e-prints, arXiv:0902.0429 (2009)

Heitmann, Katrin, et al., The Coyote Universe I: Precision Determination of the Nonlinear Matter Power Spectrum, ArXiv e-prints, arXiv:0812.1052 (2008)

Dalal, Neal, et al., Halo Assembly Bias in Hierarchical Structure Formation, Astrophysical Journal, 687, 12 (2008)

Heitmann, Katrin, et al., The cosmic code comparison project, Computational Science and Discovery, 1, 015003 (2008)

Seo, Hee-Jong, et al., Nonlinear Structure Formation and the Acoustic Scale, Astrophysical Journal, 686, 13 (2008)

Kowalski, M., et al. Improved Cosmological Constraints from New, Old, and Combined Supernova Data Sets. ApJ, 686, 749-778 (2008). [10/2008]

Barbary, K., et al. Discovery of an Unusual Optical Transient with the Hubble Space Telescope. ApJ, 690, 1358-1362 (2009). [1/2009]

Rubin, D., et al. Looking Beyond Lambda with the Union Supernova Compilation. ApJ, 695, 391-403 (2009). [4/2009]

**PI Steven Pieper **

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

**PI Mitch Pindzola **

Intermediate-coupling R-matrix calculations of electron-impact excitation of Fe+5, C. P. Ballance and D. C. Griffin, Journal of Physics B 41, 195205 (October 2008)

Dirac R-matrix calculations of electron-impact excitation of neon-like krypton D. C. Griffin, C. P. Ballance, D. M. Mitnik, and J. C. Berengut, Journal of Physics B 41, 215201 (November 2008)

Differential cross sections for the ionization of oriented H_2 molecules by electron-impact, J. P. Colgan, M. S. Pindzola, F. J. Robicheaux, C. Kaiser, A. J. Murray, and D. H. Madison, Physical Review Letters 101, 233201 (December 2008)

Energy and angle differential cross sections for the electron-impact double ionization of He, M. S. Pindzola, F. J. Robicheaux, and J. P. Colgan, Journal of Physics B 41, 235202 (December 2008)

Double photoionization of Be and Mg atoms using the R-matrix with pseudo-states method, D. C. Griffin, M. S. Pindzola, C. P. Ballance, and J. P. Colgan, Physical Review A 79, 023413 (February 2009)

Splitting a Bose-Einstein condensate in two translating traps, B. Sun and M. S. Pindzola, Physical Review A 79, 033608 (March 2009)

Triple differential cross sections for the electron-impact ionization of H_2 molecules for symmetric and asymmetric outgoing electron energies, J. P. Colgan, O. Al-Hagan, D. H. Madison, C. Kaiser, A. J. Murray, and M. S. Pindzola, Physical Review A 79, 052704 (May 2009)

Energy and angular differential probabilities for photoionization of He using chirped attosecond soft X-ray pulses, T. G. Lee, M. S. Pindzola, and F. J. Robicheaux, Physical Review A 79, 053420 (May 2009)

Inelastic scattering of electrons by black hole atoms, M. S. Pindzola, Journal of Physics B 42, 095202 (May 2009)

Triple differential cross sections for the electron-impact ionization of He at 102 eV incident energy, J. P. Colgan, M. Foster, M. S. Pindzola, I. Bray, A. T. Stelbovics, and D. V. Fursa, Journal of Physics B 42, 145002 (July 2009)

Merging and splitting of Bose-Einstein condensates in two translating traps, B. Sun and M. S. Pindzola, Journal of Physics B 42, 145502 (July 2009)

Deep interference minima in non-coplanar triple differential cross sections for the electron-impact ionization of small atoms and molecules, J. P. Colgan, O. Al-Hagan, D. H. Madison, A. J. Murray, and M. S. Pindzola, Journal of Physics B 42, 171001 (September 2009)

Electron-impact ionization of ground and metastable neon, C. P. Ballance, J. A. Ludlow, M. S. Pindzola, and S. D. Loch, Journal of Physics B 42, 175202 (September 2009)

Observing collapse in colliding two dipolar Bose-Einstein condensates, B. Sun and M. S. Pindzola, Journal of Physics B 42, 175301 (September 2009)

**PI Tomasz Plewa **

Guzman, J., and Plewa, T., "Non-spherical core collapse supernovae: evolution toward homologous expansion", submitted to Nonlinearity

Guzman, J., Plewa, T., and Kifonidis, K., "Non-spherical core collapse supernovae III. Evolution toward homology and structure of young SNR", submitted to Astronomy and Astrophysics

Kasen, D., "Seeing the collision of a supernova with its companion star", submitted to Astrophysical Journal

**PI Alan Poon **

"Measurement of the Cosmic Ray and Neutrino-Induced Muon Flux at the Sudbury Neutrino Observatory" (SNO Collaboration) Accepted for publication by Phys. Rev. D.

"The calibration of the Sudbury Neutrino Observatory using uniformly distributed radioactive sources", K. Boudjemline et al., submitted to Nucl. Instr. Meth. for publication

**PI Ruth Pordes **

D.A. Paggi, et al., "Computer simulation and SERR detection of cytochrome c dynamics at SAM-coated electrodes", Electrochim. Acta (2009), doi:10.1016/j.electacta.2009.02.050

D. F. Gauto, et el., "Carbohydrate-Binding Proteins: Dissecting Ligand Structures through Solvent Environment Occupancy, " J. Phys. Chem. B 2009, 113 (25), pp 8717"8724.

**PI Alex Pothen **

Mahantesh Halappanavar, Florin Dobrian and Alex Pothen, Matchings in massive graphs on terascale computers via approximation, Supercomputing 2009 (SC09), IEEE and ACM, Electronic Poster.

Umit Catalyurek, Florin Dobrian, Assefaw Gebremedhin, Mahantesh Halappanavar, and Alex Pothen, Scalable parallel algorithms for matching and coloring, Preprint, 15 pages, 2009. (Submitted for Publication).

**PI Larry Pratt **

Lawrence M. Pratt, Darryl D. Dixon, Marcus A. Tius Mixed Aggregates of 1-Methoxyallenyllithium with Lithium Chloride Submitted for publication

Darryl D. Dixon, Marcus A. Tius, Lawrence M. Pratt Gas Phase and Solution Structures of 1-Methoxyallenyllithium J. Org. Chem. 2009, 74, 5881

Lawrence M. Pratt, Ngan Van Nguyen, Ohyun Kwon Fritsch-Buttenberg-Wiechell (FBW) Reaction of 1-Halovinyllithium Carbenoids: A Computational Study Chem. Lett. 2009, 38, 574

Lawrence M. Pratt, Phuong Thao Tho Tran, Ngan Van Nguyen, B. Ramachandran Cyclopropanation Reactions of Halomethyllithium Carbenoids: A Computational Study of the Effects of Aggregation and Solvation Bull. Chem. Soc. Japan, 2009, 82, 1107

Lawrence M. Pratt, Shin-ichi Fujiwara, Nobuaki Kambe Structure, bonding, and Aggregation of Selenium-Containing Organolithium Species Tetrahedron 2009, 65, 1017

Lawrence M. Pratt, Darrel Jones, Andrea Sease, Donta Busch, Emmanuel Faluade, Son C. Nguyen, Bui T. Thanh Calculation of the solvation state of organolithium compounds: Effects of basis sets and electron correlation methods. Int. J. Quant. Chem. 2009, 109, 34

**PI Joel Primack **

Ceverino, Daniel, & Klypin, Anatoly 2009, The Role of Stellar Feedback in the Formation of Galaxies, ApJ, 695, 292

Dekel, Avishai, Sari, Re'em, & Ceverino, Daniel 2009, Formation of Massive Galaxies at High Redshift: Cold Streams, Clumpy Disks, and Compact Spheroids, ApJ, 703, 785

**PI Fritz Prinz **

Holme, Pornprasertsuk, and Prinz, "Interpretation of low temperature solid oxide fuel cell electrochemical impedance spectra," submitted to the Journal of the Electrochemical Society.

Pornprasertsuk, Holme, and Prinz, "KINETIC MONTE CARLO SIMULATIONS OF SOLID OXIDE FUEL CELL," accepted for publication in Journal of the Electrochemical Society.

Zhou, Pasquarelli, Holme, Berry, Ginley, O'Hayre, "Improving PEM fuel cell catalyst activity and durability using nitrogen-doped carbon supports," accepted for publication in J Mater Chem.

Timothy Holme, Yingke Zhou, Robert Pasquarelli, Ryan O'Hayre, "First principles study of doped carbon supports for enhanced platinum catalysts," submitted to Phys. Chem. Chem. Phys.

**PI Philip Protchett **

P.L. Pritchett, "Energetic Electron Acceleration During Multi-Island Coalescence," Phys. Plasmas, 15, 102105, 2008.

F.S. Mozer and P.L. Pritchett, "Regions Associated with Electron Physics in Asymmetric Magnetic Field Reconnection," Geophys. Res. Lett., 36, L07102, doi:10.1029/2009GL037463, 2009.

P.L. Pritchett and F.S. Mozer, "The Magnetic Field Reconnection Site and Dissipation Region," Phys. Plasmas, 16, 080702, 2009.

P.L. Pritchett and F.S. Mozer, "Asymmetric Magnetic Reconnection in the Presence of a Guide Field," J. Geophys. Res., 114, in press, 2009.

**PI Dale Pullin **

R. Deiterding. A parallel adaptive method for simulating shock-induced combustion with detailed chemical kinetics in complex domains, Computers & Structures 87: 769-783, 2009.

C. Pantano, R. Deiterding, D.J. Hill, and D.I. Pullin. A low numerical dissipation patch-based adaptive mesh refinement method for large-eddy simulation of compressible flows. J. Comput. Phys., 221(1):63-87, 2007.** **

## Q

**PI Ji Qiang **

"A high-order fast method for computing convolution integral with smooth kernel" by J. Qiang, Computer Physics Communications, vol. 181, p. 313 (2010)

## R

**PI Abhay Ram **

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", Physics of Plasmas 16, 055906 (2009). Invited paper YI2 3, Bull. Am. Phys. Soc. 53, 323 (2008).

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).

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.

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).

D. R. Ernst, N. P. Basse, W. Dorland, C. L. Fiore, L. Lin, A. Long, E. S. Marmar, M. Porkolab, and K. Zhurovich, "Direct comparison of density fluctuation wavelength spectra from nonlinear gyrokinetic simulations and experiment in a tokamak plasma", submitted to Physical Review Letters.

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 **

Benedict, J., and D. A. Randall, 2009: MJO Structure in the Superparameterized CAM. J. Climate (in press).

DeMott, C., and D. A. Randall, 2009: Implied ocean heat transports in the standard and super- parameterized Community Atmosphere Models. J. Climate (in press).

Teixeira,J., S. Cardoso, M. Bonazzola, J. Cole, A. DelGenio, C. DeMott, C. Franklin, C. Hannay, C. Jakob, Y. Jiao, J. Karlsson, H. Kitagawa, M. Koehler, A. Kuwano-Yoshida, C. LeDrian, A. Lock, M. J. Miller, P. Marquet, J. Martins, C. R. Mechoso, E. v. Meijgaard, I. Meinke, P. M. A. Miranda, D. Mironov, R. Neggers, H. L. Pan, D. A. Randall, P. J. Rasch, B. Rockel, W. B. Rossow, B. Ritter, A. P. Siebesma, P. Soares, F. J. Turk, P. Vaillancourt, A. Von Engeln, M. Zhao, 2009: Tropical and sub-tropical cloud transitions in weather and climate prediction models: the GCSS/WGNE Pacific Cross-section Intercomparison (GPCI). Submitted to J. Climate.

Khairoutdinov, M. F., S. K. Krueger, C.-H. Moeng, P. Bogenschutz, and D. A. Randall, 2009: Large-eddy simulation of maritime deep tropical convection. Submitted to JAMES.

**PI Sergey Rashkeev **

Michael V. Glazoff, Sergey N. Rashkeev, Yuri P. Pytev, Jeong-Whan Yoon, and Simon Sheu. Interplay between plastic deformations and optical properties of surfaces. Appl. Phys. Lett. 95, N8, 084106 (2009).

E.A.Kotomin, Yu.A.Mastrikov, S.N.Rashkeev, and P. Van Uffelen. Implementing first principles calculations of defect migration in a fuel performance code for UN simulations. Journal of Nuclear Materials 393, N2, 292-299 (2009).

Yanting Wang and Sergey N. Rashkeev. Melting phase transitions and catalytic activity of bilayer gold nanoclusters. The Journal of Physical Chemistry C 113, N 24, 10517-10520 (2009).

L.M.Petkovic, S.N.Rashkeev, and D.M.Ginosar. Ethanol oxidation on metal oxide supported platinum catalysts. Catalysis Today 147, N2, 107-114 (2009).

G.M.Veith, A.R.Lupini, S.Rashkeev, S.J.Pennycook, D.R.Mullins, V.Schwartz, C.A.Bridges, and N.J. Dudney. Thermal stability and catalytic activity of gold nanoparticles supported on silica. Journal of Catalysis 262, N1, 92-101 (2009).

M.M.Kuklja and S.N.Rashkeev. Interplay of decomposition mechanisms at shear-strain interface. The Journal of Physical Chemistry C (Letter) 113, N 1, 17-20 (2009).

S.N.Rashkeev, D.M.Ginosar, L.M.Petkovic, and H.H.Farrell. Catalytic activity of supported metal particles for sulfuric acid decomposition reaction. Catalysis Today 139, N4, 291-298 (2009).

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. Garcia-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 367, 3709-3733 (2009)(review article).

Ligen Wang and Maija M. Kuklja, First-principles study of small aluminum clusters: Oxygen adsorptions, oxidation and phase stability, (to appear in Journal of Physics and Chemistry of Solids, 2009).

A.V.Kimmel, P.V.Sushko, A.L.Shluger, and M.M.Kuklja, Modeling proton transfer and polarons in molecular crystal diamino-dinitroethylene, (Phys. Rev. B, to appear, 2009).

A.V.Kimmel, P.V.Sushko, A.L.Shluger, and M.M.Kuklja, The effect of molecular and lattice structure on hydrogen transfer in molecular crystals diamino-dinitroethylene and triamino-trinitrobenzene, J. Phys. Chem. A 112 (19), 4496-4450 (2008).

Maija M. Kuklja and Sergey N. Rashkeev, Modeling of defect induced phenomena in energetic materials, book chapter in Hydrostatic Compression of Energetic Materials, editors: S. Peiris and G. Piermarini, Springer-Verlag, Chapter 8, pp. 322-361 (2008) (review article).

**PI Lawrence Rauchwerger **

S. Rus, M. Pennings and L. Rauchwerger, ``Implementation of Sensitivity Analysis for Automatic Parallelization'', Proc. of the 21-th Workshop on Languages and Compilers for Parallel Computing (LCPC), Edmonton, Canada, Aug. 2008.

A. Jula and L. Rauchwerger, ``Two Memory Allocators that Use Hints to Improve Locality'', Int. Symposium on Memory Management(ISMM'09), Dublin, Ireland, June 2009.

A. Buss, T. Smith, G. Tanase, N. Thomas, M. Bianco, N. Amato and L. Rauchwerger, ``Design for Interoperability in STAPL'', Proc. of the 21-th Workshop on Languages and Compilers for Parallel Computing (LCPC), Edmonton, Canada, Aug. 2008.

**PI Fernando Reboredo **

Quasiparticle gaps and exciton Coulomb energies in Si nanoshells: First-principles calculations Kimberly Frey, Juan C. Idrobo, Murilo L. Tiago, Fernando Reboredo, and Serdar Öğüt Phys. Rev. B 80 153411 (2009).

Many-body electronic structure and Kondo properties of cobalt-porphyrin molecules Luis G. G. V. Dias da Silva, Murilo L. Tiago, Sergio E. Ulloa, Fernando A. Reboredo, and Elbio Dagotto Phys. Rev. B 80 155443 (2009).

Controlling the gap of fullerene microcrystals by applying pressure: Role of many-body effects Murilo L. Tiago and Fernando A. Reboredo Phys. Rev. B 79 195410 (2009).

**PI John Rehr **

"Real space calculation of optical constants from optical to x-ray frequencies," M. P. Prange, J. J. Rehr, G. Rivas, J. J. Kas, and John W. Lawson, Phys. Rev. B. (in press) 2009.

"Ab initio theory and calculations of X-ray spectra," John J. Rehr, Joshua J. Kas, Micah P. Prange, Adam P. Sorini, Yoshinari Takimoto, Fernando Vila, Comptes Rendus Physique, doi:10.1016/j.crhy.2008.08.004 (2008).

