# 2008 Publications Resulting from the Use of NERSC Resources

On their Allocation Year 2009 ERCAP Request Forms Principal Investigators reported 1,487 refereed publications (published or submitted) for the preceding 12 months, based on using, at least in part, NERSC resources.

## A

**PI Mowfak Al-Jassim**

Juarez L. F. Da Silva, Yanfa Yan, and Su-Huai Wei, Rules of Structure Formation for the Homologous InMO3(ZnO)n Compounds Phys. Rev. Lett. 100, 255501 (2008).

Yanfa Yan and S.-H. Wei, Doping asymmetry in wide-bandgap semiconductors: Origins and solutions, Phys. Stat. Sol. (b) 245, 641-652 (2008).

Aron Walsh, Yanfa Yan, M. M. Al-Jassim, and Su-Huai Wei Electronic, Energetic, and Chemical Effects of Intrinsic Defects and Fe-Doping of CoAl2O4: A DFT+U Study J. Phys. Chem. C 112; 12044 (2008)

Yanfa Yan, C.-S. Jiang, R. Noufi, Su-Huai Wei, H. R. Moutinho, and M. M. Al-Jassim Electrically Benign Behavior of Grain Boundaries in Polycrystalline CuInSe2 Films Phys. Rev. Lett. 99, 235504 (2007)

**PI Greg Aldering**

Improved Cosmological Constraints from New, Old and Combined Supernova Datasets, Kowalski, M., Rubin, D., Aldering, G., Agostinho, R. J., Amadon, A., Amanullah, R., Balland, C., Barbary, K., Blanc, G., Challis, P. J., Conley, A., Connolly, N. V., Covarrubias, R., Dawson, K. S., Deustua, S. E., Ellis, R., Fabbro, S., Fadeyev, V., Fan, X., Farris, B., Folatelli, G., Frye, B. L., Garavini, G., Gates, E. L., Germany, L., Goldhaber, G., Goldman, B., Goobar, A., Groom, D. E., Haissinski, J., Hardin, D., Hook, I., Kent, S., Kim, A. G., Knop, R. A., Lidman, C., Linder, E. V., Mendez, J., Meyers, J., Miller, G. J., Moniez, M., Mourao, A. M., Newberg, H., Nobili, S., Nugent, P. E., Pain, R., Perdereau, O., Perlmutter, S., Phillips, M. M., Prasad, V., Quimby, R., Regnault, N., Rich, J., Rubenstein, E. P., Ruiz-Lapuente, P., Santos, F. D., Schaefer, B. E., Schommer, R. A., Smith, R. C., Soderberg, A. M., Spadafora, A. L., Strolger, L. -., Strovink, M., Suntzeff, N. B., Suzuki, N., Thomas, R. C., Walton, N. A., Wang, L., Wood-Vasey, W. M. and Yun, J. L., 2008, Astrophysical Journal, in press

A New Determination of the High-Redshift Type Ia Supernova Rates with the Hubble Space Telescope Advanced Camera for Surveys, Kuznetsova, N., Barbary, K., Connolly, B., Kim, A. G., Pain, R., Roe, N. A., Aldering, G., Amanullah, R., Dawson, K., Doi, M., Fadeyev, V., Fruchter, A. S., Gibbons, R., Goldhaber, G., Goobar, A., Gude, A., Knop, R. A., Kowalski, M., Lidman, C., Morokuma, T., Meyers, J., Perlmutter, S., Rubin, D., Schlegel, D. J., Spadafora, A. L., Stanishev, V., Strovink, M., Suzuki, N., Wang, L. and Yasuda, N., 2008, Astrophysical Journal, 673, 981.

Using Visual Analytics to Maintain Situational Awareness in Astrophysics, Aragon, C., Poon, S., Aldering, G., Thomas, R. C. and Quimby, R., 2008, IEEE Visual Analytics Science and Technology 2008, in press.

Datataking in a Virtual Control Room: the SNfactory Example, Antilogus, R., Thomas, R. C., Aldering, G., Aragon, C., Hornero, E., Pecontal, A., Poon, S., Runge, K., Bailey, S., Baltay, C., Buton, C. Bongard, S., Childress, M., Copin, Y., Gangler, E., Loken, S., Nugent, P., Pain, R., Pecontal, E., Pereira, R., Perlmutter, S., Rabinowitz, D., Rigaudier, G., Scalzo, R., Smadja, G., Tao, C., Wu, C., 2008, SPIE Instrumentation in Astronomy, in press.

The Subaru/XMM-Newton Deep Survey (SXDS). V. Optically Faint Variable Object Survey, Morokuma, T., Doi, M., Yasuda, N., Akiyama, M., Sekiguchi, K., Furusawa, H., Ueda, Y., Totani, T., Oda, T., Nagao, T., Kashikawa, N., Murayama, T., Ouchi, M., Watson, M. G., Richmond, M. W., Lidman, C., Perlmutter, S., Spadafora, A. L., Aldering, G., Wang, L., Hook, I. M. and Knop, R. A. 2008, Astrophysical Journal, 676, 163.

SN 2005ap: A Most Brilliant Explosion, Quimby, R. M., Aldering, G. Wheeler, C., Akerloff, C. W., & Rykoff, E. S. (2007), Astrophysical Journal, 668, 99.

**PI Yoram Alhassid**

Spin Projection in the Shell Model Monte Carlo Method and the Spin Distribution of Nuclear Level Densities, Y. Alhassid, S. Liu, and H. Nakada, Phys. Rev. Lett. 99, 162504 (2007).

Effect of a Zeeman Field on the Superconductor-Ferromagnet Transition in Metallic Grains, S. Schmidt, Y. Alhassid, and K. Van Houcke, Europhys. Lett. 80, 47004 (2007).

Scrambling of Hartree-Fock Levels as a universal Brownian-Motion Process, Y. Alhassid, H. A. Weidenmueller, and A. Wobst, Phys. Rev. B 76, 193110 (2007).

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, arXiv: 0802.0901, submitted to Phys. Rev. Lett. (2008).

**PI Richard Andersen**

Laurent Maron, Odile Eisenstein, Richard A. Andersen "The Bond Between CO and Cp3U in Cp3U(CO) involves Backbonding from the Cp3U Ligand-based Orbitals of Pi-Symmetry", submitted to Organometallic.

**PI Ioan Andricioaei**

J. Wereszczynski and I. Andricioaei, "Mechanisms and Energetics of DNA Supercoil Relaxation by Human Topoisomerase I" (to be submitted to PNAS)

M. Mills, B. Orr, M Banaszak Holl and I Andricioaei, "Free Energy Profile, Forces, and Compaction of DNA by Amine Dendrimers" (to be submitted to Nano Letters)

J. Nummela and I. Andricioaei, "Energy landscape for DNA rotation and sliding through a bacteriophage portal" (to be submitted to Biophysical Journal)

**PI Jonathan Arons**

Sironi, L. & Spitkovsky, A. 2008, "Particle Acceleration in Relativistic Magnetized Collisionless Pair Shocks: Dependence of Shock Acceleration on Magnetic Obliquity," ApJ, submitted

Riquelme, M. & Spitkovsky, A. 2008, "Non-Linear Study of Bell's Cosmic Ray Current-Driven Instability," ApJ, submitted

Medvedev, M. & Spitkovsky, A. 2008, "Radiative Cooling in Relativistic Collisionless Shocks: Can Simulations and Experiments Probe Relevant GRB Physics?" ApJ, submitted

Spitkovsky, A. 2008, "Particle Acceleration in Relativistic Collisionless Shocks: Fermi Process at last?" ApJ Lett., 682, L5

Spitkovsky, A. 2008, "On the Structure of Relativistic Collisionless Shocks in Electron-Ion Plasmas," ApJ Lett., 673, L39

Keshet, U., Katz, B., Spitkovsky, A. & Waxman E. 2008, "Magnetic field evolution in relativistic unmagnetized collisionless shocks" ApJ Lett., submitted, arXiv: 0802.3217

Riquelme, M & Spitkovsky, A. 2008, "Kinetic Simulations of the Current-Driven Instability in Cosmic Ray Modified Shocks," Int. J. Modern Physics, in press

Chang P., Spitkovsky, A., and Arons J. 2008, "Long Term Evolution of Magnetic Turbulence in Relativistic Collisionless Shocks: Electron-Positron Plasmas," ApJ, 674, 378

## B

**PI Dmitri Babikov**

M. Zhao and D. Babikov, "On coherent and optimal control of adiabatic motion of ions in a trap", Phys. Rev. A 77, 012338 (5 pages), 2008.

E. Vetoshkin and D. Babikov, "Semiclassical wavepacket study of anomalous isotope effect in ozone formation", J. Chem. Phys. 127, 154312 (14 pages), 2007.

**PI Scott Baden**

"Performance Modeling Tools for Parallel Linear Algebra Computations," Pietro Cicotti, ACM Student Research Competition, Tapia Conference Portland, Oregon, April 1-4, 2009

**PI Prosenjit Bagchi**

Doddi, S.K., & Bagchi, P. 2008. Effect of inertia on the hydrodynamic interaction between liquid capsules in shear flow. International Journal of Multiphase Flow. 34, 375 - 392.

Doddi, S.K., & Bagchi, P. 2008. Lateral migration of a capsule in a plane Poiseuille flow in a channel. International Journal of Multiphase Flow, 34, 966-986.

Pappu, V., Doddi, S.K., & Bagchi, P. 2008. A computational study of leukocyte adhesion and its effect on flow pattern in microvessels. Journal of Theoretical Biology, 254, 483-498.

Doddi, S.K., Kalluri, R.M., & Bagchi, P. 2008. Direct numerical simulation of 1000 deformable capsules in a channel flow at finite inertia. FEDSM2008-55104. Proceedings of ASME Fluids Engineering Division Summer Conference. August 10-14, 2008. Jacksonville, FL.

**PI David Bailey**

David H. Bailey, Jonathan M. Borwein, David Broadhurst and M. L. Glasser, "Elliptic Integral Evaluations of Bessel Moments," Journal of Physics A: Mathematical and General, vol. 41 (2008), pg. 205203; LBNL-63719, available at http://crd.lbl.gov/~dhbailey/dhbpapers/b3g.pdf.

David H. Bailey, "Resolving Numerical Anomalies in Scientific Computation," manuscript, Jan 2008; LBNL-548E, available at http://crd.lbl.gov/~dhbailey/dhbpapers/numerical-bugs.pdf.

David H. Bailey and Jonathan M. Borwein, "High-Precision Numerical Integration: Progress and Challenges," Proceedings of the Milestones in Computer Algebra, to appear, Apr 2008; LBNL-547E, available at http://crd.lbl.gov/~dhbailey/dhbpapers/hp-num-int.pdf

[Carrington] L. Carrington, A. Snavely, D. Komatitsch, M. Laurenzano, M. Tikir, D. Micha, N. Le Goff, and J. Tromp, High-Frequency Simulations of Global Seismic Wave Propagation Using SPECFEM3D_GLOBE on 62K Processors, Supercomputing 2008.

[Chame] Jacqueline Chame, Chun Chen, Jack Dongarra, Mary Hall, Jeff Hollingsworth, Paul Hovland, Shirley Moore, Keith Seymour, Jaewook Shin, Ananta Tiwari, Sam Williams, Haihang You, "PERI Auto-tuning", SCIDAC Review 2008 (to appear).

[Michalakes2008] J Michalakes, J Hacker, R Loft, M O McCracken, A Snavely, N J Wright, T Spelce, B Gorda and R Walkup, "WRF Nature Run", 2008 Journal of Physics: Conference Series 125 012022.

[Wang] Lin-Wang Wang, Byounghak Lee, Hongzhang Shan, Zhengji Zhao, Juan Meza, Erich Strohmaier, David Bailey, "Linearly Scaling 3D Fragment Method for Large-Scale Electronic Structure Calculations", Proceedings of SC08, Nov 2008; LBNL-959E. Recipient of the 2008 ACM Gordon Bell Prize in the "Special" category for "algorithmic innovation." Also available at http://crd.lbl.gov/~dhbailey/ls3df-main.pdf.

**PI V. Balaji**

"Simulations of global hurricane climatology, interannual variability, and response to global warming using a 50 km resolution GCM" by Ming Zhao, Isaac M. Held, Shian-Jiann Lin and Gabriel A. Vecchi, submitted to Journal of Climate.

**PI Krishnan Balasubramanian**

Inorganic Chemistry: Theoretical: Theoretical Studies on Structures of Neptunyl Carbonates: NpO2(CO3)m(H2O)nq- (m=1-3, n =0-3) in Aqueous Solution Krishnan Balasubramanian, Zhiji Cao Inorg. Chem., 2007, 46(25), 10510-10519

ZHIJI CAO and KRISHNAN BALASUBRAMANIAN,"GEOMETRIES AND ENERGY SEPARATIONS OF ELECTRONIC STATES OF In3N, InN3, AND THEIR IONS", Journal of Theoretical and Computational Chemistry Vol. 7, No. 4 (2008) 751-765

Z. Cao, K. Balasubramanian, M. Calvert and H. Nitsche, Computational Studies of curium(III) with multidentate ligands: PPA complexes", Submitted for publication

**PI Perla Balbuena**

Diego A. Gomez-Gualdron and Perla B. Balbuena, Effect of metal cluster-cap interaction on the catalyzed growth of single-wall carbon nanotubes, submitted, J. Phys. Chem. C.

Diego A. Gomez-Gualdron and Perla B. Balbuena, Role of cap chirality on the growth mechanism of single-wall carbon nanotubes, submitted, Nanotechnology.

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).

A. Martinez-Limia, J. Zhao, and P. B. Balbuena, Molecular dynamics study of the initial stages of catalyzed single-wall carbon nanotubes growth: Force field development ,J. Mol. Mod., 13, 595-600, (2007).

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, submitted, J. Chem. Phys., August 8, 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, in press.

Yuguang Ma and Perla B. Balbuena, A kinetic model of surface segregation in Pt-based alloys, submitted, J. Chem. Theory and Comp.

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).

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

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

Y. Ma and P. B. Balbuena, OOH dissociation on Pt clusters, Chem. Phys. Lett.,447,289-294, (2007).

Z. Gu and P. B. Balbuena, Chemical environment effects on the atomic oxygen absorption into Pt(111) surfaces, J. Phys. Chem C., 111, 17388-17396, (2007).

**PI Arun Bansil**

Jouko Nieminen, Hsin Lin, R.S. Markiewicz, A. Bansil, "Importance of Matrix Element Effects in the Scanning Tunneling Spectra of High-Temperature Superconductors", arXiv:0805.1675v1 (2008), submitted to Phys. Rev. Lett.

Tanmoy Das, R. S. Markiewicz, A. Bansil, "Strong correlation effects and optical conductivity in electron doped cuprates", arXiv:0807.4257v1, submitted to Phys. Rev. Lett.

L. Spanu, D. Nissenbaum, C. Attaccalite, B. Barbiellini and A. Bansil "The Resonating-Valence-Bond Ground-State of Li Nanoclusters", submitted to Phys. Rev. Lett.

W. Al-Sawai, R.S. Markiewicz, M.Z. Hasan, A. Bansil, "Resonant Inelastic X-ray Scattering (RIXS) Spectra for Ladder Cuprates", arXiv:0801.0604v1, submitted to Phys. Rev. B

B. Barbiellini and T. Jarlborg, "The importance of local band effects for ferromagnetism in hole doped La$_2$CuO$_4$", arXiv:0809.3246v1, accepted for publication in Phys. Rev. Lett.

Tanmoy Das, R. S. Markiewicz, A. Bansil, "Superconductivity and topological Fermi surface transitions in electron-doped cuprates near optimal doping", arXiv:0711.1504 , Journal of Physics and Chemistry of Solids (2008, in press).

S. Sahrakorpi, R.S. Markiewicz, Hsin Lin, M. Lindroos, X. J. Zhou, T.Yoshida, W. L. Yang, T. Kakeshita, H. Eisaki, S. Uchida, Seiki Komiya, Yoichi Ando, F. Zhou, Z. X. Zhao, T. Sasagawa, A. Fujimori, Z. Hussain, Z.-X. Shen, and A. Bansil, "Appearance of Universal Metallic Dispersion in a Doped Mott Insulator", Phys. Rev. B 78, 104513 (2008)

Y. W. Li, D. Qian, L. Wray, D. Hsieh, Y. Xia, Y. Kaga, T. Sasagawa, H. Takagi, R. S. Markiewicz, A. Bansil, H. Eisaki, S. Uchida, and M. Z. Hasan, "X-ray imaging of dispersive charge modes in a doped Mott insulator near the antiferromagnet/superconductor transition ", Phys. Rev. B 78, 073104 (2008)

Z. Sun, J. F. Douglas, Q. Wang, D. S. Dessau, A. V. Fedorov, H. Lin, S. Sahrakorpi, B. Barbiellini, R. S. Markiewicz, A. Bansil, H. Zheng, and J. F. Mitchell, "Electronic structure of the metallic ground state of La2-2xSr1+2xMn2O7 for x~0.59 and comparison with x=0.36,0.38 compounds as revealed by angle-resolved photoemission", Phys. Rev. B 78, 075101 (2008)

Tanmoy Das, R. S. Markiewicz, and A. Bansil, "Erratum: Competing order scenario of two-gap behavior in hole-doped cuprates [Phys. Rev. B 77, 134516 (2008)]", Phys. Rev. B 77, 219904 (2008)

Tanmoy Das, R. S. Markiewicz, and A. Bansil,"Competing order scenario of two-gap behavior in hole-doped cuprates", Phys. Rev. B 77, 134516 (2008)

R. S. Markiewicz, M. Z. Hasan, and A. Bansil, "Acoustic plasmons and doping evolution of Mott physics in resonant inelastic x-ray scattering from cuprate superconductors", Phys. Rev. B 77, 094518 (2008)

R. Saniz, B. Barbiellini, P. M. Platzman, and A. J. Freeman, "Erratum: Physisorption of Positronium on Quartz Surfaces [Phys. Rev. Lett. 99, 096101 (2007)]" , Phys. Rev. Lett. 100, 019902 (2008)

R. S. Markiewicz, S. Sahrakorpi, and A. Bansil, "Paramagnon-induced dispersion anomalies in the cuprates", Phys. Rev. B 76, 174514 (2007)

Patrick H.-L. Sit, Christophe Bellin, Bernardo Barbiellini, D. Testemale, J.-L. Hazemann, T. Buslaps, Nicola Marzari and Abhay Shukla, "Hydrogen bonding and coordination in normal and supercritical water from X-ray inelastic scattering", Phys. Rev. B 76, 245413 (2007)

**PI Michael Barad**

Barad, M.F., P. Colella, and S.G. Schladow, 2008. An adaptive cut-cell method for environmental fluid mechanics, International Journal for Numerical Methods in Fluids, 44 pages (in press).

Barad, M.F. and O.B. Fringer. Identifying bedforms from free-surface observations: a numerical study, 30 pages. (Submitted to Physics of Fluids).

Barad, M.F. and O.B. Fringer. Simulations of shear instabilities in interfacial internal gravity waves, 35 pages. (Submitted to the Journal of Fluid Mechanics).

**PI Edward Baron**

E. Baron, D. J. Jeffery, D. Branch, E. Bravo, D. Garcia-Senz, & P. H. Hauschildt, Detailed Spectral Modeling of a 3-D Pulsating Reverse Detonation Model: Too Much Nickel, ApJ, (2008), 672, 1038--1042.

W. Ketchum, E. Baron, & D. Branch, Detailed Spectral Analysis of the Type Ib Supernova 1999dn. Paper I: Hydrogen-free Models ApJ, (2008), 674, 371--377.

D. Casebeer, E. Baron, K. Leighly, D. Jevremovic, & D. Branch, A Self-Consistent NLTE-Spectra Synthesis Model of FeLoBAL QSOs, ApJ, (2008), 676, 857--867.

S. Bongard, E. Baron, G. Smadja, D. Branch, & P. H. Hauschildt, Multi-layered Spectral Formation in SNe Ia Around Maximum Light, ApJ, (2008), in press.

Aaron Dotter, Brian Chaboyer, Darko Jevremovic, Veselin Kostov, E. Baron, J. W. Ferguson, The Dartmouth Stellar Evolution Database, ApJS, (2008), in press.

P. Hauschildt & E. Baron, A 3D Radiative Transfer Framework: III. Periodic Boundary Conditions, A&A, (2008), in press.

**PI Klaus Bartschat**

Time-dependent R-matrix calculations for multi-photon ionization of argon atoms in intense laser pulse X. Guan, C.J. Noble, O. Zatsarinny, K. Bartschat, and B.I. Schneider, Phys. Rev. A 78 (2008), 053402.

An Arnoldi-Lanczos program to propagate the time-dependent Schroedinger equation X. Guan, C.J. Noble, O. Zatsarinny, K. Bartschat, B.I. Schneider, submitted to Comp. Phys. Commun. (2009)

Time-Dependent B-Spline R-Matrix Approach to Double Ionization of Atoms by XUV Laser Pulses X. Guan, O. Zatsarinny, C.J. Noble, K. Bartschat, and B.I. Schneider, submitted to J. Phys. B (2009)

**PI Don Batchelor**

E.F. Jaeger et al, "Simulation of high-power electromagnetic wave heating in the ITER burning plasma", Physics of Plasmas, 15, 072513 (2008).

**PI Victor Batista**

J. Am. Chem. Soc. (in press), 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, 7034R, 2008-- (in press) Physical Chemistry of Interfaces and Nanomaterials VII, Laura Sharic Editor (Aug. 10-14, 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.

Ann. Rev. Phys. Chem. (in press), 2009 Coherent Control of Quantum Dynamics with Sequences of Unitary Phase-Kick Pulses, Luis G.C. Rego, Lea F. Santos and Victor S. Batista.

Current Opinion Struct. Biol. 17, 173-180, 2007 Structural Models of the Oxygen-Evolving Complex of Photosystem II, by Eduardo M. Sproviero, Jose A. Gascon, James P. McEvoy, Gary W. Brudvig and Victor S. Batista.

J. Phys. Chem. B 111, 11982-11990, 2007 Ultrafast Photooxidation of a Mn(II)-terpyridine complex covalently attached to TiO2 Nanoparticles, Sabas G. Abuabara, Clyde W. Cady, Jason B. Baxter, Charles A. Schmuttenmaer, Robert H. Crabtree, Gary W. Brudvig and Victor S. Batista.

Photochem. Photobiol. 190, 274-282, 2007 The MP/SOFT Methodology for Simulations of Quantum Dynamics: Model Simulations of the Photoisomerization of the Retinyl Chromophore in Rhodopsin, by Xin Chen and Victor S. Batista.

J. Mod. Optics. 54: 2617-2627, 2007 Multiple Unitary Pulses for Coherent Control of Tunneling and Decoherence, Luis G.C. Rego, Sabas G. Abuabara and Victor S. 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.

Photosynthesis. Energy from the Sun. 14th International Congress on Photosynthesis. Eds. J. F. Allen, E. Gautt, J.H. Golbeck and B. Osmond, p. 363-368, 2008, Springer. Ligation of the C-terminus of the D1-polypeptide of photosystem II to the Oxygen Evolving Complex of Photosystem II, by Jose A. Gascon, Eduardo M. Sproviero, 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.

Photosyn. 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.

**PI Pat Behling**

Zhong, Y., Z. Liu, and R. Jacob, 2008: Origin of Pacific Multidecadal Variability in Community Climate System Model, Version 3 (CCSM3): A Combined Statistical and Dynamical Assessment. J. Climate, 21, 114-133.

Liu, Z., N. Wen, and Y. Liu, 2008: On the Assessment of Nonlocal Climate Feedback. Part I: The Generalized Equilibrium Feedback Assessment. J. Climate, 21, 134-148.

Lee, D.E., Z. Liu, and Y. Liu, 2008: Beyond Thermal Interaction between Ocean and Atmosphere: On the Extratropical Climate Variability due to the 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.

Pan A., Q. Liu and Z. Liu, 2008: Formation mechanism of the "stability Gap" and the North Pacific Central mode water. Chinese Journal of Geophysics, 47, 461-470.

Liu Z. and N. Wen, 2008: On the assessment of non-local climate feedback: II: EFA-SVD analysis and optimal feedback. J. Climate, 21, 5404-5418.

Bayler E. and Z. Liu, 2008: Wind-forced Dynamics of the Seasonal Southern South China Sea Gyre. J. Geophys. Res., 113, C07014, doi:10.029/2007JC00519

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., in press

Zhong Y. F. and Z. Liu, 2008: On the mechanism of Pacific multidecadal variability in the CCSM3: the subpolar pathway. J. Clim., submitted

**PI John Bell**

P. Colella, D. Graves, T. Ligocki, D. Trebotich and B.Van Straalen "Embedded boundary algorithms and software for partial differential equations", 2008 J. Phys.: Conf. Ser. 125 01208

T.J. Ligocki, P.O. Schwartz, J. Percelay, P. Colella, "Embedded boundary grid generation using the divergence theorem, implicit functions, and constructive solid geometry", 2008 J. Phys.: Conf. Ser. 125 012080

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

Martin, D.F., Colella, P., and Graves, D.T. "A Cell-Centered Adaptive Projection Method for the Incompressible Navier-Stokes Equations in Three Dimensions", LBNL-62025, Journal of Computational Physics Vol 227 (2008) pp. 1863-1886.

D. T. Graves, D Trebotich, G. H. Miller, P. Colella, "An efficient solver for the equations of resistive MHD with spatially-varying resistivity", Journal of Computational Physics Vol 227 (2008) pp.4797-4804.

S. E. Woosley, A. J. Aspden, J. B. Bell, A. R. Kerstein, and V. Sankaran, "Numerical simualtion of low Mach number reacting flows", SciDAC 2008, J. of Physics: Conference Series, 125, Seattle Washington, July 2008.

M. Day, J. Bell, P.-T. Bremer, V. Pascucci, V. Beckner, M. Lijewski, "Turbulence effects on cellular burning structures in lean premixed hydrogen flames", submitted for publication.

G. H. Weber, P.-T. Bremer, M. S. Day, J. B. Bell, V. Pascucci, "Feature Tracking Using Reeb Graphs", submitted for publication

J. F. Grcar, J. B. Bell, M. S. Day, "The Soret Effect in Naturally Propagating, Premixed, Lean, Hydrogen-Air Flames", LBNL Report LBNL-669E, Proc. Combust. Inst., 32, to appear.

A. J. Aspden, J. B. Bell, M. S. Day, S. E. Woosley, M. Zingale, "Turbulence-Flame Interactions in Type Ia Supernovae", to appear, Astrophysical Journal.

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", submitted for publication. LBNL Report LBNL-176E.

A. J. Aspden, N. Nikiforakis, S. B. Dalziel, and J.B.Bell, "Characterising Implicit LES Methods", submitted for publication.

J. B. Bell, R. K. Cheng, M. S. Day, V. E. Beckner and M. J. Lijewski, "Interaction of turbulence and chemistry in a low-swirl burner", SciDAC 2008, J. of Physics: Conference Series, 125, 012027, Seattle Washington, July 2008.

**PI Roy Benedek**

Phase stability of cation doped LiMnO2 within the GGA+U approximation, by N. N. Shukla, R. Shukla, R. Prasad, and R. Benedek, Modelling and Simulation in Materials Science and Engineering 16, 55008 (2008).

Free energies for acid attack reactions of lithium cobaltate, by R. Benedek and A. van de Walle, Journal of the Electrochemical Society, in press.

Free energy for protonation rection in lithium-ion battery cathode materials, by R. Benedek, M. M. Thackeray, and A. van de Walle, Chemistry of Materials, in press.

Li2MnO3-stabilized LiMO2 (M = Mn, Ni, Co) electrodes for lithium-ion batteries, Thackeray MM (Thackeray, Michael M.), Kang SH (Kang, Sun-Ho), Johnson CS (Johnson, Christopher S.), Vaughey JT (Vaughey, John T.), Benedek R (Benedek, Roy), Hackney SA (Hackney, S. A.) JOURNAL OF MATERIALS CHEMISTRY, 3112-3125 (2007)

Studies of layered lithium metal oxide anodes in lithium cells, Vaughey JT (Vaughey, J. T.), Geyer AM (Geyer, Andrea M.), Fackler N (Fackler, Nathanael), Johnson CS (Johnson, Christopher S.), Edstrom K (Edstrom, K.), Bryngelsson H (Bryngelsson, H.), Benedek R (Benedek, Roy), Thackeray MM (Thackeray, Michael M.), JOURNAL OF POWER SOURCES 174, 1052-1056 (2007)

**PI Dan Bergmann**

Shindell, D..T., H. Teich, M. Chin, F. Dentener, R. M. Doherty, G. Faluvegi, A. M. Fiore, P. Hess, I. A. MacKenzie, M. G. Sanderson, M. G. Schultz, M. Schulz, D. S. Stevenson, C. Textor, O. Wild, D. J. Bergmann, I. Bey, H. Bian, C. Cuvelier, B. N. Duncan, L. W. Horowitz, J. Jonson, J. W. Kaminski, E. Marmer, R. Park, K. J. Pringle, S. Schroeder, S. Szopa, T. Takemura, G. Zeng, T. J. Keating, A. Zuber 2008: A multi-model assessment of pollution transport to the Arctic. 2008 Atmospheric Chemistry and Physics Discussions.

Sanderson, M.G. Dentener, A. Fiore, K. Cuvelier, T. Keating, A. Zuber, Hess, J.-E. Jonson, D. Simpson, O. Wild, M.J. Prather, R. Hu, D. Jacob, C. Atherton, D.J. Bergmann. Horowitz, I. Mackenzie, R.M. Doherty, K.J. Pringle 2008: A multi-model source-receptor study of the hemispheric transport and deposition of oxidised nitrogen. Geophysical Research Letters, 35, L17815, doi:10.1029/2008GL035389.

**PI Wes Bethel**

Daniela Ushizima, Oliver Ruebel, Prabhat, Gunther Weber, E. Wes Bethel, Cecilia Aragon, Cameron Geddes, Estelle Cormier-Michel, Bernd Hamann, Peter Messmer, Hans Hagen. "Automated Analysis for Detecting Beams in Laser Wakefield Simulations". 2008 Seventh International Conference on Machine Learning and Applications, Proceedings of IEEE ICMLA'08, 2008. LBNL-960E.

E. Wes Bethel, Hank Childs, Ajith Mascarenhas, Valerio Pascucci, and Prabhat. Scientific Data Managment Challenges in High Performance Visual Data Analysis. In Arie Shoshani and Doron Rotem, editors, Scientific Data Management: Challenges, Existing Technology, and Deployment. Chapman & Hall/CRC Press, 2008.

Luke J. Gosink, John C. Anderson, E. Wes Bethel, Kenneth I. Joy. "Query-Driven Visualization of Time-Varying Adaptive Mesh Refinement Data." IEEE Transactions on Visualization and Computer Graphics, 14(6), Proceedings of IEEE Visualization 2008 (To appear). LBNL-803E.

Luke J. Gosink, Kesheng Wu, E. Wes Bethel, John D. Owens, Kenneth I. Joy. "Bin-Hash Indexing: A Parallel Method for Fast Query Processing." Technical Report LBNL-729E, Lawrence Berkeley National Laboratory, Berkeley CA, USA, 94720, 2008.

O. Ruebel, Prabhat, K. Wu, H. Childs, J. Meredith, C.G.R. Geddes, E. Cormier-Michel, S. Ahern, G.H. Weber, P. Messmer, H. Hagen, B. Hamann and E.W. Bethel, "Application of High-performance Visual Analysis Methods to Laser Wakefield Particle Acceleration Data." Poster at IEEE Visualization 2008, Columbus, Ohio, October 19-24, 2008. (To appear) LBNL-952E.

O. Ruebel, Prabhat, K. Wu, H. Childs, J. Meredith, C.G.R. Geddes, E. Cormier-Michel, S. Ahern, G.H. Weber, P. Messmer, H. Hagen, B. Hamann and E.W. Bethel, "High Performance Multivariate Visual Data Exploration for Extremely Large Data." SC08, Austin TX, November, 2008

Sarah Poon, Rollin Thomas, Cecilia Aragon, and Brian Lee, "Context-Linked Virtual Assistants for Distributed Teams: An Astrophysics Case Study." CSCW 2008: ACM Conference on Computer Supported Cooperative Work. (To appear, 2008.) Best Paper Award Nominee

Cecilia Aragon, Stephen Bailey, Sarah Poon, Karl Runge, and Rollin Thomas, "Sunfall: A Collaborative Visual Analytics System for Astrophysics." J. Phys.: Conf. Ser. 125 012091 (Proceedings of SciDAC 2008). LBNL-657E.

Cecilia Aragon, Sarah Poon, Gregory Aldering, Rollin Thomas, and Robert Quimby, "Using Visual Analytics to Maintain Situation Awareness in Astrophysics." Proceedings of the IEEE Symposium on Visual Analytics Science and Technology (IEEE VAST 2008).

E. Wes Bethel, Chris Johnson, Charles Hansen, Claudio Silva, Steven Parker, Allen Sanderson, Lee Myers, Martin Cole, Xavier Tricoche, Sean Ahern, George Ostrouchov, Dave Pugmire, Jamison Daniel, Jeremy Meredith, Valerio Pascucci, Hank Childs, Peer-Timo Bremer, Ajith Mascarenhas, Ken Joy, Bernd Hamann, Christoph Garth, Cecilia Aragon, Gunther Weber, and Prabhat. "Seeing the Unseeable." SciDAC Review, Number 8, Summer 2008, pp 24-33. LBNL-472E.

O. Ruebel, G. H. Weber, M-Y Huang, E. W. Bethel, M. D. Biggin, C. C. Fowlkes, C. Luengo Hendriks, S. V. E. Ker??nen, M. Eisen, D. Knowles, J. Malik, H. Hagen and B. Hamann, "Integrating Data Clustering and Visualization for the Analysis of 3D Gene Expression Data." IEEE Transactions on Computational Biology and Bioinformatics. 2008. (To appear) LBNL-382E.

C. C. Fowlkes, C. L. Luengo Hendriks, S. V. E. Ker??nen, G. H. Weber, O. Ruebel, M.-Y. Huang, S. Chatoor, A. H. DePace, L. Simirenko, C. Henriquez, A. Beaton, R. Weiszmann, S. Celniker, B. Hamann, D. W. Knowles, M. D. Biggin, M. B. Eisen, J. Malik. "A Quantitative Spatio-temporal Atlas of Gene Expression in the Drosophila Blastoderm." Cell Vol 133, 364-374, 18 April 2008.

**PI Amitava Bhattacharjee**

P. Zhu, J. Raeder, K. Germaschewski, and C. C. Hegna, Initiation of ballooning instability by reconnection in the near-Earth plasma sheet, submitted to Ann. Geophys. (2008).

C.-S. Ng, D. Rosenberg, K. Germaschewski, A. Pouquet, and A. Bhattachar- jee, A comparison of spectral element and finite difference simulations with ad- aptive mesh refinement for the MHD island coalescence instability problem, Astrophys. J. Suppl. 177 (2008) 613-625

L.-J. Chen, N. Bessho, B. Lefebvre, H. Vaith, A. Fazakerley, A. Bhattacharjee, P. A. Puhl-Quinn, A. Runov, Y. Khotyaintsev, A. Vaivads, E. Georgescu, and R. B. Torbert (2008), Evidence of an extended electron current sheet and its neighboring magnetic island during magnetotail reconnection, J. Geophys. Res., doi:10.1029/2008JA013385, in press.

J. Dorelli and A. Bhattacharjee, Defining and identifying three-dimensional magnetic reconnection in resistive MHD simulations of Earths magnetosphere, Physics of Plasmas 15, 056504 (2008).

C.-S. Ng and A. Bhattacharjee, A constrained tectonics model for coronal heating, The Astrophysical Journal 675, 899 (2008).

**PI Erik Boman**

Optimizing Parallel Sparse Matrix-Vector Multiplication by Corner Partitioning, M. M. Wolf, E.G. Boman and B. Hendrickson, PARA08, Trondheim, Norway, May 2008. To appear in Springer LNCS.

**PI Paul Bonoli**

"Simulation of High Power Electromagnetic Wave Heating in the ITER Burning Plasma", E. F. Jaeger, L. A. Berry, E. F. D'Azevedo, R. F. Barrett, S. D. Ahern, D. W. Swain, D. B. Batchelor, R. W. Harvey, J. R. Myra, D. A. D'Ippolito, C. K. Phillips, E. Valeo, D. N. Smithe, P. T. Bonoli, J. C. Wright, M. Choi, Phys. Plasmas 15, 072513 (2008) - cover article.

"High Harmonic Fast Wave Heating Efficiency Enhancement and Current Drive at Longer Wavelength on the National Spherical Torus Experiment," J. Hosea, R. E. Bell, B. P. LeBlanc, et. al., Phys. Plasmas 15, 056104 (2008).

"Full Wave Simulations of Lower Hybrid Waves in Toroidal Geometry with Non-Maxwellian Electrons", J. C.Wright, E. J. Valeo, C. K. Phillips, P. T. Bonoli, and M. Brambilla, Communications in Computational Physics, Vol. 4(3) 545 (2008).

"Far-field sheaths due to fast waves incident on material boundaries," D. A. D'Ippolito, J. R. Myra, E. F. Jaeger, L. A. Berry, accepted for publication in Phys. Plasmas (2008).

"Complex Version of High Performance Computing LINPACK Benchmark (HPL)", R. Barrett, T. Chan, E. F. D'Azevedo, E. F. Jaeger et al., submitted to Concurrency Computat.: Pract. Exper. (2008).

**PI Julian Borrill**

"High resolution CMB power spectrum from the complete ACBAR data set", C. Reichardt, et al. submitted to Astrophysical Journal; arXiv:0801.1491

"CMB Polarization Systematics due to Beam Asymetry: Impact on Inflationary Science" M. Shimon, B. Keating, N. Ponthieu, E. Hivon, Phys. Rev. D 77, 083003 (2008); arXiv:0709.1513

"New Measurements of Fine-Scale CMB Polarization Power Spectra from CAPMAP at Both 40 and 90 GHz" CAPMAP collaboration - Astrophysical Journal 84, 771 (Sep 10, 2008); arXiv:0802.0888

"The White Mountain Polarimeter Telescope and an Upper Limit on Cosmic Microwave Background Polarization", Levy, A.R. et al. 2008, ApJS, 177, 419L; arXiv:0804.3634v1

"Making Maps from Planck LFI 30GHz Data with Asymmetric Beams and Cooler Noise" M.A.J.Ashdown et al, Submitted to Astronomy & Astrophysics

"PReBeaM for Planck: A Polarized Regularized Beam Deconvolution Map-Making Method" Charmaine Armitage-Caplan & Benjamin D. Wandelt, submitted to Astrophysical Journal Supplement

**PI Joel Bowman**

Yimin Wang, Bastiaan J.~Braams, Joel M.~Bowman, Stuart Carter, and David P.~Tew. Full-dimensional quantum calculations of ground-state tunneling splitting of malonaldehyde using an accurate ab initio potential energy surface. {\it Journal of Chemical Physics} 128 \#224314, 2008.\hfil\break http://dx/doi/org/10.1063/1.2937732

Lucas Koziol, Yimin Wang, Bastiaan J.~Braams, Joel M.~Bowman, and Anna I.~Krylov. The theoretical prediction of infrared spectra of trans- and cis-hydroxycarbene calculated using full dimensional ab initio potential energy and dipole moment surfaces. Journal of Chemical Physics 128 #204310, 2008. http://dx/doi.org/10.1063/1.2925452

Brianna R.~Heazlewood, Meredith J.~T.~Jordan, Scott H.~Kable, Talitha M.~Selby, David L.~Osborn, Benjamin C.~Shepler, Bastiaan J.~Braams, and Joel M.~Bowman. Roaming is the dominant mechanism for molecular products in acetaldehyde photodissociation. Proceedings of the National Academy of Sciences 105, 12719--12724, 2008. http://dx.doi.org/10.1073/pnas.0802769105

Jennifer E.~Mann, Zhen Xie, John D.~Savee, Bastiaan J.~Braams, Joel M.~Bowman, and Robert E.~Continetti. Probing the Structure of CH5+ by Dissociative Charge Exchange. Journal of the American Chemical Society 130, 3730--3731, 2008. http://dx/doi.org/10.1021/ja0782504

Paulo H.~Acioli, Zhen Xie, Bastiaan J.~Braams, and Joel M.~Bowman. Vibrational ground state properties of H5+ and its isotopomers from diffusion Monte Carlo calculations. Journal of Chemical Physics 128 \#104318, 2008. http://dx/doi.org/10.1063/1.2838847

Benjamin C.~Shepler, Bastiaan J.~Braams, and Joel M.~Bowman. ``Roaming'' Dynamics in CH3CHO Photodissociation Revealed on a Global Potential Energy Surface. Journal of Physical Chemistry A 112, 9344--9351, 2008. http://dx/doi.org/10.1021/jp802331t

Yimin Wang, Stuart Carter, Bastiaan J.~Braams, and Joel M.~Bowman. MULTIMODE quantum calculations of intramolecular vibrational energies of the water dimer and trimer using ab initio-based potential energy surfaces. Journal of Chemical Physics 128 #071101, 2008. http://dx/doi/org/10.1063/1.2839303

X.~Huang, Bastiaan J.~Braams, Joel M.~Bowman, Ross E.~A.~Kelly, Jonathan Tennyson, Gerrit C.~Groenenboom, and Ad van der Avoird. New ab initio potential energy surface and the vibration-rotation-tunneling levels of (H2O)2 and (D2O)2. Journal of Chemical Physics 128, #034312, 2008. http://dx.doi.org/10.1063/1.2822115

Bastiaan J. Braams and Hua-Gen Yu. Potential energy surface and quantum dynamics study of rovibrational states for HO3 (X2A). Phys. Chem. Chem. Phys. 10, 3150--3155, 2008. http://dx/doi.org/10.1039/b801928b

Benjamin C.~Shepler, Bastiaan J.~Braams and Joel M.~Bowman. Quasiclassical Trajectory Calculations of Acetaldehyde Dissociation on a Global Potential Energy Surface Indicate Significant Non-transition State Dynamics. Journal of Physical Chemistry A 111, 8282--8285, 2007. http:://dx.doi.org/10.1021/jp074646q

Chao Chen, Benjamin C.~Shepler, Bastiaan J.~Braams and Joel M.~Bowman. Quasiclassical trajectory calculations of the OH + NO2 association reaction on a global potential energy surface. Journal of Chemical Physics} 127, #104310, 2007. http:://dx/doi.org/10.1063/1.2764076

**PI Bastiaan Braams**

Jennifer E.~Mann, Zhen Xie, John D.~Savee, Bastiaan J.~Braams, Joel M.~Bowman, and Robert E.~Continetti. Probing the Structure of CH5+ by Dissociative Charge Exchange. Journal of the American Chemical Society 130, 3730--3731, 2008. http://dx/doi.org/10.1021/ja0782504

Ralf I.~Kaiser, Leonid Belau, Stephen R.~Leone, Musahid Ahmed, Yimin Wang, Bastiaan J.~Braams, and Joel M.~Bowman. A Combined Experimental and Computational Study on the Ionization Energies of the Cyclic and Linear C$_3$H Isomers. ChemPhysChem 8:1236--1239, 2007. http://dx.doi.org/10.1002/cphc.200700109

Kurt M.~Christoffel, Zhong Jin, Bastiaan J.~Braams and Joel M.~Bowman. Quasiclassical trajectory study of the CH3+ + HD -> CH2D+ + H2 reaction. Journal of Physical Chemistry A, 111:6658--6664, 2007. http://dx.doi.org/10.1021/jp068722

**PI Dylan Brennan**

R. Takahashi, D.P. Brennan and C.C. Kim, "Kinetic Effects of Energetic Particles on Resistive MHD Stability," submitted to Phys. Rev. Lett. (9/2008)

**PI David Bruhwiler**

G.I. Bell, D.L. Bruhwiler, A. Fedotov, A. Sobol, R.S. Busby, P. Stoltz, D.T. Abell, P. Messmer, I. Ben-Zvi and V. Litvinenko, "Simulating the dynamical friction force on ions due to a briefly co-propagating electron beam," J. Comput. Phys. (2008), doi:10.1016/j.jcp.2008.06.019.

J.R. Cary, P. Spentzouris, J. Amundson, L. McInnes, M. Borland, B. Mustapha, B. Norris, P. Ostroumov, Y. Wang, W. Fischer, A. Fedotov, I. Ben-Zvi, R. Ryne, E. Esarey, C.G.R. Geddes, J. Qiang, E. Ng, S. Li, C. Ng, R. Lee, L. Merminga, H. Wang, D.L. Bruhwiler, D. Dechow, P. Mullowney, P. Messmer, C. Nieter, S. Ovtchinnikov, K. Paul, P. Stoltz, D. Wade-Stein, W.B. Mori, V. Decyk, C.K. Huang, W. Lu, M. Tzoufras, F. Tsung, M. Zhou, G.R. Werner, T. Antonsen, T. Katsouleas, "COMPASS, the COMmunity Petascale project for Accelerator Science and Simulation, a broad computational accelerator physics initiative," J. Physics: Conf. Series 78, 012009 (2007). http://www.iop.org/EJ/article/1742-6596/78/1/012009/jpconf7_78_012009.pdf

**PI Patrick Burns**

"A Fast, Portable, Parallel LFG Random Number Generator." By Joshua Ladd and Patrick J. Burns, submitted.

## C

**PI Philip Cameron-Smith**

"TransCom Model Simulations of hourly CO2: Experimental Overview and Diurnal Cycle Results for 2002", R.M. Law, and 34 other authors including P. J. Cameron-Smith and D. J. Bergmann, Global Biogeo. Cycles, 22, GB3009, doi:10.1029/2007GB003050, 2008.

"TransCom continuous experiment: 2. Comparison of CO2 transports at synoptic timescale", P. K. Patra, and 34 other authors including P. J. Cameron-Smith and D. J. Bergmann, Global Biogeo. Cycles, in press.

**PI Andrew Canning**

C. Voemel, O Marques, A. Canning, L.W. Wang, J. Dongarra, State-of-the-art eigensolvers for electronic structure calculations of large scale nanosystems J. Comp. Phys. 223, 774 (2007) [LBNL-60147].

A. Canning, J. Dongarra, J. Langou, O. Marques, S. Tomov, C. Voemel, and L.-W. Wang, Interior State Computation of Nanstructures, submitted to proceedings of PARA2008 (2008)

A. Canning, Scalable Parallel 3d FFTs for Electronic Structure Codes, submitted to VecPar08 conference proceedings, to be published in Springer Series, Lecture Notes in computer Science (2008)

Lee, Byounghak; Wang, Lin-Wang; Canning, Andrew Effects of semicore d-states in screened exchange density functional method J. Appl, Phys, 103, 113713 (2008) LBNL-6133

A. Canning, J. Dongarra, J. Langou, O. Marques, S. Tomov, C. Voemel, and L.-W. Wang New Eigensolvers for Large Scale Nanoscience Simulations, Submitted to Journal of Physics, Proc. Scidac conference, Seattle (2008)

The Use of Bulk States to Accelerate the Band Edge State Calculation of a Semiconductor Quantum Dot, C. Voemel, O. Marques, S. Tomov, L.-W.-Wang and J. Dongarra. J. Comp. Phys. 223, 774 (2007)

**PI Joseph Carlson**

Self-consistent description of spontaneous fission in multidimensional collective space, A. Staszczak, A. Baran, J. Dobaczewski and W. Nazarewicz, Submitted to Nature

Deformed Coordinate-Space Hartree-Fock-Bogoliubov Approach to Weakly Bound Nuclei and Large Deformations, J.C. Pei, M.V. Stoitsov, G.I. Fann, W. Nazarewicz, N. Schunck, F.R. Xu, Submitted to PRC

Broyden Method in Nuclear Structure Calculations, Baran, A. Bulgac, M. McNeil Forbes, G. Hagen, W. Nazarewicz, N. Schunck, and M. V. Stoitsov, Phys. Rev. C78 014318 (2008)

`Dependence of two-nucleon momentum densities on total pair momentum', R. B. Wiringa, J. Carlson, Steven C. Pieper, and J. Carlson, Phys. Rev. C78, 021001(R).

`Strongly Paired Fermions: Cold Atoms and Neutron Matter', Alexandros Gezerlis and J. Carlson, Phys. Rev. C77, 032801(R) (2008).

T. Dytrych, K.D. Sviratcheva, C. Bahri, J.P. Draayer and J.P. Vary, "Highly deformed modes in the ab initio symplectic no-core shell model," J. Phys. G. 35, 095101 (2008).

Systematics of the first 2+ excitation in spherical nuclei with the Skryme quasiparticle random-phase approximation J. Terasaki, J. Engel, and G.F. Bertsch, to appear in Phys. Rev. C (2008).

P. Sternberg, E.G. Ng, C. Yang, P. Maris, J.P. Vary, M. Sosonkina and H. V. Le, "Accelerating Configuration Interaction Calculations for Nuclear Structure", accepted for publication in Proceedings of Super Computing 2008.

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," Submitted to Phys. Rev. C, arXiv 0806.4018

P. Maris, J.P. Vary and A. M. Shirokov, "Ab Initio no-core full configuration calculations of light nuclei," Submitted for publication to Phys. Rev. C., arXiv 0808.3420.

**PI Alfredo Caro**

B. Sadigh, P. Erhart, E. Martinez, L. Zepeda-Ruiz, and A. Caro, "Large-scale Monte-Carlo simulations of microstructural evolution in Fe-Cu alloys", to be submitted

B. Sadigh and P. Erhart, "The fluctuation-controlled semi grand-canonical Monte Carlo method for simulation of heterogeneous precipitation in alloys", to be submitted

N. Q. Vo, R.S. Averback, P. Bellon, S. Odunuga, A. Caro, Phys. Rev. B 77, 134108 (2008)

**PI Laura Carrington**

High-Frequency Simulations of Global Seismic Wave Propagation Using SPECFEM3D_GLOBE. L. Carrington, D.Komatitsch, M. Laurenzano, M. Tikir, D. Miche,N. Le Goff, A. Snavely, J. Tromp SC08 International Conference for High Performance Computing November 2008

**PI Paul Cassak**

K. Malakit, P. A. Cassak, M. A. Shay, and J. F. Drake, "The Hall effect in magnetic reconnction: Hybrid vs. Hall-less hybrid simulations," submitted to Geophysical Research Letters, September 2008.

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," submitted to Journal of Geophysical Research, August 2008.

P. A. Cassak and M. A. Shay, "The Scaling of Asymmetric Hall Reconnection," accepted to Geophys. Res. Lett., August 2008.

P. A. Cassak and M. A. Shay, "Scaling of Asymmetric Magnetic Reconnection: General Theory and Collisional Simulations," Phys. Plasmas, 14, 102114, 2007.

**PI Fausto Cattaneo**

"The influence of horizontal boundaries on ekman circulation and angular momentum transport in a cylindrical annulus" Aleksandr V Obabko, Fausto Cattaneo and Paul F Fischer, 2008, to appear in topical issue of Physica scripta (volume T131) (http://www.iop.org/EJ/journal/-page=forthart/1402-4896#Special_IsTMBW)

**PI Paola Cessi**

Cessi P., 2007. Regimes of thermocline scaling: The interaction of wind stress and surface buoyancy. J. Phys. Oceanogr., Vol. 37, 2009-2021.