"On the Frequency and Solvent Dependence of Non-Linear Optical Properties of Molecules," Yoshi Takimoto, Christine M. Isborn, B.E. Eichinger, J. J. Rehr, Xiaosong Li, and B. H. Robertson, Journal of Physical Chemistry C, 112, 8016 (2008).

Ab initio Real Space Calculations of Electron Energy Loss Spectra," A. P. Sorini, J. J. Rehr and K. Jorissen, AIP Conference Proceedings 999, 47 (2008).

**PI Chuang Ren **

R. Yan, A. Maximov, C. Ren, and F. Tsung, "The growth and saturation of convective modes of the two- plasmon decay instability in inertial confinement fusion," submitted to Phys. Rev. Lett.

**PI Patrick Rinke **

E. Kioupakis, P. Rinke, A. Schleife, F. Bechstedt and C. G. Van de Walle, "Free-carrier absorption in nitrides from first principles", submitted to Physical Review Letters

Q. Yan, P. Rinke and C. G. Van de Walle, "Strain effects in group-III nitrides: deformation potentials for AlN, GaN, and InN", Applied Physics Letters (in press).

G. B. Wilson-Short, A. Janotti, K. Hoang and C. G. Van de Walle, submitted to Physical Review B

**PI Barrett Rogers **

``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, to appear in Phys Plasmas (2009)

``Magnetic Reconnection at the Dayside Magnetopause in Global LFM Simulations'', J. E. Ouellette, B. N. Rogers, M. Wiltberger, and J. G. Lyon, submitted to JGR (2009)

``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)

``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); doi:10.1063/1.3155085

**PI Tony Rollett **

T. Haxhimali, D. Buta, M. Asta, P. W. Voorhees and J. J. Hoyt, "Size-Dependent Nucleation Kinetics at Non-planar Nanowire Growth Interfaces," Phys. Rev. E, Rapid Communications (submitted).

"Dynamics of grain boundary motion coupled to shear deformation: An analytical model and its verification by molecular dynamics," V. A. Ivanov and Y. Mishin, Phys. Rev. B 78, 064106 (2008).

"Temperature dependence of the surface free energy and surface stress: An atomistic calculation for Cu(110)," T. Frolov and Y. Mishin, Phys. Rev. B 79, 045430 (2008).

"Solid-liquid interface free energy in binary systems: Theory and atomistic calculations for the(110) Cu-Ag interface," T. Frolov and Y. Mishin, J, Chem. Phys. 131, 054702 (2009).

"Thermodynamics of grain boundary premelting in alloys. I. Phase-field modeling," Y. Mishin, W. J. Boettinger, J. A. Warren, G. B. McFadden, Acta Materialia 57, 3771-3785 (2009).

"Thermodynamics of grain boundary premelting in alloys. II. Atomistic simulation," P. L. Williams and Y. Mishin, Acta Materialia 57, 3786-3794 (2009).

"Molecular dynamics modeling of self-diffusion along a triple junction ," T. Frolov and Y. Mishin, Phys. Rev. B 79, 174110 (2009).

"Atomistic simulation of CdTe solid-liquid coexistence equilibria," C. Henager and J. R. Morris, submitted to Phys. Rev. B.

**PI Edward Rubin **

Aklujkar M et al. The genome sequence of Geobacter metallireducens: features of metabolism, physiology and regulation common and dissimilar to Geobacter sulfurreducens. BMC Microbiol. 2009 May 27;9:109.

Allen MA et al. The genome sequence of the psychrophilic archaeon, Methanococcoides burtonii: the role of genome evolution in cold adaptation. ISME J. 2009 Sep;3(9):1012-35. Epub 2009 Apr 30.

Alvarez Retuerto AI et al. Association of common variants in the Joubert syndrome gene (AHI1) with autism. Hum Mol Genet. 2008 Dec 15;17(24):3887- 96.

Anderson I et al. Genomic characterization of methanomicrobiales reveals three classes of methanogens. PLoS One. 2009 Jun 4;4(6):e5797.

Anderson IJ et al. The complete genome sequence of Staphylothermus marinus reveals differences in sulfur metabolism among heterotrophic Crenarchaeota. BMC Genomics. 2009 Apr 2;10:145

Anderson SJ et al. Development of simple sequence repeat markers for the soybean rust fungus, Phakopsora pachyrhizi. Mol Ecol Res. 2008 Nov;8(6):1310- 1312

Barabote RD et al. Complete genome of the cellulolytic thermophile Acidothermus cellulolyticus 11B provides insights into its ecophysiological and evolutionary adaptations. Genome Res. 2009 Jun;19(6):1033-43. Epub 2009 Mar

Bickel RD et al. Contrasting Patterns of Sequence Evolution at the Functionally Redundant bric A brac Paralogs in Drosophila melanogaster. J Mol Evol. 2009 Aug;69(2):194-202. Epub 2009 Jul 29.

Birney E et al. Prepublication data sharing. Nature. 2009 Sep 10;461(7261):168- 70.

Blazewicz J et al. Whole genome assembly from 454 sequencing output via modified DNA graph concept. Comput Biol Chem. 2009 Jun;33(3):224-30. Epub 2009 May 3.

Bluhm BH et al. Analyses of expressed sequence tags from the maize foliar pathogen Cercospora zeae-maydis identify novel genes expressed during vegetative, infectious, and reproductive growth. BMC Genomics. 2008 Nov 4;9:523.

Bowler C et al. The Phaeodactylum genome reveals the evolutionary history of diatom genomes. Nature. 2008 Nov 13;456(7219):239-44. Epub 2008 Oct 15.

Bressler J et al.The INSIG2 rs7566605 genetic variant does not play a major role in obesity in a sample of 24,722 individuals from four cohorts. BMC Med Genet. 2009 Jun 12;10:56.

Breznak JA et al. Spirochaeta cellobiosiphila sp. nov., a facultatively anaerobic, marine spirochaete. Int J Syst Evol Microbiol. 2008 Dec;58(Pt 12):2762-8.

Cai ZQ et al. Extensive Reorganization of the Plastid Genome of Trifolium subterraneum (Fabaceae) Is Associated with Numerous Repeated Sequences and Novel DNA Insertions. J Mol Evol. 2008 Dec;67(6):696-704.

Calton MA et al. Association of functionally significant Melanocortin-4 but not Melanocortin-3 receptor mutations with severe adult obesity in a large North American case-control study. Hum Mol Genet. 2009 Mar 15;18(6):1140-7. Epub 2008 Dec 17.

Campbell BJ et al. Adaptations to submarine hydrothermal environments exemplified by the genome of Nautilia profundicola. PLoS Genet. 2009 Feb;5(2):e1000362. Epub 2009 Feb 6.

Carbon S et al. AmiGO: online access to ontology and annotation data. Bioinformatics. 2009 Jan 15;25(2):288-9. Epub 2008 Nov 25.

Chivian D et al. Environmental genomics reveals a single-species ecosystem deep within Earth. Science. 2008 Oct 10;322(5899):275-8.

Clum A et al. Complete genome sequence of Acidimicrobium ferrooxidans type strain (ICPT). Standards in Genomic Sciences. 2009:1(1):38- 45.

Coleman JJ et al. The genome of Nectria haematococca: contribution of supernumerary chromosomes to gene expansion. PLoS Genet. 2009 Aug;5(8):e1000618. Epub 2009 Aug 28.

Copeland A et al. Complete genome sequence of Desulfomicrobium baculatum type strain (XT). Standards in Genomic Sciences. 2009:1(1):29-37.

Coyne RS et al. Refined annotation and assembly of the Tetrahymena thermophila genome sequence through EST analysis, comparative genomic hybridization, and targeted gap closure. BMC Genomics. 2008 Nov 26;9:562.

De Val S et al. Combinatorial regulation of endothelial gene expression by ets and forkhead transcription factors. Cell. 2008 Dec 12;135(6):1053-64.

Drainas C et al. Characterization and whole genome sequencing of Arthrobacter phenanthrenivorans, a new phenanthrene degrading bacterium. FEBS J. 2009 Jul;276(Suppl. 1):101-101.

Dubchak I et al. Multiple whole-genome alignments without a reference organism. Genome Res. 2009 Apr;19(4):682-9. Epub 2009 Jan 28.

Engelbrektson A et al. Probiotics to minimize the disruption of faecal microbiota in healthy subjects undergoing antibiotic therapy. J Med Microbiol. 2009 May;58(Pt 5):663-70.

Field D et al. Meeting Reports from the Genomic Standards Consortium (GSC) Workshops 6 and 7. Standards in Genomic Sciences. 2009:1(1):21-28.

Foster JT et al. Whole-genome-based phylogeny and divergence of the genus Brucella. J Bacteriol. 2009 Apr;191(8):2864-70. Epub 2009 Feb 6.

Gray J et al. A Recommendation for Naming Transcription Factor Proteins in the Grasses. Plant Physiol. 2009 Jan;149(1):4-6.

Gomez LD et al. Analysis of saccharification in Brachypodium distachyon stems under mild conditions of hydrolysis. Biotechnol Biofuels. 2008 Oct 22;1(1):15.

Grimson A et al. Early origins and evolution of microRNAs and Piwi- interacting RNAs in animals. Nature. 2008 Oct 30;455(7217):1193-7. Epub 2008 Oct 1.

Han C et al. Complete genome sequence of Pedobacter heparinus type strain (HIM 762-3T). Standards in Genomic Sciences. 2009:1(1):54-62.

Harris DR et al. Directed Evolution of Ionizing Radiation Resistance in Escherichia coli. J Bacteriol. 2009 Aug 19;1(16):5240-52. Epub 2009 Jun 5.

Herlemann DP et al. Genomic analysis of "Elusimicrobium minutum," the first cultivated representative of the phylum "Elusimicrobia" (formerly termite group 1). Appl Environ Microbiol. 2009 May;75(9):2841-9. Epub 2009 Mar 6.

Hooper SD et al. Microbial co-habitation and lateral gene transfer: what transposases can tell us. Genome Biol. 2009;10(4):R45. Epub 2009 Apr 24.

Hooper SD et al. Integration of phenotypic metadata and protein similarity in Archaea using a spectral bipartitioning approach. Nucleic Acids Res. 2009 Apr;37(7):2096-104. Epub 2009 Feb 17.

Horton A et al. Conservation of linkage and evolution of developmental function within the Tbx2/3/4/5 subfamily of T-box genes: implications for the origin of vertebrate limbs. Dev Genes Evol. 2008 Dec;218(11-12):613-28.

Hugenholtz P et al. Focus: Synergistetes. Environ Microbiol. 2009 Jun;11(6):1327-9.

Hugenholtz P et al. A changing of the guard. Environ Microbiol. 2009 Mar;11(3):551-3.

Ivanova N et al. Spreading of aqueous solutions of trisiloxanes and conventional surfactants over PTFE AF coated silicone wafers. Langmuir. 2009 Apr 9;25(6):3564-70.

Isabel S et al. Divergence among Genes Encoding the Elongation Factor Tu of Yersinia Species. J Bacteriol. 2008 Nov;190(22):7548-58.

Jiang Z et al. Old can be new again: HAPPY whole genome sequencing, mapping and assembly. Int J Biol Sci. 2009;5(4):298-303. Epub 2009 Apr 15. Review.

Jongsik Chun et al. Comparative genomics reveals mechanism for short- term and long-term clonal transitions in pandemic Vibrio cholerae. PNAS. August 31, 2009. [Epub ahead of print]

Kataeva IA et al. Genome Sequence of the Anaerobic, Thermophilic, and Cellulolytic Bacterium "Anaerocellum thermophilum" DSM 6725. J Bacteriol. 2009 Jun;191(11):3760-1. Epub 2009 Apr 3.

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Kazakov AE et al. Comparative genomics of regulation of fatty acid and branched-chain amino acid utilization in proteobacteria. J Bacteriol. 2009 Jan;191(1):52-64.

Kislyuk A et al. Frameshift detection in prokaryotic genomic sequences. Int J Bioinform Res Appl. 2009;5(4):458-77.

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Lane TW et al. Digital transcriptomic analysis of silicate starvation induced triacylglycerol formation in the marine diatom Thalassiosira pseudonana. Phycologia. 2009 Jul; 48(4):71-71. Suppl. S

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Larsson P et al. Molecular Evolutionary Consequences of Niche Restriction in Francisella tularensis, a Facultative Intracellular Pathogen. PLoS Pathog. 2009 Jun;5(6):e1000472. Epub 2009 Jun 12.

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Le Crom S et al. Tracking the roots of cellulase hyperproduction by the fungus Trichoderma reesei using massively parallel DNA sequencing. Proc Natl Acad Sci U S A. Epub 2009 Sept 2.

Leary RJ, Lin JC, Cummins J, et al. Integrated analysis of homozygous deletions, focal amplifications, and sequence alterations in breast and colorectal cancers. Proc Natl Acad Sci U S A. 2008 Oct 21;105(42):16224-9. Epub 2008 Oct 13.

Lin-Jones J et al. Identification and Localization of Myosin Superfamily Members in Fish Retina and Retinal Pigmented Epithelium. J Comp Neurol. 2009 Mar 10;513(2):209-23.

Macey JR et al. Socotra Island the forgotten fragment of Gondwana: Unmasking chameleon lizard history with complete mitochondrial genomic data. Mol Phylogenet Evol. 2008 Dec;49(3):1015-8.

Markowitz VM et al. IMG ER: a system for microbial genome annotation expert review and curation. Bioinformatics. 2009 Sep 1;25(17):2271-8. Epub 2009 Jun 27.

Martin F et al. The long hard road to a completed Glomus intraradices genome. New Phytol. 2008 Nov 6;180(4):747-50.

Martinez D et al. Genome, transcriptome, and secretome analysis of wood decay fungus Postia placenta supports unique mechanisms of lignocellulose conversion. Proc Natl Acad Sci U S A. 2009 Feb 10;106(6):1954-9. Epub 2009 Feb 4.

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Mavrommatis K et al. Genome analysis of the anaerobic thermohalophilic bacterium Halothermothrix orenii. PLoS One. 2009;4(1):e4192. Epub 2009 Jan 15.

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]

Merritt WM et al. Dicer, Drosha, and outcomes in patients with ovarian cancer. N Engl J Med. 2008 Dec 18;359(25):2641-50.

Novichkov PS et al. Trends in prokaryotic evolution revealed by comparison of closely related bacterial and archaeal genomes. J Bacteriol. 2009 Jan;191(1):65-73. Epub 2008 Oct 31.

Novichkov PS et al. ATGC: a database of orthologous genes from closely related prokaryotic genomes and a research platform for microevolution of prokaryotes. Nucleic Acids Res. 2009 Jan;37(Database issue):D448-54. Epub 2008 Oct 9.

Oda Y et al. Multiple genome sequences reveal adaptations of a phototrophic bacterium to sediment microenvironments. Proc Natl Acad Sci U S A. 2008 Nov 25;105(47):18543-8. Epub 2008 Nov 19.

Paterson AH et al. The Sorghum bicolor genome and the diversification of grasses. Nature. 2009 Jan 29;457(7229):551-6.

Pavlopoulos GA et al. jClust: a clustering and visualization toolbox. Bioinformatics. 2009 Aug 1;25(15):1994-6. Epub 2009 May 19.

Penn K et al. Genomic islands link secondary metabolism to functional adaptation in marine Actinobacteria. ISME J. 2009 May 28. [Epub ahead of print]

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Peterson SB et al. Environmental distribution and population biology of Candidatus Accumulibacter, a primary agent of biological phosphorus removal. Environ Microbiol. 2008 Oct;10(10):2692-703.

Pierce E et al. The complete genome sequence of Moorella thermoacetica (f. Clostridium thermoaceticum). Environ Microbiol. 2008 Oct;10(10):2550-73. Epub 2008 Jun 9.

Podar M et al. A genomic analysis of the archaeal system Ignicoccus hospitalis-Nanoarchaeum equitans. Genome Biol. 2008;9(11):R158. Epub 2008 Nov 10.

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Ratnere I et al. Obtaining comparative genomic data with the VISTA family of computational tools. Curr Protoc Bioinformatics. 2009 Jun;Chapter 10:Unit 10.6.

Rodrigues DF et al. Architecture of thermal adaptation in an Exiguobacterium sibiricum strain isolated from 3 million year old permafrost: A genome and transcriptome approach. BMC Genomics. 2008 Nov 18;9:547.

Romeo S et al. Rare loss-of-function mutations in ANGPTL family members contribute to plasma triglyceride levels in humans. J Clin Invest. 2009 Jan;119(1):70-9. Epub 2008 Dec 15.

Romeo S et al. Genetic variation in PNPLA3 confers susceptibility to nonalcoholic fatty liver disease. Nat Genet. 2008 Dec;40(12):1461-5. Epub 2008 Sep 25.

Salinero KK et al. Metabolic analysis of the soil microbe Dechloromonas aromatica str. RCB: indications of a surprisingly complex life-style and cryptic anaerobic pathways for aromatic degradation. BMC Genomics. 2009 Aug 3;10:351.

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Sela DA et al. The genome sequence of Bifidobacterium longum subsp. infantis reveals adaptations for milk utilization within the infant microbiome. Proc Natl Acad Sci U S A. 2008 Dec 2;105(48):18964-9. Epub 2008 Nov 24.

Silby MW et al. Genomic and genetic analyses of diversity and plant interactions of Pseudomonas fluorescens. Genome Biol. 2009;10(5):R51. Epub 2009 May 11.

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Wu D et al. Complete genome sequence of the aerobic CO-oxidizing thermophile Thermomicrobium roseum. PLoS One. 2009;4(1):e4207. Epub 2009 Jan 16.

Wu M et al. A simple, fast, and accurate method of phylogenomic inference. Genome Biol. 2008 Oct 13;9(10):R151. [Epub ahead of print]

Yan HH et al. Intergenic Locations of Rice Centromeric Chromatin. PLoS Biol. 2008 Nov 25;6(11):e286.

Yang JC et al. The complete genome of Teredinibacter turnerae T7901: an intracellular endosymbiont of marine wood-boring bivalves (shipworms). PLoS One. 2009 Jul 1;4(7):e6085.

Yoder-Himes DR et al. Mapping the Burkholderia cenocepacia niche response via high-throughput sequencing. Proc Natl Acad Sci U S A. 2009 Mar 10;106(10):3976-81. Epub 2009 Feb 20.

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Zhou K et al. Proteomics for validation of automated gene model predictions. Methods Mol Biol. 2009;492:447-52.

**PI Yoram Rubin **

Rubin Y., X. Chen, H. Murakami, M. Hahn, "A Bayesian approach for inverse modeling, data assimilation and conditional simulation of spatial random fields." submitted to Water Resources Research

Murakami1, 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", submitted to the 2009 AGU Fall conference

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", submitted to the 2009 AGU Fall conference

Murakami1, H., X. Chen, M.S. Hahn, Y. Liu, M.L. Rockhold, V.R. Vermeul, Y. Rubin, "Bayesian Geostatistical Inversion Framework for Characterizing Three-Dimensional Hydraulic Conductivity Field: An Application to the Hanford 300 Area", submitted to the WM symposia, 2010

**PI Robert Ryne **

J. Qiang, R. D. Ryne, M. Venturini, A. A. Zholents, I. V. Pogorelov "High resolution simulation of beam dynamics in electron linacs for x-ray free electron lasers," accepted by Phys. Rev. ST Accel. Beams (2009).

## S

**PI Yousef Saad **

P. Carrier, Phys. Rev. B, 80, 075319 (2009)

**PI Sayeef Salahuddin **

1. Y. Yoon and S. Salahuddin, "Non linear temperature dependence in the tunneling current of Graphene Nanoribbon Tunneling Transistor" UNDER REVIEW - ASK WHERE

**PI Martin Savage **

Meson-Baryon Scattering Lengths from Mixed-Action Lattice QCD, Aaron Torok, Silas R. Beane, William Detmold, Thomas C Luu, Kostas Orginos, Assumpta Parreno, Martin J. Savage, Andre Walker-Loud, e-Print: arXiv:0907.1913 [hep-lat]

High Statistics Analysis using Anisotropic Clover Lattices. II. Three- Baryon Systems, Silas R. Beane, William Detmold, Thomas C Luu, Kostas Orginos, Assumpta Parreno, Martin J. Savage, Aaron Torok, Andre Walker-Loud, e-Print: arXiv:0905.0466 [hep-lat]

High Statistics Analysis using Anisotropic Clover Lattices: (I) Single Hadron Correlation Functions. Silas R. Beane, William Detmold, Thomas C. Luu, Kostas Orginos, Assumpta Parreno, Martin J. Savage, Aaron Torok, Andre Walker-Loud, Published in Phys.Rev.D79:114502,2009, e-Print: arXiv:0903.2990 [hep-lat]

**PI Richard Saykally **

David Prendergast and Steven G. Louie, "Shirley interpolation - optimal basis sets for detailed Brillouin Zone sampling revisited", Phys Rev B (submitted).

Janel S. Uejio, Craig P. Schwartz, Andrew M. Duffin, Alice H. England, David Prendergast, and Richard J. Saykally "Peptides vs. Peptoids: Insights on Structure and Hydration of Aqueous Alanine and Sarcosine via X-ray Absorption Spectroscopy" JACS (submitted)

Craig P. Schwartz, Janel S. Uejio, Andrew M. Duffin, Alice H. England, David Prendergast, and Richard J. Saykally, "Auto-oligomerization and hydration of pyrrole revealed by x-ray absorption spectroscopy", J Chem Phys 131, 114509 (2009).

C. P. Schwartz, J. S. Uejio, R. J. Saykally, and D. Prendergast, "On the importance of Nuclear Quantum Motion in Near Edge X-ray Absorption Fine Structure (NEXAFS) Spectroscopy of Molecules", Journal of Chemical Physics 130, 184109 (2009).

J. S. Uejio, C. P. Schwartz, R. J. Saykally, and D. Prendergast, "Effects of vibrational motion on core-level spectra of prototype organic molecules", Chemical Physics Letters 467, 195 (2008).

**PI Henry Schaefer **

A. C. Simmonett, H. F. Schaefer and W. D. Allen, "The Enthalpy of Formation and Anharmonic Force Field of Diacetylene", J. Chem. Phys., 130, 044301 (2009).

T. Lu, A. C. Simmonett, F. A. Evangelista, Y. Yamaguchi and H. F. Schaefer, "Diphosphene and Diphosphinylidene", J. Phys. Chem. A, (ASAP article, DOI 10.1021/jp904028a).

A. C. Simmonett, N. J. Stibrich, B. N. Papas, H. F. Schaefer and W D. Allen, "The Barrier To Linearity and Anharmonic Force Field of the Ketenyl Radical", J. Phys. Chem. A, (ASAP article, DOI 10.1021/jp9024365).

Q. Cheng, F. A. Evangelista, A. C. Simmonett, Y. Yamaguchi and H. F. Schaefer, "The Water Dimer Radical Cation: Structures, Vibrational Frequencies, and Energetics", J. Phys. Chem. A. (submitted).

S. E. Wheeler and H. F. Schaefer, "Thermochemistry of the HOSO Radical, a Key Intermediate in Fossil Fuel Combustion", J. Phys. Chem. A, 113, 6779 (2009).

J. C. Hargis, F. A. Evangelista, J. B. Ingels, and H. F. Schaefer, "Short Intramolecular Hydrogen Bonds: Derviatives of Malonaldehyde with Symmetrical Substituents", J. Am. Chem. Soc., 130, 17471 (2008).

**PI Timohy Scheibe **

Palmer, B., V. Gurumoorthi, A. Tartakovsky, and T. Scheibe, "A Component Based Framework for Smoothed Particle Hydrodynamics Simulations of Reactive Fluid Flow in Porous Media," accepted for publication pending minor revision in International Journal of High Performance Computing Applications, in revision.

Palmer,B., Y. Fang, V. Gurumoorthi, G. Hammond, J.Fort and T. Scheibe, 2009. Developing a component-based framework for subsurface simulation using the Common Component Architecture, Journal of Physics: Conference Series 180: 012064.

**PI Rocco Schiavilla **

S. Pastore, R. Schiavilla, and J.L. Goity, "Electromagnetic Currents of One- and Two-Pion Range", Phys. Rev. C78, 064002 (2008)

S. Pastore, L. Girlanda, R. Schiavilla, M. Viviani, and R.B. Wiringa, "Electromagnetic Currents and Magnetic Moments in chiEFT", Phys. Rev. C in press, arXiv:0906:1800

**PI David Schultz **

Electron-impact ionization of Li_2 and Li+_2, M. S. Pindzola, F. J. Robicheaux, C. P. Ballance, and J. P. Colgan, Physical Review A 78, 042703 (October 2008)

Recombination rate coefficients of Be-like neon, I. Orban, S. Bohm, S. D. Loch, and R. Schuch, Astronomy and Astrophysics 489, 829 (October 2008)

Electron-impact ionization of C+ in its ground and metastable states, J. A. Ludlow, S. D. Loch, M. S. Pindzola, C. P. Ballance, D. C. Griffin, M. E. Bannister, and M. Fogle, Physical Review A 78, 052708 (November 2008)

Electron-impact single ionization of Mg and Al+, J. A. Ludlow, C. P. Ballance, S. D. Loch, M. S. Pindzola, and D. C. Griffin, Physical Review A 79, 032715 (March 2009)

Elastic and related transport cross sections for singly charged ion-atom scattering of light metals (Li,Be,B) and hydrogen, P. S. Krstic and D. R. Schultz, Journal of Physics B 42, 06520 (March 2009)

Scandium and chromium in the strontium filament in the homunculus of n Carinae, M A Bautista, C. P. Ballance, T. R. Gull, H. Hartman, K. Lodders, M. Martinez, and M. Melendez, Monthly Notices of the Royal Astronomical Society 393, 1503 (March 2009)

Electron-impact excitation of Ar+2, J. M. M. Burgos, S. D. Loch, C. P. Ballance, and R. F. Boivin, Astronomy and Astrophysics 500, 1253 (June 2009)

The role of excited state ionization data on H and He generalized collisional radiative coefficients, S. D. Loch, C. P. Ballance, M. S. Pindzola, and D. P. Stotler, Plasma Physics and Controlled Fusion 51, 105006 (September 2009)

**PI Annabella Selloni **

Authors: F. Zipoli, R. Car, M. H. Cohen, and A. Selloni Title: Hydrogen Production by the Naked Active Site of the Di-iron Hydrogenases in Water Journal: J. Phys. Chem. B, published on the web on September 9th, 2009

**PI John Shalf **

G. Hendry, S. Kamil, A. Biberman, J. Chan, B. Lee, M. Mohiyuddin, A. Jain, K. Bergman, L. Carloni, J. Kubiatowicz, L. Oliker, J. Shalf , "Analysis of Photonic Networks for a Chip Multiprocessor Using Scientific Applications", International Symposium on Networks-on-Chip (NOCS), 2009

S. Kamil, C. Chan, S. Williams, L. Oliker, J. Shalf, M. Howison, E. Wes Bethel, Prabhat, "A Generalized Framework for Auto-tuning Stencil Computations", Cray User Group (CUG), 2009. (LBNL-2078E) (Best Paper Award Winner)

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

K. Datta, M. Murphy, V. Volkov, S. Williams , J. Carter, L. Oliker. D. Patterson, J. Shalf, K. Yelick, Stencil Computation Optimization and Autotuning on State-of-the-Art Multicore Architectures, SC08: International Conference for High-Performance Computing, Networking, Storage, and Analysis, Nov, 2008

A. Canning, M. Gajbe, J. Shalf, L. Wang, H. Wasserman, "A Comparison of Different Communication Structures for Scalable Parallel Three Dimensional FFTs in First Principles Codes," ParCo, 2009.

**PI Shunli Shang **

S. L. Shang, G. Sheng, Y. Wang, L. Q. Chen, and Z. K. Liu, "Elastic properties of cubic and rhombohedral BiFeO3 from first-principles calculations", Phys. Rev. B., Vol. 80 (2009) 052102.

Y. Wang, L.G. Hector, Jr., H. Zhang, S. L. Shang, L. Q. Chen, and Z. K. Liu, "Thermodynamic Framework for a System with Itinerant-Electron Magnetism", J. Phys.: Condens. Matter, Vol. 21 (2009) 326003.

D. E. Kim, S. L. Shang, Z. K. Liu, "Effects of alloying elements on elastic properties of Ni by first-principles calculations", Comput. Mater. Sci., http://dx.doi.org/10.1016/j.commatsci.2009.07.014

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", Comput. Mater. Sci., (Submitted).

S. L. Shang, Y. Wang, Z. G. Mei, and Z. K. Liu, "Fluctuations among competing magnetic states: First-principles thermodynamics of fcc Ni", Appl. Phys. Lett. (Submitted)

S. L. Shang, Y. Wang, Y. Du, and Z. K. Liu, "Entropy favored ordering: Phase stability of Ni3Pt revisited", Phys. Rev. B. (Submitted)

**PI Michael Shay **

Cassak, P. A., Shay, M. A., and J. F. Drake, Scaling of Sweet-Parker Reconnection with Secondary Islands, The Astrophysical Journal, submitted.

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, In press, 2009.

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.

Cassak, P. A. and M. A. Shay, Response to "Comment on 'Scaling of Asymmetric Magnetic Reconnection: General Theory and Collisional Simulations'", Physics of Plasmas, Vol. 16, 034702, 2009.

Malakit, K., P. A. Cassak, M. A. Shay, and J. F. Drake The Hall effect in magnetic reconnection: Hybrid vs. Hall-less hybrid simulations, Geophysical Research Letters, Vol. 36, L07107, doi:10.1029/2009GL037538, 2009.

Parashar, T. N., M. A. Shay, P. A. Cassak, and W. H. Matthaeus, Kinetic dissipation and anisotropic heating in a turbulent collisionless plasma, Physics of Plasmas, Vol. 16, 032310, 2009.

8. Cassak, P. A. and M. A. Shay, Structure of the dissipation region in fluid simulations of asymmetric magnetic reconnection, Physics of Plasmas, Vol. 16, 055704, 2009.

9. Cassak, P. A. and M. A. Shay, The scaling of asymmetric hall magnetic reconnection, Geophysical Research Letters, Vol. 35, L19102, doi:10.1029/2008GL035268, 2008.

**PI Junko Shigemitsu **

``High Precision Determination of the pi, K, D and D(s) Decay Constants from Lattice QCD''; E.Follana, C.Davies, P.Lepage, J.Shigemitsu, Phys. Rev. Lett. \underbar{100}:062002 (2008).

``High-Precision Charm-Quark Mass and QCD Coupling from Current-Current Correlators in Lattice and Continuum QCD''; I.Allison, E.Dalgic, C.Davies, E.Follana, R.Horgan, K.Hornbostel, P.Legage,C.McNeile, J.Shigemitsu, H.Trottier, R.Woloshyn, K.Chetyrkin, J.Kuehn, M.Steinhauser and C.Sturm; Phys. Rev. D\underbar{78}:054513 (2008).

``Update: Accurate Determinations of $\alpha_s$ from Realistic Lattice QCD''; C.Davies, I.Kendall, P.Lepage, C.McNeile, J.Shigemitsu and H.Trottier; Phys. Rev. D\underbar{78}:114507 (2008).

``Neutral B Meson Mixing in Unquenched Lattice QCD''; E.Gamiz, C.Davies, P.Lepage, J.Shigemitsu and M.Wingate; Phys. Rev. D\underbar{80}:014503 (2009).

**PI Donald Sinclair **

D.K.Sinclair and J.B.Kogut, ``Thermodynamics of lattice QCD with 2 flavours of colour-sextet quarks: A model of walking/conformal Technicolor,'' Argonne preprint, ANL-HEP-PR-09-95 (2009)

D.K.Sinclair, ``Separating the scales of confinement and chiral-symmetry breaking in lattice QCD with fundamental quarks,'' Phys. Rev. D78, 054512 (2008)

J.B.Kogut and D.K.Sinclair, ``Lattice QCD at finite temperature and density in the phase-quenched approximation,'' Phys. Rev. D77}, 114503 (2008)

**PI George Smoot **

T.K. Fletcher, K.A. James, J.L. Christiansen, Search for Cosmic Strings in the COSMOS Survey, Poster presentation at the American Astronomical Society 213th meeting in Long Beach, CA, Jan 2009.

J.L. Christiansen, E. Albin, K.A. James, J. Goldman, D. Maruyama, G.F. Smoot, Phys. Rev. D 77, 123509 (2008), astro-ph/0803.0027.

**PI Randall Snurr **

C.-Y. Sung, R.Q. Snurr, L.J. Broadbelt, A DFT study of deNOx reactions in the gas phase: Mimicking the reaction mechanism over BaNaY zeolites, J. Phys. Chem. A 113, 6730-6739 (2009).

C.-Y. Sung, L.J. Broadbelt, R.Q. Snurr, A QM/MM study of the effect of local environment on dissociative adsorption in BaY zeolites, J. Phys. Chem. C 113, 15643-15651 (2009).

**PI Masha Sosonkina **

Fang (Cherry) Liu, Masha Sosonkina, Dane Coffey "Coupling Multi-level Component Interfaces for Parallel Sparse Linear System Solvers", accepted in proceedings of Component-Based High Performance Computing Workshop Nov 15-16, 2009, Portland Oregon

Nikhil Laghave, Masha Sosonkina, Pieter Maris, James P. Vary "Benefits of Parallel I/O in Ab Initio Nuclear Physics Calculations", in Proc of International Conference on Computational Science (ICCS'2009), May, 2009 Baton-Rouge LA.