Cessi P., 2008. An Energy-Constrained Parameterization of Eddy Buoyancy Flux, J. Phys. Oceanogr., Vol. 38, 1807-1819.

Wolfe, C.L. and P. Cessi, 2008. Overturning Circulation in an Eddy-Resolving Model: The Effect of the Pole-to-Pole Temperature Gradient. In press on J. Phys. Oceanogr., 47pp.

P. Cessi and C.L. Wolfe, 2008. Eddy-driven buoyancy gradients on eastern boundaries. Submitted to J. Phys. Oceanogr.

Wolfe, C.L., P. Cessi, J.L. McClean and M.E. Maltrud 2008. Vertical heat transport in eddying ocean models. Submitted to Geophys. Res. Lett.}, 17pp.

**PI Yuen-Dat Chan**

A Generic Surface Sampler for Monte Carlo Simulations J. A. Detwiler, R. Henning, R. A. Johnson, and M. G. Marino IEEE TRANSACTIONS ON NUCLEAR SCIENCE, VOL. ?, NO. ?, ? 2008

Validation of spallation neutron production and propagationwithin Geant4, M.G. Marino, J.A. Detwiler, R. Henning, R.A. Johnson, A.G. Schubert, and J.F. Wilkerson

**PI Choong-Seock Chang**

C.S. Chang, S. Ku, Spontaneous rotation sources in a quiescent tokamak edge plasma, Phys. Plasmas 15, 062510 (2008)

J. Cummings, A. Pankin, N. Podhorszki, G. Park, S. Ku, R. Barreto5, S. Klasky5, C. S. Chang, et al, Plasma Edge Kinetic-MHD Modeling in Tokamaks Using Kepler Workflow for Code Coupling, Data Management and Visualization, Commun. Comput. Phys.4, 675 (2008)

C S Chang, S Klasky, J Cummings, et al, Toward a first-principles integrated simulation of tokamak edge Plasmas, J. Phys: Conf. Series 125, 012042 (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)

Y. Chen, S.E. Parker, G. Rewoldt, S. Ku, G.Y. Park and C-S Chang, Coarse-graining the electron distribution in turbulence simulations of tokamak plasmas. Phys. Plasmas 15, 055905 (2008)

J. Lang, Y. Chen and S. Parker, Gyrokinetic delta-f particle simulation of trapped electron mode driven turbulence, Physics of Plasmas 14, 082315 (2007).

Y. Chen and S. Parker, Coarse-graining phase space in delta-f particle-in-cell simulations, Physics of Plasmas 14, 082301 (2007).

D. C. Barnes, J. Cheng, and S. E. Parker, Low-noise particle algorithms for extended magnetohydrodynamic closure, Phys. Plasmas 15, 055702 (2008)

Z. Lin, Y. Nishimura, Y. Xiao, I. Holod, W. L. Zhang, and L. Chen, "Global gyrokinetic particle simulations with kinetic electrons," Plasma Phys. Contr. Fusion 49, B163-B172 (2007).

Z. Lin, I. Holod, L. Chen, P. H. Diamond, T. S. Hahm, and S. Ethier, "Wave-particle decorrelation and transport of anisotropic turbulence in collisionless plasmas," Phys. Rev. Lett. 99, 265003 (2007).

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

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

**PI James Chelikowsky**

M.M.G. Alemany, M. Jain, M. L. Tiago, Y. Zhou, Y. Saad and J.R. Chelikowsky: "Efficient first principles calculations of the electronic structure of periodic systems," Comp. Phys. Commun. 177, 339 (2007).

A. Sitt, L. Kronik, S. Ismail-Beigi and J.R. Chelikowsky: "Excited state forces within time-dependent density functional theory: A real-space, frequency domain approach," Phys. Rev. A 76, 054501 (2007).

H. Kwak, M. L. Tiago and J. R. Chelikowsky: "Quantum Confinement and Strong Coulombic Correlation in ZnO Nanocrystals," Solid State Commun. 145, 227 (2008).

L. Kong, J.R. Chelikowsky, J.B. Neaton, and S.G. Louie: "Real-space pseudopotential calculations of spin-dependent electron transport in quantum point contacts," Phys. Rev. B 76, 235422 (2007).

D. Naveh, L. Kronik, M.L. Tiago and J.R. Chelikowsky: "Real-Space Pseudopotential method for Spin-Orbit Coupling within Density Functional Theory," Phys. Rev. B 76, 153407 (2007).

M. M. G. Alemany, R. C. Longo, L. J. Gallego, D. J. Gonzalez, L. E. Gonzalez, M. L. Tiago and J.R. Chelikowsky: "Ab initio molecular dynamics simulations of the static, dynamic and electronic properties of liquid lead. A study based on a real-space implementation of density-functional theory," Phys. Rev. B 76, 214203 (2007).

T.-L. Chan, M. L. Tiago, E. Kaxiras and J.R. Chelikowsky, "Size Limits on Doping Phosphorus into Silicon Nanocrystals," Nano Letters 8, 596 (2008).

M. Lopez del Puerto, M.L. Tiago, and J.R. Chelikowsky: "Ab initio methods for the optical properties of CdSe clusters," Phys. Rev. B 77, 045404 (2008).

L. Kong and J.R. Chelikowsky: "Transport properties of transition-metal-encapsulated Si cages," Phys. Rev. B 77, 073401 (2008).

A.T. Zayak, S. Beckman, M. Tiago, P. Entel, and J.R. Chelikowsky: "Switchable Heusler Clusters," J. Appl. Phys. (in press).

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).

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 20, 337-340 (2008).

J. Han, M. L. Tiago, T.-L. Chan, and J. R. Chelikowsky: "Real-space method for the electronic structure of one dimensional periodic systems," J. Chem. Phys. (in press).

H. Kwak, M. L. Tiago, T.-L. Chan, James R. Chelikowsky: "The Role of Quantum Confinement in Li Doped ZnO Nanocrystals," Phys. Rev. B (in press).

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. (submitted).

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 (submitted).

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).

T.-L. Chan, A. T. Zayak, G. M. Dalpian, and J. R. Chelikowsky: ``Size effects on diffusion barriers in semiconductor nanocrystals,'' Phys. Rev. Lett.

M.M.G. Alemany, X. Huang, M.L. Tiago, and J.R. Chelikowsky: "p-type Doping in Indium Phosphide Nanowires: the Role of Dimensionality and Quantum Confinement in the Acceptor Impurity States," Nano Lett. 7, 1878 (2007).2. J.R. Chelikowsky, M.L. Tiago, Y. Saad, and Y. Zhou: "Algorithms for the Evolution of Electronic Properties in Nanocrystals," Comp. Phys. Comm. 177, 1 (2007).

M. Lopez del Puerto, M.L. Tiago and J.R. Chelikowsky: "Ab initio calculation of temperature effects in the optical response of open-shell sodium clusters," J. Chem. Phys. 27, 144311 (2007).

G. Rollmann, M.E. Gruner, A. Hucht, P. Entel, M.L. Tiago and J.R. Chelikowsky: "Shell-wise Mackay transform ation in iron nano-clusters," Phys. Rev. Lett. 99, 083402 (2007).

**PI Jacqueline Chen**

F. Bisetti, J. Y. Chen, E. R. Hawkes, and J. H. Chen, "Probability Density Function Treatment of Turbulence-Chemistry Interactions during the Ignition of a Temperature-Stratified Mixture for Application to HCCI Engine Modeling,"accepted Combust. Flame (2008).

E. R. Hawkes, R. Sankaran, J. H. Chen, S. Kaiser, and J. H. Frank, "An Analysis of Lower-Dimensional Approximations to the Scalar Dissipation Rate using DNS of Plane Jet Flames," accepted Proceedings of the Combustion Institute, 32 (2008).

F. Bisetti, J. Y. Chen, E. R. Hawkes, and J. H. Chen, "Differential Diffusion Effects During the Ignition of a Thermally Stratified Premixed Hydrogen-Air Mixture Subject to Turbulence," accepted Proceedings of the Combustion Institute, 32 (2008).

N. Chakraborty, E. R. Hawkes, J. H. Chen, and S. Cant, "The Effects of Strain Rate and Curvature on Surface Density Function Transport in Turbulent Premixed Methane-Air and Hydrogen-Air Flames: A Comparative Study," Combust. Flame, 154:259-280 (2008).

D. J. Cook, H. Pitsch, J. H. Chen, and E. R. Hawkes, "Flamelet-Based Modeling of Autoignition with Thermal Inhomogeneities for Application to HCCI Engines," Proceedings of the Combustion Institute, 31: 2903-2911 (2007).

E. Hawkes, R. Sankaran, J. Sutherland, and J. H. Chen, "Scalar Mixing in DNS of Temporally-Evolving Plane Jet Flames with Detailed CO/H2 Kinetics," Proc. of the Combustion Institute, 31:1633-1640 (2007).

J. C. Sutherland, P. J. Smith, and J. H. Chen, "A quantitative method for apriori evaluation of combustion reaction models," Combust. Theory and Modelling, 11, 287-303, (2007).

**PI Liu Chen**

"The Formation of Coronal Loops by Thermal Instability in Three Dimensions", Y. Mok, Z. Mikic, R. Lionello and J.A. Linker, Astrophysical Journal Lett. 679, L161,2008.

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

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).

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).

Theory of charged particle heating by low-frequency Alfven waves, Z. H. Guo, C. Crabtree, L. Chen, Phys. Plasmas 15, 032311 (2008).

Radial structures and nonlinear excitation of geodesic acoustic modes, F. Zonca and L. Chen, EPL 83, 35001 (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).

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

**PI Yang Chen**

Role of zonal flows in TEM turbulence through nonlinear gyrokinetic particle and continuum simulation, D.R. Ernst, J. Lang, W. Nevins, M. Hoffman, Y. Chen, W. Dorland and S. Parker, submitted to 22nd IAEA Fusion Energy Conference, Geneva, Switzerland, 13-18 October 2008

Toward a first principle integrated simulation of tokamak edge plasmas, C. S. Chang, S. Klasky, J. Cummings et al, J. Phys: Conf. Series 125 012042 (2008).

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

Coarse-graining the electron distribution in turbulence simulations of tokamak plasmas. Y. Chen, S.E. Parker, G. Rewoldt, S. Ku, G.Y. Park and C-S Chang, Phys. Plasmas 15, 055905 (2008)

Gyrokinetic delta-f particle simulation of trapped electron mode driven turbulence, J. Lang, Y. Chen and S. Parker, Physics of Plasmas 14, 082315 (2007).

Coarse-graining phase space in delta-f particle-in-cell simulations, Y. Chen and S. Parker, Physics of Plasmas 14, 082301 (2007).

Low-noise particle algorithms for extended magnetohydrodynamic closure D. C. Barnes, J. Cheng, and S. E. Parker Phys. Plasmas 15, 055702 (2008)

**PI Hai-Ping Cheng**

Proximity of antiferromagnetism and superconductivity in LaFeAsO1-xFx: Effective Hamiltonian from ab initio studies, Chao Cao, P.J. Hirschfeld, and Hai-Ping Cheng, Phys. Rev. B77 Rapid Comm, 220506 (2008).

Determining gap nodal structures in Fe-based superconductors: Theory of the angle dependence of the low-temperature specific heat in an applied magnetic field, S. Graser, G.R. Boyd, Chao Cao, Hai- Ping Cheng, et al. Phys.Rev.B77, Rapid Comm, 180514 (2008).

Structure of Bi2Sr2CaCu2O8+x supermodulation from ab initio calculations, Y. He, S. Graser, P. J. Hirschfeld and H.-P. Cheng, Phys. Rev. B77, Rapid Comm. 220507 (2008).

Predictive first-principles simulations of strain-induced phenomena at water-silica nanotube interfaces, Yao He, Chao Cao, S.B. Trickey, and Hai-Ping Cheng, J. Chem. Phys. 129, 011101 (2008).

Strongly correlated electrons in the {Ni(hmp)(ROH)X}(4) single molecule magnet: A DFT+U study, C. Chao, S. Hills, and H.-P. Cheng, Phys. Rev. Lett. 100, 167206 (2008).

First-principles simulations of dissociated and molecular H-2 adsorption on Pd-4-cluster- functionalized carbon nanotubes, C. Chao, Y. He, and H.-P. Cheng, Phy. Rev. B77, 045412 (2008). accpeted

First-Principles Determination of the Effects of Intermolecular Interactions on the Electronic Transport through Molecular Monolayers, L. Agapito, C. Cao, and H-P. Cheng, (PRB, in press).

Dynamics of Ag clusters on complex surfaces: Molecular dynamics simulations, S. Alkis, J.L. Krause, J.N. Fry, H.-P. Cheng (PRB) submitted

Finding stable alpha-quartz (0001) surface structures via simulation, YW Chen, Chao Cao and Hai- Ping Cheng (to APL).

Fen-doped C60 Monolayer on h-BN/Ni (111), Lan Li and Hai-Ping Cheng (to PRB).

Non-equilibrium Green's function study of Pd4-cluster-functionalized carbon nanotubes as hydrogen sensors, Chao Cao, Alexander Kemper, Jian-Wei Zhang, Yao He, Andrew Rinzler, Hai-Ping

Cheng, X.-G. Zhang, Alexandre Reily Rocha and Stefano Sanvito, (Phys. Rev. B). Curvature effect on the interaction between folded graphitic surface and silver clusters

A. F. Kemper, H-P. Cheng, N. K??ba??li, S. Benrezzak, M. Schmidt, A. Masson, C. Br??chignac (PRB) Insensitivity of superconductivity to disorder in the cuprates

A.F. Kemper, D.G.S.P. Doluweera, T.A. Maier, M. Jarrell, P.J. Hirschfeld, H-P. Cheng (PRL)

Controlling Au atom penetration through alkanethiol self-assembled monolayers (SAM)s on the Au(111) surface, Sabri Alkis, Chao Cao, Hai-Ping Cheng and Jeffrey L. Krause (JPC C).

**PI Wai-Yim Ching**

R. F. Rajter, W.Y. Ching, R. H. French, W. C. Carter, and Y.M. Chiang, "van der Waals-London dispersion interactions of optically uniaxial metallic and semiconducting carbon nanotubes determined from ab initio optical properties", J. Appl. Phys., 101, 54303-1-5 (2007).

A. Misra, L. Ouyang, J. Chen and W.Y. Ching, "Ab initio calculations of strain field and failure pattern in silicon nitride intergranular glassy films", Philosophical Magazine A. 87(25), 3839-3852 (2007).

Hongzhi Yao, L. Ouyang and W.Y. Ching, "Ab initio Calculation of the elastic constants of ceramic crystals", J. Am. Ceram. Soc. 90 [10] 3194-3204 (2007) .

R. F. Rajter, R. Podgornik, A. Parsegian, R.H. French, and W.Y. Ching, "van der Waals-London dispersion interactions for optically anisotropic cylinders: Metallic and semiconducting single wall carbon nanotubes", Phys. Rev. B76, 045417-1-16 (2007).

T. Mizoguchi, A. Seko, M. Yoshiya, H. Yoshida, W.Y. Ching and I.Tanaka, "X-ray absorption near-edge structure of disordered Mg1-xZnxO solid solutions First-principles", Phys. Rev. B76, 195125-1-7 (2007).

P. Rulis, Hongzhi Yao, L. Ouyang, and W.Y. Ching. Electronic structure, bonding, charge distribution and X-ray absorption spectra of the (001) surfaces of fluorapatite and hydroxyapatite. Phys. Rev. B76, 245410-1-15,(2007).

Sitaram Aryal, Paul Rulis and W. Y. Ching. Density functional calculation of the electronic structure and optical properties of Aluminosilicate polymorphs (Al2SiO5). American Mineralogist, 93, 114-123 (2008).

W.Y. Ching, and P. Rulis. Ab initio calculation of the O-K, N-K, Si-K, Si-L3, Y-K, Y-L3 edges in the Y-Si-O-N system: A new strategy for ELNES/XANES spectral modeling in complex materials. Phys. Rev. B. 77, 35125-1-17 (2008).

W.Y. Ching, and P. Rulis. Large differences in the electronic and spectroscopic properties of the three phases of AlPO4. Phys. Rev. B77, 125116-1-7 (2008).

S.K. Arora, H. C. Wu, R.J. Choudhary, I.V. Shvets, O.N. Mryasov, H. Yao, and W.Y. Ching. Giant magnetic moment in epitaxial magnetite thin films grown by molecular beam epitaxy. Phys. Rev. B77, 134443-1-5 (2008).

W.Y. Ching, L. Ouyang, Paul Rulis, and Hongzhi Yao. Ab initio study of the physical properties of alpha-Al2O3: lattice dynamics, bulk properties, electronic structures and bonding, optical properties and ELNES/XANES spectra, Phys. Rev. B 78, 014106-1-13 (2008).

R. F. Rajter, R.H. French, R. Podgornik, W.Y. Ching, A.Parsegian. Mixing of optical properties for the determination of accurate far-limit effective vdW-Ld spectra and total vdW-Ld interaction energies, J. Appl. Phys. 104, 053513 (2008).

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, DOE LRI Workshop Report, submitted to Review of Modern Physics.

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. (accepted, 2009)

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, submitted to Phys. Rev. B.

W.Y. Ching and Paul. Rulis, XANES/ELNES calculation using the supercell OLCAO method, (Review article) submitted for J. Phys. Condensed Matter.

**PI Mei-Yin Chou**

"First-Principles Study of Cation and Hydrogen Arrangements in the Li-Mg-N-H Hydrogen Storage System," Y. Wang and M. Y. Chou, Phys. Rev. B 76, 014116/1-6 (2007).

"Electronic and Vibrational Properties of gamma-AlH3," Y. Wang and M. Y. Chou, Phys. Rev. B 77, 014101/1-8 (2008).

"Low-Energy Ordered Structures of Li2Mg(NH)2," Z. Ma and M. Y. Chou, J. Appl. Phys., in press.

"First-Principles Investigation of Sodium and Lithium Alloyed Alanates," Z. Ma and M. Y. Chou, J. Appl. Phys., submitted.

"Size and Orientation Dependence in the Electronic Properties of Silicon Nanowires," J.-A. Yan, L. Yang, and M. Y. Chou, Phys. Rev. B 76, 115319/1-6 (2007).

"Variational Calculation of the Depolarization of the Maximum Density Droplet in Two-Dimensional Quantum Dots," W. Geist and M. Y. Chou, Phys. Rev. B 76, 235306/1-7 (2007).

"Phonon Dispersions and Vibrational Properties of Monolayer, Bilayer, and Trilayer Graphene," J. A. Yan, W. Y. Ruan, and M. Y. Chou, Phys. Rev. B 77, 125401/1-7 (2008).

"Quantum Confinement Effect in Si/Ge Core-Shell Nanowires," L. Yang, R. N. Musin, X.-Q. Wang, and M. Y. Chou, Phys. Rev. B 77, 195325/1-5 (2008).

"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. of Phys. Chem., in press.

**PI Daryl Chrzan**

Elif Ertekin, Murray S. Daw, and D.C. Chrzan, "Topological description of the Stone-Wales defect formation energy in carbon nanotubes and graphene," submitted to Physical Review B.

**PI Catherine Chuang**

Kelly, J.T., C.C. Chuang, and A.S. Wexler, 2007: Influence of dust composition on cloud droplet formation. Atmos. Environment, 41: 2904-2916 doi:10.1016/j.atmosenv.2006.12.008.

**PI Bruce Cohen**

E. B. Hooper, B. I. Cohen, D. N. Hill, L. L. LoDestro, H. S. McLean, C. A. Romero-Talamas, R. D. Wood, and C. R. Sovinec, "Magnetic Reconnection in the Spheromak: Physics and Consequences," J. Fusion Energy 26, 71 (2007).

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)

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

B. Hudson R.D. Wood, H.S. McLean, E.B. Hooper, D.N. Hill, J. Jayakumar, J. Moller, C. Romero-Talamas, T.A. Casper, J.A. Johnson III, L.L. LoDestro, E. Mezonlin, L.D. Pearlstein, "Energy confinement and magnetic field generation in the SSPX spheromak," Phys. Plasmas 15, 056112 (2008)

J.L. Terry, S.J. Zweben, M.V. Umansky et al, "Spatial structure of scrape-off-layer filaments near the midplane and X-point regions of Alcator C-Mod" submitted to J. Nucl. Mater. (2008)

M.V.Umansky, R.H.Cohen, L.L.LoDestro, and X.Q.Xu "Suite of Verification Test Problems for Edge Turbulence Simulations" Contributions to Plasma Physics 48 (1-3) 27-31 (2008)

X Q Xu et. al. Commun. Comput. Phys. 4(5) (2008), 949-979

A.M. Dimits, W.M. Nevins, D.E. Shumaker, G.W. Hammett, T. Dannert, F. Jenko, M.J. Pueschel, W. Dorland, S.C. Cowley, J.N. Leboeuf, T.L. Rhodes, J. Candy and C. Estrada-Mila, "Gyrokinetic simulations of ETG and ITG turbulence," 2007 Nucl. Fusion 47, 817-824, DOI 10.1088/0029-5515/47/8/012.

P.B. Snyder, K.H. Burrell, H.R. Wilson, M.S. Chu, M.E. Fenstermacher, A.W. Leonard, R.A. Moyer, T.H. Osborne, M. Umansky, W.P. West, X.Q. Xu, "Stability and dynamics of the edge pedestal in the low collisionality regime: physics mechanisms for steady-state ELM-free operation," Nuclear Fusion 47, 8, 961-968

W. M. Nevins, S. E. Parker, Y. Chen, J. Candy, A. Dimits, W. Dorland, G. W. Hammett, and F. Jenko, "Verification of gyrokinetic delta-f simulations of electron temperature gradient turbulence," Phys. Plasmas 14, 084501 (2007).

[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", submitted to Phys. Plasmas

[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, R. E. Waltz,2 J. Candy, G. R. McKee, M. W. Shafer, A. E. White, L. Schmitz, G. R. Tynan, "Validation of gyrokinetic transport simulations using DIIID core turbulence measurements", submitted to Phys Plasmas

J. Candy, R.E. Waltz, M.R. Fahey and C. Holland, The effect of ion-scale dynamics on electron-temperature-gradient turbulence, Plasma Phys. Control. Fusion 49 (2007) 1209

J. Candy, R.E. Waltz, M.R. Fahey and C. Holland, Plasma microturbulence simulation of instabilities at highly disparate scales, J. Phys.: Conf. Ser. 78 (2007) 012008

R.E. Waltz, J. Candy, and M.R. Fahey, Coupled ion temperature gradient and trapped electron mode to electron temperature gradient mode gyrokinetic simulations, Phys. Plasmas 14 (2007) 056116

Howes GG, Dorland W, Cowley SC, Hammett GW, Quataert E, Schekochihin AA, Tatsuno T. Kinetic simulations of magnetized turbulence in astrophysical plasmas. Phys Rev Lett. 2008 Feb 15;100(6):065004 (2008)

Yong Xiao, Peter J. Catto, William Dorland Effects of finite poloidal gyroradius, shaping, and collisions on the zonal flow residual Phys. Plasmas 14, 055910 (2007)

B. N. Rogers and S. Kobayashi, P. Ricci, W. Dorland, J. Drake, and T. Tatsuno Gyrokinetic simulations of collisionless magnetic reconnection Phys. Plasmas 14, 092110 (2007)

D J Applegate, C M Roach, J W Connor, S C Cowley, W Dorland, R J Hastie and N Joiner Micro-tearing modes in the mega ampere spherical tokamak Plasma Phys. Control. Fusion 49 1113-1128 (2007)

**PI Marvin Cohen**

B. D. Malone, J. D. Sau, and M. L. Cohen, "Ab initio survey of the electronic structure of tetrahedrally bonded phases of silicon," Phys. Rev. B, 78, 035210 (2008).

B. D. Malone, J. D. Sau, and M. L. Cohen, "Ab initio study of the optical properties of Si-XII," submitted to Phys. Rev. B.

K.T. Chan, J.B. Neaton, and M.L. Cohen, "First-principles study of metal adatom adsorption on graphene," Phys. Rev. B 77, 235430 (2008).

C.-H. Park, L. Yang, Y.-W. Son, M.L. Cohen, and S.G. Louie, "Anisotropic behaviours of massless Dirac fermions in graphene under periodic potentials," Nature Physics 4, 213 (2008).

C-H. Park, Y.-W. Son, L. Yang, M.L. Cohen, and S. G. Louie, "Electron Beam Supercollimation in Graphene Superlattices," Nano Lett. 8, 2920 (2008).

C.-H. Park, L. Yang, Y.-W. Son, M.L. Cohen, and S.G. Louie, "New Generation of Massless Dirac Fermions in Graphene under External Periodic Potentials," Phys. Rev. Lett. 101, 126804 (2008) .

L. Yang, C.-H. Park, Y.-W. Son, M.L. Cohen, and S.G. Louie, "Quasiparticle energies and band gaps of graphene nanoribbons," Phys. Rev. Lett. 99, 186801 (2007).

Li Yang, Marvin L. Cohen, and Steven G. Louie, "Magnetic Edge-state Excitons in Zigzag Graphene Nanoribbons", submitted to Phys. Rev. Lett.

J. Noffsinger, F. Giustino, S. G. Louie, and M. L. Cohen, "Origin of superconductivity in boron-doped silicon carbide", submitted to Phys. Rev. Lett.

J. Noffsinger, F. Giustino, S. G. Louie, and M. L. Cohen, "First-principles study of superconductivity and Fermi-surface nesting in ultrahard transition metal carbides", Phys. Rev. B 77, 180507(R) (2008) .