J. He, A. Verstak, M. Sosonkina, and L.T. Watson, "Performance modeling and analysis of a massively parallel DIRECT -- Part 2", International Journal of High Performance Computing Applications, Vol. 23, pp. 29-41, 2009.

J. He, A. Verstak, L.T. Watson, and M. Sosonkina, "Performance modeling and analysis of a massively parallel DIRECT -- Part 1", International Journal of High Performance Computing Applications, Vol. 23, pp. 14-28, 2009.

**PI Ivo Souza **

"Orientation Dependence of the Intrinsic Anomalous Hall Effect in hcp Cobalt", Eric Roman, Yuriy Mokrousov, and Ivo Souza, Phys. Rev. Lett. 103, 097203 (2009).

**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," submitted to Physics of Plasmas (2009).

P. Zhu, C. C. Hegna, C. R. Sovinec, A. Bhattacharjee, and K. Germaschewski, "Intermediate nonlinear regimes of line-tied g mode and ballooning instability," Nuclear Fusion 49, 095009 (2009).

P. Zhu, C. C. Hegna, and C. R. Sovinec, "Exponential growth of nonlinear ballooning instability," Physical Review Letters 102, 235003 (2009).

C. S. Carey and C. R. Sovinec, "Rotational stabilization of magnetically collimated jets," the Astrophysical Journal 699, 362 (2009).

J.-Y. Ji, E. D. Held, and C. R. Sovinec, "Moment approach to deriving parallel heat flow for general collisionality," Physics of Plasmas 16, 22312 (2009).

W. Guttenfelder, J. Lore, D.T. Anderson, F.S.B. Anderson, J.M. Canik, W. Dorland, K.M. Likin, J.N. Talmadge, "Effect of Quasihelical Symmetry on Trapped-Electron Mode Transport in the HSX Stellarator," Phys. Rev. Lett. 101, 215002 (2008).

**PI Panagiotis Spentzouris **

E. G. Stern, J. F. Amundson, P. G. Spentzouris, A. A. Valishev, 3D multiple beam dynamics processes simulation for the Fermilab Tevatron, e-Print: arXiv: 0906.0513, submitted to PRSTAB

L . Ge, K. Ko, Z. Li, C.-K. Ng, D. Li, R. B.. Palmer, Multipacting and Dark Current Simulation for Muon Collider Cavity, Particle Accelerator Conference 2009(PAC09)

Z. Li, et al, Dark Current Simulation for the CLIC T18 High Gradient Structure, PAC09

Z. Li, L. Xiao, A Compact Alternative Crab Cavity Design at 100-MHz for the LHC Upgrade, PAC09

Liling Xiao, Zenghai Li, Cho-Kuen Ng, Andrei Seryi, 800MHz Crab Cavity Conceptual Design for the LHC Upgrade, PAC09 A.C. Kabel, Simulation of Compensation Mechanisms for Head-On and. Parasitic Beam-Beam Collisions at LHC, PAC09

L. Xiao, C.-K. Ng, J. C. Smith, Trapped Mode Study for a Rotable Collimator Design for the LHC upgrade, PAC09

A.E. Candel, A.C. Kabel, K. Ko, L. Lee, Z. Li, C.-K. Ng, G.L. Schussman, I. Syratchev, Wakefield Simulation of CLIC PETS Structure Using Parallel 3D Finite Element Time-Domain Solver T3P, PAC09

A.E. Candel, A.C. Kabel, K. Ko, L. Lee, Z. Li, C.-K. Ng, G.L. Schussman, I. Ben- Zvi, J. Kewisch, Parallel 3D Finite Element Particle-in-Cell Simulations with Pic3P, PAC09

V. Akcelik, K. Ko, L. Lee, Z. Li, C.-K. Ng, G. Cheng, R.A. Rimmer, H. Wang, Thermal Analysis of SCRF Cavity Couplers Using Parallel Multi-Physics Tools TEM3P, PAC09

V. Akcelik, L.Q. Lee, Z. Li, C.-K Ng. L. Xiao and K. Ko, Large Scale Shape Optimization for Accelerator Cavities, SciDAC 2009 Conference, 2009

A. Candel, A. Kabel, Lie-Quan Lee, Zenghai Li, Cho Ng, Greg Schussman, Kwok Ko, State of the art in Electromagnetic Modeling for Compact Linear Collider, SciDAC 2009 Conference, 2009

C.G.R. Geddes, E. Cormier-Michel, E.H. Esarey, C.B. Schroeder, J.-L. Vay, W.P. Leemans, D.L. Bruhwiler, J.R. Cary, B. Cowan, M. Durant, P. Hamill, P. Messmer, P. Mullowney, C. Nieter, K. Paul, S. Shasharina, S. Veitzer, G. Weber, O. Rubel, D. Ushizima, Prabhat and W. Bethel, "Laser-plasma particle accelerators: Large fields from smaller sources," SciDAC Review (2009).

K. Wu, A. Shoshani, E.J. Otoo, O. Rubel, Prabhat, H. Childs, J. Meredith, C.G.R. Geddes, E. Cormier-Michel, S. Ahern, G.H. Weber, P. Messmer, H. Hagen, B. Hamann, J. Hules and E.W. Bethel, "FastBit: A Lightning- Fast Index Drives Massive Data Analysis," SciDAC Review (2009).

N. Xiang and J. R. Cary, Second harmonic generation of electron Bernstein waves in an inhomogeneous plasma, Phys. Rev. Lett., 100, 085002 (2008); doi:10.1103/PhysRevLett.100.085002

G. R. Werner and J. R. Cary, Extracting Degenerate Modes and Frequencies from Time Domain Simulations, J. Comp. Phys. 227, 5200-5214 (2008), http://dx.doi.org/10.1016/j.jcp.2008.01.040

C.G.R. Geddes, D.L. Bruhwiler, J.R. Cary, W.B. Mori, J-L. Vay, S.F. Martins, T. Katsouleas, E. Cormier-Michel, W.M. Fawley, C. Huang, X. Wang, B. Cowan, V.K. Decyk, E. Esarey, R.A. Fonseca, W. Lu, P. Messmer, P. Mullowney, K. Nakamura, K. Paul, G.R. Plateau, C.B. Schroeder, L.O. Silva, Cs. Toth, F.S. Tsung, M. Tzoufras, T. Antonsen, J. Vieira and W.P. Leemans, Computational studies and optimization of wakefield accelerators, Journal of Physics: Conference Series 125, 12002 (2008).

C. A. Bauer, G. R. Werner, and J. R. Cary, Optimization of a photonic crystal cavity, J. Appl. Phys. 4 (105), 053107 (2008); DOI:10.1063/1.2973669.

**PI Frank Spera **

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, Vol 94, p 975- 980, 2009 .

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, Vol 94, p 693-703, 2009.

Spera, F., Nevins, D., Ghiorso, M, Cutler, I. (2009) Structure, Thermodynamic and Transport Properties of CaAl2Si2O8 Liquid: Part I. Molecular Dynamics Simulations, Geochimica et Cosmochimica Acta, in press.

Ghiorso, M., Nevins, D., Cutler, I., Spera, F. (2009), Molecular Dynamics Studies of CaAl2Si2O8 Liquid: II. Equation of State and a Thermodynamic Model, Geochimica et Cosmochimica Acta, in press.

**PI Don Spong **

"Clustered frequency analysis of shear Alfven modes in stellarators," D. A. Spong, Ed D'Azevedo, Y. Todo, submitted to Physics of Plasmas, 2009.

"Energetic-Electron-Driven Instability in the Helically Symmetric Experiment," C. B. Deng, ... D. A. Spong, et al., Physical Review Letters, Vol. 103, 025003 (2009).

"Measurements, modeling and electron cyclotron heating modification of Alfven eigenmode activity in DIII-D," M. A. Van Zeeland, ... D. A. Spong, et al., Nuclear Fusion, Vol. 49 (2009) 065003.

"Numerical Analyses of Energetic Particles in LHD," Y. Todo, ... D. A. Spong, et al., submitted to Fusion Science and Technology LHD special issue, 2009.

"Simulation Study of Energetic Ion Transport due to Alfvin Eigenmodes in LHD Plasma," Yasushi Todo, ... D. A. Spong, , Plasma and Fusion Research, Vol. 3, S1074 (2008).

**PI Garrison Sposito **

Bourg I.C., Richter F.M., Christensen J.N. and Sposito G. (2009) Isotopic mass-dependence of metal cation diffusion coefficients in liquid water. Submitted to Geochimica et Cosmochimica Acta.

Pena J., Kwon K.D., Bargar J., Refson K. and Sposito G. (2009) Nickel sorption to bacteriogenic manganese oxides: A X-ray absorption spectroscopy and density functional theory study. Submitted to Geochimica et Cosmochimica Acta.

Kwon K.D., Refson K., and Sposito G., (2009) On the role of Mn(IV) vacancies in the photoreductive dissolution of birnessite, Geochimica et Cosmochimica Acta, 73, 4142-4150.

Kwon K.D., Refson K., and Sposito G., (2009) Zinc surface complexes on birnessite: A density functional theory study, Geochimica et Cosmochimica Acta, 73, 1273-1284.

**PI Phillip Sprangle **

D. F. Gordon, B. Hafizi, and A. Ting, "Nonlinear conversion of photon spin to photon orbital angular momentum," accepted for publication in Optics Letters.

**PI Malcolm Stocks **

T. Kawakami, Y. Tsujimoto, H. Kageyamo, X.Q. Chen, C.L. Fu, C. Tassel, A. Kitada, S. Suto, K. Hirama, Y. Sekiya, Y. Makino, T. Okada, T. Yagi, N. Hayashi, K. Yoshimura, S. Nasu, R. Podloucky, and M. Takano, "Spin Transition in a four-coordinate oxide compound", Nature Chemistry 1, 371 (2009).

Xing-Qiu Chen, C.L. Fu, C. Franchini, and R. Podloucky, "Hybrid density functional calculation of the electronic and magnetic structure of tetragonal CuO", (accepted for publication by Physical Review B).

Li Gao, Xin Jiang, D. M.C. Nicholson, Teya Topuria, and Stuart S. P. Parkin, "Role of the electronic structure on the relationship between the crystallinity of CoFe and its Tunneling magnetoresistance", Applied Physics Letters, 95, 012508 (2009).

Paul F. Becher, Naoya Shibata, Gayle S. Painter, Frank Averill, Klaus van Benthem, Hua-Tay Lin and Shirley B. Waters, "Observations on the Influence of Secondary Me Oxide Additives (Me = Si, Al, Mg) on the Microstructural Evolution and Mechanical Behavior of Silicon Nitride Ceramics Containing RE2O3 (RE = La, Gd, Lu)", accepted for publication in J. Am. Ceramic Soc. (Sept. 2009).

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

D. E. Jiang, V. R. Cooper and S. Dai "Porous gaphene as the ultimate membrane for gas separation"(under review Nano Letters 2009).

Yoon M, Yang SY, Zhang ZY, "Interaction between hydrogen molecules and metallofullerenes", J. Chem. Phys. 131, 064707 (2009).

Chen H, Zhu WG, Kaxiras E, et al., "Optimization of Mn doping in group-IV-based dilute magnetic semiconductors by electronic codopants", Phys. Rev. B 79, 235202 (2009).

Li MZ, Yao YG, Wu BA, et al., "Strain effect on the instability of island formation in submonolayer heteroepitaxy", EPL 86, 16001 (2009).

Zhao K, Troparevsky MC, Xiao D, et al., "Electronic Coupling and Optimal Gap Size between Two Metal Nanoparticles", Phys. Rev. Lett. 102, 186804 (2009).

Song YL, Zhao K, Jia Y, et al., "Finite size effects on the electromagnetic field enhancement from low-dimensional silver nanoshell dimer arrays", J. Chem. Phys. 129, 204506 (2008).

Song YL, Zhao K, Jia Y, et al., "Finite size effects on the electromagnetic field enhancement from low-dimensional silver nanoshell dimer arrays", J. Chem. Phys. 129, 204506 (2008).

Guo Y, Qu ZH, Braiman Y, et al., "Nanotribology and Nanoscale Friction SMOOTH SLIDING THROUGH FEEDBACK CONTROL", IEEE CONTROL SYSTEMS MAGAZINE 28, 92-100 (2008).

Mo YN, Zhu WG, Kaxiras E, et al., "Electronic Nature of Step-Edge Barriers against Adatom Descent on Transition-Metal Surfaces", Phys. Rev. Lett. 101, 216101 (2008).

Shegai T, Li ZP, Dadosh T, et al., "Managing light polarization via plasmon-molecule interactions within an asymmetric metal nanoparticle trimer", PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA 105, 16448-16453 (2008).

Yang SY, Yoon MN, Wang E, et al., "Energetics and kinetics of Ti clustering on neutral and charged C-60 surfaces", J. Chem. Phys. 129, 134707 (2008).

**PI Alberto Striolo **

D. Konatham and A. Striolo, Thermal Boundary Resistance at the Graphene-Oil Interface, Applied Physics Letters (2009) submitted.

D. Argyris, D.R. Cole, and A. Striolo, Dynamics Behavior of Interfacial Water at the Silica Surface, Journal of Physical Chemistry C, (2009) in Press.

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. Also featured in Virtual Journal of Nanoscale Science & Technology, Vol. 20, Issue 11, September 14th, 2009.

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. Argyris, D.R. Cole, and A. Striolo, Hydration Structure on Silica Crystalline Substrates, Langmuir 25 (2009) 8025-8035.

N.R. Tummala and A. Striolo, SDS Surfactants on Carbon Nanotubes: Aggregate Morphology, ACS Nano 3 (2009) 595-602.

D. Konatham and A. Striolo, Molecular Design of Stable Graphene Nano-Sheets Dispersions, Nano Letters 8 (2008) 4630.

A. Striolo, On the Solution Self-Assembly of Colloidal Brushes: Insights from Simulations, Nanotechnology 19 (2008) 445606.

D. Argyris, N.R. Tummala, A. Striolo, and D.R. Cole, Molecular Structure and Dynamics in Thin Water Films at the Silica and Graphite Surfaces, Journal of Physical Chemistry C, 112 (2008) 13587-13599. Also featured in the cover art of J. Phys. Chem. C, issue # 35, September 4th, 2008.

## T

**PI John Tainer **

Interdomain communication in the Mycobacterium tuberculosis environmental phosphatase Rv1364c. Greenstein AE, Hammel M, Cavazos A, Alber T. J Biol Chem. 2009 Aug 20. [Epub ahead of print]

Mechanism of DNA substrate recognition by the mammalian DNA repair enzyme, Polynucleotide Kinase. Bernstein NK, Hammel M, Mani RS, Weinfeld M, Pelikan M, Tainer JA, Glover JN. Nucleic Acids Res. 2009 Aug 11

Structure and flexibility within proteins as identified through small angle X-ray scattering. Pelikan M, Hura GL, Hammel M. Gen Physiol Biophys. 2009 Jun;28(2):174-89.

**PI Bhupender Thakur **

B. Thakur, S. Pittel and N. Sandulescu "Density matrix renormalization group study of 48Cr and 56Ni" Phys. Rev. C 78, 041303 (2008)

**PI Jason Tillett **

Jason C. Tillett, Mohammad I. Daoud, James C. Lacefield, and Robert C. Waag, A k-space method for acoustic propagation using coupled first-order equations in three dimensions, Journal of the Acoustical Society of America, 126(3) 1231-1244 (2009).

**PI Doug Toussaint **

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, "Full nonperturbative QCD simulations with 2+1 flavors of improved staggered quarks", Submitted to Reviews of Modern Physics.

D. Toussaint and W. Freeman (for the MILC Collaboration), "The strange quark condensate in the nucleon in 2+1 flavor QCD", Phys. Rev. Lett. 103, 2009, 122002.

Jon A. Bailey, C. Bernard, C. DeTar, M. Di Pierro, A. X. El-Khadra, R. T. Evans, E. D. Freeland, E. Gamiz, Steven Gottlieb, U. M. Heller, J. E. Hetrick, A. S. Kronfeld, J. Laiho, L. Levkova, P. B. Mackenzie, M. Okamoto, J. N. Simone, R. Sugar, D. Toussaint, R. S. Van de Water, "The B -> pi l nu semileptonic form factor from three-flavor lattice QCD: A model-independent determination of |V(ub)|", Phys. Rev. D79: 054507, 2009

C. Bernard, C. DeTar, M. Di Pierro, A.X. El-Khadra, R.T. Evans, E.D. Freeland, E. Gamiz, Steven Gottlieb, U.M. Heller, J.E. Hetrick, A.S. Kronfeld, J. Laiho, L. Levkova, P.B. Mackenzie, M. Okamoto, J. Simone, R. Sugar, D. Toussaint, R.S. Van de Water, "The B -> D* l nu form factor at zero recoil from three-flavor lattice QCD: A model independent determination of |V_cb|", Phys. Rev. D79: 014506, 2009.