F. Giustino, M.L. Cohen, and S.G. Louie, "Electron-phonon interaction using Wannier functions," Phys. Rev. B 76, 165108 (2007).

H.J. Choi, M.L. Cohen, and S.G. Louie, "First-principles scattering-state approach for nonlinear electrical transport in nanostructures," Phys. Rev. B 76, 155420 (2007).

Y.-W. Son, M.L. Cohen, and S.G. Louie, "Electric field effects on spin transport in defective metallic carbon nanotubes," Nano Letters 7, 3518 (2007).

P. Zhang, S. Saito, S.G. Louie, and M.L. Cohen, "Theory of the electronic structure of alternating MgB2 and graphene layered structures," Phys. Rev. B 77, 052501 (2008).

Y.M. Byun, H.J. Choi, S.G. Louie, and M.L. Cohen, "Low-energy structures of K atoms in expanded K3C60 monolayers: Ab initio pseudopotential density-functional calculations," Phys. Rev. B 77, 115418 (2008).

C.-H. Park, F. Giustino, J.L. McChesney, A. Bostwick, T. Ohta, E. Rotenberg, M.L. Cohen, and S.G. Louie, "Van Hove singularity and apparent anisotropy in the electron-phonon interaction in graphene," Phys. Rev. B 77, 113410 (2008).

F. Giustino, M.L. Cohen, and S.G. Louie, "Small phonon contribution to the photoemission kink in the copper oxide superconductors," Nature 452, 975 (2008).

E. Kioupakis, P. Zhang, M.L. Cohen, and S.G. Louie, "GW quasiparticle corrections to the LDA+U/GGA+U electronic structure of bcc hydrogen," Phys. Rev. B 77, 155114 (2008).

J.D. Sau, J.B. Neaton, H.J. Choi, S.G. Louie, and M.L. Cohen, "Electronic energy levels of weakly coupled nanostructures: C-60-metal interfaces," Phys. Rev. Lett. 101, 026804 (2008).

**PI Michael Colvin**

V.V. Krishnan, E.Y. Lau, J. Yamada, D.P. Denning, S.S. Patel, M.E. Colvin and M.F. Rexach (2008) Intra-molecular Cohesion of Coils Mediated by Phenylalanine-Glycine Motifs in the Natively Unfolded Domain of a Nucleoporin PLOS Computational Biology 4: e1000145. (doi:10.1371/journal.pcbi.1000145).

J. Phillips, M. Colvin, E.Y. Lau, and S. Newsam (2008) "Analyzing Dynamical Simulations of Intrinsically Disordered Proteins Using Spectral Clustering" (accepted for publication in the IEEE-published proceedings of the 2008 Computational Structural Bioinformatics Workshop at the IEEE International Conference on Bioinformatics and Biomedicine, Philadelphia, PA, November, 2008.)

**PI Gil Compo**

Whitaker, J.S., G.P.Compo, and J.-N. Thepaut, 2008: A comparison of variational and ensemble-based data assimilation systems for reanalysis. Mon. Wea. Rev., submitted.

**PI Jennifer Comstock**

"IceFormation in Arctic Mixed-Phase Clouds - Insights from a 3-D Cloud-Resolving Model with Size- Resolved Aerosol and Cloud Microphysics" by Fan, Ovtchinnikov, Comstock, McFarlane, and Khain. Submitted to Journal of Geophysical Research - Atmospheres. This paper is currently under revision.

**PI Peter Cummings**

Qing Pu, Yongsheng Leng, Xiongce Zhao, and Peter T. Cummings, "Molecular simulations of stretching gold nanowires in solvents," Nanotechnology 18, 424007 (2007).

Yongsheng Leng, "Hydration force and dynamic squeeze-out of hydration water under subnanometer confinement," Journal of Physics: Condensed Matter, 20, 354017 (2008).

Xiongce Zhao, Christina M. Payne, Peter T. Cummings, and James W. Lee, "Single-strand DNA molecule translocation through nanoelectrode gaps," Nanotechnology 18 (2007) Art. No. 424018.

Xiongce Zhao, Tauna R. Rignall, Clare McCabe, William S. Adney, and Michael E. Himmel, "Molecular Simulation Evidence for Processive Motion of Trichoderma reesei Cel7A I during Cellulose Depolymerization," Chemical Physics Letters, 460 284-288 (2008).

Peter J. Dyer, Hugh Docherty, Peter T. Cummings , "The importance of polarizability in the modeling of solubility: Quantifying the effect of solute polarizability on the solubility of small nonpolar solutes in popular models of water," Journal of Chemical Physics 129, 024508 (2008). Also

Molecular dynamics simulations of stretched gold nanowires: The relative utility of different semi-empirical potentials, Pu, Q., Leng, Y. S., Tsetseris, L., Park, H. S., Pantelides, S. T. and Cummings, P. T., J. Chem. Phys. 126 (2007) Art. No. 144707.

Evidence of Coulomb blockade behavior in a finite, zero-dimensional quantum well, Vincent Meunier, M.H. Pan, F. Moreau, K.T. Park, and E.W. Plummer, Proc. Nat. Ac. Science, under consideration (2008)

First-principles study of quantum transport of multiterminal junctions, Kamal K. Saha, Wenchang Lu, Jerry Bernholc, and Vincent Meunier, submitted to Physical Review B (2008)

Covalent Metal-Nanotube Heterojunctions as Ultimate Nano-Contacts, J. A. Rodr??guez-Manzo, F. Banhart, M. Terrones, H. Terrones, N. Grobert, P.M. Ajayan, B.G. Sumpter, V. Meunier, submitted to Nature Materials (2008)

Enhancement of the transverse conductance in DNA nucleotides, Vincent Meunier and Predrag S. Krstic, J. Chem. Phys., 128, 041103 (2008)

Electronic flexoelectricity in low dimensional systems, S. Kalinin and V. Meunier, Physical Review B. 77, 033403 (2008)

New insight into carbon nanotube electronic structure selectivity, B.G. Sumpter, De-en Jiang, and Vincent Meunier, Small, in press (2008)

Hetero-doped Nanotubes: Theory, Synthesis and Characterization of Phosphorus-Nitrogen Doped Multiwalled Carbon Nanotubes, Cruz-Silva, Eduardo; Cullen, David; Gu, Lin; Romo-Herrera, Jose; Munoz-Sandoval, E; Lopez-Urias, Florentino; Sumpter, Bobby; Meunier, Vincent ; Charlier, Jean-Christophe; Smith, David; Terrones, Humberto; Terrones, Mauricio, ACS Nano, 2, 441 (2008)

An Atomistic Branching Mechanism for Carbon Nanotubes: Sulfur as triggering agent, J.M. Romo-Herrera, B.G. Sumpter, D.A. Cullen, H. Terrones , E. Cruz, D.J. Smith, V. Meunier, and M. Terrones, Angewandte Chemie, 47, 2948 (2008)

Electron transport in open systems from finite-size calculations: Examination of the principal layer method applied to linear gold chains, Ariana Beste, Vincent Meunier, and Robert J. Harrison, J. Chem. Phys., 128, 154713 (2008)

Quantum Length Dependence of the Electrical Rectification in Betaine Derivatives, Aldilene Saraiva-Souza, Antonio G. Souza Filho, Bobby G. Sumpter, Vincent Meunier, and Jordan Del Nero, J. Phys. Chem. C, 112, 12008 (2008)

Structure and properties of one-dimensional molybdenum nanowires in a confined environment, V. Meunier, H. Terrones, M. Terrones, B. Sumpter, submitted to Physical Review Letters (2008).

Effect of phase breaking events on electron transport in mesoscopic and nano devices, T. Jayasekera, P. Pillahamarri, J.W. Mintmire, and V. Meunier, Int. J. Quant. Chem., in press (2008).

Electron transport properties of ordered networks using carbon nanotubes, Jose Romo-Herrera, H. Terrones, M. Terrones, and V. Meunier, Nanotechnology, 19, 315704 (2008)

The Role of Sulfur in the Synthesis of Novel Carbon Morphologies: From Covalent Y-junctions to Sea Urchinlike Structures. J.M. Romo-Herrera, D. Cullen, E. Cruz-Silva, B.G. Sumpter, V. Meunier, H. Terrones, D. Smith, and M. Terrones, submitted to Functional Advanced Material (2008)

Guiding electronic current through Organic Nanocircuits: Defects engineering in ON-CNTs, J.M. Romo-Herrera, M. Terrones, H. Terrones and Vincent Meunier, submitted to ACS Nano (2008)

Massless Fermions in multilayer graphitic systems with misoriented layers, S. Latil, V. Meunier, and L. Henrard, Phys. Rev. B 76, 201402(R) (2007)

Nitrogen-mediated carbon nanotube growth: Diameter reduction, metallicity, bundle dispersability, and bamboo-like structure formation, B.G. Sumpter, V. Meunier, J.M. Romo-Herrera, E. Cruz-Silva , D.A. Cullen, H. Terrones, D. J. Smith, M. Terrones, ACS Nano 1, 369 (2007)

A New Class of Supramolecular Wires, B. Sumpter, Vincent Meunier, E. Valeev, A. Lampkins, Li Hengfeng, and R. Castellano, J. Phys. Chem. C. 111, 18912 (2007)

Nonvolatile Memory Element Based on Carbon Nanotubes Intercalated with Organic Molecules, V. Meunier, S. K. Kalinin, B.G. Sumpter, Phys. Rev. Lett., 98, 056401 (2007)

Tuning the Conductance of Carbon Nanotube with Encapsulated Molecules, Vincent Meunier and Bobby G Sumpter, Nanotechnology 18, 424032 (2007)

Covalent 2D and 3D Networks from 1D Nanostructures: Designing New Materials, Jose Romo-Herrera, Mauricio Terrones, Humberto Terrones, Sefa Dag, and Vincent Meunier, Nano Letters, 7(3), 570 - 576 (2007)

Tuning the Electronic Properties of Coaxial Nanoscale Cables through Chemical Doping, A. G. Souza Filho, Vincent Meunier, T. Terrones, Bobby G. Sumpter, E. B. Barros, F. Villalpando, Y. A. Kim, H. Muramatsu, T. Hayashi, M. Endo, and M. S. Dresselhaus, Nanoletters, 7 (8), 2383 -2388 (2007)

Conductivity Properties of Benzo-homologated DNA Bases, Miguel Fuentes-Cabrera, Vincent Meunier, and Bobby G. Sumpter, Nanotechnology 18, 424019 (2007)

Scanning tunneling microscopy fingerprints of point defects in graphene: A theoretical prediction, H. Amara, S. Latil, V. Meunier, Ph. Lambin, and J.-C. Charlier, Phys. Rev. B 76, 115423 (2007) selected for publication in the Virtual Journal of Biological Physics Research.

Christina M. Payne, Xiongce Zhao, Lukas Vlcek, and Peter T. Cummings, "Molecular Dynamics Simulation of ss-DNA Translocation between Copper Nanoelectrodes Incorporating Electrode Charge Dynamics," Journal Physical Chemistry B, 112 (6), 1712 -1717 (2008)

Xiongce Zhao, Christina M. Payne, and Peter T. Cummings, "Controlled Translocation of DNA Segments through Nanoelectrode Gaps from Molecular Dynamics," Journal Physical Chemistry C, 112 (1), 8 -12 (2008)

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, in press (2008).

Qing Pu, Yongsheng Leng, and Peter T. Cummings, "The rate-dependent energy release mechanism of gold nanowires under elongation," Journal of the American Chemical Society, submitted (2008).

Kevin R. Hadley and Clare McCabe, "Coarse-Grained Model of Amorphous and Crystalline Free Fatty Acids," Journal of Chemical Physics, submitted (2008).

Mamontov, E., Wesolowski, D. J., Vlcek, L., Cummings, P. T., Rosenqvist, J., Wang, W., Cole, D. R., "Dynamics of hydration water on rutile studied by backscattering neutron spectroscopy and molecular dynamics simulation," Journal of Physical Chemistry C 112 (2008) 12334-12341.

Vlcek, L., Cummings, P. T., "Adsorption of water on TiO2 and SnO2 surfaces: Molecular dynamics study," Collection of Czechoslovak Chemical Communications, 73 (2008) 575-589.

**PI Larry Curtiss**

S. Adiga, P. Zapol, and L. Curtiss, "Structure and Morphology of Hydroxylated Alumina Surfaces" J. Phys. Chem. C 111 7422 (2007). S. Vajda, M. J. Pellin, J. P. Greeley, C. L. Marshall, L. A. Curtiss, G. A. Ballantine, J. W. Elam, S. Murcherie, P. Redfern, and P. Zapol, "Subnanometer Platinum Clusters: Highly Active and Selective Catalysts for Oxidative Dehydrogenation", Nature Materials, submitted.

## D

**PI Valerie Daggett**

Benson N. and Daggett V. Dynameomics: Large-Scale Assessment of Native Protein Flexibility. Protein Science In Press, 2008. http://dx.doi.org/10.1110/ps.037473.108

Beck D.A.C., Jonsson A.L., Schaeffer R.D., Scott K.A., Day R., Toofanny R.D., Alonso D.O.V., and Daggett V. Dynameomics: mass annotation of protein dynamics and unfolding in water by high-throughput atomistic molecular dynamics simulations. Protein Engineering Design & Selection 21: 353-368, 2008. http://dx.doi.org/10.1093/protein/gzn011

Simms A.M., Toofanny R.D., Kehl C., Benson N.C., and Daggett V. Dynameomics: design of a computational lab workflow and scientific data repository for protein simulations. Protein Engineering Design & Selection 21: 369-377, 2008.http://dx.doi.org/10.1093/protein/gzn012

Kehl C., Simms A.M., Toofanny R.D., and Daggett V. Dynameomics: a multi-dimensional analysis-optimized database for dynamic protein data. Protein Engineering Design & Selection 21: 379-386, 2008. http://dx.doi.org/10.1093/protein/gzn015

Anderson P.C. and Daggett V. Molecular Basis for the Structural Instability of Human DJ-1 Induced by the L166P Mutation Associated with Parkinson's Disease. Biochemistry 47:9380-9393, 2008. http://dx.doi.org/10.1021/bi800677k

Beck D.A.C., Alonso D.O.V., Inoyama D., and Daggett V. The intrinsic conformational propensities of the 20 naturally occurring amino acids and reflection of these propensities in proteins. Proceedings of the National Academy of Sciences USA 105: 12259-12264, 2008. http://dx.doi.org/10.1073/pnas.0706527105

**PI Ronald Davidson**

E. V. Belova, 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, Nucl. Fusion 48, 032001 (2008).

S. P. Gerhardt, E. V. Belova, M. Yamada, H. Ji, M. Inomoto et al., Inductive sustainment of a field-reversed configuration stabilized by shaping, magnetic diffusion, and finite-Larmor radius effects, Phys. Rev. Lett. 99, 245003 (2007).

H. Ji, E. Belova, S. P. Gerhardt, and M. Yamada, Recent advances in the SPIRIT (Self-organized Plasma with Induction, Reconnection, and Injection Techniques) concept, J. Fusion Energy 26, 93 (2007).

Cothran, C. D., J. Fung, M. R. Brown, M.J. Schaffer, E. Belova, Spectroscopic flow and ion temperature studies of a large-s FRC, J. Fusion Energy 26, 37 (2007).

Brown, M. R., C. D. Cothran, J. Fung, M. J. Schaffer, E. Belova, Novel dipole trapped spheromak configuration, J. Fusion Energy 26, 37 (2007).

Yamada, M., H. Ji, S. P. Gerhardt, E. V. Belova, R. C. Davidson, and D. Mikkelsen, A Self-organized Plasma with Induction, Reconnection, and Injection Techniques: the SPIRIT concept for Field-Reversed Configuration Research, Plasma and Fusion Research 2, 004 (2007).

Streaming Instabilities of Intense Charged Particle Beams Propagating along a Solenoidal Magnetic Field in Background Plasma, E. A. Startsev, R. C. Davidson and M. Dorf, Physics of Plasmas 15, 062107 (2008).

Weight Growth Due to Resonant Simulation Particles and a Modified Delta-f Algorihm with Smooth Switch Between Delta-f and Total-f Methods, H. Qin, R. C. Davidson and E. A. Startsev, Physics of Plasmas15, 063101 (2008).

Advanced Plasma Flow Simulations of Cathodic-Arc and Ferroelectric Plasma Sources for Neutralized Drift Compression, A. B. Sefkow, R. C. Davidson and E. P. Gilson, Physical Review Special Topics on Accelerators and Beams 11, 070101 (2008).

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, submitted for publication (2008).

"Dynamics of Electromagnetic Two-Stream Interaction Processes During Longitudinal and Transverse Compression of an Intense Ion Beam Pulse Propagating Through Background Plasma", E. A. Startsev and R. C. Davidson, submitted for publication (2008).

"Advanced Numerical Simulations of Temperature Anisotropy Instabilities and Collective Interaction Processes for High-Intensity Bunched Ion Beams", H. Qin, R. C. Davidson and E. A. Startsev, submitted for publication (2008).

Charge and Current Neutralization of an Ion Beam Pulse Propagating in a Background Plasma along a Solenoidal Magnetic Field, I.D. Kaganovich, E. A. Startsev, A. B. Sefkow and R. C. Davidson, Physical Review Letters 99, 235002 (2007).

Collective Temperature Anisotropy Instabilities in Intense Charged Particle Beam, E.A. Startsev, R. C. Davidson and H Qin, Physics of Plasmas 14, 056705 (2007).

Nonlinear Delta-f Particle Simulations of Collective Excitations and Energy Anisotropy-Driven Instabilities in High-Intensity Bunched Beams, H. Qin, R. C. Davidson and E. A. Startsev, Physical Review Special Topics on Accelerators and Beams 10, 064201 (2007).

**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 21 (2009) 045401

**PI Eric DeWeaver**

Lorenz, D. J., E. T. DeWeaver, and D. J. Vimont, 2008: Evaporation change and global warming - the role of net radiation and relative humitidy. J. Climate, submitted.

Durner, G. M., D. C. Douglas, R. M. Neilson, S. C. Amstrup, T. L. McDonald, I. Stirling, M. Mauritzen, E. W. Born, O. Wiig, E. DeWeaver, M. C. Serreze, S. E. Belikov, M. M. Holland, J. Maslanik, J. Aars, D. A. Bailey, and A. E. Derocher, 2008: Predicting 21st Century Polar Bear Habitat Distribution from Global Climate Models. Ecological Monographs, in press.

DeWeaver, E. T., E. C. Hunke, and M. M. Holland, 2008: Sensitivity of Arctic Sea Ice Thickness to Inter-Model Variations in the Surface Energy Budget. In "Arctic Sea Ice Decline: Observations, Projections, Mechanisms and Implications", E. T. DeWeaver, C. M. Bitz, and B. Tremblay, eds, in press.

DeWeaver E. T., E. C. Hunke, M. M. Holland, 2008, Comment on "On the reliability of simulated Arctic sea ice in global climate models" by I. Eisenman, N. Untersteiner, and J. S. Wettlaufer, Geophys. Res. Lett., 35, L04501, doi:10.1029/2007GL031325. abstract/download from AGU website

DeWeaver, E, 2007: Uncertainty in climate model projections of Arctic sea ice decline: an evaluation relevant to polar bears. download from USGS website

**PI David Dean**

"Broyden's method in nuclear structure calculations", Andrzej Baran, Aurel Bulgac, Michael McNeil Forbes, Gaute Hagen, Witold Nazarewicz, Nicolas Schunck, and Mario V. Stoitsov, Phys. Rev. C 78, 014318 (2008)

"Computational Nuclear Physics", D.J. Dean, G. Hagen, M. Hjorth-Jensen and T. Papenbrock, Comput. Sci. Disc. (2008), in press.

**PI Viktor Decyk**

A. M. Dimits, W. M. Nevins, D. E. Shumaker, G. W. Hammett, T. Dannert, F. Jenko, W. Dorland, J. N. Leboeuf, T. L. Rhodes, J. Candy, and C. Estrada-Mila, "Gyrokinetic Simulations of ETG and ITG Turbulence", Nuclear Fusion 47 No 8 (August 2007) 817-824.

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

**PI James Demmel**

J. Demmel, Y. Hida, X. S. Li, and E. J. Riedy. Extra-precise iterative refinement for overdetermined least squares problems. ACM Transactions on Mathematical Software, 35(4) (to appear in 2009).

J. Demmel, M. F, Hoemmen, Y. Hida, and E. J. Riedy. Non-Negative Diagonals and High Performance on Low-Profile Matrices from Householder QR. Submitted to SIAM journal on Scientific Computing, short version of LAPACK Working Note (LAWN) 203 and UCB/EECS-2008-76.

J. Demmel, L. Grigori, M. F. Hoemmen, and J. Langou, Communication-optimal parallel and sequential QR and LU factorizations, Submitted to SIAM journal on Scientific Computing, short version of UCB-EECS-2008-89 and LAWN 204 (available on arxiv)

J. Demmel, L. Grigori, M. F. Hoemmen, and J. Langou, Implementing communication-optimal parallel and sequential QR factorizations, Submitted to SIAM journal on Scientific Computing, short version of UCB-EECS-2008-89 and LAWN 204 (available on arxiv)

**PI Stephen Derenzo**

S. Derenzo, M. Boswell, R. Boutchko A. Canning et al. Design and Implementation of a Facility for Discovering New Scintillator Materials, IEEE transactions on nuclear science, vol 55, p1458 (2008) [LBNL-753E)

A. Canning, A. Chaudhry R. Boutchko and S. E. Derenzo First-Principles Studies and Predictions for New Ce doped Gamma Detector Materials submitted to IEEE transaction on nuclear science (2008)

A. Chaudhry, A. Canning, R. Boutchko, S. E. Derenzo et. al First principles calculations for Ce-doped rare-earth oxyhalides REOX (RE = Y, La; X = F, Cl, Br, I) for Gamma Detector Materials, submitted to IEEE transaction on nuclear science. (2008)

R. Boutchko, A. Chaudhry, A. Canning et. al. Cerium Activated Scintillation in Yttrium Halides: First Principles Theory and Prediction, submitted to IEEE transaction on nuclear science. (2008)

A. Canning, A. Chaudhry, L.-W. Wang, R. Boutchko, S. E. Derenzo, and M. J. Weber, "Electronic structure studies and predictions for new Ce-doped gamma detector materials," in IEEE Nuclear Science Symp. Conf. Rec., 2007, pp. 2466-2468 (2007)

**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 . NT@UW-08-18, DAMTP-2008-94, Dec 2008. e-Print: arXiv:0812.2583 [hep-lat] http://arXiv.org/abs/0812.2583, submitted to Nuclear Physics B

**PI Thomas Devereaux**

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, "High-energy anomaly dichotomy in electron- and hole-doped high temperature superconductors," arXiv:0807.3359v1 [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 and homogenization of plasma angular momentum, O. D. Gurcan, P. H. Diamond, and T. S. Hahm, Phys. Rev. Lett. 100, 135001 (2008).

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).

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).

Electron thermal transport analysis in Tokamak ?? Configuration Variable, E. Asp, J.-H. Kim, W. Horton, L. Porte, S. Alberti, A. Karpushov, Y. Martin, O. Sauter, G. Turri, and the TCV TEAM, Phys. Plasmas 15, 082317 (2008).

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**

K. Paul, D.A. Dimitrov, R. Busby, D.L. Bruhwiler, D. Smithe, J.R. Cary, J. Kewisch, D. Kayran, R. Calaga and I. Ben-Zvi, "Half-Cell RF Gun Simulations with the Electromagnetic Particle-in-Cell Code VORPAL", in the proceedings of the Advanced Accelerator Concepts, 13th Workshop, Santa Cruz, California (2008)

**PI Sebastian Doniach**

Critical Assessment of Nucleic Acid Electrostatics via Experimental and Computational Investigation of an Unfolded State Ensemble Bai, Y.; Chu, V. B.; Lipfert, J.; Pande, V. S.; Herschlag, D.; Doniach, S. J. Am. Chem. Soc.; (Article); 2008; 130(37); 12334-12341.

**PI William Dorland**

Howes, GG, Inertial range turbulence in kinetic plasmas, PHYSICS OF PLASMAS, 15 (5): Art. No. 055904 MAY 2008.

Howes, GG; Cowley, SC; Dorland, W; Hammett, GW; Quataert, E; Schekochihin, AA, A model of turbulence in magnetized plasmas: Implications for the dissipation range in the solar wind, JOURNAL OF GEOPHYSICAL RESEARCH-SPACE PHYSICS, 113 (A5): Art. No. A05103 MAY 23 2008.

Howes, GG; Dorland, W; Cowley, SC; Hammett, GW; Quataert, E; Schekochihin, AA; Tatsuno, T, Kinetic simulations of magnetized turbulence in astrophysical plasmas, PHYSICAL REVIEW LETTERS, 100 (6): Art. No. 065004 FEB 15 2008.

Stantchev, G; Juba, D; Dorland, W; Varshney, A, Confluent volumetric visualization of gyrokinetic turbulence, IEEE TRANSACTIONS ON PLASMA SCIENCE, 36 (4): 1112-1113 Part 1 AUG 2008.

Rogers, BN; Kobayashi, S; Ricci, P; Dorland, W; Drake, J; Tatsuno, T, Gyrokinetic simulations of collisionless magnetic reconnection, PHYSICS OF PLASMAS, 14 (9): Art. No. 092110 SEP 2007.

Dimits, AM; Nevins, WM; Shumaker, DE; Hammett, GW; Dannert, T; Jenko, F; Pueschel, MJ; Dorland, W; Cowley, SC; Leboeuf, JN; Rhodes, TL; Candy, J; Estrada-Mila, C, Gyrokinetic simulations of ETG and ITG turbulence, NUCLEAR FUSION, 47 (8): 817-824 AUG 2007.

Applegate, DJ; Roach, CM; Connor, JW; Cowley, SC; Dorland, W; Hastie, J; Joiner, N, Micro-tearing modes in the mega ampere spherical tokamak, PLASMA PHYSICS AND CONTROLLED FUSION, 49 (8): 1113-1128 AUG 2007.

Nevins, WM; Parker, SE; Chen, Y; Candy, J; Dimits, A; Dorland, W; Hammett, GW; Jenko, F, Verification of gyrokinetic delta f simulations of electron temperature gradient turbulence, PHYSICS OF PLASMAS, 14 (8): Art. No. 084501 AUG 2007.

M. A. Shay, J. F. Drake, and W. Dorland, Equation free projective integration: A multiscale method applied to a plasma ion acoustic wave, J. Comp. Phys. 226, 571, 2007.

P. Cassak, J. F. Drake and M. A. Shay, Catastrophic onset of fast magnetic reconnection with a guide field, Phys. Plasmas 14, 054502, 2007.

P. Cassak, J. F. Drake, M. A. Shay and B. Eckhardt, Onset of fast magnetic reconnection, Phys. Rev. Lett. 98, 215001, 2007.

M. Swisdak, J. F. Drake and M. A. Shay, Development of a Turbulent Outflow during Electron-Positron Magnetic Reconnection, Astrophy. J. 680, 999, 2008.

M. A. Shay, J. F. Drake and M. Swisdak, Two-scale structure of the electron dissipation region during collisionless reconnection, Phys. Rev. Lett. 99, 155002, 2007.

J. P. Eastwood, D. A. Brain, J. S. Halekas, J. F. Drake, T. D. Phan, M. Oieroset, D. L. Mitchell, R. P. Lin and M. Acuna, Evidence for collisionless magnetic reconnection at Mars, Geophys. Res. Lett. 35, L02106, 2007.

T. D. Phan, J. F. Drake, M. A. Shay, F. S. Mozer and J. P. Eastwood, Evidence for an elongated (>60 ion skin depths) electron diffusion region during fast magnetic reconnection, Phys. Rev. Lett. 99, 255002, 2007.

J. F. Drake, M. A. Shay and M. Swisdak, The Hall fields and fast magnetic reconnection, Phys. Plasmas 15, 042306, 2008.

Choi, S; Guzdar, PN; Case, A; Ellis, R; Hassam, AB (Hassam, A. B.); Lunsford, R; Teodorescu, C; Uzun-Kaymak, I; Observations and analysis of magnetic fluctuations in the Maryland centrifugal experiment, PHYSICS OF PLASMAS, 15 (4): Art. No. 042507 APR 2008

Guzdar, PN; Chakrabarti, N; Singh, R; Kaw, PK; Excitation of geodesic acoustic modes by ion temperature gradient modes, PLASMA PHYSICS AND CONTROLLED FUSION, 50 (2): Art. No. 025006 FEB 2008

Kleva, RG; Guzdar, PN; Turbulent anti-resistivity and the zonal magnetic field dynamo in drift-ballooning turbulence, PHYSICS OF PLASMAS, 14 (11): Art. No. 112307 NOV 2007

**PI John Drake**

**PI Barry Dunietz**

Perrine, T. and Dunietz, B. D. "Conductance of a coblat(II) terpyridine complex based molecular transistor: A computational analysis" J. of Phys. Chem. A., 112, 2043, 2008.

Perrine, T. M. and Smith, R. G. and Marsh, C. and Dunietz, B. D. "Gating of single molecule transistors: Combining field-effect and chemical control" J. Chem. Phys., 128, 154706, 2008.

**PI Michel Dupuis**

R. Devanathan, A. Venkatnathan and M. Dupuis, "Atomistic simulation of nafion membrane. 2. Dynamics of water molecules and hydronium ions", Journal of Physical Chemistry B, 111(45), 13006-13013, (2007).

A. Venkatnathan, R. Devanathan, R. Rousseau, M. Dupuis, T. Frigato, W. Gu and V. Helms, "Simulation of proton transport in hydrated Nafion membrane using the Quantum Hopping Molecular Dynamics (Q-HOP MD) method", Phys. Chem. Chem. Phys. (submitted 2008)

## E

**PI Charlotte Elster**

Faddeev and Glauber Calculations at Intermediate Energies in a Model for n+d Scattering, Ch. Elster, T. Lin, W. Glockle, S. Jeschonnek, Phys. Rev. C{\bf 78}, 034002 (2008).

Poincare Invariant Three-Body Scattering at Intermediate Energies, T. Lin, Ch. Elster, W.N. Polyzou, H. Wital a, W. Glockle, Phys. Rev. C{\bf 78}, 024002 (2008).

Relativistic Effects in Exclusive pd Breakup Scattering at Intermediate Energies, T. Lin, Ch. Elster, W.N. Polyzou, W. Glockle, Phys. Lett. {\bf B~660}, 345 (2008).

First Order Relativistic Three-Body Scattering, T. Lin, Ch. Elster, W. Polyzou, W. Glockle, Phys. Rev. C{\bf 76}, 014010 (2007).

A New Approach to the 3D Faddeev Equation for Three-Body Scattering, Ch. Elster, W. Glockle, H. Witala, arXiv:0805.2010 [nucl-th], to appear in Few Body Systems.

## F

**PI Roland Faller**

Jayeeta Ghosh and Roland Faller: Comparing the density of states of binary Lennard Jones glasses in bulk and film, J. Chem. Phys. 128 (12) 124509 (2008).

Jayeeta Ghosh, and Roland Faller: Density of States Simulations of Various Glass Formers, AIP Proceedings 982 142-147 (2008).

Florence R. Pon, Qi Sun and Roland Faller: Static and Dynamic Heterogeneities in Polyisoprene-Polystyrene Blends: A Molecular Dynamics Simulation, submitted to Eur Pol J

Jayeeta Ghosh, Masaomi Hatakeyama, Petra Traskelin, Chenyue Xing and Roland Faller: Molecular Modeling in Confined Polymer and Biomembrane Systems, submitted to Songlakarin J Sci (refereed version of Proc of Thai Nanotech Conf)

Petra Traskelin, Roland Faller: Molecular dynamics simulations of grafted polystyrene in toluene solutions in preparation

**PI William Fawley**

``Production of Ultrashort FEL XUV Pulses via a Reverse Undulator Taper''. 2008, in Proc. ``Frontiers in FEL Physics and Related Topics''} (Elba Island, Italy, Sept. 2007), Nucl. Instr. Meth., A593}, 111 (also LBNL-63588).

**PI Andrew Felmy**

Marat Valiev, Eric J. Bylaska, Michel Dupuis, and Paul G. Tratnyek (2008) "Combined Quantum Mechanical and Molecular Mechanics Studies of the Electron-Transfer Reactions Involving Carbon Tetrachloride in Solution," J. Phys. Chem. A 2008, 112, 2713-2720

Eric J. Bylaska, Michel Dupuis, and Paul G. Tratnyek (2008) "One-Electron-Transfer Reactions of Polychlorinated Ethylenes: Concerted and Stepwise Cleavages," J. Phys. Chem. A 2008, 112, 3712-3721

Patrick Nichols, Eric J. Bylaska, Gregory K. Schenter, and Wibe de Jong (2008) "Equatorial and apical solvent shells of the UO22+ ion," THE JOURNAL OF CHEMICAL PHYSICS 128, 124507, 2008.

Patrick Nichols, Niri Govind, Eric J. Bylaska, and Wibe A. De jong (2008) "Gaussian Basis Set and Planewave Relativistic Spin-Orbit Methods in NWChem," Submitted to Journal of Chemical Theory and Computation

Eric J. Bylaska, Mike Holst and John H. Weare (2008) "Adaptive Finite Element Method for Solving the Exact Schr??dinger Equation of Density Functional Theory: Is it Computable?" Submitted to Journal of Chemical Theory and Computation

Stuart Bogatko, Eric Bylaska, John Weare (2008) "1st principles simulation of the bonding, vibrational, and electronic properties of the hydration shells of high spin Fe3+ ions," Submitted to THE JOURNAL OF CHEMICAL PHYSICS

**PI Graham Fleming**

Y.-C. Cheng, G. S. Engel, and G. R. Fleming, Elucidation of population and coherence dynamics using cross-peaks in two-dimensional electronic spectroscopy. Chem. Phys. 341, 285 (2007).

Y.-C. Cheng and G. R. Fleming, Coherence quantum beats in two-dimensional electronic spectroscopy. J. Phys. Chem. A 112, 4254 (2008).

E. L. Read, G. S. Schlau-Cohen, G. S. Engel, J. Wen, R. E. Blankenship, and G. R. Fleming, Visualization of excitonic structure in the Fenna-Matthews-Olson photosynthetic complex by polarization-dependent two-dimensional electronic spectroscopy. Biophys. J. 95, 847 (2008).

Y.-C. Cheng, T. Ahn, T. J. Avenson, D. Zigmantas, K. K. Niyogi, M. Ballottari, R. Bassi, and G. R. Fleming, Kinetic Modeling of Charge-Transfer Quenching in the CP29 Minor Complex. J. Phys. Chem. B, ASAP Article, doi:10.1021/jp802730c.

**PI Michael Fox-Rabinovitz**

Fox-Rabinovitz, M., J. Cote, B. Dugas, M. Deque, and J. L. McGregor, and A. Belochitski, 2008: Stretched-Grid Model Intercomparison Project: Decadal Regional Climate Simulations with Enhanced Variable and Uniform-Resolution GCMs, Meteorology and Atmospheric Physics, Springer, Wien, 14.08.2008, vol. 100, no. 1, pp. 159-178.

Krasnopolsky, V. M., M. S. Fox-Rabinovitz, and A. A. Belochitski, 2008: "Decadal Climate Simulations Using Accurate and Fast Neural Network Emulation of Full, Long- and Short Wave, Radiation.", Monthly Weather Review, Vol. 136, No. 10, 3683-3695.

**PI Alberto Franceschetti**

Q. Zhao, P.A. Graf, W.B. Jones, A. Franceschetti, J. Li, L.W. Wang, and K. Kim, "Shape Dependence of Band-Edge Exciton Fine Structure in CdSe Nanocrystals", Nano Letters 7, 3274 (2007).

A. Franceschetti, "First-Principles Calculations of the Temperature Dependence of the Band Gap of Si Nanocrystals", Phys. Rev. B (Rapid Communications) 76, 161301 (2007).

M.C. Troparevsky and A. Franceschetti, "An Optimized Configuration Interaction Method for Calculating Electronic Excitations in Nanostructures", J. Phys. Cond. Matter 20, 055211 (2008).

A. Franceschetti and Y. Zhang, "Multiexciton Absorption and Multiple Exciton Generation in CdSe Nanocrystals", Phys. Rev. Lett. 100, 136805 (2008).

A. Franceschetti, "Structural and Electronic Properties of PbSe Nanocrystals from First Principles", Phys. Rev. B 78, 075418 (2008).

A. Franceschetti, S. Lany, and G. Bester, "Quantum-Dot Intermediate-Band Solar Cells with Inverted Band Alignment", J. Phys. E 41, 15 (2008).

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 (in press).

A. Franceschetti and M.C. Troparevsky, "Pseudopotential Theory of Electronic Excitations in Semiconductor Nanostructures", Journal of Theoretical and Computational Nanoscience (in press).

**PI Stuart Freedman**

S. Abe et al. [KamLAND Collaboration], "Precision Measurement of Neutrino Oscillation Parameters with KamLAND", Phys. Rev. Lett. 100, 221803 (2008) [arXiv:0801.4589 [hep-ex]].

Z. Djurcic et al., "Uncertainties in the Anti-neutrino Production at Nuclear Reactors", Submitted to Phys. Rev. C (August 2008).

C. Arnaboldi et al. (the CUORICINO Collaboration), "Results from a search for the 0 neutrino beta beta- decay of Te-130", Phys.Rev.C78:035502,2008.

**PI Arthur Freeman**

S. H. Rhim, R. Saniz, Jaejun Yu, Lin-Hui Ye, and A. J. Freeman, Interface electronic structure, two-dimensional metallicity, and possible interface superconductivity in CuCl/Si superlattices, Phys. Rev. B 76, 184505 (2007).

S.H. Rhim, R. Saniz, and A. J. Freeman, Interface 2D metallicity but lack of superconductivity in hetero-bonded semiconductors: ZnS/Si and GaP/Si, submitted to Phys. Rev. B

R. Saniz, M. R. Norman, and A. J. Freeman, Orbital mixing and nesting in the bilayer manganites La2-2xSr1+2xMn2O7 , submitted to Phys. Rev. Lett.

K. Nakamura, T. Akiyama, T. Ito, and A.J. Freeman, Magnetic structures and half-metallicity at zincblende ferromagnetic/antiferromagnetic interfaces: Role of tetragonal distortions , J. Magn. Magn. Mater. 310, 2186 (2007)

K. Nakamura, N. Mizuno, T. Akiyama, T. Ito, and A. J. FreemanNoncollinear magnetism, magnetocrystalline anisotropy, and spin-spiral structures in Fe/W(110) , J. Appl. Phys. 101, 09G521 (2007)

R. Saniz, B. Barbiellini, P. M. Platzman, and A. J. Freeman, Physisorption of Positronium on Quartz Surfaces , Phys. Rev. Lett. 99, 096101 (2007)

M. I. Bertoni, T. O. Mason, J. E. Medvedeva, Y. Wang, A. J. Freeman, and K. R. Poeppelmeier, Enhanced electronic conductivity in Si-substituted calcium aluminate , J. Appl. Phys. 102, 113704 (2007)

M. I. Bertoni, J. E. Medvedeva, A. J. Freeman, K. R. Poeppelmeier, and T. O. Mason, An insight into the insulator to metal transition in Ca12Al14O33 , submitted to Phys. Rev. B.

Joo-Hyoung Lee, Arthur J. Freeman, and Michael Weinert, Magnetically driven structural transformation of iron, submitted to Nature Materials

**PI James Freericks**

J. K. Freericks, H. R. Krishnamurthy, and Th. Pruschke. Theoretical description of time-resolved photoemission spectroscopy: application to pump-probe experiments. arXiv:0806.4781, 2008.

J. K. Freericks, V. M. Turkowski, and V. Zlati??c. Nonequilibrium dynamical mean-field theory. Phys. Rev. Lett., 97:266408, 2006. J. K. Freericks. Quenching Bloch oscillations in a strongly correlated material: The dynamical mean-field theory approach. Phys. Rev. B, 77:075109, 2008.

J. K. Freericks, V.M. Turkowski, and V. Zlati??c. Nonlinear response of strongly correlated materials to large electric fields. In D. E. Post, editor, Proceedings of the HPCMP Users Group Conference 2006, Denver, CO, June 26-29, 2006, pages 218-226. IEEE Computer Society, Los Alamitos, CA, 2006.

J. K. Freericks. Transient response of strongly correlated materials to large electric fields: Utilizing the large memory capacity of ARSCs midnight machine in a capability applications project. In D. E. Post, editor, Proceedings of the HPCMP Users Group Conference 2007, Pittsburgh, PA, June 18-21, 2007, pages 222-230. IEEE Computer Society, Los Alamitos, CA, 2007.

V. M. Turkowski and J. K. Freericks. Spectral moment sum rules for strongly correlated electrons in time-dependent electric fields. Phys. Rev. B, 73:075108, 2006.

V. M. Turkowski and J. K. Freericks. Nonequilibrium sum rules for the retarded self-energy of strongly correlated electrons. Phys. Rev. B, 77:205102, 2008.

**PI Alex Friedman**

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 matterphysics and inertial fusion energy" Nuclear Instruments and Methods in Physics Research (to bepublished).

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 PhysicsResearch (to be published).

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, a platform for studying ion beam-heated matter," Nuclear Instruments and Methods in Physics Research(to be published).

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

S. M. Lund, "Beam stability and control in solenoidal transport channels," Nuclear Instruments andMethods in Physics Research (to be published).

J.-L. Vay, "Simulation of beams or plasmas crossing at relativistic velocity," Physics of Plasmas 15, 056701 (2008).

J.-L. Vay, "Noninvariance of Space- and Time-Scale Ranges under a Lorentz Transformation -Implications for the Study of Relativistic Interactions," Phys. Rev. Lett. 98, 130405 (2007).

K. Gomberoff, J. Fajans, A. Friedman, D. P. Grote, and J.-L. Vay, "Simulations of plasma confinement inan antihydrogen trap," Physics of Plasmas 14, 102111 (2007).

K. Gomberoff , J. Wurtele, A. Friedman, D. P. Grote, J.-L. Vay, "A method for obtaining three-dimensional computational equilibrium of non-neutral plasmas using WARP," J. of Comput. Phys., 225, 1736-1752 (2007).

C. M. Celata, M. A. Furman, J.-L. Vay, and J. W. Yu, "Electron Cyclotron Resonances in Electron Cloud Dynamics", Physical Review Special Topics Accel. Beams (to be published 2008).

**PI Guoyong Fu**

Chen Y, Parker SE, Rewoldt G et al., "Coarse-graining the electron distribution in turbulence simulations of tokamak plasmas", Phys. Plasmas 15, 055905 (2008).

Fu GY, Park W, Strauss H, et al, "Gobal Hybrid Simulations of Energetic Particle Effects on the n=1 Mode in Tokamaks: Internal Kink and Fishbone Instability" Phys Plasmas 13 052517 (2006)

Fu GY, "Energetic Particle-driven Geodesic Acoustic Mode", Phys. Rev. Lett, accepted (2008).

Lang J, Chen Y, and Parker S, "Gyrokinetic delta-f particle simulation of trapped electron mode driven turbulence", Physics of Plasmas 14, 082315(2007).

**PI Miguel Furman**

C. M. Celata , Miguel A. Furman, J.-L. Vay, and Jennifer W. Yu, "Electron Cloud Cyclotron Resonances in the Presence of a Short-bunch-length Relativistic Beam," LBNL-1002E, CBP-795, July 2008, PRST-AB 11, 091002 (2008).

## G

**PI Giulia Galli-Gygi**

"Electronic properties of MoS2 nanoparticles", T.Li and G.Galli,

J.Phys.Chem.C 2007 111, 16192 (2007) [carried out with previous year allocations]

"Single functional group interactions with individual carbon nanotubes", Raymond W. Friddle1,Melburne C. LeMieux1,Giancarlo Cicero, Alexander B. Artyukhin, Vladimir V. Tsukruk, Jeffrey C. Grossman, Giulia Galli, and Aleksandr Noy, Nature Nanotechnology 2, 692 (2007).[carried out with previous year allocations]

A First-Principles Study of Aromatic Isocyanide Self-Assembled Monolayers on Au(111) Surface, Yan Li and Deyu Lu, Giulia Galli, Sally A. Swanson and J. Campbell Scott J. Phys. Chem. C 112, 6413 (2008).

"Structural characterization of aldehyde-terminated self-assembled monolayers", A.Riposan, Y. Li, Y.Tan, G. Galli and G. Liu, J.Phys.Chem.A , 111, 12727 (2007).

"Effect of Nitrogen on the Stability of Silicon Nanocrystals Produced by Decomposition of Alkyl Silanes", N. Zaitseva, S. Hamel, Zu R. Dai, C. Saw, A. Williamson, and G. Galli, J. Phys. Chem. C 112, 3585 (2008).

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

**PI Bruce Garrett**

G. S. Fanourgakis and S. S. Xantheas, "Development of Transferable Interaction Potentials for Water: V. Extension of the flexible, polarizable, Thole-type Model potential (TTM3-F, v. 3.0) to describe the vibrational spectra of water clusters and liquid water", Journal of Chemical Physics 128, 074506 (2008).

M. V. Kirov, G. S. Fanourgakis and S. S. Xantheas, "Identifying the Most Stable Networks in Polyhedral Water Clusters", Frontiers article (invited), Chemical Physics Letters 461, 180 (2008). Journal cover.

G. S. Fanourgakis, V. Tipparaju, J. Nieplocha and S. S. Xantheas, "An efficient parallelization scheme for molecular dynamics simulations with many-body, flexible, polarizable empirical potentials: Application to water", Theoretical Chemistry Accounts 117, 73 (2007)

S. M. Kathmann, G. K. Schenter and S. S. Xantheas, "On the Determination of Monomer Dissociation Energies of Small Water Clusters from Photoionization Experiments", Letter to the Editor, Journal of Physical Chemistry A, 112, 1851 (2008)

M. L. Lipciuc, F. Wang, X. Yang and T. N. Kitsopoulos, G. S. Fanourgakis and S. S. Xantheas, "Cluster-Controlled Photofragmentation: The Case of the Xe-Pyrrole Cluster", Communication to the Editor, ChemPhysChem 9, 1838 (2008)

C. D. Wick and S. S. 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 (accepted)

S. S. Xantheas, "Low-lying energy isomers and global minima of the pentagonal dodecahedron (H2O)20 and the (H3O)+(H2O)20 clusters: Structures and spectroscopic features", Special Issue on Aqueous solutions and their Interfaces (invited), Journal of Physical Chemistry B (submitted)

J. Nieplocha, S. Krishnamoorthy, M. Valiev, M. K. Krishnan, B. J. Palmer, and P. Sadayappan, "Integrated Data and Task Management for Scientific Applications." In Proceedings of ICCS, pp. 20-31. Springer-Verlag, Berlin, Germany (2008).

M. Valiev. B. C. Garrett, M. K. Tsai, K. Kowalski, S. M. Kathmann, G. K. Schenter, M. Dupuis, Journal of Chemical Physics, 127, 051102 (2007).

**PI Silvina Gatica**

Ordering transition of gases adsorbed on a C60 surface: Monte Carlo simulations and lattice-gas models, Silvina M. Gatica, Milen K. Kostov and Milton W. Cole Phys. Rev. B 78, 205417 (2008)

A Corresponding States Principle for Physisorption and Deviations for Quantum Fluids, Hye-Young Kim, Angela D. Lueking, Silvina M. Gatica, J. Karl Johnson and Milton W. Cole, Molecular Physics, Volume 106, Issue 12 & 13 June 2008 , pages 1579 – 1585

Xe Adsorption on a C60 Monolayer on Ag(111), S. M. Gatica, H. I. Li, R. A. Trasca, M. W. Cole and R. D. Diehl, Phys. Rev. B 77, 045414 (2008)

**PI Cameron Geddes**

C.G.R. Geddes, K. Nakamura, G.R. Plateau, Cs. Toth, E. Cormier-Michel, E. Esarey, C.B. Schroeder, J.R. Cary, and W.P. Leemans, "Stable low momentum spread electron bunches from plasma density gradient injection," PRL V 100, 215004 (2008).

E. Cormier-Michel, B.A. Shadwick, C.G.R. Geddes, E. Esarey, C.B Schroeder, and W.P. Leemans, "Unphysical Kinetic effects in particle-in-cell modeling of laser wakefield accelerators", PRE 78, 016404 (2008).

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,' J. Phys. Conf. Series V 125 pp. 12002/1-11 (2008).

O. Rubel, Prabhat, K. Wu, H. Childs, J. Meredith, C.G.R. Geddes, E. Cormier-Michel, S. Ahearn, G.H. Weber, P. Messmer, H. Hagen, B. Hamann, E.W. Bethel, "High Performance Multivariat Visual Data Exploration for Extremely Large Data, " Proc. Supercomputing Conference 2008 in press.

**PI Philip Geissler**

B. Gin, J. Garrahan, and P.L. Geissler. "Dynamical irrelevance of non-native contacts in a lattice model of protein folding." Biophysical Journal, submitted (2008).

**PI Giorgio Gratta**

Oceanic Ambient Noise as Background to Acoustic Neutrino Detection N. Kurahashi and G. Gratta Phys. Rev. D 78, 092001 (2008)

**PI Stephen Gray**

A. Saracibar, E. M. Goldfield, and S. K. Gray, Quantum mechanical capture/phase space theory calculation of the rate constants for the complex-forming CH + H2 reaction, J. Phys. Chem. A, in press (2008).

M. E. Stewart, C. R. Anderton, L. B. Thompson, J. Maria, S. K. Gray, J. Rogers, and R. G. Nuzzo, Nanostructured plasmonic sensors, Chemical Reviews 108, 494-521 (2008).

J. M. McMahon, J. Henzie, T. Odom, G. C. Schatz, and S. K. Gray, Tailoring the sensing capabilties of nanohole arrays in gold films with Rayleigh anomaly-surface plasmon polaritons, Optics Express 15, 18119-18129 (2007).

J. T. Bahns, Q. Guo, J. M. Montgomery, S. K. Gray, H. M. Jaeger, and L. Chen, High fidelity nano-hole enhanced Raman spectroscopy, submitted to J. Am. Chem. Soc. (2008).

**PI Chris Greene**

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

L. Pagani, C. Vastel, E. Hugo, V. Kokoouline, C. H. Greene, E. Bayet, A. Bacmann, S. Schlemmer, C. Ceccarelli. Chemical modeling of L183 (=L134N): an estimate of the ortho/para H2 ratio. Essentially accepted for publication in Astronomy & Astrophysics; preprint is at http://www.physics.ucf.edu/~slavako/publ/AA.pdf

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

V. Kokoouline, R. Curik, and C. H. Greene. Non-adiabatic effects in dissociative recombination of molecular ions. Accepted for publication in J. Phys.: Conf. Series; preprint: http://www.physics.ucf.edu/~slavako/publ/Kokoouline_Curik_Greene.pdf

A. Faure, J. Tennyson, V. Kokoouline and C.H Greene. Rotational excitation of interstellar molecular ions by electrons. Accepted for publication in J. Phys.: Conf. Series; preprint: http://www.physics.ucf.edu/~slavako/publ/faure-dr2007.pdf

J. J. Zirbel, K.-K. Ni, S. Ospelkaus, J. P. D'Incao, C. E. Wieman, J. Ye, and D. S. Jin. Collisional stability of Fermionic Feshbach Molecules. Phys. Rev. Lett 100, 143201 (2008)

D. J. Haxton and C. H. Greene. Indirect dissociative recombination of LiH2+. Submitted to Phys Rev A. Preprint at arxiv:0807.5046

L. Caron, S. Tonzani, C. H. Greene, and L. Sanche. Diffraction in low-energy electron scattering from DNA: bridging gas phase and solid-state theory. In press, Phys Rev A. Online at arxiv:0710.2854.