C. Bernard, C. DeTar, M. Di Pierro, A.X. El-Khadra, R.T. Evans, E.D. Freeland, E. Gamiz, Steven Gottlieb, U.M. Heller, J.E. Hetrick, A.S. Kronfeld, J. Laiho, L. Levkova, P.B. Mackenzie, M. Okamoto, M.B. Oktay, J.N. Simone, R. Sugar, D. Toussaint, R.S. Van de Water, "Visualization of semileptonic form factors from lattice QCD", Phys. Rev. D80: 034026, 2009.

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, "Equation of state and QCD transition at finite temperature", Phys. Rev. D80: 014504, 2009.

**PI Trevor Tyson **

T. A. Tyson, Z. Chen, M. A. DeLeon, S. Yoong, and S. W. Cheong, "Local structure of multiferroic RMn2O5: Important role of the R site", J. Magn. Magn. Mater. 321, 1714 (2009).

T. A. Tyson, Z. Chen, Q. Jie, Q. Li, and J. J. Tu, "Local structure of thermoelectric Ca3Co4O9", Phys. Rev. B: Condens. Matter Mater. Phys. 79, 024109/1 (2009).

## V

**PI Goerge Vahala **

G. Vahala, M. Soe, J. Yepez, L. Vahala, J. Carter and S. Ziegeler, "MHD Turbulence Studies using Lattice Boltzmann Algorithms", Comm. in Comput, Phys. 4, 624-646 (2008)

G. Vahala, J. Yepez, M. Soe, L. Vahala, J. Carter and S. Ziegeler, "MHD Turbulence Studies Using Lattice Boltzmann Methods " CAP Simulations using 9000 cores on the AFRL/Hawk Supercomputer", IEEE Computer Society, 978-0-7695-3515-9/08, p. 138-142 (2008)

G. Vahala, B. Keating, M. Soe, J. Yepez, L. Vahala and S. Ziegeler, "Entropic, LES and boundary conditions in lattice Boltzmann simulations of turbulence", Eur. Phys. J. Special Topics 171, 167-171 (2009)

J. Yepez, G. Vahala and L. Vahala, "Vortex-antivortex pair in a Bose-Einstein condensate", Eur. Phys. J. Special Topics 171, 9-14 (2009)

J. Yepez, G. Vahala, L. Vahala and M. Soe, "Superfluid Turbulence from Quantum Kelvin Wave to Classical Kolmogorov Cascades", Phys. Rev. Lett. 103, 084501 (2009)

**PI Chris Van de Walle **

"Atomic and electronic structure of hydrogen-related centers in hydrogen storage materials," C. G. Van de Walle, A. Peles, A. Janotti, and G. B. Wilson-Short, Physica B 404, 793 (2009).

"Formation and migration of charged native point defects in MgH2: First-principles calculations," M. S. Park, A. Janotti, and C. G. Van de Walle, Phys. Rev. B 80, 064102 (2009).

"First-principles investigations of F and Cl impurities in NaAlH4," G. B. Wilson-Short, A. Janotti, A. Peles, and C. G. Van de Walle, J. Alloys Compd. (in press, 2009). (DOI: 10.1016/j.jallcom.2009.04.091), in press.

"Hydrogen interactions with vacancies in Al and Mg: A comparative analysis based on density functional theory," M. S. Park, L Ismer, A. Janotti, and C. G. Van de Walle (Phys Rev. B), submitted.

"Formation and migration of native defects in NaAlH4," G. B. Wilson-Short, A. Janotti, K. Hoang, A. Peles, and C. G. Van de Walle (Phys. Rev. B), submitted.

"Hydrogen-related defects and the role of metal additives in the kinetics of complex hydrides: A first- principles study," K. Hoang and C. G. Van de Walle (Phys Rev. B), submitted.

**PI Kalman Varga **

J. Driscoll, and K. Varga, Calculation of self-energy matrices using complex absorbing potentials in electron transport calculations, Phys. Rev. B, 2008. A

J. Mitroy, J.Y. Zhang, and K. Varga, Elastic scattering using an artificial confining potential, Phys. Rev. Lett. 101 123201 (2008). B

J. Y. Zhang, J. Mitroy, and K. Varga, Development of a confined variational method for elastic scattering, Phys. Rev. A 78 042705 (2008). B

K. Varga: Solution of few-body problems with the stochastic variational method: Two dimensional systems, Computer Physics Communications 179 591 (2008). A

K. Varga, J. Mitroy, Zs. Mezei and A.T. Kruppa, Desciption of positron-hydrogen resonances Phys. Rev. A 77 044502 (2008). B

K. Varga and S. T. Pantelides, Quantum transport in molecules and carbon nanotubes, Phys. Rev. Lett. 98 078804 (2007). A

J. Z. Mezei, A. T. Kruppa and K. Varga, Charged exciton resonances, Few-Body Systems, 41 233 (2007). B

X.-G. Zhang, K. Varga, and S. T. Pantelides, Extending Bloch theorem to complex periodic potentials for transport study, Phys. Rev. B76 038108 (2007). B M.W.J. Bromley, J. Mitroy, and K. Varga, Positronic complexes with unnatural parity, Phys. Rev. A75 062505 (2007). B.

K. Varga, and Pantelides Lagrange-function approach to real-space order-N electronic-structure calculations, Physica Status Solidi B 243, 1110 (2006). A

E. Armour, Jean-Marc Richard and K. Varga, Stability of correlated few-particle systems, Physics Reports 413 , 1 (2005). B

Varga K., Zhang Z., and Pantelides S.T., "Lagrange Functions": A Family of Powerful Basis Sets for Real-Space Order-N Electronic Structure Calculations, Phys. Rev. Lett., 93 176403 (2004). A

Mina Yo, Varga K., T. Kaxiras, and Z. Zhang, Kinetic pathway for the formation of Fe nanowires on stepped Cu(111) surfaces, Phys. Rev. Lett. 94, 155503 (2004). B

Varga K., Wang L.G., Pantelides S.T., Zhang Zhenyu, Critical layer thickness in Stranski- Krastanow growth of Ge on Si(001), Surface Science Letters 562, 225 (2004). A

**PI James Vary **

"Ab initio no-core full configuration calculations of light nuclei," P. Maris, J.P. Vary and A.M. Shirokov, Phys. Rev. C 79, 014308 (2009).

"Ab initio shell model with a core," A.F. Lisetskiy, B.R. Barrett, M.K.G. Kruse, P. Navratil, I. Stetcu, J. P. Vary, Phys. Rev. C 78, 044302 (2008).

"Accelerating Configuration Interaction Calculations for Nuclear Structure," P. Sternberg, E.G. Ng, C. Yang, P. Maris, J.P. Vary, M. Sosonkina and H.V. Le, Proceedings of the 2008 ACM/IEEE Conference on Supercomputing (Austin, Texas, November 15 - 21, 2008) , (2008).

"Inverse scattering J-matrix approach to nucleon-nucleus scattering and the shell model," A.M. Shirokov, A.I. Mazur, J.P. Vary and E.A. Mazur, Phys. Rev. C 79, 014610 (2009).

"Light nuclei from chiral EFT interactions," P. Navratil, V. G. Gueorguiev, J.P.Vary, W. E. Ormand, A. Nogga, and S. Quaglioni, Few Body Syst. 43, 129 (2008).

"The Ab Initio No-core Shell Model," C. Forssen, J. Christensson, P. Navratil, S. Quaglioni, S. Reimann, J. Vary and S. Aberg, Few-Body Systems 45, 111 (2009).

"Effective operators from exact many-body renormalization," A. F. Lisetskiy, M. K. G. Kruse, B. R. Barrett, P. Navratil, I. Stetcu and J.P. Vary, accepted for publication in Phys. Rev. C.

"Hamiltonian light-front field theory in a basis function approach," J.P. Vary, H. Honkanen, J. Li, P. Maris, S.J. Brodsky, A. Harindranath, G.F. de Teramond, P. Sternberg, E.G. Ng and C. Yang," submitted for publication to Phys. Rev. C.; arXiv: 0905.1411

## W

**PI Ronald Waltz **

[Waltz 2007b] R.E. Waltz, G. M. Staebler, J. Candy, and F. Hinton, "Gyrokinetic Theory and Simulation of Toroidal Angular Momentum Transport", Phys. Plasmas 14 (2007)122507

[Waltz 2008a] R.E. Waltz, G. M. Staebler, and J. Candy, "Gyrokinetic Theory and Simulation of Turbulent Energy Exchange, Phys. Plasmas 15 (2008) 014505

[Waltz 2008b] R. E. Waltz and C. Holland, "Numerical experiments on the drift wave -zonal flow paradigm", Phys. Plasmas 15 (2008) 0122503

[Waltz 2009] R.E. Waltz, A. Casati, and G.M. Staebler, "Gyrokinetic simulation tests of quasilinear and tracer transport", Phys. Plasmas 16 072303 (2009)

[Kinsey 2008] J.E. Kinsey, G.M. Staebler, and R.E. Waltz, "First test of the TGLF transport model" Plasmas 15, 0055908 (2008) APS07 Issue.

[Holland 2008] C Holland, , A E White, G R McKee, M W Shafer, J Candy, R E Waltz,L Schmitz and G R Tynan, "Implimentation and applications of two synthetic diagnostics for validating simulations of core tokamak turbulence", Phys. Plasmas 16, 052301 (2009)

[Holland 2009] C Holland1, J Candy2, R E Waltz2, A E White3, G R McKee4, M W Shafer4, L Schmitz3 and G R Tynan, "Validating simulations of core tokamak turbulence: status an dfuture directions", Journal of Physics: Conf. Series 125 (2008) 012043

[White 2008] A. E. White et al. "Measurements of core electron temperature and density fluctuations in DIII-D and comparison to nonlinear gyrokinetic simulations", Phys. Plasmas 15 056116 (2008)

[Belli 2008] E. Belli and J. Candy, "Kinetic calculation of neoclassical transport and self-consistent electron and transport and impurity dynamics" Plasma Phys. Control. Fusion 50, 095010 (2008).

[Belli 2009] E. A. Belli and J. Candy, "An Eulerian method for the solution of the multi-species drift-kietuc equation", Plasma Phys. Control. Fusion 51, 075018 (2009).

[Casati 2009a] 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)

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

[Lin2009a] 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)

[Lin2009b] 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 carparisons with GYRO", PPCF 51, 065006 (2009)

[Choi 2009] M. Choi, et al, "Comparison of the Monte Carlo ion cyclotron heating model with the full-wave linear absorption model", "Physics of Plasmas 16, 052513 (2009)

[Izzo 2009] V.A. Izzo, P.B. Parks, and L.L. Lao, "DIII-D and ITER rapid shutdown with radially uniform deuterium delivery" Plasma Phys. Control. Fusion 51 (2009) 105004.

**PI Cai-Zhuang Wang **

S. Y. Wang, C. Z. Wang, M. Z. Li, L. Huang, R. T. Ott, M. J. Kramer, D. J. Sordelet, and K. M. Ho, "Short- and medium-range order in a Zr73Pt27 glass: experimental and simulation Studies", Phys. Rev. B 78, 184204 (2008)

S. G. Hao, M. J. Kramer, C.Z. Wang, K. M. Ho, and A. I. Goldman, V. Wessel, K. K. Sahu, K. F. Kelton , R. W. Hyers, S Canepari, and J. R. Rogers, "Experimental and ab Initio structural studies of liquid Zr2Ni", Phys. Rev. B 79, 104206 (2009).

Songyou Wang, C. Z. Wang, C. X. Zheng, and K. M. Ho, "Structure and dynamics of liquid Al1-xSix alloys by Ab initio molecular dynamics Simulations", J. Non-Crys. Sol. 355, 340-347 (2009).

S. Y. Wang, M. J. Kramer, M. Xu, S. Wu, S. G. Hao, D. J. Sordelet, K. M. Ho, and C. Z. Wang, "Experimental and ab initio molecular dynamics simulation studies of liquid Al60Cu40 alloy", Phys. Rev. B 79, 144205 (2009).

Li Huang, C.Z. Wang, S.G. Hao, M.J. Kramer, and K.M. Ho, "Atomic Size and Chemical Effects on the Local Order of Zr2M (M= Co, Ni, Cu, Ag) Binary Liquids", Phys. Rev. B, submitted

M. Li, C. Z. Wang, S. G. Hao, M. J. Kramer, and K. M. Ho, "Structural Heterogeneity and Medium-Range Order in ZrxCu1-x Metallic Glasses", Phys. Rev. B. (submitted).

Shaogang Hao, C. Z. Wang, Maozhi Li, M. J. Kramer, and Kai-Ming Ho "Structure of Zr1-xCux Metallic Liquids and Origin of Slow Diffusion at the Good-Glass-Forming Composition Range", Phys. Rev. B, Submitted

S. Q. Wu, C. Z. Wang, Z. Z. Zhu, and K. M. Ho, "Structural and dynamical heterogeneity in molten Si-rich oxides", Appl. Phys. Lett., submitted

**PI Haobin Wang **

H. Wang and M. Thoss, ``From coherent motion to localization: Dynamics of the spin-boson model at zero temperature'', Focus issues: Quantum Dissipation in Unconventional Environments. New J. Phys., 10, 115005 (2008).

Y. Zhang, T. Irshaidat, H. X. Wang, K. V. Waynant, H. Wang, J. W. Herndon, ``Coupling of Fischer carbene complexes with conjugated enediynes featuring radical traps; Novel structure and reactivity features of chromium complexed arene diradical species'', J. Organometallic Chem., 693, 3337 (2008).

Z. G. Yu, M. A. Berding, and H. Wang, ``Spatially correlated fluctuations and coherence dynamics in phototsynthesis'', Phys. Rev. E, 78, 050902 (2008).

X. G. Song, H. Wang, and T. Van Voorhis, ``A Langevin equation approach to electron transfer reqctions in the diabatic basis'', J. Chem. Phys., 129, 144502 (2008).

D. Egorova, M. F. Gelin, M. Thoss, H. Wang, and W. Domcke, ``Effects of intense femtosecond pumping on ultrafast electronic-vibrational dynamics in molecular systems with relaxation'', J. Chem. Phys., 129, 214303 (2008).

F. Ding, J. M. Smith, and H. Wang, ``First-Principles Calculation of pK_a Values for Organic Acids in Nonaqueous Solution'', J. Org. Chem., 74, 2679 (2009).

H. Wang and M. Thoss, ``Numerically Exact Quantum Dynamics for Indistinguishable Particles: The Multilayer Multiconfiguration Time-Dependent Hartree Theory in Second Quantization Representation'', J. Chem. Phys., 131, 024114 (2009).

K. A. Velizhanin and H. Wang, ``Dynamics of electron transfer reactions in the presence of mode-mixing: Comparison of a generalized master equation approach with the numerically exact simulation'', J. Chem. Phys., 131, 094109 (2009).

**PI Lin-Wang Wang **

J. Schrier, B. Lee, L.W. Wang, "Mechanical and electronic structure properties of compressed CdSe tetrapod nanocrystals", J. Nanosci. Nanotech. 8, 1994 (2008).

C. Yang, J. Meza, B. Lee, L.W. Wang, "A MATLAB toolbox for solving the Kohn-Sham equations", ACM Trans. On Math. Software 36, Article 10 (2009).

J. Sun, W.E. Buhro, L.W. Wang, J. Schrier, "Electronic structure and spectroscopy of cadmium telluride quantum wires", Nano Lett. 8, 2913 (2008).

A. Garcia-Lekue, L.W. Wang, "Self-consistent non-equilibrium transport using planewaves", Comp. Mat. Sci. 45, 1016 (2009).

S. Dag, L.W. Wang, "Modlling of Nanoscale morphology of regioregular poly(3-hexylthiophene) on ZnO (10-10) surface", Nano Lett. 8, 4185 (2008).

L.W. Wang, B. Lee, H. Shan, Z. Zhao, J. Meza, E. Strohmaier, D. Bailey, "Linear scaling 3D fragment method for large scale electronic structure calculations", Porc. 2008 ACM/IEEE Conf. supercomp. (ACM Gordon Bell), Article 65 (2008).

L.W. Wang, "Ab initio calculation of shallow acceptor levels in Si", J. Appl. Phys. 105, 123712 (2009).

L.W. Wang, "Large scale ab initio nanostructure electronic structure calculations for energy applications", J. Phys.: Conf. Series 125, 012059 (2008).