**PI Jeffrey Grossman**

L.K. Wagner and J.C. Grossman, "A microscopic description of light induced defects in amorphous silicon solar cells", under review at Phys. Rev. Lett.

Zhigang Wu, J. C. Grossman, and J. B. Neaton, "Quantum confinement and electronic structures of tapered silicon nanowires", Phys. Rev. Lett. 100, 246804 (2008).

Y. Kanai and J. C. Grossman, "Role of Semiconducting and Metallic Tubes in P3HT/Carbon-Nanotube Photovoltaic Heterojunctions: Density Functional Theory Calculations", NanoLetters 8, 909 (2008).

J.-H. Lee, J. C. Grossman, J. Reed and G. A. Galli, Lattice thermal conductivity of nanoporous Si: molecular dynamics study, Appl. Phys. Letts., v.91, 223110 (2007)

J.-H. Lee, G. A. Galli and J. C. Grossman, Nanoporous Si as an efficient thermoelectric material, Nano Letters, submitted.

**PI Hua Guo**

C. Xu, B. Jiang, D. Xie, S. C. Farantos, S. Y. Lin, and H. Guo, J. Phys. Chem. A (Wyatt Festschrift), 111, 10353 (2007), Analysis of the HO2 vibrational spectrum on an accurate ab initio potential energy surface.

S. Y. Lin, H. Guo, P. Honvault, C. Xu, and D. Xie, J. Chem. Phys., 128, 014303 (2008), Accurate quantum mechanical calculations of differential and integral cross sections and rate constant for the O + OH reaction using an ab initio potential energy surface.

S. Y. Lin, Z. Sun, H. Guo, D. H. Zhang, P. Honvault, D. Xie, and S.-Y. Lee, J. Phys. Chem. A., 112, 602 (2008), Fully Coriolis coupled quantum studies of the H + O2 (i=0-2, ji=0,1) OH + O reaction on an accurate potential energy surface: integral cross sections and rate constants.

S. Y. Lin, H. Guo, P. Honvault, Chem. Phys. Lett., 453, 140 (2008), Quantum dynamics of C(3P) + OH(2) H(2S) + CO(X1+) reaction.

S. Zhou, D. Xie, D. Xu, H. Guo, R. W. Field, Chem. Phys. Lett., 455, 145 (2008), Theoretical emission spectra of HNC( ) on a new ab initio potential energy surface.

G. Lendvay, D. Xie, and H. Guo, Chem. Phys., 349, 181 (2008) (Special issue on electron correlation and molecular dynamics for excited state and photochemistry in honor of Hans Lischka), Mechanistic insights into the H + O2 OH + O reaction from quasi-classical trajectory studies on a new ab initio potential energy surface.

S. Zhou, D. Xie, S. Y. Lin, and H. Guo, J. Chem. Phys., 128, 224316 (2008), A new ab initio potential-energy surface for NH2(X2A) and quantum studies of NH2 vibrational spectrum and rate constant for the N(2D) + H2-NH + H reaction.

Z. Li, L. Wang, H. Ran, D. Xie, N. Blinov, P.-N. Roy, and H. Guo, J. Chem. Phys., 128, 224513 (2008), Path integral Monte Carlo study of CO2 solvation in 4He clusters.

D. Quan, E. Herbst, T. Millar, S. Y. Lin, H. Guo, P. Honvault, and D. Xie, Astrophys. J. 68, 1318 (2008), New theoretical results concerning the interstellar abundance of molecular oxygen.

**PI William Gutowski**

Abiodun BJ, Gutowski WJ, and Prusa JM, 2008a: Implementation of a non-hydrostatic, adaptive grid dynamics core in CAM3. Part II: dynamical influences on ITCZ behavior and tropical precipitation. Clim. Dynamics [DOI: 10.1007/s00382-008-0381-y].

Abiodun BJ, Prusa JM, and Gutowski WJ, 2008b: Implementation of a non-hydrostatic, adaptive grid dynamics core in CAM3. . Clim. Dynamics [DOI: 10.1007/s00382-008-0382-x].

Prusa JM, Smolarkiewicz PK and Wyszogrodzki AA, 2008: EULAG, a computational model for multiscale flows. Computers and Fluids, V. 37, 1193-1207.

## H

**PI Stephan Haas**

P. Sengupta, C. D. Batista, R.D. McDonald, S. Cox, J. Singleton, L. Huang, T. P. Papageorgiou, O. Ignatchik, T. Herrmannsd{\"o}rfer, J. L. Manson, J. A. Schlueter, K. A. Funk, and J. Wosnitza, ``Non-monotonic Field dependence of the N{\'e}el temperature in the quasi-2D magnet [Cu(HF$_2$)(pyz)$_2$]BF$_4$'', submitted to {\it Phys. Rev. Lett.}

Leonid P. Pryadko, and Pinaki Sengupta, ``Second-order shaped pulses for solid-state quantum computation'' to appear in {\it Phys. Rev. A}.

S. E. Sebastian, N. Harrison, P. Sengupta, C. D. Batista, S. Francoul, E. Palm, T. Murphy, H. A. Dabkowska, and B. D. Gaulin, ``Fractalization drives crystalline states in a frustrated spin system'' to appear in {\it Proc. Natl. Acad. Sci.}.

S. Cox, R.D. McDonald, P. Sengupta, C.D. Batista, J. Singleton, A. Paduan-Filho, ``Unusual magneto-optical phenomenon reveals low energy spin dispersion in NiCl$_2$-4SC(NH$_2$)$_2$'' to appear in {\it Phys. Rev. Lett.}.

P. A. Goddard, J. Singleton,C.~Maitland, S.~J.~Blundell, T. Lancaster, P.~J.~Baker, R. D. McDonald, S. Cox, P. Sengupta, J. L. Manson, K.~A.~Funk, and J. A. Schlueter, `` Isotope effect in quasi-two-dimensional metal-organic antiferromagnets'', {\it Phys. Rev. B} {\bf 78}, 052408 (2008).

6. P. A. Goddard, J. Singleton, P. Sengupta, R. D. McDonald, T. Lancaster, S. J. Blundell, F. L. Pratt, S. Cox, N. Harrison, J. L. Manson, H. I. Southerland, and J. A. Schlueter, `` Experimentally determining the exchange parameters of quasi-two-dimensional Heisenberg magnets'', {\it New J. Phys.} {\bf 10}, 083025 (2008).

E. C. Samulon, Y.-J. Jo, P. Sengupta, C. D. Batista, M. Jaime, L. Balicas, and I. R. Fisher, ``Ordered magnetic phases of the frustrated spin-dimer compound Ba$_3$Mn$_2$O$_8$'', {\it Phys. Rev. B} {\bf 77}, 214441 (2008).

Pinaki Sengupta, and Cristian Batista, ``Ground state and thermal transitions in a Field-induced spin-Supersolid phase'', {\it Journal of Applied Physics} {\bf 103}, 07C709 (2008). Proceedings of the 52nd Magnetism and Magnetic Materials Conference, Nov.5-9, Tampa, Fl.

V. S. Zapf, V. F. Correa, P. Sengupta, C. D. Batista, M. Tsukamoto, N. Kawashima, P. Egan, C. Pantea, A. Migliori, J. B. Betts, M. Jaime, A. Paduan-Filho, ``A direct measurement of spin correlations using magnetostriction'', {\it Phys. Rev. B} {\bf 77}, R020404 (2008).

Pinaki Sengupta, and Cristian Batista, ``Spin Supersolid in Anisotropic Spin-One Heisenberg Chain'', {\it Phys. Rev. Lett.} {\bf 99}, 217205 (2007).

**PI Bruce Harmon**

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).

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

Photonic crystal enhanced light-trapping in thin film solar cells, D. Zhou, R. Biswas, J. Applied Physics 103, 093102 (2008).

Mechanisms underlying extraordinary transmission in sub-wavelength hole arrays, R. Biswas, S. Neginhal, C. G. Ding, I. Puscasu, E. Johnson, J. Opt. Soc. of America B 24, 2489-95 (October, 2007).

Improved Photon Absorption in a-Si:H Solar Cells using Photonic Crystal Architectures, R. Biswas, D. Zhou, Proceedings MRS Symposium A MRS 1066 (2008) .

Harvesting Photons in Thin Film Solar Cells with Photonic Crystals, D. Zhou, R. Biswas, Proceedings MRS Symposium KK 1101E (2008).

"Crystallographic phase transition and island height selection in In/Si(111) growth", J. Chen, M. Hupalo, M. Ji, C. Z. Wang, K. M. Ho, and M. C. Tringides, Phys. Rev. B, 77, 233302 (2008).

"Honeycomb chain structure of the Au/Si(111)-(5x2) surface reconstruction: a first-principles study", Feng-Chuan Chuang, Chia-Hsiu Hsu, C. Z. Wang, and K. M. Ho, Phys. Rev. B, 77, 153409 (2008).

"The formation of pentagon-hepatagon pair defect by the reconstruction of vacancy defects in carbon nanotube", Gun-Do Lee, C. Z. Wang, Jaejun Yu, Euijoon Yoon, Nong-Moon Hwang, Kai-Ming Ho, Appl. Phys. Lett, 92, 043104 (2008).

"Strongly-Driven Coarsening of Height-Selected Pb Islands on Si(111)", Maozhi Li, J. Evans, C. Z. Wang, M. Hupalo, M. C. Tringides, T. L. Chan, K. M. Ho, Surf. Sci. Lett. 601 (23) L140-L144 (2007).

"Formation of Carbon Nanotube Semiconductor-Metal Intramolecular Junctions by Self-Assembly of Vacancy Defects", Gun-Do Lee, C. Z. Wang, Jaejun Yu, Euijoon Yoon, Nong-Moon Hwang, Kai-Ming Ho, Phys. Rev. B 76, 165413 (2007).

"New mofif of silocon segregation in silicon monoxide clusters", H. Wang, W. C. Lu, Z. S. Li, C. C. Sun, C. Z. Wang, and K. M. Ho, J. Phys. Chem. 112, 7097 (2008).

"Size- and strain-dependent electronic structures in H-passivated Si [112] nanowires" Li Huang, Ning Lu, Jia-An Yan, Mei-Yin Chou, C. Z. Wang, K. M. Ho, J. Phys. Chem. C Accepted

"Core Properties of Dislocation in YCu and YAg B2 Intermetallic Compounds", Q. Chen, M. Ji, C. Z. Wang, K. M. Ho, and S. B. Biner Intermetallics, submitted.

"Atomic and electronic structures of Ag/Si(111)-c(12x2) Surface: A first-principles study" Feng-Chuan Chuang, Chia-Hsiu Hsu, Cai-Zhuang Wang, and Kai-Ming Ho Phys. Rev. B, submitted

**PI Charles Harris**

K.R. Sawyer, R.P. Steele, E.A. Glascoe, J.F. Cahoon, J.P. Schlegel, M. Head-Gordon, C.B. Harris, "Direct observation of photoinduced bent nitrosyl excited-state complexes", J. Phys. Chem. A, 112, 8505-8514 (2008).

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., in press.

K.R. Sawyer, E.A. Glascoe, J.F. Cahoon, J.P. Schlegel, C.B. Harris, "The mechanism of iron-catalyzed alkene isomerization in solution", Organometallics, 27, 4370-4379 (2008).

J.F. Cahoon, K.R. Sawyer, J.P. Schlegel, C.B. Harris, "Determining Transition-state Geometries in Liquids Using 2D-IR", Science 319, 1820-1823 (2008).

**PI Martin Head-Gordon**

Miller, T.F., E. Vanden-Eijnden and D. Chandler, "Solvent coarse-graining and the string method applied to the hydrophobic collapse of a hydrated chain," Proc. Natl Acad. Sci. USA 104, 14559-14564 (2007)

Maibaum, L. and D. Chandler, "Segue between favorable and unfavorable solvation," J. Phys. Chem. B 111, 9025 (2007)

Willard, A.P., D. Chandler, "The Role of Solvent Fluctuations in Hydrophobic Assembly," J. Phys. Chem. B 112, 6187-6192 (2008)

Willard, A.P., and D. Chandler, "Coarse Grained Modeling of The Interface Between Water and Heterogeneous Surfaces," Faraday Discussion 141, Accepted for publication.

Willard, A.P., S.K. Reed, P.A. Madden, and D. Chandler, "Water at an electrochemical interface - a simulation study," Faraday Discussion 141, Accepted for publication

"A two-parameter Coulomb attenuator with a cutoff radius for two-electron repulsion integrals: the effect of attenuation on correlation energies", A.D. Dutoi and M. Head-Gordon, J. Phys. Chem A (in press for Bill Lester Special Issue, 2008)

"The limits of local correlation theory: electronic delocalization and chemically smooth potential energy surfaces", J.E. Subotnik, A. Sodt and M. Head-Gordon, J. Chem. Phys. 128, 034103 (2008)

"The analytical gradient of dual basis resolution-of-the-identity second order Moller-Plesset perturbation theory", R.A. DiStasio Jr., R.P. Steele, and M. Head-Gordon, Mol. Phys. 105, 2731-2742 (2007)

"Hartree-Fock exchange computed using the atomic resolution of the identity approximation", A. Sodt and M. Head-Gordon. J. Chem. Phys. (in press, 2008)

"Systematic optimization of long-range corrected hybrid density functionals", Jeng-Da Chai and M. Head-Gordon, J. Chem. Phys. (in press, 2008)

**PI Teresa Head-Gordon**

M.E. Johnson and T. Head-Gordon (2008). Assessing thermodynamic theories of liquid dynamics. Nature submitted.

M.E. Johnson, C. Malardier-Jugroot, R.K. Murarka, and T. Head-Gordon (2008). Hydration water dynamics near biological interfaces. J. Phys. Chem. B accepted.

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 (Cover article).

N. Lux Fawzi, A. Phillips, J. Z. Ruscio, M. Doucleff, D. E. Wemmer & T. Head-Gordon (2008). Structure and dynamics of the Alzheimer's Ab21-30 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. JPC-B 112, 179-186.

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

**PI Eric Held**

Moment approach for deriving parallel heat flow for general collisionality, submitted to Physics of Plasmas, Jeong-Young Ji and Eric D. Held

**PI Brian Hingerty**

Ding S, Wang Y, Kolbanovskiy A, Durandin A, Bolton JL, van Breemen RB, Broyde S, Geacintov NE. Determination of absolute configurations of 4-hydroxyequilenin-cytosine and -adenine adducts by optical rotatory dispersion, electronic circular dichroism, density functional theory calculations, and mass spectrometry. Chem Res Toxicol. 2008 Sep;21(9):1739-48.

Dimitri A, Jia L, Shafirovich V, Geacintov NE, Broyde S, Scicchitano DA. Transcription of DNA containing the 5-guanidino-4-nitroimidazole lesion by human RNA polymerase II and bacteriophage T7 RNA polymerase. DNA Repair (Amst). 2008 Aug 2;7(8):1276-88.

Xu P, Oum L, Geacintov NE, Broyde S. Nucleotide selectivity opposite a benzo[a]pyrene-derived N2-dG adduct in a Y-family DNA polymerase: a 5'-slippage mechanism. Biochemistry. 2008 Mar 4;47(9):2701-9.

Dimitri A, Goodenough AK, Guengerich FP, Broyde S, Scicchitano DA. Transcription processing at 1,N2-ethenoguanine by human RNA polymerase II and bacteriophage T7 RNA polymerase. J Mol Biol. 2008 Jan 11;375(2):353-66.

Watt DL, Utzat CD, Hilario P, Basu AK. Mutagenicity of the 1-nitropyrene-DNA adduct N-(deoxyguanosin-8-yl)-1-aminopyrene in mammalian cells. Chem Res Toxicol. 2007 Nov;20(11):1658-64.]

Mocquet V, Kropachev K, Kolbanovskiy M, Kolbanovskiy A, Tapias A, Cai Y, Broyde S, Geacintov NE, Egly JM. The human DNA repair factor XPC-HR23B distinguishes stereoisomeric benzo[a]pyrenyl-DNA lesions. EMBO J. 2007 Jun 20;26(12):2923-32.

Jia L, Shafirovich V, Geacintov NE, Broyde S. Lesion specificity in the base excision repair enzyme hNeil1: modeling and dynamics studies. Biochemistry. 2007 May 8;46(18):5305-14.

Wang L, Yu X, Hu P, Broyde S, Zhang Y. A water-mediated and substrate-assisted catalytic mechanism for Sulfolobus solfataricus DNA polymerase IV. J Am Chem Soc. 2007 Apr 18;129(15):4731-7.

Rodriguez FA, Cai Y, Lin C, Tang Y, Kolbanovskiy A, Amin S, Patel DJ, Broyde S, Geacintov NE. Exocyclic amino groups of flanking guanines govern sequence-dependent adduct conformations and local structural distortions for minor groove-aligned benzo[a]pyrenyl-guanine lesions in a GG mutation hotspot context. Nucleic Acids Res. 2007;35(5):1555-68.

Ding S, Shapiro R, Geacintov NE, Broyde S. 4-hydroxyequilenin-adenine lesions in DNA duplexes: stereochemistry, damage site, and structure. Biochemistry. 2007 Jan 9;46(1):182-91.

Perlow-Poehnelt RA, Likhterov I, Wang L, Scicchitano DA, Geacintov NE, Broyde S. Increased flexibility enhances misincorporation: temperature effects on nucleotide incorporation opposite a bulky carcinogen-DNA adduct by a Y-family DNA polymerase. J Biol Chem. 2007 Jan 12;282(2):1397-408.

**PI Kai-Ming Ho**

"Optimal doping control via subsurfactant epitaxy", C. Zeng, Z.Y. Zhang, K. van Benthem, M.F. Chisholm, and H.H. Weitering, Phys. Rev. Lett. 100, 066101 (2008).

"Crystallographic phase transition and island height selection in In/Si(111) growth",J. Chen, M. Hupalo, M. Ji, C. Z. Wang, K. M. Ho, and M. C. Tringides, Phys. Rev. B, 77, 233302 (2008).

"Dopant-assisted concentration enhancement of substitutional Mn in Si and Ge, W. Zhu, Z. Y. Zhang, and E. Kaxiras, Phys. Rev. Lett. 100, 027205 (2008).

"Stability of metallic thin films studied with a free electron model", B. Wu and Z. Y. Zhang, Phys. Rev. B 77, 035410 (2008).

"Calcium as the superior coating metal in functionalization of carbon fullerenes for high-capacity hydrogen storage", M. Yoon, S. Yang, C. Hicke, E. G. Wang, D. Geohegan, and Z. Y. Zhang , Phys. Rev. Lett. 100, 206806 (2008).

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

"Step Line Tension and Step Morphological Evolution on the Si(111) (1x1) Surface," A.B. Pang, K.L. Man, M.S. Altman, T.J. Stasevich, F. Szalma, and T.L. Einstein, Phys. Rev. B 77, 115424 (2008).

"Strongly-Driven Coarsening of Height-Selected Pb Islands on Si(111)", Maozhi Li, J. W. Evans, C. Z. Wang, M. Hupalo, M. C. Tringides, T.-L. Chan, and K. M. Ho, Surf. Sci. Lett. 601 (23) L140-L144 (2007).

"Analytic Formulas for the Orientation Dependence of Step Stiffness and Line Tension: Key Ingredients for Numerical Modeling," T.J. Stasevich and T.L. Einstein, [SIAM-] Multiscale Model. Simul. 6, 90-100 (2007).

"Scanning tunneling microscopy and density functional theory study of initial bilayer growth of Ag films on NiAl(110)" B. Unal, F. Qin, Y. Han. D.-J. Liu, D. Jing, A.R. Layson, C.J. Jenks, J.W. Evans, P.A. Thiel, Phys. Rev. B 76, 195410(2007).

"Synthesis of Carbon Nanotubes by Rolling Up Patterned Graphene Nanoribbons Using Selective Atomic Adsorption", Decai Yu and Feng Liu, Nano Lett. 7, 3046(2007).

"Size- and strain-dependent electronic structures in H-passivated Si [112] nanowires", Li Huang, Ning Lu, Jia-An Yan, Mei-Yin Chou, C. Z. Wang, K. M. Ho, J. Phys. Chem. C Accepted

"Concerted diffusion, clustering, and magnetic properties of Mn dopants on a 2x2-T4 GaN(0001) substrate", Shiqiang Hao and Zhenyu Zhang, Phys Rev. Lett. 99, 166101 (2007).

"Upward self-diffusion of adatoms and small clusters on facets of fcc metal (110) surfaces", Haili Yang, Qiang Sun, Zhenyu Zhang, and Yu Jia, Phys. Rev. B 76, 115417 (2007).

"Metal-diboride nanotubes as high-capacity hydrogen storage media", S. Meng, E. Kaxiras, Z. Y. Zhang, Nano Lett, 7 (3), 663 (2007).

"Formation of Carbon Nanotube Semiconductor-Metal Intramolecular Junctions by Self-Assembly of Vacancy Defects", Gun-Do Lee, C. Z. Wang, Jaejun Yu, Euijoon Yoon, Nong-Moon Hwang, Kai-Ming Ho, Phys. Rev. B 76, 165413 (2007).

"Tuning the quantum stability and superconductivity of ultrathin metal alloys", M. M Ozer, Y. Jia, Z. Y. Zhang , J. R. Thompson, H. H. Weitering, SCIENCE 316 (5831): 1594-1597 2007

"Dynamics of step bunching in heteroepitaxial growth on vicinal substrates", M. Yoon, H. N. Lee, W. Hong, H. M. Christen , Z. Y. Zhang, Z. G. Suo, Phys. Rev. Lett. 99 (5): 055503 (2007)

"Initial interactions between water molecules and Ti-adsorbed carbon nanotubes, Y. Lei, Z. X. Guo, W. Zhu, S. Meng, and Z. Y. Zhang, Appl. Phys. Lett. 91, 161906 (2007)

"Charged fullerenes as high-capacity hydrogen storage media," M. Yoon, S. Yang, E. G. Wang, and Z. Y. Zhang, Nano Lett. 7, 2578 (2007).

**PI Roald Hoffmann**

The double-diamond structure for NaAl: Hume-Rothery reasoning at work, Ji Feng, Roald Hoffmann and N. W. Ashcroft, submitted to Physical Review Letters

## I

**PI Hong Im**

P. Narayanan, A. Trouve, "Radiation-driven flame weakening effects in sooting turbulent diffusion flames," Proc. Combust. Inst. 32 (2008), in press.

D.O. Lignell, J.H. Chen, P.J. Smith, T. Lu, C.K. Law, "The effect of flame structure on soot formation and transport in turbulent nonpremixed flames using direct numerical simulation," Combust. Flame 151 (2007) 2-28.

**PI Valerie Izzo**

V. A. Izzo, D. G. Whyte, R. S. Granetz, P. B. Parks, E. M. Hollmann, L. L. Lao, and J. C. Wesley, "Magnetohydrodynamic simulations of massive gas injection into Alcator C-Mod and DIII-D plasmas" Physics of Plasmas 15, 056109 (2008)

## J

**PI Stephen Jardin**

Jardin, Stephen J. Breslau, C. Sovinec, and S. C. Jardin, "An Improved Tokamak Sawtooth Benchmark for 3D Nonlinear MHD", Communications in Computational Physics, 4, p647-658 (2008)

H. R. Strauss, B. Hientzsh, J. Chen, "A spectral element implementation for the M3D extended MHD code", Communications in Computational Physics, 4, p506-518 (2008)

S. C. Jardin, N. Ferraro, X. Luo, J. Chen, J. Breslau, et al, "The M3D-C1 approach to simulating 3D 2-fluid magnetohydrodynamics in magnetic fusion experiments", Journal of Physics: Conference Series 125 (2008) 012044

S. R. Hudson and J. Breslau, "Temperature contours and ghost services for chaotic magnetic fields", Phys Rev Lett 100 095001 (2008)

S. Jardin, J. Breslau, N. Ferraro, "A high-order implicit finite element method for integrating the two-fluid magnetohydrodynamic equations in two dimensions", J. Comput. Phys. 226 p 2146-2174 (2007)

F. Najmabadi, A. R. Raffray, ARIES-CS Team, "The ARIES-CS Compact Stellarator Fusion Power Plant," Fusion Science and Technology, 54, 3, 655 (2008).

L. P. Ku, P. R. Garabedian, J. Lyon et al., "Physics Design for ARIES-CS," Fusion Science and Technology, 54, 3, 673 (2008).

J. F. Lyon, L. P. Ku, L. El-Guebaly et al., "Systems Studies and Optimization of the ARIES-CS Power Plant," Fusion Science and Technology, 54, 3, 694 (2008).

T. K. Mau, T. B. Kaiser, A. A. Grossman et al., "Divertor Configuration and Heat Load Studies for the ARIES-CS Fusion Power Plant," Fusion Science and Technology, 54, 3, 771 (2008).

L. El-Guebaly, P. Wilson, d. Henderson et al., "Designing ARIES-CS Compact Radial Build and Nuclear System: Neutronics, Shielding and Activation," Fusion Science and Technology, 54, 3, 747 (2008).

Reynolds, Samtaney, Woodward, "Operator based preconditioning of stiff hyperbolic systems", SIAM J. of Scientific Computing, sub judice.

**PI Julius Jellinek**

STATIC POLARIZABILITIES AND OPTICAL ABSORPTION SPECTRA OF GOLD CLUSTERS (Au_n, n=2-14 and 20) FROM FIRST PRINCIPLES J. C. Idrobo, W. Walkosz, S. F. Yip, S. Ogut, J. Wang, and J. Jellinek Phys. Rev. B 76, 205422(1-12) (2007)

SITE-SPECIFIC ANALYSIS OF DIELECTRIC PROPERTIES OF FINITE SYSTEMS K. A. Jackson, M. Yang, and J. Jellinek J. Phys. Chem. C 111, 17952-17960 (2007) (R. E. Smalley Memorial Issue)

PRESSURE AND SIZE EFFECTS IN ENDOHEDRALLY CONFINED HYDROGEN CLUSTERS J. Soullard, R. Santamaria, and J. Jellinek J. Chem. Phys. 128, 064316(1-7) (2008)

NANOALLOYS: FROM THEORY TO APPLICATIONS OF ALLOY CLUSTERS AND NANOPARTICLES R. Ferrando, J. Jellinek, and R. L. Johnston Chem. Rev. 108, 845-910 (2008)

NANOALLOYS: TUNING PHYSICAL AND CHEMICAL PROPERTIES THROUGH SIZE AND COMPOSITION J. Jellinek Faraday Discuss. 138, 11-35 (2008)

SITE-SPECIFIC ANALYSIS OF RESPONSE PROPERTIES OF SODIUM CLUSTERS K. A. Jackson, M. Yang, and J. Jellinek in "Latest Advances in Atomic Cluster Collisions: Structure and Dynamics from Nuclear to the Biological Scale", J.-P. Connerade and A. V. Solov'yov, Eds., Imperial College Press, London, 2008, pp. 72-86

OPTICAL ABSORPTION SPECTRA OF INTERMEDIATE SIZE SILVER CLUSTERS FROM FIRST PRINCIPLES K. Baishya, J. C. Idrobo, S. Ogut, M. Yang, K. Jackson, and J. Jellinek Phys. Rev. B 78, 075439(1-9), (2008)

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

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", AIP Press (in press)

**PI Puru Jena**

Li, S. and Jena, P.: “"Dehydrogentaion from Ti-activated Sodium Alanate" in Materials Issues in a Hydrogen Economy, eds. P. Jena, A. K. Kandalam, and Q. Sun, World Scientific (2009) (in press).

Li, S. and Jena, P.: "Origin of the anatase to rutile phase conversion in metal doped TiO2", submitted to Phys. Rev. Lett.

**PI Chueng-Ryong Ji**

H.~M.~Choi and C.~R.~Ji, %``Conformal Symmetry and Pion Form Factor: Space- and Time-like Region,'' Phys.\ Rev.\ D {\bf 77}, 113004 (2008) [arXiv:0803.2604 [hep-ph]].

J.~Yu, T.~Wang, C.~R.~Ji and B.~Q.~Ma, %``Zero-Mode Contribution in Nucleon-Delta Transition,'' Phys.\ Rev.\ D {\bf 76}, 074009 (2007) [arXiv:0708.0172 [hep-ph]].

H.~M.~Choi and C.~R.~Ji, %``Perturbative QCD analysis of exclusive $J/\psi+\eta_c$ production in %$e^+e^-$ annihilation,'' Phys.\ Rev.\ D {\bf 76}, 094010 (2007) [arXiv:0707.1173 [hep-ph]].

**PI De-en Jiang**

Jiang, D. E.*; Dai, S. "Circumacenes versus periacenes: boundary shape and critical size." Chemical Physics Letters, submitted.

Jiang, D. E.*; Du, M. H.; Dai, S. "First principles study of the graphene/Ru(0001) interface."Journal of Chemical Physics, submitted.

Jiang, D. E.*; Luo, W. D.; Tiago, M. L.; Dai, S. "In Search of a Structural Model for a Thiolate-protected Au38 Cluster." J. Phys. Chem. C, ASAP.

Jiang, D. E.*; Dai, S. "First principles molecular dynamics simulation of a task-specific ionic liquid based on silver-olefin complex: atomistic insight into separation process." J. Phys. Chem. B, 112, 10202 (2008).

Jiang, D. E.*; Dai, S. "Spin States of Zigzag-edged Mobius Graphene Nanoribbons from First Principles." J. Phys. Chem. C, 112, 5348 (2008).

Jiang, D. E.*; Tiago, M. L.; Luo, W. D.; Dai, S. "The 'Staple' Motif: a Key to Stability of Thiolate-Protected Gold Nanoclusters." J. Am. Chem. Soc. (Communication), 130, 2777 (2008).

Jiang, D. E.*; Dai, S. "Electronic ground state of higher acenes." J. Phys. Chem. A, 112, 332 (2008).

Chen, Z. F.*; Jiang, D. E.*; Lu, X.; Bettinger, H. F.; Dai, S.; Schleyer, P. v. R.; Houk, K. N. "Open-Shell Singlet Character of Cyclacenes and Short Zigzag Nanotubes." Org. Lett., 9, 5449 (2007).

**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, Impacts of background ozone production on Houston and Dallas, TX Air Quality during the TexAQS field mission, Submitted to J. Geophy. Res., Oct, 2008.

**K**

**PI Andrey Kalinichev**

P.Kumar, A.G.Kalinichev, R.J.Kirkpatrick (2007) Dissociation of carbonic acid: Gas phase energetics and mechanism from ab initio metadynamics simulations. J.Chem.Phys., 126, 204315-1-7.

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

**PI Martin Karplus**

Intrinsic Motions Along An Enzymatic Reaction Trajectory, Nature 450, 838-U13 (2007), by V. Thai, K. Henzler-Wildman, M. Lei, M. Wunderlich, M. Wolf-Watz, T. Fenn, E. Pozharski, M. A. Wilson, G. A. Petsko, M. Karplus, C. G. Hubner and D. Kern.

A Hierarchy of Timescales in Protein Dynamics Linked to Enzyme Catalysis, Nature, 450, 913-U27 (2007), by K. Henzler-Wildman, M. Lei, V. Thai, M. Karplus, C. G. Hubner and D. Kern.

How Subunit Coupling Produces the gamma-Subunit Rotary Motion in F1-ATPase, Proc. Natl. Acad. Sci. USA 105, 1192-1197 (2008), by J. Pu and M. Karplus.

The Elastic Properties of the Structurally Characterized Myosin II S2 Sub-domain: A Molecular Dynamics and Normal Mode Analysis, Biophys. J. 94, 3779-3789 (2008), by I. Adamovic, S. M. Mijailovich and M. Karplus.

The Human Cytomegalovirus UL44 C Clamp Wraps Around DNA, Structure 16, 1214-1225 (2008), by G. Komazin-Meredith, R. J. Petrella, W. L. Santos, D. J. Filman, J. M. Hogle, G. L. Verdine, M. Karplus and D. M. Coen.

Bayesian Estimates of Free Energies from Nonequilibrium Work Data in the Presence of Instrument Noise, J. Chem. Phys. 129, 024102 (2008), by P. Maragakis, F. Ritort, C. Bustamante, M. Karplus and G. E. Crooks.

A Differential Fluctuation Theorem, J. Phys. Chem. B 112, 6168-6174 (2008), by P. Maragakis, M. Spichty and M. Karplus.

Force Generation in Kinesin Hinges on Cover-Neck Bundle Formation, Structure 16, 62-71 (2008), by W. Hwang, M. J. Lang and M. Karplus.

The Signaling Pathway of PDZ Domains, Proteins: Struct. Funct. Bioinformatics, in press, by Y. Kong and M. Karplus.

The Mechanism of the Translocation Step in DNA Replication by DNA Polymerase I: A Computer Simulation Analysis, submitted, by Andrei A. Golosov, Martin Karplus, Joshua Warren, and Lorena Beese.

**PI Paul Kent**

"Charge-order fluctuations in one-dimensional silicides". Changgan Zeng, P. R. C. Kent, Tae- Hwan Kim, An-Ping Li, and Hanno H. Weitering. Nature Materials 7 539 (2008).

"The origin of nanoscale phase stability reversals in titanium oxide polymorphs" Daniel R. Hummer, James D. Kubicki, Paul R. C. Kent, Jeffrey E. Post, and Peter J. Heaney. Submitted to Physical Review Letters (2008)

"Computational Challenges of Large-Scale Long-Time First-Principles Molecular Dynamics". P. R. C. Kent. Journal of Physics: Conference Series 125 012058 (2008).

"Neutral and charged excitations in carbon fullerenes from first-principles many-body theories". Murilo L. Tiago, P.R.C. Kent, Randolph Q. Hood, and Fernando A. Reboredo. Journal of Chemical Physics 129 084311 (2008).

"An effective potential for graphene-fluid interactions" Zhao XC. Langmuir. Submitted (2008).

"Electrophoresis of ssDNA through Nanoelectrode Gaps from Molecular Dynamics: Impact of Gap Width and Chain Length" Christina M. Payne, Xiongce Zhao, and Peter T. Cummings. J. Phys. Chem. B ASAP 10.1021/jp802258v (2008)

"Molecular simulation evidence for processive motion of Trichoderma reesei Cel7A during cellulose depolymerization" Zhao X, Rignall TR, McCabe C, Adney WS, and Himmel ME. Chem. Phys. Lett. 460 284 (2008)

"Interaction of C-60 derivatives and ssDNA from simulations", X. C. Zhao. J. Phys. Chem. C 112 8898 (2008)

"A molecular dynamics simulation study on trapping ions in a nanoscale Paul trap" X. C. Zhao, P. S. Krstic Nanotechnology 19 195702 (2008)

"Molecular dynamics simulation of ss-DNA translocation between copper nanoelectrodes incorporating electrode charge dynamics" Payne CM, Zhao X, Vlcek L, and Cummings PT. J. Phys. Chem. B 112 1712 (2008)

"Controlled translocation of DNA segments through nanoelectrode gaps from molecular dynamics" X. Zhao, C. M. Payne, P. T. Cummings. J. Phys. Chem. C 112 8 (2008)

"Molecular simulations of stretching gold nanowires in solvents" Q. Pu, Y.S. Leng, X.C. Zhao, P. T. Cummings Nanotechnology 18 424007 (2007)

"Single strand DNA molecule translocation through nanoelectrode gaps" X. C. Zhao, C. M. Payne, P. T. Cummings, J. W. Lee. Nanotechnology 18 424018 (2007)

"A first-principles investigation of the effect of Pt cluster size on CO and NO oxidation intermediates and energetics" Y. Xu, R.B. Getman, W.A. Shelton, W.F. Schneider, Physical Chemistry Chemical Physics, in press (2008)

"Bimetallic and ternary alloys for improved oxygen reduction catalysis" A.U. Nilekar, Y. Xu, J. Zhang, M.B. Vukmirovic, K. Sasaki, F. Uribe, R.R. Adzic, M. Mavrikakis, Topics in Catalysis, 46 (2007) 276-284.

"Influence of preformed Asp23-Lys28 salt bridge on the conformational fluctuations for rates of fibril formation" G. Reddy, J.E. Straub, D. Thirumalai. Submitted to J. Molecular Biology (2008)

"Simulation of Fen-doped C60 Monolayer on h-BN/Ni (111)". Lan Li, and H. P. Cheng. Submitted to Physical Review B (2008)

"Insensitivity of superconducticity to disorder in the cuprates", A.F. Kemper, D.G.S.P. Doluweera, T.A. Maier, M. Jarrell, P.J.Hirschfeld, H.P.Cheng. Submitted to Phys. Rev. Lett. (2008)

"Finding stable alpha-quartz (0001) surface structures via simulation" Y. Chen, H. P. Cheng. Submitted to Appl. Phys. Lett. (2008) (continued in 18.2)

**PI Kwiseon Kim**

P. Piquini, P. A. Graf, and A. Zunger, 2008, Band-gap Design of Quaternary (In,Ga)(As,Sb) Semiconductors Via the Inverse-band-structure Approach, Phys. Rev. Lett. Vol. 100, 2008; pp. 186403.

P. A. Graf and W. B. Jones, K. Kim, Optimization of semiconductor alloy properties using the virtual crystal approximation, J. Comput. Phys. (accepted).

P. A. Graf, W. B. Jones, and Kwiseon Kim, 2008, A Scatter Search Based Inverse Band Structure Method for Semiconductor Alloys, J. Comput. Phys. (submitted).

Chang, CH and Kim, K. (in review) Density Functional Theory Calculation of Bonding and Charge Parameters for Molecular Dynamics Studies on [FeFe] Hydrogenases. J. Chem. Theory Comput.

**PI Joanna Kiryluk**

A. Achterberg A. et al., "Search for neutrino-induced cascades from gamma-ray bursts with AMANDA", the Astrophysical Journal 664, 397 (2007).

M. Ackermann et al.,"Search for ultra high-energy neutrinos with AMANDA-II", the Astrophysical Journal 675, 1014 (2008).

A. Achterberg et al.,"The Search for Muon Neutrinos from Northern Hemisphere Gamma-Ray bursts with AMANDA", the Astrophysical Journal, 674, 357 (2008).

A. Achterberg et al.,"Multi-year search for a diffuse flux of muon neutrinos with AMANDA-II", Phys. Rev. D76, 042008 (2007); Erratum-ibid. D77, 089904 (2008).

A. Achterberg et al.,"Detection of atmospheric muon neutrinos with the IceCube 9-string detector", Phys. Rev. D76, 027001 (2007). Klein,

**PI Richard Klein**

Offner, S. S. R., Klein, R. I., & McKee. C. F. 2008, ApJ, in press.

Offner, S. S. R., Krumholz, M. R., Klein, R. I. & McKee, C. F. 2008, AJ, 136, 440.

Offner, S. S. R. & Krumholz, M. R. 2008, ApJL, submitted.

**PI Kwok Ko**

Volkan Akcelik, Kwok Ko, Lie-Quan Lee, Zenghai Li, Cho-Kuen Ng, Liling Xiao, Shape determination for deformed electromagnetic cavities, Journal of Computational Physics, 227 (3), Pages 1722-1738, 2008

C Ng, et al, Design and optimization of large accelerator systems through high-fidelity electromagnetic simulations, J, of Physics, Conf. Series. 125 (2008) 012003

L Lee, et al, Computational science research in support of petascale electromagnetic modeling, J, of Physics, Conf. Series. 125 (2008) 012077

J Qiang, M Borland, A Kabel, R Li, R Ryne, E Stern, Y Wang, H Wasserman and Y Zhang3, "SciDAC advances in beam dynamics simulation: From light sources to colliders". Journal of Physics: Conference Series 125 (2008) 012004

X Luo, M Shephard, L-Q Lee, C Ng and L Ge, "Curved mesh correction and adaptation tool to improve COMPASS electromagnetic analyses". Journal of Physics: Conference Series 125 (2008) 012082

**PI Boris Kogan**

Samade R, Weiss JN, Shivkumar K, Kogan B. Defibrillation failure and tachycardia-induced early afterdepolarizations: a simulation study. In: ICCB'08, IAENG Press, San Francisco, CA, 2008.

Huffaker RB. Tachycardia-induced early afterdepolarizations: ionic mechanisms and effects on wave propagation in 1, 2, and 3D tissue (computer simulation study), in: Computer Science, University of California, Los Angeles, CA, 2008.

**PI Joel Koplik**

Y. Yan, J. F. Morris and J. Koplik, Interaction of two particles in confined linear shear flow at finite Reynolds number, Phys. Fluids 19, 113305 (2007).

Y. Yan and J. Koplik, Flow of power-law fluids in self-affine fracture channels, Phys. Rev. E 77, 036315 (2008)

Y. Yan and J. Koplik, Transport and sedimentation of suspended particles in inertial pressure-driven flow, submitted to Phys. Fluids (2008).

**PI V. Rao Kotamarthi**

Zubrow, A., L. Chen, and V. R. Kotamarthi, EAKF-CMAQ: Introduction and evaluation of a data assimilation for CMAQ based on the ensemble adjustment Kalman filter, J. Geophys. Res., 113, D09302, doi:10.1029/2007JD009267, 2008

**PI Henry Krakauer**

Finite-size correction in many-body electronic structure calculations, Hendra Kwee, Shiwei Zhang and Henry Krakauer, Physical Review Letters 100, 126404 (2008).

**PI Petr Kral**

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

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

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

**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.

C S Chang, S Klasky, J Cummings, R Samtaney, A Shoshani, et al. (2008) Toward a first-principles integrated simulation of tokamak edge plasmas, J. Phys.: Conf. Ser. 125 (2008) 012042.

**PI Leeor Kronik**

S. Kemmel and L. Kronik, Rev. Mod. Phys. 80, 3 (2008)

**PI Scott Kruger**

V.A. Izzo and I. Joseph, Nucl. Fusion 48 (2008.) 115004.

V. A. Izzo, D. G. Whyte, R. S. Granetz, P. B. Parks, E. M. Hollmann, L. L. Lao, and J. C. Wesley, PHYSICS OF PLASMAS 15, 056109 (2008)

S. Shasharina, J. R. Cary, A. Hakim, G. R. Werner, S. Kruger, A. Pletzer, "FACETS: A Multiphysics Parallel Component Framework", COMPFRAME 2008 (Karlsruhe, Germany).

J R Cary, J Candy, R H Cohen, S Krasheninnikov, D C McCune, D J Estep, J Larson, A D Malony, A. Pankin, P H Worley, J A Carlsson, A H Hakim, P Hamill, S Kruger, M Miah, S Muzsala, A Pletzer, S Shasharina, D Wade-Stein, N Wang, S. Balay, L McInnes, H Zhang, T Casper, L Diachin, T Epperly, T D Rognlien, M R Fahey, J Cobb, A Morris, S Shende, G W Hammett, K Indireshkumar, D Stotler, A Yu Pigarov, First results from core-edge parallel composition in the FACETS project, J. Physics: Conf. Series, accepted (2008).

## L

**PI Andrew Lacis**

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).

Q. Ma, R. H. Tipping, C. Boulet, and J. Bonamy, Vibration-Dependent Trajectories and Their Effects on Vibrational Dephasing, J. Mol. Spec. 243, 105 (2007).

Q. Ma, R. H. Tipping, and C. Boulet, Modification of the Robert-Bonamy Formalism in Calculating Lorentzian Half-Widths and Shifts. J.Q.S.R.T, 103, 588 (2007).

A. Goldman, R. H. Tipping, Q. Ma, C. D. Boone, P. F. Bernath, P. Demoulin, F. Hase, M. Schneider, J. W. Hannigan, M. T. Coffey, and C. P. Rindland, On the Line Parameters for the X1??g+ (1-0) Infrared Quadrupolar Transitions of 14N2. J.Q.S.R.T. 103, 168 (2007).

**PI Jean-Francois Lamarque**

Lamarque, J.-F., D. E. Kinnison, P. G. Hess, and F. M. Vitt (2008), Simulated lower stratospheric trends between 1970 and 2005: Identifying the role of climate and composition changes, J. Geophys. Res., 113, D12301, doi:10.1029/2007JD009277.

Lamarque, J.-F. and S. Solomon, Identifying the role of vertical velocity trends in explaining tropical lower stratospheric trends in ozone. Submitted for publication in Geophys. Res. Lett., 2008.

**PI Don Lamb**

**PI Uzi Landman**

Bonding, Conductance, and Magnetization of Oxygenated Au Nanowires, Chun Zhang, Robert N. Barnett, and Uzi Landman, Phys. Rev. Lett. 100, 046801 (2008).

Electric Field Control of Structure, Dimensionality, and Reactivity of Gold Nanoclusters on Metal-Supported MgO Films, Bokwon Yoon and Uzi Landman, Phys. Rev. Lett. 100, 056102 (2008)

Nonuniversal Transmission Phase Lapses through a Quantum Dot: An Exact Diagonalization of the Many-Body Transport Problem, Leslie O. Baksmaty, Constantine Yannouleas, and Uzi Landman, Phys. Rev. Lett. 101, 136803 (2008)

**PI Michael Langston**

Eblen, J.D., Gerling, I.C., Saxton, A.M., Wu, J., Snoddy, J.R., Langston, M.A., 2008. Graph Algorithms for Integrated Biological Analysis, with Applications to Type 1 Diabetes Data. In: Clustering Challenges in Biological Networks, W.A. Chaovalitwongse, ed. World Scientific, accepted for publication.

Langston, M.A., Perkins, A.D., Saxton, A.M., Scharff, J.A., Voy, B.H., 2008. Innovative Computational Methods for Transcriptomic Data Analysis: A Case Study in the Use of FPT for Practical Algorithm Design and Implementation. The Computer Journal. 51, 26-38.

Zhang, Y., Chesler, E.J., Langston, M.A., 2008. On Finding Bicliques in Bipartite Graphs: a Novel Algorithm with Application to the Integration of Diverse Biological Data Types. In: Proceedings, Hawai'i International Conference on System Sciences, Big Island, HI. Lany, Stephan

**PI Stephan Lany**

K. Biswas, A. Franceschetti, and S. Lany, "Generalized valence-force-field model of (Ga,In)(N,P) ternary alloys" Phys. Rev. B 78, 085212 (2008).

**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, "On the nature of transport across sheared zonal flows in electrostatic ion-temperature-gradient gyrokinetic plasma turbulence", Phys. Rev. Letters., Submitted for Publication, May 14, 2008.

**PI Frank Lee**

Magnetic moments of vector, axial, and tensor mesons in lattice QCD F.X. Lee, S. Moerschbacher, W. Wilcox, submitted to Phys. Rev. D. hep-lat/0807.4150

Tests of Electric Polarizability using 2+1 Flavor Dynamical Configurations F.X. Lee, V. Guerrero, W. Wilcox, and J. Christensen, Proceedings of Science (Lattice 2008) 150

Maximum entropy analysis of lattice QCD correlation functions T. Harsono and F.X. Lee, Proceedings of Science (Lattice 2008)

The background field method on the lattice A. Alexandru and F.X. Lee, Proceedings of Science (Lattice 2008)

Octet baryon magnetic moments from QCD sum rules Lai Wang, F.X. Lee, Phys. Rev. D 78, 013003 (2008). arXiv:0804.1779 [hep-ph]

Dominance of Sign Geometry and the Homogeneity of the Fundamental Topological Structure I. Horvath, A. Alexandru and T. Streuer, arXiv:0809.2834 [hep-lat].

Classical Limits of Scalar and Tensor Gauge Operators Based on the Overlap Dirac Matrix A. Alexandru, I. Horvath and K.F. Liu, accepted for publication in Phys. Rev. D, arXiv:0803.2744 [hep-lat].

New results using the canonical approach to finite density QCD A. Li, A. Alexandru and K.F. Liu, Proceedings of Science (LAT07), 203 (2007), arXiv:0711.2692 [hep-lat].

Finite density simulations using a determinant estimator A. Alexandru, A. Li and K.F. Liu, Proceedings of Science (LAT07), 167 (2007), arXiv:0711.2678 [hep-lat].

Gauge Field Strength Tensor from the Overlap Dirac Operator K.F. Liu, A. Alexandru and I. Horvath, Phys. Lett. B 659, 773 (2008), arXiv:hep-lat/0703010.

**PI T. S. Harry Lee**

Dynamical Coupled-channel Model of \pi N scattering in the W <= 2 GeV nucleon resonance region B. Julia-Diaz, T.-S.H. Lee, A. Matsuyama, T. Sato Phys.Rev.C76, 065201 (2007)

Dynamical coupled-channels effects on pion photoproduction B. Julia-Diaz, T.-S.H. Lee, A. Matsuyama, T. Sato, L.C. Smith Phys.Rev.C77, 045205 (2008).

Coupled-channels study of the $\pi^- p \rightarrow \eta n$ process J. Durand, B. Julia-Diaz, T.-S.H. Lee, B. Saghai, T. Sato Phys.Rev.C78, 025204 (2008).

Regge Approach to Charged-Pion Photoproduction at Invariant Energies above 2-GeV A. Sibirtsev, J. Haidenbauer, S. Krewald, T.-S.H. Lee, U.-G. Meissner, and A.W. Thomas Phy.Eur.Phys.J.A34, 49 (2007)

Measurement of the polarized gamma p ->K \Lambda reaction at backward angles. K. Hicks.., . Julia-Diaz, T.-S. H. Lee et al. Phys.Rev.C76 042201 (2007)

Extraction of Resonances from Meson-Nucleon Reactions N. Suzuki, T. Sato, T.-S.H. Lee submitted to Phys. Rev. C, e-Print: arXiv:0806.2043 [nucl-th]

Dynamical coupled-channels study of \pi N -> \pi \pi N reactions H. Kamano, B. Julia-Diaz, T.-S.H. Lee, A. Matsuyama, T. Sato submitted to Phys. Rev. C, e-Print: arXiv:0807.2273 [nucl-th]

**PI Wei-li Lee**

W. W. Lee et al., "Nonlinear Turbulent Transport in Magnetic Fusion Plamsas," submitted to Computational Science and Discovery (2008).

W. W. Lee et al., "Multiscale Turbulence Simulation and Steady State Transport," Invited talk, Joint Varenna-Lausanne International Workshop on Theory of Fusion Plasmas, Varenna, Italy, August 25-29, 2008.