N. Vukmirovic, L.W. Wang, "Electronic structure of disordered conjugated polymers: polythiophenes", J. Phys. Chem. B 113, 409 (2009).

Y. Zhang, A. Mascarenhas, L.W. Wang, "Interplay of alloying and ordering on the electronic structure of Ga_xIn_(1-x)P alloys", Phys. Rev. B 78, 235202 (2008).

B. Sadtler, D.O. Demchenko, H. Zheng, S.M. Hughes, M.G. Merkle, U. Dahmen, L.W. Wang, A.P. Alivisatos, "Selective facet reactivity during cation exchange in cadmium sulfide nanorods", J. Am. Chem. Soc. 131, 5285 (2009).

F. Tao, S. Dag, L.W. Wang, Z. Liu, D.R. Butcher, M. Salmeron, G.A. Somorjai, "Restructuring of hex-Pt(100) under CO gas environments: formation of 2-D nanoclusters", Nano Lett. 9, 2167 (2009).

L.W. Wang, "Computational challenges for nanostructure solar cells", Energy & Env. Sci. 2, 944,(2009)(cover story).

D. Alloyeau, B. Freitag, S. Dag, L.W. Wang, C. Kisielowski, "Atomic resolution three dimensional imaging of germanium self-interstitials near a surface: Aberration corrected transmission electron microscopy", Phys. Rev. B 80. 014114 (2009).

Y. Zhang, A. Mascarenhas, S.H. Wei, L.W. Wang, "Comparison of atomistic simulations and statistical theories for variable degree of long-range order in semiconductor alloys", Phys. Rev. B 80, 045208 (2009).

L.W. Wang, "Divide and conquer: New algorithm promises to unleash the power of nanotechnology by enabling electronic structure calculations with hundreds of thousands of atoms", SciDAC review, Issue 14, P.22, Fall 2009.

**PI Yi Wang **

S. L. Shang, G. Sheng, Y. Wang, L. Q. Chen, and Z. K. Liu, "Elastic properties of cubic and rhombohedral BiFeO3 from first-principles calculations", Phys. Rev. B., Vol. 80, 2009, 052102, http://dx.doi.org/10.1103/PhysRevB.80.052102

Y. Wang, L.G. Hector, Jr., H. Zhang, S. L. Shang, L. Q. Chen, and Z. K. Liu, "Thermodynamic Framework for a System with Itinerant-Electron Magnetism", J. Phys.: Condens. Matter, Vol.21, 2009, 326003, http://dx.doi.org/10.1088/0953-8984/21/32/326003

Y. Wang, S. L. Shang, L. Q. Chen, and Z. K. Liu, "Thermodynamic Fluctuations among Magnetic States in BaFe2As2 (Submitted to J. Am. Chem. Soc.)

Y. Wang, S. L. Shang, L. Q. Chen, and Z. K. Liu, ???Origin of Invar Anomalies??? (Submitted to Nat. Mater.)

**PI Warren Washington **

Washington W. M., R. Knutti, G. A. Meehl, H. Teng, C. Tebaldi, D. Lawrence, L. Buja, W. G. Strand (2009), How much climate change can be avoided by mitigation?, Geophys. Res. Lett., 36, L08703, doi:10.1029/2008GL037074\

Williams, D.N., R. Ananthakrishnan, D.E. Bernholdt, S. Bharathi, D. Brown, M. Chen, A.L. Chervenak, L. Cinquini, R. Drach, I.T. Foster, P. Fox, D. Fraser, J. Garcia, S. Hankin, P. Jones, D.E. Middleton, J. Schwidder, R. Schweitzer, R. Schuler, A. Shoshani, F. Siebenlist, A. Sim, *W. G. Strand*, M. Su, and N. Wilhelmi, 2009: The Earth System Grid: Enabling Access to Multimodel Climate Simulation Data. Bull. Amer. Meteor. Soc., 90, 195-205. doi:10.1175/2008BAMS2459.1

Xie, S.-P., C. Deser, G.A. Vecchi, J. Ma, H. Teng, A. T. Wittenberg, 2009, Global warming pattern formation: sea surface temperature and rainfall. Submitted to J. Climate.

Teng, H. and G. Branstator, 2009, Initial value predictability in prominent modes of North Pacific subsurface temperature in a coupled GCM. Submitted to Climate Dynamics.

Hu, A., G. A. Meehl, W. Han, and J. Yin, 2009, Transient Response of the MOC and Climate to Potential Melting of the Greenland Ice Sheet in the 21st Century, Geophys. Res. Lett., 36, L10707, doi:10.1029/2009GL037998.

Okumura, Y. M., C. Deser, A. Hu, Axel Timmermann and Shang-Ping Xie, 2009, North Pacific Climate Response to Freshwater Forcing in the Subarctic North Atlantic: Oceanic and Atmospheric Pathways, J Clim., 22, 1424-1445.

Washington, W.M., L. Buja and A. Craig, 2009: The computational future for climate and earth system models: On the path to petaflop and beyond. Philosophical Transactions of the Royal Society A, The environmental eScience revolution, Royal society Publishing, London, UK (367) 833-846.

**PI William Weber **

R. Devanathan, "Radiation damage evolution in ceramics", Nuclear Instruments and Methods 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(17) (2009) Art. No. 174502.

J. Yu, R. Devanathan and W. J. Weber, "Unified Interatomic Potential for Zircon, Zirconia and Silica Systems", Journal of Materials Chemistry 19(23) (2009) 3923-3930. doi:10.1039/b902767j

H. Y. Xiao, X. T. Zu, F. Gao and W. J. Weber, "First-Principles Study of Energetic and Electronic Properties of A2Ti2O7 (A= Sm, Gd, Er) Pyrochlore," J. Applied Physics 104 [7] (2008) Art. No. 075303.

Z. L. Zhang, H. Xiao, X. T. Zu, F. Gao, and W. J. Weber, "First-principles calculation of structural and energetic properties for A2Ti2O7 (A =Lu, Er, Y, Gd, Sm, Nd, La)," J. Materials Research 24 [4] (2009) 1335-1341.

H. Y. Xiao, F. Gao, X. T. Zu, and W. J. Weber, Ab Initio Molecular Dynamics Simulation of a Pressure Induced Zinc Blende to Rocksalt Phase Transition in SiC, J. Phys.: Condens. Matter 21 (2009) Art. No. 245801.

H. Y. Xiao, F. Gao, X. T. Zu, and W. J. Weber, "Threshold Displacement Energy in GaN: Ab Initio Molecular Dynamics Study," J. Applied Physics 105 [12] (2009) Art. No. 123527.

F. Gao, H. Y. Xiao, X. T. Zue, M. Posselt, and W. J. Weber, "Defect-Enhanced Charge Transfer by Ion-Solid Interactions in SiC using Large-Scale Ab Initio Molecular Dynamics Simulations," Phys. Rev. Letters 102 [2] (2009) Art. No. 027405.

J. Yu, R. Devanathan and W. J. Weber, "First-principles study of defects and phase transition in UO2 in the GGA+U formalism", Journal of Physics: Condensed Matter (2009) in press.

P. A. Moreira, R. Devanathan, J. Yu and W. J. Weber, "Molecular dynamics simulation of threshold displacement energies in zircon", Nuclear Instruments and Methods B (2009) doi:10.1016/j.nimb.2009.07.023

**PI Suhuai Wei **

H. Peng, H. J. Xiang, S.-H. Wei, et al., Origin and Enhancement of Hole-Induced Ferromagnetism in First-Row d0 Semiconductors, Phys. Rev. Lett. 102, 017201 (2009).

Y. Gai, J. Li, S. S. Li, J. B. Xia, and S.-H. Wei, Design of Narro-Gap TiO2: A Passivated Codoping Approach for Enhanced Photoelectrochemical Activity, Phys. Rev. Lett. 102, 036402 (2009).

L. Zhang, Y. Yan, and S.-H Wei, Enhancing Dopant Solubility via Epitaxial Surfactant Growth, Phys. Rev. B 80, 073305 (2009).

Y. Zhang, A. Mascarenhas, S.-H. Wei, and L. W. Wang, Comparision of Atomistic Simulations and Statistical Theories for Variable Degree of Long Range Order in Semiconductor Alloys, Phys. Rev. B 80, 045206 (2009).

G. M. Dalpian, J. L. F. Da Silva, and S.-H. Wei, Ferrimagentic Fe-doped GaN: An Unusual Magnetic Phase in Dilute Magnetic Semiconductors, Phys. Rev. B (Rapid Communications) 79, 241201(R) (2009).

A. Walsh, J. L. F. Da Silva, Y. Yan, M. M. Al-Jassim, and S.-H. Wei, Origin of Electronic and Optical Trends in Ternary In2O3(ZnO)n transparent conducting oxides (n=1,3,5): Hybrid Density Functional Theory Calculations, Phys. Rev. B 79, 073105 (2009).

Y. Zhao, Y.-H. Kim, S. B. Zhang, M. J. Heben, 'Theory of Hydrogen Storage in Nanoscale Materials' in The Oxford Handbook of Nanoscience and Technology, Frontiers and Advances, Vol. 3, pp 700-736 (Oxford University Press, 2009)

H. J. Xiang, S.-H. Wei, S. Chen, and X. G. Gong, Ordered Ground State Wurtzite Alloys from Zinc-Blende Parent Compounds, Phys. Rev. B (in press).

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, submitted to Phys. Rev. Lett.

**PI Michael Weinert **

FLAPW: Applications and implementations. M. Weinert, G. Schneider, R. Podlucky, and J. Redinger, J. Phys. Condens. Matter 21, 084201 (2009).

Atomic and Electronic Structure of Polar Fe_2O_3(0001)/MgO(111) Interfaces, K. Pande, M. Gajdardziska-Josifovska, and M. Weinert, Phys. Rev. B (in press).

Effecs of unreconstructed polar surface termination on growth, structure, and magnetic properties of hematite films, S. H. Chung, A. Celik-Aktas, P. Dey, M. Weinert, B. Kabius, D. J. Keavney, V. K. Lazarov, S. A. Chambers, and M. Gajdardziska-Josifovska, Phys. Rev. B (submitted).

Electronic structures of Mn-induced phases on GaN(0001), Y. Qi, G.F. Sun, M. Weinert, L. Li, Phys. Rev. B (submitted)

**PI Harold Weitzner **

M. Adams, S. Ku, P. Worley, D'Azevedo, J. Cummings, C.S. Chang, "Scaling to 150K cores: recent algorithm and performance engineering developments enabling XGC1 to run at scale," Journal of Physics: Conference Series 180 (2009) 012036

C. S. Chang,, S. Ku, P. H. Diamond, Z. Lin, S. Parker, T. S. Hahm and N. Samatova, "Compressed ion temperature gradient turbulence in diverted tokamak edge," Phys. Plasmas 16, 056108 (2009)

C.S. Chang, S. Ku, et al, "Whole Volume Integrated Simulation of Plasma Turbulence in Realistic Diverted-Tokamak Geometry," Journal of Physics: Conference Series 180 (2009) 012057.

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," Nucl. Fusion, accepted.

X. Q. Xu, E. Belli, K. Bodi, J. Candy, C. S. Chang, et al, "Dynamics of kinetic Geodesic-Acoustic modes and the radial electric _eld in tokamak neoclassical plasmas," Nuclear Fusion, 49 065023 (2009). 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 (2009) 055025.

E.M. Hollmann, P.S. Krstic, R.P. Doerner, D. Nishijima, A.Yu. Pigarov, C.O. Reinhold, and S.J. Stuart, Measurement and modeling of hydrogen molecule ro-vibrational accommodation on graphite, Plasma Phys. Control. Fusion 50, 102001 (2008).

P.S. Krstic, C.O. Reinhold, and S.J. Stuart, Energy and Angle Spectra of Sputtered Particles for Low-Energy Deuterium Impact of Carbon, J. Appl. Phys. 104, 103308 (2008).

J.A. Ludlow, S.D. Loch, M.S. Pindzola, C.P. Ballance, D.C. Griffin, M.E. Bannister,M. Fogle, Electron-impact ionization of C+ in both ground and metastable states, Phys. Rev. A 78, 052708 (2008). P.S. Krstic, C.O. Reinhold, and S.J. Stuart, "Plasma-surface interactions of hydrogenated carbon," Nucl.Instr. Meth. B 267, 704 (2009).

S.D. Loch, C.P. Ballance, M.S. Pindzola, and D.P. Stotler, "The role of excited state ionization data on H and He generalized collisional radiative coefficients," Plasma Physics and Controlled Fusion 51, 105006 (2009).

C.O. Reinhold, P.S. Krstic, and S.J. Stuart, Hydrogen reflection in low-energy collisions with amorphous carbon, Nucl. Instr. Meth. B 267, 691 (2009).

P.S. Krstic, E.M. Hollmann, C.O. Reinhold, S.J. Stuart, R.P. Doerner, D. Nishijima, and A.Yu. Pigarov, Transfer of Rovibrational Energies in Hydrogen Plasma-Carbon Surface Interactions, J. Nuclear Materials 390-391, 88 (2009).

S.J. Stuart, M. Fallet, P.S. Krstic, and C.O. Reinhold, Evolution of carbon surfaces under simulated bombardment by deuterium, Submitted to J. Phys. Conf. (2009).

P.S. Krstic and C.O. Reinhold, Burning Plasma Wall Interactions, Submitted to AIP Conference Proceedings.

C.P. Ballance, J.A. Ludlow, M.S. Pindzola, and S.D. Loch, "Electron-impact ionization of ground and metastable neon," J. Phys. B 42, 175202 (2009).

J.A. Ludlow, C.P. Ballance, S.D. Loch, M.S. Pindzola, and D.C. Griffin, Electron-impact single ionization of Mg and Al+, Phys. Rev. A 79, 032715 (2009)

**PI Gerhard Wellein **

T. Zeiser, G. Hager, G. Wellein: Vector computers in a world of commodity clusters, massively parallel systems and many-core many-threaded CPUs: recent experience based on advanced lattice Boltzmann flow solvers, (In: W. E. Nagel, D. B. Kr??ner, M. Resch (editors), High Performance Computing in Science and Engineering '08, Transactions of the High Performance Computing Center, Stuttgart (HLRS) 2008), Springer, ISBN 978-3-540-88301-2, (2009) 333-347. doi:10.1007/978-3-540-88303-6.

**PI Zhaofang Wen **

"Parallel Phase Model for Manycore Parallel Machines," Zhaofang Wen and Junfeng Wu, Workshop on Theory and Many-Cores (T&MC), May 2009, University of Maryland, College Park, Maryland

"Parallel Phase Model: A Programming Model for High-end Parallel Machines with Manycores," Ron Brightwell1, Mike Heroux1, Zhaofang Wen, Junfeng Wu, THE 38th INTERNATIONAL CONFERENCE ONPARALLEL PROCESSING (ICPP-2009)

**PI Dan Werthimer **

Siemion, A., Von Korff, J., McMahon, P., Korpela, E., Werthimer, D., Anderson, D., Bower, G., Cobb, J., Foster, G., Lebofsky, M., van Leeuwen, J., Mallard, W., Wagner, M., ``New SETI Sky Surveys for Radio Pulses", in Acta Astronautica Special Issue: Life Signatures, submitted

**PI Myung Whangbo **

Y. Zhang, H. J. Xiang and M.-H. Whangbo, "Interplay between Jahn-Teller instability, uniaxial magnetism and ferroelectricity in Ca3CoMnO6", Phys. Rev. B 79, 054432 (2009).

J. L. Manson, K. H. Stone, H. I. Southerland, T. Lancaster, A. J. Steele, S. J. Blundell, F. L. Pratt, Peter J. Baker, R. D. McDonald, P. Sengupta, J. Singleton, P. A. Goddard, C. Lee, M.-H. Whangbo, M. M. Warter, C. H. Mielke and P. W. Stephens, "Characterization of the antiferromagnetism in Ag(pyz)2(S2O8) (pyz = pyrazine) with a two-dimensional square lattice of Ag2+ ions", J. Am. Chem. Soc. 131, 4590 (2009).

C. Lee, J. Kang, K. H. Lee and M.-H. Whangbo, "Symmetry-dependent strong reduction of the spin exchange interactions in Cs2CuCl4 by the 6p orbitals of Cs+ ions", Inorg. Chem. 48, 4185 (2009).

J. L. Manson, J. A. Schlueter, K. A. Funk, H. I. Southerland, B. Twamley, T. Lancaster, S.n J. Blundell, P. J. Baker, F. L. Pratt, J. Singleton, R. D. McDonald, P. A. Goddard, P. Sengupta, C. D. Batista, L. Ding, C. Lee, M.-H. Whangbo, I. Franke, S. Cox, C. Baines, and D. Triala, "?Strong H...F hydrogen bonds as synthons in polymeric quantum magnets: Structural, magnetic and theoretical characterization of [Cu(HF2)(pyrazine)2]SbF6, [Cu2F(HF)(HF2)(pyrazine)4](SbF6)2 and [CuAg(H3F4)(pyrazine)5](SbF6)2", J. Am. Chem. Soc. 131, 6733 (2009).

C. Lee, J. Kang, K. H. Lee and M.-H. Whangbo, "Density functional investigation of the antiferromagnetic ordering, spin orientation and ferroelectric polarization of rare-earth iron borate TbFe3(BO3)4", Chem. Mater. 21, 2534 (2009).

F. Wu, E. J. Kan, H. J. Xiang, S.-H. Wei, M.-H. Whangbo and J. L. Yang, "On the Magnetic States of Zigzag Graphene Nanoribbons", Appl. Phys. Lett. 94, 223105 (2009).

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).

M. G. Banks, R. K. Kremer, C. Hoch, A. Simon, B. Ouladdiaf, J.-M. Broto, H. Rakoto, C. Lee, and M.-H. Whangbo, "Magnetic ordering in the frustrated Heisenberg chain system cupric chloride CuCl2", Phys. Fev. B 80, 024404 (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, in press.

C. Tian, C. Lee, H. J. Xiang, Y. Zhang, C. Payen, S. Jobic, and M.-H. Whangbo, "Magnetic structure and ferroelectric polarization of MnWO4 investigated by density functional calculations and classical spin analysis", Phys. Rev. B, in press.

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., in press.

K. Tomiyasu, H. Kageyama, C. Lee, M.-H. Whangbo, Y. Tsujimoto, T. Watanabe, K. Yoshimura, J. W. Taylor, A. Llobet, F. Trouw, K. Kakurai, and K. Yamada, "Spin waves and orbital magnons in infinite-layer antiferromagnetic insulator", Phys. Rev. Lett., submitted for publication.

O. Mentre, E. Janod, P. Rabu, M. Hennion, F.Leclercq-Hugeux, J. Kang, C. Lee, M.-H. Whangbo, S. Petit, "BiCu2PO6: Frustration driven incommensurate dispersion in a gapped quantum spin ladder", Phys. Rev. B: Rapid Commun., submitted for publication.

**PI Martin White **

Carlson, Jordan, White, Martin, & Padmanabhan, Nikhil, Critical look at cosmological perturbation theory techniques, Physical Review D, 80, 043531 (2009)

Padmanabhan, Nikhil, et al., 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, 1862 (2009)

White, Martin, Song, Yong-Seon, & Percival, Will J., Forecasting cosmological constraints from redshift surveys, Monthly Notices of the Royal Astronomical Society, 397, 1348 (2009)

Wetzel, Andrew R. & White, Martin, What determines satellite galaxy disruption?, ArXiv e-prints, arXiv:0907.0702 (2009)

White, Martin & Padmanabhan, Nikhil, Breaking halo occupation degeneracies with marked statistics, Monthly Notices of the Royal Astronomical Society, 395, 2381 (2009)

Slosar, Anze, et al., The Acoustic Peak in the Lyman Alpha Forest, ArXiv e-prints, arXiv:0906.2414 (2009)

Padmanabhan, Nikhil & White, Martin, Calibrating the Baryon Oscillation Ruler for Matter and Halos, ArXiv e-prints, arXiv:0906.1198 (2009)

Wetzel, Andrew R., Cohn, J. D., & White, Martin, Simulating subhaloes at high redshift: merger rates, counts and types, Monthly Notices of the Royal Astronomical Society, 395, 1376 (2009)

Wetzel, Andrew R., Cohn, J. D., & White, Martin, The clustering and host haloes of galaxy mergers at high redshift, Monthly Notices of the Royal Astronomical Society, 394, 2182 (2009)

Cohn, J. D. & White, Martin, Issues in joint SZ and optical cluster finding, Monthly Notices of the Royal Astronomical Society, 393, 393 (2009)

Percival, Will J. & White, Martin, Testing cosmological structure formation using redshift-space distortions, Monthly Notices of the Royal Astronomical Society, 393, 297 (2009)

Heitmann, Katrin, et al., The Coyote Universe II: Cosmological Models and Precision Emulation of the Nonlinear Matter Power Spectrum, ArXiv e-prints, arXiv:0902.0429 (2009)

Heitmann, Katrin, et al., The Coyote Universe I: Precision Determination of the Nonlinear Matter Power Spectrum, ArXiv e-prints, arXiv:0812.1052 (2008)

White, Martin, Martini, Paul, & Cohn, J. D., Constraints on the correlation between QSO luminosity and host halo mass from high-redshift quasar clustering, Monthly Notices of the Royal Astronomical Society, 390, 1179 (2008)

Dalal, Neal, et al., Halo Assembly Bias in Hierarchical Structure Formation, Astrophysical Journal, 687, 12 (2008)

Heitmann, Katrin, et al., The cosmic code comparison project, Computational Science and Discovery, 1, 015003 (2008)

Seo, Hee-Jong, et al., Nonlinear Structure Formation and the Acoustic Scale, Astrophysical Journal,

**PI John Wilkins **

Quantum Monte Carlo for minerals at high pressures: Phase stability, equations of state, and elasticity of silica. K. P. Driver, R. E. Cohen, Zhigang Wu, B. Militzer, P. Lopez Rios, M. D. Towler, R. J. Needs, and J. W. Wilkins. Submitted to Nature (2009).

The energy landscape of silicon systems and its description by force fields, tight binding schemes, density functional methods and Quantum Monte Carlo methods. S. Alireza Ghasemi, M. Amsler, R. G. Hennig, S. Roy, S. Goedecker, C. J. Umrigar, L. Genovese, T. J. Lenosky, T. Morishita, K. Nishio. Submitted to PRB (2009).

Relative stability of extended interstitial defects in silicon. Hyoungki Park and John W. Wilkins. Phys. Rev. B 79, 241203(R) (2009)).

Classical potential describes martensitic phase transformations between the alpha, beta, and omega titanium phases. R. G. Hennig, T. J. Lenosky, D. R. Trinkle, S. P. Rudin, and J. W. Wilkins. Phys. Rev. B 78, 054121 (2008).

**PI Simon Woodruff **

S. Woodruff, A. I. D. Macnab, K. E. Miller, T. M. Ziemba Spheromak formation and sustainment with a repetitively pulsed source, Journal of Fusion Volume 28, Number 2 / June, 2009 229-234

A. I. D. Macnab and S. Woodruff Extended MHD simulations of the compression and stability of spheromaks for current drive, Journal of Fusion Energy Volume 28, Number 2 / June, 2009 183-186

Scott C. Hsu Technical Summary of the First U.S. Plasma Jet Workshop Journal of Fusion Energy Volume 28, Number 3 / September, 2009 246-257

**PI Stan Woosley **

Almgren, A. S., Bell, J. B., Nonake, A., and Zingale, M. ``Low Mach Number Modeling of Type Ia Supernovae. III. Reactions'' Astrophys. J., 684, 449 - 470, (2008).

Almgren, A. S., Bell, J. B., Nonaka, A., and Zingale, M., ``A New Low Mach Number Approach in Astrophysics'', Computing in Science and Engineering}, in press, (2009).

Aspden, A. J., Bell, J. B., Day, M. S., Woosley, S. E., and Zingale, M., ``Turbulence-Flame Interactions in Type Ia Supernovae'', Astrophys. J., {\bf 689}, 1173 - 1185, (2008).

Dessart, L., Burrows, A., Livne, E., and Ott, C.D., ``The Protoneutron Star Phase of the Collapsar Model and the Route to Long-Soft Gamma-ray Bursts and Hypernovae'', Astrophys. J., {\bf 673}, L43- L46, (2008).

Dessart, L., Ott, C.D., Burrows, A., Rosswog, S., and Livne, E., ``Neutrino Signatures of Binary Neutron Star Mergers'', Astrophys. J., Astrophys. J., 690, 1681, 2009 (astroph-0806.4380).

Hoffman, R. D., Muller, B., and Janka, H. T., ``Nucleosynthesis in O-Ne-Mg Supernovae'', Astrophys. J., 676, L127 - 130, (2008).

Kasen, D., Ropke, F., and Woosley, S. E., ``Brighter Makes Broader: Theory Agrees with Observations for Type Ia Supernovae'', Nature, 460, 869 (2009).

Kasen, D. and Woosley, S.E., ``Type IIP Supernovae: Light Curves and Standard Candle Relations'', Astrophys. J., accepted (2009).

McKinney, J., and Blandford, R. D., ``Stability of Relativistic Jets from Rotating, Accreting Black Holes via Fully Three-Dimensional Magnetohydrodynamic Simulations'', MNRAS, 394, 126 (2009).

Murphy. J.M. and Burrows, A., ``BETHE-Hydro: An Arbitrary Lagrangian-Eulerian Multi-dimensional Hydrodynamics Code for Astrophysical Simulations'', Astrophys. J. Suppl., 179, 209 - 241, (2008).

Murphy, J.M. and Burrows, A., ``Criteria for Core-Collapse Supernova Explosions by the Neutrino Mechanism'', Astrophys. J., 688, 1159 - 1175, (2008).

Ott, C.D., Burrows, A., Dessart, L., and Livne, E., ``2D Multi-Angle, Multi-Group Neutrino Radiation-Hydrodynamic Simulations of Postbounce Supernova Cores'', Astrophys. J., 685, 1069 - 1088, (2008).

Spitkovsky, A., ``On the Structure of Relativistic Collisionless Shocks in Electron-Ion Plasmas'', Astrophys. J., 673, L39 - L42, (2008).

Spitkovsky, A., ``Particle Acceleration in Relativistic Collisionless Shocks: Fermi Process at Last?'', Astrophys. J., 682, L5 - L8, (2008).

Woosley, S. E., Kerstein, A. R., Sankaran, V., and Roepke, F. K., ``Type Ia Supernova: Calculations of Turbulent Flames Using the Linear Eddy Model'', Astrophys. J., in press, astroph-0811.3610, (2009).

Woosley, S. E., Aspden, A. J., Bell, J. B., Kerstein, A. R., and Sankaran, V., `` Numerical Simulation of low Mach Number Reacting Flows'', in SciDAC 2008, Journal of Physics Conf. Ser., in press, (2008).

**PI Jianzhong Wu **

J. Jin, J. Wu, A. L. Frischknecht, "Modeling microscopic morphology and mechanical properties of block copolymer/nanoparticle composites", Macromolecules, in press, 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.

T. Jiang and J. Wu, "Self-organization of multivalent counterions in polyelectrolyte brushes", Journal of Chemical Physics, 129: 084903, 2008.

J. Wu and J. M. Prausnitz, "Pairwise additive hydrophobic effect for alkanes in water", Proceedings of National Academy of Science of the United States, 105(28): 9512"9515, 2008.

Z. Li, J. Wu and Z. G. Wang, ''Osmotic pressure and packaging structure of caged DNA,'' Biophysical Journal, 94: 737-746, 2008.

Z. Li and J. Wu, ''Towards a quantitative theory of ultra"small liquid droplets and vapor"liquid nucleation,'' Industrial & Engineering Chemistry Research, 47 (15): 4988"4995, 2008.

J. Jin and J. Wu, "A theoretical study for nanoparticle partitioning in the lamellae of diblock copolymers", Journal of Chemical Physics, 128, 074901, 2008.

T. Jiang and J. Wu, "Ionic effects in collapse of polyelectrolyte brushes", The Journal of Physical Chemistry B, 112 (26), 7713-7720, 2008.

**PI Meng-Shiou Wu **

Joseph Kenny, Kevin Huck, Lo Li, Lois Curfman McInnes, Heather Netzloff, Boyana Norris, Meng-Shiou Wu, "Computational Quality of Service in Quantum Chemistry", Posters session, the Supercomputing Conference (SC08), Austin, Texas, 2008.

Li Li , Joseph P. Kenny, Meng-Shiou Wu , Kevin Huck, Alexander Gaenko, Mark S. Gordon , Curtis L. Janssen, Lois Curfman McInnes, Hirotoshi Mori, Heather M. Netzloff , Boyana Norris, and Theresa L. Windus, Adaptive Application Composition in Quantum Chemistry, Argonne National Laboratory Preprint ANL/MCS- P1575-0209, the 5th International Conference on the Quality of Software Architectures (QoSA 2009), East Stroudsburg University, Pennsylvania, USA, June 22-26, 2009.

L. Seshagiri, M.-S.Wu, M. Sosonkina, Z. Zhang "Exploring Tuning Strategies for Quantum Chemistry Computations," to appear in The 4th International Workshop on Automatic Performance Tuning, Tokyo, Japan, October 1-2, 2009.

Meng-Shiou Wu, Colin Campbell, "Automating the Knowledge Discovery Process for Computational Quality of Service Research with Scientific Workflow Systems," to appear in the poster session of Supercomputing Conference 2009 (SC09), Portland, OR, USA, November 15-20, 2009.

**PI Ruqian Wu **

A. T. Costa, R. B. Muniz, J. X. Cao, R. Q. Wu, and D. L. Mills, "Magnetism of an Fe monolayer on W(110)", Phys. Rev. B 78, 054439 (2008).

Y. Zhu, J. X. Cao, Z. Q. Yang, and R. Q. Wu, "Origin of the co-dopant induced enhancement of ferromagnetism in (Zn,Mn)O", Phys. Rev. B 79, 085206 (2009).

J.H. Wang, Y.S. Shi, J.X. Cao, and R.Q. Wu, "Magnetization and magnetic anisotropy of metallophthalocyanine molecules from the first principles calculations", Appl. Phys. Lett. 95, 122502 (2009). (on Journal cover)

J. X. Cao, Y. Zhu, Z. Q. Yang, and R. Q. Wu, "Origin of the magnetism in CaB6: A first-principles study", Phys. Rev. B 79, 132404 (2009).

C.S. Tian, Y.Z. Wu, Z. Tian, J. Wu, G.S. Dong, X.F. Jin, C.Y. Won, Z.Q. Qiu, S.C. Hong, R.Q. Wu, "Frustrated Spin Structure at Mn/Ni/Cu(001)", Phys. Rev. Lett. Submitted (2008).

Li Zeng, Juexian Cao, Erik Helgren, Julie Karel, Elke Arenholz, David J. Smith, Ruqian Wu, Frances Hellman, "Localized Electronic Structure and Magnetism for Transition Metal (Mn) in Group IV Semiconductor Matrices", Nat. Mater. To be 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", Phys. Rev. B, submitted.

J. X. Cao, J. Lindner, A. Ney and R. Q. Wu, "Characterization of Co distribution in ZnO by x-ray magnetic circular dichroism", Phys. Rev. Lett. Submitted (2009).

A. Shinde, J.X. Cao, R.Q. Wu, and R. Ragan, Understanding of Self-Assembled Disilicide Nanowire Precursor Structures via Scanning Probe Microscopy and First Principles Studies, Israel Journal of Chemistry 48, 73 (2008).

A.A. Shinde, J.X. Cao, R. Ragan, and R.Q. Wu, An atomistic view of structural and electronic properties of rare earth disilicide nanostructures on Si(001) substrates, Chem. Phys. Lett., 466, 159 (2008).

A Shinde, J Cao, W Ouyang, R Wu, and R Ragan, Determination of preferential rare earth adatom adsorption geometries on Si (001), Phys. Lett. A 373, 3459 (2009).

**PI Donald Wuebbles **

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. (in review, available in Atmos. Chem. Phys. Discuss. at http://www.atmos-chem-phys-discuss.net/9/15511/2009/)

CHECK Several reports have been written for the DOE H2 project, but we do not as yet have a journal article prepared for publication concerning the DOE-funded project. In addition, the paper regarding the methyl iodide and trifluoroiodomethane Ozone Depletion Potential is nearly ready for submission, as are three papers resulting from the EPA-sponsored air quality studies.

**X**

**PI Nong Xiang **

N. Xiang and J. R. Cary, "Second harmonic generation of electron Bernstein waves in an inhomogeneous plasma," PRL., v.100, 085002 (2008);

J. R. Cary and N. Xiang, "Edge Electron Heating by the nonlinear Landau damping", Fusion Sherwood meeting, 2009;

N. Xiang and J. R. Cary, " Electron heating at half-harmonic cyclotron frequencies", to be submitted to POP.

## Y

**PI Yanfa Yan **

Muhammad N. Huda, Yanfa Yan, Aron Walsh, Su-Huai Wei, and Mowafak M. Al-Jassim, Symmetry-breaking-induced enhancement of visible light absorption in delafossite alloys Applied Physics Letters 94, 251907 (2009)

Muhammad N. Huda, Yanfa Yan, Aron Walsh, Su-Huai Wei, and Mowafak M. Al-Jassim, Group-IIIA versus IIIB delafossites: Electronic structure study Phys. Rev B 80, 035205 (2009)

Aron Walsh, K.-S. Ahn, S. Shet, M. N. Huda, T. G. Deutsch, H. Wang John A. Turner, Su-Huai Wei, Yanfa Yana and M. M. Al-Jassim, Ternary cobalt spinel oxides for solar driven hydrogen production: Theory and Experiment Energy Environ. Sci., 2, 774???782 (2009)

Aron Walsh, Juarez L. F. Da Silva, Yanfa Yan, M. M. Al-Jassim, and Su-Huai Wei Origin of electronic and optical trends in ternary In2O3(ZnO)n transparent conducting oxides (n=1,3,5): Hybrid density functional theory calculations Phys. Rev. B 79, 073105 (2009)

Aron Walsh, Yanfa Yan, Muhammad N. Huda, Mowafak M. Al-Jassim, and Su-Huai Wei Band Edge Electronic Structure of BiVO4: Elucidating the Role of the Bi s and V d Orbitals Chem. Mater., 21, 547???551(2009)

**PI Chao Yang **

L. Lin, J. Lu, R. Car and W. E. Multipole representation of the Fermi Operator with application to the electronic structure analysis of metallic systems. Phy. Rev. B. 115133, 2009.

L. Lin, J. Lu, L. Ying, R. Car and W. E., Fast algorithm for extracting the diagonal of the inverse matrix with application to the electronic structure of metallic systems, Comm. Math. Sci., to appear 2009

**PI Weiming Yao **

T. Aaltonen et al, The CDF Collaboration, Search for a Higgs Boson Produced in Association with a W Boson at CDF, Accepted by Phys. Rev. Lett. arXiv:0906.5613

T. Aaltonen et al, The CDF Collaboration, Search for Standard Model Higgs Boson Production in Association with a W Boson using a Neural Network Discriminant at CDF, Phys. Rev. D80, 012002 (2009)

T. Aaltonen et al, The CDF Collaboration, Top Quark Mass Measurement in the Lepton Plus Jets Channel using a Modified Matrix Element Method. Phys. Rev. D79, 072001(2009)

First Observation of B-bar0_s ->D+/-_sK-/+ and Measurement of the Ratio of Branching Fractions B(B-bar0_s ->D+/-_sK-/+)/B(B-bar0_s ->D+/-_spi-/+), Submitted to Phys. Rev. Lett. arXiv:0809.0080

**PI Katherine Yelick **

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.

Dan Bonachea, Paul Hargrove, Michael Welcome, Katherine Yelick, "Porting GASNet to Portals: Partitioned Global Address Space (PGAS) Language Support for the Cray XT," Proceedings of the Cray User Group (CUG), Atlanta, GA, May 2009.

"Scaling Communication-Intensive Applications on BlueGene/P Using One-Sided Communication and Overlap," R. Nishtala, P. Hargrove, D. Bonachea, K. Yelick. 23rd International Parallel & Distributed Processing Symposium (IPDPS), 2009.

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.

Rajesh Nishtala, Katherine Yelick, "Optimizing Collective Communication on Multicores," HotPar 2009, Berkeley, CA, March 2009.

**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 and J.S. Francisco, Theoretical study of the reaction of CH3 with HOCO radicals, J. Phys. Chem. A 113, 3844 (2009).

H.-G. Yu, J.S. Francisco and J.T. Muckerman, Ab initio and direct dynamics study of the reaction of Cl atoms with HOCO, J. Chem. Phys. 129, 064301 (2008).

H.-G. Yu and J.S. Francisco, Energetics and kinetics of the reaction of HOCO with hydrogen atoms, J. Chem. Phys. 128, 244315 (2008).

H.-G. Yu, G. Poggi, J.S.Francisco and J. T. Muckerman, Energetics and molecular dynamics of the reaction of HOCO with HO2 radicals, J. Chem. Phys. 129, 214307 (2008).

H.-G. Yu, Product branching ratios of the reaction of CO with H3+ and H2D+, Astrophys. J. Lett. (submitted, 2009).

## Z

**PI Bin Zhang **

Bin Zhang, "Thermalization through parton transport", Submitted to the Proceedings of the 10th International Conference on Nucleus-Nucleus Collisions (NN2009), arXiv:0909.0780 [nucl-th].

Bin Zhang "Kinetic equilibration from a radiative transport", Submitted to the Proceedings of the 25th Winter Workshop on Nuclear Dynamics, arXiv:0903.2055 [nucl-th].

Bin Zhang, "Recent results from parton cascade and microscopic transport", Eur. Phys. J. C 62, 25 (2009), [arXiv:0809.0446 [nucl-th]].

**PI Guoping Zhang **

G. P. Zhang, Laser-induced orbital and spin excitations in ferromagnets: Insights from a two-level system, Phys. Rev. Lett. 101, 187203 (2008).

G. P. Zhang and Thomas F. George, Total angular momentum conservation in laser-induced femtosecond magnetism, Phys. Rev. B 78, 052407 (2008).

G. P. Zhang, Yihua Bai, W. H\"ubner, Georg Lefkidis and Thomas F. George, Understanding laser-induced ultrafast magnetization in ferromagnets: First-principles investigation, J. Appl. Physics 103, 07B113 (2008).

G. P. Zhang, W. Hubner, Georg Lefkidis, Yihua Bai, and T. F. George, Paradigm of the time-resolved magneto-optical Kerr effect for femtosecond magnetism, Nature Physics 5, 499 (2009). See also: News and Views by Bovensiepen, http://www.nature.com/nphys/journal/v5/n7/index.html.

T. Hartenstein, G. Lefkidis, W. Hubner, G. P. Zhang and Yihua Bai, Time-resolved and energy-dispersed spin excitation in ferromagnets and clusters under influence of femtosecond laser pulses, J. Appl. Physics 105, 07D305 (2009). This paper has been selected for the March 2009 issue of Virtual Journal of Ultrafast Science. http://www.vjultrafast.org

G. P. Zhang, X. Sun and T. F. George, Nonlinear optical response and ultrafast dynamics in C_60, Journal of Physical Chemistry A 13, (7), pp 1175-1188 (2009) (INVITED FEATURE ARTICLE, COVER PAGE).

**PI Zhenyu Zhang **

Y. Mo, W. G. Zhu, E. Kaxiras, and Z. Y. Zhang Electronic nature of step-edge barriers against adatom descent on transition-metal surfaces Phys. Rev. Lett. 101,216101 (2008).

K. Zhao, M. C. Troparevsky, D. Xiao, A. G. Eguiluz, and Z. Y. Zhang Electronic Coupling and Optimal Gap Size between Two Metal Nanoparticles Phys. Rev. Lett. 102, 186804 (2009)

H. Chen, W. G. Zhu, E. Kaxiras, and Z. Y. Zhang Optimization of Mn doping in group-IV-based dilute magnetic semiconductors by electronic codopants Phys. Rev. B 79, 235202 (2009).

M. Z. Li, Y. G. Yao, B. Wu, Z. Y. Zhang, and E. G. Wang Strain effect on the instability of island formation in submonolayer heteroepitaxy Euro. Phys. Lett. 86 16001 (2009).

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 Bandgap narrowing of titanium oxide semiconductors by non-compensated anion-cation codoping for enhanced visible-light photoactivity Submitted to Phys. Rev. Lett.

Y. Jia, B. Wu, T. L. Einstein, H. H. Weitering, and Z. Y. Zhang Persistent Oscillations in the Interlayer Lattice Relaxation of Pb(111) Films Submitted to Phys. Rev. Lett.

J. Y. Lee, J. H. Cho, and Z. Y. Zhang Quantum size effects in competing charge and spin orderings of dangling-bond wires on Si(001) Submitted to Phys. Rev. Lett.

M. C. Troparevsky, K. Zhao, D. Xiao, Z. Zhang, and A. G. Eguiluz Tuning the electronic coupling and magnetic moment of a metal nanoparticle dimer in the nonlinear dielectric-response regime Submitted to Nano Letters.

A. Khajetoorians, W. Zhu, J. Kim, S. Y. Qin, H. Eisele, Z. Y. Zhang, and C.-K. Shih Adsorbate-induced Restructuring of Pb mesas Grown on Vicinal Si(111) in the Quantum Regime Submitted to Phys. Rev. B.

Kinetic Monte Carlo simulations of nanocolumn formation in two-component epitaxial growth S. Zheng, W. G. Zhu, G. M. Stocks, and Z. Y. Zhang Submitted to Appl. Phys. Lett.

Nanotribology and Nanoscale Friction Smooth Sliding Through Feedback Control, Guo Y, Qu ZH, Braiman Y, et al., IEEE CONTROL SYSTEMS MAGAZINE 28, 92 (2008).

Managing light polarization via plasmon-molecule interactions within an asymmetric metal nanoparticle trimer, Shegai T, Li ZP, Dadosh T, et al., PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA 105, 16448 (2008).

Energetics and kinetics of Ti clustering on neutral and charged C-60 surfaces, Yang SY, Yoon MN, Wang E, et al., JOURNAL OF CHEMICAL PHYSICS 129, 134707 (2008).

Electron transfer and localization in endohedral metallofullerenes: Ab initio density functional theory calculations, Yang SY, Yoon M, Hicke C, et al., PHYSICAL REVIEW B 78, 115435 (2008).

Theory of the excitation of the vibrational mode of an adatom-substrate system under a resonant laser field, Ma J, Wang EG, Zhang ZY, et al., PHYSICAL REVIEW B 78, 125303 (2008).

**PI Linjin Zheng **

A. Y. Aydemir, "An intrinsic source of radial electric field and edge flows in tokamaks", Nucl. Fusion 49, 065001 (2009).

P. Brady, T. Ditmire, W. Horton, et al. "Laboratory experiments simulating solar wind driven magnetospheres", Phys. Plasmas 16, 043112 (2009)

L. J. Zheng, M. Kotschenreuther, and J. W. Van Dam, "Gyrokinetic Theory for Kinetic Analysis of Resistive Wall Modes in ITER," paper TH/P9-32, 22nd IAEA Fusion Energy Conference, Geneva, Switzerland, 13-18 October 2008.

M. Kotschenreuther, P. Valanju, and S. M. Mahajan, "The Super X Divertor (SXD) and High Power Density Experiment (HPDX)," 2008 IAEA Fusion Energy Conference, paper IC/P4-7, submitted to Nucl. Fusion (2008).

J.M. Canik, R. Maingi, L. Owen, J. Menard, R. Goldston, M. Kotschenreuther, S. Mahajan, and P. Valanju, "2D divertor design calculations for the National High-power Advanced Torus Experiment," to be published, Journal of Nuclear Materials (available online 24 January 2009).

M. Kotschenreuther, P. M. Valanju, S. M. Mahajan, and E. A. Schneider "Fusion-Fission Transmutation Scheme-Efficient Destruction of Nuclear Waste," Fusion Engineering and Design 84, 83-88 (2009).

P. Valanju, M. Kotschenreuther, and S. M. Mahajan, "Super X Divertors for solving heat and neutron flux problems of fusion devices", Fus. Eng. Des. (2009), in press.

P. M. Valanju, M. Kotschenreuther, S. M. Mahajan, and J. Canik, "Super-X divertors and high power density fusion devices," Phys. Plasmas 16, 056110 (2009).

M. Kotschenreuther, P. Valanju, and S. M. Mahajan, "Fusion-Fission Transmutation Scheme --- efficient destruction of nuclear waste," Fus. Eng. Des. 84, 83 (2009).

P. Valanju, M. Kotschenreuther, and S. Mahajan, "Super-X Divertors and high power density fusion devices", Invited talk at 2008 APS Division of Plasma Physics Annual Meeting, Phys. Plasmas 16, 056110 (2009).

E. Schneider, M. Kotschenreuther, S. Mahajan, and P. Valanju, "Exploitation of a breakthrough in magnetic confinement fusion to improve transuranic incineration", in Proceedings of Global 2009 (The Nuclear Fuel Cycle: Sustainable Options and Industrial Perspectives), 6-11 September 2009, Paris, France.

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, 075021 (2009)

L. J. Zheng, M. T. Kotschenreuther, and J. W. Van Dam, "AEGIS-K code for linear kinetic analysis of toroidally axisymmetric plasma stability", submitted to J. Comp. Phys.

**PI Ping Zhu **

P. Zhu, C.C. Hegna, C.R. Sovinec, A. Bhattacharjee, and K. Germaschewski, Intermediate nonlinear regimes of line-tied g mode and ballooning instability, Nucl. Fusion 49, 095009 (2009).

P. Zhu, C. C. Hegna, and C. R. Sovinec, Exponential growth of nonlinear ballooning instability, Phys. Rev. Lett. 102, 235003 (2009).

P. Zhu, J. Raeder, K. Germaschewski, and C. C. Hegna, Initiation of ballooning instability in the near-Earth plasma sheet prior to the 23 March 2007 THEMIS substorm expansion onset, Ann. Geophys. 27, 1129-1138 (2009).

**PI Alex Zunger **

V. Mlinar and A. Zunger, Effect of atomic-scale randomness on the optical polarization of semiconductor quantum dots, Phys. Rev. B 79, 115416 (2009).

V. Mlinar, A. Franceschetti, and A. Zunger, Rules of peak multiplicity and peak alignment in multiexcitonic spectra of (In,Ga)As quantum dots, Phys. Rev. B 79, 121307(R) (2009).

V. Mlinar and A. Zunger, Spectral barcoding of quantum dots: Deciphering structural motifs from the excitonic spectra, Phys. Rev. B 80, 035328 (2009).

V. Mlinar et al., Structure of quantum dots as seen by excitonic spectroscopy and structural characterization: Using theory to close the loop, submitted to Phys. Rev. B (2009).

V. Mlinar et al. Internal electronic structure and fine structure of multiexcitons in semiconductor quantum dots, submitted to Phys. Rev. B (2009).

S.L. Sewall, A. Franceschetti, R.R. Cooney, A. Zunger, and P. Kambhampati, Direct observation of the structure of band-edge biexcitons in colloidal semiconductor CdSe quantum dots, Phys. Rev. B 80, 081310(R) (2009).

J. W. Luo, A. Franceschetti, and A. Zunger, Phys. Rev. B 79, Nonmonotonic size dependence of the dark/bright exciton splitting in GaAs nanocrystals, 201301(R) (2009).

J. W. Luo, A. Franceschetti, and A. Zunger, Direct-bandgap InAs quantum dots have long-range electron-hole exchange whereas indirect gap Si dots have short-range exchange, Nano Letters 9, 2648 (2009).

J.W. Luo, G. Bester, and A. Zunger, submitted to New J. Phy. (2009).

J.W. Luo, A. N. Chantis, M. van Schilfgaarde, G. Bester, and A. Zunger, Prediction of large linear-k spin splitting for holes in the 2D GaAs/AlAs system, submitted to Phys. Rev. Lett. (2009).

J.A. Chan, J.Z. Liu, H. Raebiger H, and A. Zunger, Relative stability, electronic structure, and magnetism of MnN and (Ga,Mn)N alloys, Phys. Rev. B 78, 184109 (2008).

J.A. Chan and A. Zunger, II-VI Oxides phase-separate whereas the corresponding carbonates order: The stabilizing role of anionic groups, Phys. Rev. B (accepted, 2009).

X.W Zhang, G. Trimarchi, and A. Zunger, Possible pitfalls in theoretical determination of ground-state crystal structures: The case of platinum nitride, Phys. Rev. B 79, 092102 (2009).

J.Z. Liu and A. Zunger, Thermodynamic theory of epitaxial alloys: first-principles mixed-basis cluster expansion of (In, Ga)N alloy film, J. Phys. COnd. Matt. 21, 295402 (2009).

P. Piquini and A. Zunger, Using superlattice ordering to reduce the band gap of random (In,Ga)As/InP alloys to a target value via the inverse band structure approach, Phys. Rev. B 78, 161302 (2008).

"Assessment of correction methods for the band-gap problem and for finite-size effects in supercell defect calculations: Case studies for ZnO and GaAs", S. Lany and A. Zunger, Phys. Rev. B 78, 235104 (2008).

"Electronic structure, donor and acceptor transitions, and magnetism of 3d impurities in In2O3 and ZnO", H. Raebiger, S. Lany, and A. Zunger, Phys. Rev. B 79, 165202 (2009).

"Polaronic hole localization and multiple hole binding of acceptors in oxide wide-gap semiconductors", S. Lany and A. Zunger, Phys. Rev. B 80, 085202 (2009).

"Accurate prediction of defect properties in density functional supercell calculations", S. Lany and A. Zunger, submitted to Modelling and Simulation in Materials Science and Engineering (2009).