W. X. Wang et al., "Relationship between Toroidal Momentum and Heat Transport in Tokamaks" Proceedings of 35th EPS Plasma Physics Conference, 9 - 13 June 2008, Hersonissos, Crete, Greece

W. X. Wang et al., "Interaction between Turbulence and Neoclassical Dynamics and Its Effect on Tokamak Transport: Gyrokinetic Simulations and Theory" Proceedings of 22nd IAEA Fusion Energy Conference, 13-18 October 2008, Geneva, Switzerland

W. X. Wang et al., "Gyrokinetic Turbulence Driven Toroidal Momentum Transport and Comparison to Experimental Observations", Invited talk, 50th Annual Meeting of American Physical Society, the Division of Plasma Physics, November 17-21, 2008, Dallas, Texas

**PI Xuhui Lee**

Huang, J., X. Lee, E. G. Patton: 2008, "A modelling study of flux imbalance and the influence of entrainment in the convective boundary layer", Boundary-Layer Meteorology, 127, pp. 273-292, DOI: 10.1007/s10546-007-9254-x.

Huang, J., X. Lee, E. G. Patton: 2008, "Dissimilarity of scalar transport in the convective boundary layer in inhomogeneous landscapes", submitted to Boundary-Layer Meteorology.

**PI Sanjiva Lele**

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

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

**PI Yongsheng Leng**

Pu, Q., Leng, Y.S., Cummings, P.T. "The rate-dependent energy release mechanism of gold nanowires under elongation" (submitted to JACS, under review)

Leng, Y.S. "Hydration force and dynamic squeeze-out of hydration water under subnanometer confinement," Journal of Physics: Condensed Matter,20, 354017 (2008).

Leng, Y. S., Dyer, P. J., Krsti??, P. S., Harrison, R. J., and Cummings, P. T. "Calibration of chemical bonding between benzenedithiolate and gold: the effects of geometry and size of gold clusters," Molecular Physics 105, 293 (2007).

Pu, Q., Leng, Y.S. Tsetseris, L., Park, H.S., Pantelides, S.T. and Cummings, P.T. "Molecular dynamics simulations of stretched gold nanowires --- the relative utility of different semiempirical potentials," Journal of Chemical Physics, 126, 144707 (2007).

Pu, Q., Leng, Y.S., Zhao, X.C., and Cummings, P.T., "Molecular simulations of stretching gold nanowires in solvents," Nanotechnology 18, 424007 (2007).

**PI William Lester**

B. Austin, A. Aspuru-Guzik, R. Salomon-Ferrer, and W. A. Lester, Jr., Linear Scaling Evaluation of the Local Energy in Quantum Monte Carlo, in Proceedings of the Pacifichem Symposium on Advances in Quantum Monte Carlo, J. B. Anderson and S. M. Rothstein, eds., ACS Symposium Series 953, 55 (2007).

R. Prasad, N. Umezawa, D. Domin, R. Salomon-Ferrer, and W. A. Lester, Jr., Quantum Monte Carlo Study of First-Row Atoms using Transcorrelated Variational Monte Carlo Trial Functions, J. Chem. Phys. 126, 164109 (2007).

R. Whitesides, D. Domin, R. Salomon-Ferrer, W.A. Lester, Jr., and M. Frenklach, Graphene Layer Growth Chemistry: Five-Six-Ring Flip Reaction, J. Phys. Chem. A, 112, 2115 (2008).

M. T, Nguyen, M. H. Matus, W. A. Lester, Jr., and D. A. Dixon, Heats of Formation of Triplet Ethylene and Ethylidene, J. Phys. Chem. A, 112, 2082 (2008).

D. Domin, W. A. Lester, Jr., R. Whitesides, and M. Frenklach, Isomer Energy Differences for the C4H3 and C4H5 Isomers Using Diffusion Monte Carlo, J. Phys. Chem. A, 112, 2065 (2008).

D. Domin, B. Braida, and W. A. Lester, Jr, Breathing Orbital Valence Bond Method in Diffusion Monte Carlo: C-H Bond Dissociation of Acetylene, J. Chem. Phys. A, 112, 8964 (2008).

R. Olivares-Amaya, R. Salomon-Ferrer, W. A. Lester Jr., and C. Amador-Bedolla, "Creation of a GUI for Zori, a Quantum Monte Carlo program, using Rappture," Computing in Science and Engineering, submitted.

**PI Rui Li**

Advances on ELIC Design Studies [556 KB] S.A. Bogacz, P. Chevtsov, Ya. Derbenev, P. Evtushenko, G. Krafft, A. Hutton, R. Li, L. Merminga, J. Musson, B. Yunn, Y. Zhang, Jefferson Lab, Newport News, VA 23606, USA; H. Sayed, Old Dominion University, Norfolk, VA 23529, USA; J. Qiang, LBNL, Berkeley, CA 94720, USA Abstract http://cern.ch/AccelConf/e08/papers/wepp049.pdf

R. Li, "Curvature-induced bunch self-interaction for an energy-chirped bunch in magnetic bends", Phys. Rev. ST Accel. Beams, 11, 024401 (2008).

**PI Guang Lin**

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 review.

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 review.

Tartakovsky, D. M., M. Dentz, and P. C. Lichtner, Probability density functions for reactive transport in porous media, Water Resour. Res., (under review, 2008WR007383), 2008.

Wohlberg, B. E. and D. M. Tartakovsky, Delineation of geological facies from poorly differentiated data, Adv. Water Resour. (under review), 2008.

Neuman, S. P. and D. M. Tartakovsky, Perspective on theories of anomalous transport in heterogeneous media, Adv. Water Resour., (in press), 2008.

Short, M., L. Guadagnini, A. Guadagnini, D. M. Tartakovsky, and D. Higdon, Estimating preferential flow paths within an aquifer system, Bayesian Analysis, (under review) 2007.

Tartakovsky, A. M., D. Bolster, and D. M. Tartakovsky, Hydro-geophysical approach for identification of layered structures of the vadose zone from electrical resistivity data, Vadose Zone J., (in press), 2008.

Tartakovsky, A. M., D. M. Tartakovsky, and P. Meakin, Stochastic Langevin model for flow and transport in porous media, Phys. Rev. Lett., 101, 044502, 2008.

Dentz, M. and D. M. Tartakovsky, Four-point closure for transport in steady random flows, Phys. Rev. E, 77(6), 066307, doi:10.1103/PhysRevE.77.066307, 2008.

Winter, C. L. and D. M. Tartakovsky, A reduced complexity model for probabilistic risk assessment of groundwater contamination, Water Resour. Res., 44, W06501, doi:10.1029/2007WR006599, 2008.

Tartakovsky, D. M. and C. L. Winter, Uncertain future of hydrogeology, ASCE J. Hydrologic Engrg., 13(1), 37 -- 39, 2008.

Tartakovsky, D. M., B. E. Wohlberg, and A. Guadagnini, Nearest neighbor classification for facies delineation, Water Resour. Res., 43, W07201, doi:10.1029/2007WR005968, 2007.

Srinivasan, G., D. M. Tartakovsky, B. A. Robinson, and A. B. Aceves, Quantification of uncertainty in geochemical reactions, Water Resour. Res., 43, W12415, doi:10.1029/2007WR006003, 2007.

Neuman, S. P., A. Blattstein, M. Riva, D. M. Tartakovsky, A. Guadagnini, and T. Ptak, Type curve interpretation of late-time pumping test data in randomly heterogeneous aquifers, Water Resour. Res., 43, W10421, doi:10.1029/2007WR005871, 2007.

Tartakovsky, D. M., Probabilistic risk analysis in subsurface hydrology, Geophys. Res. Lett., 34, L05404, doi:10.1029/2007GL029245, 2007.

Sanchez-Vila, X. and D. M. Tartakovsky, Ergodicity of pumping tests, Water Resour. Res., 43, W03414, doi:10.1029/2006WR005241, 2007.

**PI Yu Lin**

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

Yoon, P. H., Y. Lin, X. Y. Wang, and A. T. Y. Lui, Drift instabilities for current sheet equilibrium with guide field, Phys. Plasmas, submitted, 2008.

Zhang, W., Z. Lin, P. H. Yoon, and X. Y. Wang, Two-fluid Formulation of Lower-Hybrid-Drift Instabilities in Current Sheet Equilibrium With a Guide Field, in press, Comm. Comput. Phys., 2008.

Lin, Y., X. Y. Wang, M. R. Brown, M. Schaffer, and C. D. Cothran, Modeling Swarthmore Spheromak Reconnection Experiment Using Hybrid Code, Plasma Physics and Controlled Fusion, 50(7), 074012, 2008.

**PI Zhihong Lin**

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).

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).

Reversed Shear Alfv??n Eigenmode Stabilization by Localized Electron Cyclotron Heating, M. A. Van Zeeland et al, Plasma Phys. Control. Fusion 50, 035009 (2008).

The physics of burning plasmas in toroidal magnetic field devices, F. Zonca, Intern. J. Modern Phys. A 23, 1165 (2008).

Basic physics of Alfv??n instabilities driven by energetic particles in toroidally confined plasmas, W. W. Heidbrink, Phys. Plasmas 15, 055501 (2008).

AWECS: A linear gyrokinetic delta-f particle-in-cell simulation code for the study of Alfv??nic instabilities in high-beta tokamak plasmas, A. Bierwage and L. Chen, Commun. Comput. Phys. 4, 457.

Central Flattening of the Fast-ion Profile in Reversed Shear DIII-D Profile in Reversed-Shear DIII-D Discharges, W. W. Heidbrink et al, Nuclear Fusion 48, 084001.

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

**PI Da-Jiang Liu**

Y. Han et al, "Kinetics of Facile Bilayer Island Formation at Low Temperature: Ag/NiAl(110)" Phys. Rev. Lett. vol 100, 116105 (2008).

Y. Han, J. W. Evans, and D.-J. Liu "Quantum stabilities and growth modes of thin metal films: unsupported and NiAl-supported Ag(110) and Ag(100)" Surf. Sci., vol 602, 2532 (2008).

M. Shen et al., "Novel self-organized structure of a Ag-S complex on the Ag(111) surface below room temperature", J. Phys. Chem. C, vol 112, 4281 (2008)

B. Unal, "Scanning tunneling microscopy and density functional theory study of initial growth of Ag films on NiAl(110)," Phys. Rev. B vol. 76 195410 (2007).

**PI Feng Liu**

Yong Han, "A jellium model analysis on quantum growth of metal nanowires and nanomesas", Front. Phys. China 3, 436 (2008).

Yong Han, Guang-Hong Lu, Byeong-Joo Lee, and Feng Liu, "Flat-surface, step- edge, facet-facet, and facet-step diffusion barriers in growth of a Pb mesa", Surf. Sci. 602, 2284 (2008).

Yong Han, Feng Liu, Shao-Chun Li, Jin-Feng Jia, Qi-Kun Xue, and Byeong-Joo Lee, "Kinetics of mesa overlayer growth: climbing of adatoms onto the mesa top", Appl. Phys. Lett. 92, 021909 (2008).

Yong Han and Feng Liu, "Coulomb sink effect on coarsening of metal nanostructures on surfaces", Front. Phys. China 3, 41 (2008).

Y. Han, M. Hupalo, M. C. Tringides, and Feng Liu, "Quantum modulation of island nucleation on top of a metal nanomesa", Surf. Sci. 602, 62 (2008).

Mobility of Charge Carriers in Biaxially Strained Silicon D. Yu, F. Liu (submitted)

Synthesis of carbon nanotubes by rolling up patterned graphene nanoribbons using selective atomic adsorption D. Yu, F. Liu, Nano Lett. 7, 3046-3050 (2007)

**PI Keh-Fei Liu**

[UK/06-14] K.F. Liu, A. Alexandru, I. Horvath, `Gauge Field Strength Tensor from the Overlap Dirac Operator', Phys. Lett. B659:773-782,2008, [hep-lat/0703010].

[UK/08-01] A. Alexandru , I. Horvath, K.F. Liu, `Classical Limits of Scalar and Tensor Gauge Operators Based on the Overlap Dirac Matrix' Phys. Rev. D, to appear, arXiv:0803.2744 [hep-lat].

[UK/08-04] K.F. Liu, `Challenges of Lattice Calculation of Scalar Mesons', AIP Conf. Proc. 1030, 305 (2008), arXiv:0805.3364 [hep-lat].

[UK/08-06] K.F. Liu, ` Neutron Electric Dipole Moment at Fixed Topology', submitted to PRD, arXiv:0807.1365 [hep-ph].

[UK/08-08] M. Deka, T. Streuer, T. Doi, S.J. Dong, T. Draper, K.F. Liu, N. Mathur, A.W. Thomas, `Moments of Nucleon's Parton Distribution for the Sea and Valence Quarks from Lattice QCD', submitted to Phys. Rev. D.

**PI Ping Liu**

M. J. Patterson, Y. Choi, P. Liu, M. G. White, "Dissociation of OCS on the Mo6S8+ Cluster Supported on Au(111)", submitted. J. X. Wang, H. Inada, L. Wu, Y. Zhu, Y. Choi, P. Liu, R. R. Adzic, "Structure-activity correlation for oxygen reduction on layer-by-layer grown Pd(core)-Pt(shell) nanoparticles", submitted.

**PI Stewart Loken**

ATLAS computing system commissioning: Real-time data processing and distribution tests. By A. Nairz, et al., J.Phys.Conf.Ser.110:092019,2008.

ATLAS inner detector alignment. By Tobias Gottfert. J.Phys.Conf.Ser.110:092012,2008.

Commissioning of the ATLAS offline software with cosmic rays. By ATLAS Collaboration J.Phys.Conf.Ser.110:092006,2008.

Overview and status of the ATLAS pixel detector. By ATLAS Collaboration J.Phys.Conf.Ser.110:092001,2008.

ATLAS discovery potential for Higgs bosons beyond the standard model. By ATLAS Collaboration J.Phys.Conf.Ser.110:072046,2008.

SUSY searches in early ATLAS data. By Davide Costanzo. J.Phys.Conf.Ser.110:072007,2008.

The ATLAS Experiment at the CERN Large Hadron Collider. By ATLAS Collaboration JINST 3 (2008) S0800.

**PI Charles Long**

Wang, Y., C. N. Long, L. R. Leung, J. Dudhia, S. McFarlane, J. H. Mather, and S. Ghan (2008) Evaluating high-resolution, regional cloud resolving simulations of the WRF ARW model for the TWP-ICE (Darwin, 2006), Journal of Geophysical Research-Atmospheres, submitted August, 2008.

Wang, Y., C. N. Long, L. R. Leung, and G. Thompson (2008) Improved cloud microphysical scheme in the WRF model from the TWP-ICE (Darwin, 2006), The U.S. Department of Energy Atmospheric Radiation Measurement Program Cloud Modeling Working Group Meeting, Princeton, New Jersey, USA, November 2008.

**PI Steven Louie**

H.J. Choi, M.L. Cohen, and S.G. Louie, "First-Principles Scattering-State Approach for Nonlinear Electrical Transport in Nanostructures," Phys. Rev. B 76, 155420 (2007).

F. Giustino, M.L. Cohen, and S.G. Louie, "Electron-Phonon Interaction Using Wannier Functions," Phys. Rev. B 76, 165108 (2007).

L. Yang, C.H. Park, Y.-W. Son, M.L. Cohen, and S.G. Louie, "Quasiparticle Energies and Band Gaps of Graphene Nanoribbons," Phys. Rev. Lett. 99, 186801 (2007).

Y.-W. Son, M.L. Cohen, and S.G. Louie, "Electric Field Effects on Spin Transport in Defective Metallic Carbon Nanotubes," Nano Letters 7, 3518 (2007).

R.B. Capaz, C.D. Spataru, S. Ismail-Beigi, and S.G. Louie, "Excitons in Carbon Nanotubes: Diameter and Chirality Trends," Phys. Stat. Sol. (b) 244, 4016 (2007).

F. Wang, D.J. Cho, B. Kessler, J. Deslippe, P.J. Schuck, S.G. Louie, A. Zettl, T.F. Heinz, and Y.R. Shen, "Observation of Excitons in One-Dimensional Metallic Single-Walled Carbon Nanotubes," Phys. Rev. Lett. 99, 227401 (2007).

B. Lee, L.-W. Wang, C.D. Spataru, and S.G. Louie, "Nonlocal Exchange Correlation in Screened-exchange Density Functional Methods," Phys. Rev. B 76, 245114 (2007).

Y.Y. Wang, E. Kioupakis, X. Lu, D. Wegner, R. Yamachika, J.E. Dahl, R.M.K. Carlson, S.G. Louie, and M.F. Crommie, "Spatially Resolved Electronic and Vibronic Properties of Single Diamondoid Molecules," Nature Mater. 7, 38 (2008).

P. Zhang, S. Saito, S.G. Louie, and M.L. Cohen, "Theory of the Electronic Structure of Alternating MgB2 and Graphene Layered Structures," Phys. Rev. B 77, 052501 (2008).

C.-H. Park, L. Yang, Y.-W. Son, M.L. Cohen, and S.G. Louie, "Anisotropic Behaviours of Massless Dirac Fermions in Graphene Under Periodic Potentials," Nature Physics 4, 213 (2008).

C.-H. Park, F. Giustino, J.L. McChesney, A. Bostwick, T. Ohta, E. Rotenberg, M.L. Cohen, and S.G. Louie, "Van Hove Singularity and Apparent Anisotropy in the Electron-phonon Interaction in Graphene," Phys. Rev. B 77, 113410 (2008).

K.H. Khoo, J.B. Neaton, H.J. Choi, and S.G. Louie, "Contact Dependence of the Conductance of H2 Molecular Junctions from First Principles," Phys. Rev. B 77, 115326 (2008).

Y.M. Byun, H.J. Choi, S.G. Louie, and M.L. Cohen, "Low-energy Structures of K Atoms in Expanded K3C60 Monolayers: Ab Initio Pseudopotential Density-functional Calculations," Phys. Rev. B 77, 115418 (2008).

E. Kioupakis, P. H. Zhang, M. L. Cohen, and S. G. Louie, "GW Quasiparticle Corrections to the LDA+U/GGA+U Electronic Structure of bcc Hydrogen," Phys. Rev. B 77, 155114 (2008).

F. Giustino, M.L. Cohen, and S.G. Louie, "Small Phonon Contribution to the Photoemission Kink in the Copper Oxide Superconductors," Nature 452, 975 (2008).

J. Noffsinger, F. Giustino, S.G. Louie, and M.L. Cohen, "First-principles Study of Superconductivity and Fermi-surface Nesting in Ultrahard Transition Metal Carbides," Phys. Rev. B 77, 180507 (2008).

J. D. Sau, J. B. Neaton, H.J. Choi, S.G. Louie, and M.L. Cohen, "Electronic Energy Levels of Weakly Coupled Nanostructures: C60 Metal Interfaces," Phys. Rev. Lett. 101, 026804 (2008).

C.-H. Park and S.G. Louie, "Energy Gaps and Stark Effect in Boron Nitride Nanoribbons," Nano Lett. 8, 2200 (2008).

C.-H. Park, Y.-W. Son, L. Yang, M.L. Cohen, and S.G. Louie, "Electron Beam Supercollimation in Graphene Superlattices," Nano Lett. 8, 2920 (2008).

C.-H. Park, L. Yang, Y.-W. Son, M.L. Cohen, and S.G. Louie, "New Generation of Massless Dirac Fermions in Graphene under External Periodic Potentials," Phys. Rev. Lett. 101, 126804 (2008).

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," submitted to Nano Lett.

L. Yang, M.L. Cohen, and S.G. Louie, "Magnetic Edge-state Excitons in Zigzag Graphene Nanoribbons," submitted to Phys. Rev. Lett.

**PI Walter Loveland**

1. Gulzari L Malli"Dramatic antibinding effects of relativity for atomization energy of molecules of superheavy elements: the existence and atomization energy of tetravalent Eka-lead tetrachloride E114Cl4 " (Submitted).,

2. 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 and atomization energy calculations for the tetravalent superheravy eka-lead tetrahydride E114H4 " ( Submitted)

3.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).

4.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**

M. Boylan-Kolchin, C.-P. Ma, and E. Quataert (2008), MNRAS, 383, 93. Dynamical Friction and Galaxy Merging Timescales

L. Desroches, E. Quataert, C.-P. Ma, and A. West (2007), MNRAS, 377, 402. Luminosity Dependence in the Fundamental Plane Projections of Elliptical Galaxies

**PI Kwan-Liu Ma**

Parallel volume rendering using 2-3 swap image compositing for an arbitrary number of processors. Hongfeng Yu, Chaoli Wang, and Kwan-Liu Ma. In Proceedings of IEEE/ACM Supercomputng 2008 Conference (SC08), November 2008.

**PI Steven Manson**

Photoionization of Doubly-Charged Scandium Ions, A. M. Sossah, H.-L. Zhou and S. T. Manson, Phys. Rev. A (submitted).

**PI Angelo Mascarenhas**

Y. Zhang, A. Mascarenhas, and L.-W. Wang, Non-Bloch Nature of Alloy States in a Conventional Semiconductor Alloy: Ga(x)In(1-x)P as an Example, Phys. Rev. Lett. 101, 036403 (2008).

Y. Zhang, A. Mascarenhas, and L.-W. Wang, Interplay of alloying and ordering on the electronic structure of Ga(x)In(1-x)P alloys, Submitted to Phys. Rev. B.

**PI Artem Masunov**

Title: Applicability of hybrid density functional theory methods to calculation of molecular hyperpolarizability Author(s): Suponitsky, KY; Tafur, S; Masunov, AE Source: JOURNAL OF CHEMICAL PHYSICS Volume: 129 Issue: 4 Article Number: 044109 Published: 2008

Title: Double excitations and state-to-state transition dipoles in pi-pi* excited singlet states of linear polyenes: Time-dependent density-functional theory versus multiconfigurational methods Author(s): Mikhailov, IA; Tafur, S; Masunov, AE Source: PHYSICAL REVIEW A Volume: 77 Issue: 1 Article Number: 012510 Published: 2008

**PI Manos Mavrikakis**

R. R. Adzic, J. Zhang, K. Sasaki, M. B. Vukmirovic, M. Shao, J. X. Wang, A. U. Nilekar, M. Mavrikakis, J. A. Valerio and F. Uribe, "Platinum Monolayer Fuel Cell Electrocatalysts", Topics In Catalysis, 46, 249 (2007).

A. U. Nilekar, Y. Xu, J. Zhang, M. B. Vukmirovic, K. Sasaki, R. R. Adzic, and M. Mavrikakis, "Bimetallic and Ternary Alloys for Improved Oxygen Reduction Catalysis", Topics In Catalysis, 46, 276 (2007).

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).

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).

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).

P. Ferrin, A. U. Nilekar, J. Greeley, J. Rossmeisl, and M. Mavrikakis, "Reactivity Descriptors for Direct Methanol Fuel Cell Anode Catalysts", Surface Science (in press).

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 (accepted).

L. R. Merte, J. Knudsen, L. C. Grabow, R. T. Vang, E. Lagsgaard, M. Mavrikakis, and F. Besenbacher, "Navigating a nanoscale superstructure with STM: Misfit dislocations as guideposts on a thin-film oxide surface" (submitted).

**PI William McCurdy**

K. Houfek, C. W. McCurdy and T. N. Rescigno, "Probing the Nonlocal Approximation to Resonant Collisions of Electrons with Diatomic Molecules" Phys. Rev. A 77, 012710 (2008).

T. N. Rescigno, C. W. McCurdy, D. J. Haxton, C. S. Trevisan and A. E. Orel "Nuclear Dynamics in Resonant Electron Collisions with Small Polyatomic Molecules," Invited Talks of the XXV International Conference on Photonic, Electronic and Atomic Collisions , Freiburg, Germany, 25-31 July, 2007 (J. Phys. Conference Series 88, 012011 (2007)).

M. S. Schoeffler, J. Titze, N. Petridis,T. Jahnke, D. Akoury, K. Cole, L. Ph. H. Schmidt, A. Czasch, O. Jagutzki, N. A. Cherepkov, S. K. Semenov, C. W. McCurdy, T. N. Rescigno, C. L. Cocke, T. Osipov, S. Lee, M. H. Prior, A. Belkacem, A. Lander, H. Schmidt-Boecking, Th. Weber, and R. Doerner, "Ultrafast probing of core hole localization in N2", Science 320, 920 (2008).

T. Osipov, T. N. Rescigno, T. Weber, S.Miyabe, T.Jahnke, A. Alnaser, M. Hertlein, O. Jagutzki, L. Schmidt, M. Schoeffler, L. Foucar, S. Schoessler, T. Havermeier, M. Odenweller, S. Voss, B. Feinberg, A. Landers, M. Prior, R. Doerner, C. L. Cocke and A. Belkacem, "Fragmentation Pathways for Selected Electronic States of the Acetylene Dication", J. Phys. B 41, 091001 (2008).

A. Palacios, T. N. Rescigno and C. W. McCurdy, "Cross sections for short-pulse single and double ionization of helium", Phys. Rev. A 77, 032716 (2008).

P. L. Bartlett, A. T. Stelbovics, T. N. Rescigno and C. W. McCurdy, "Application of Exterior Complex Scaling to Positron-Hydrogen Collisions Including Rearrangement", Phys. Rev. A 77, 032710 (2008).

D. A. Horner, T. N. Rescigno and C. W. McCurdy"Decoding sequential vs non-sequential two-photon double ionization of helium using nuclear recoil", Phys. Rev. A. 77, 030703(R) (2008).

L. Campbell, M. Brunger and T. N. Rescigno, "Carbon dioxide electron cooling rates in the atmospheres of Mars and Venus", J. Geophys. Res.-Planets 113, 2008JE003099 (2008).

F. L. Yip, C. W. McCurdy and T. N. Rescigno, "A hybrid Gaussian-discrete variable representation approach to molecular continuum processes II: application to photoionization of diatomic Li2+", Phys. Rev. A 78, 023405 (2008).

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 (accepted).

D. 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. (accepted).

D. J. Haxton, T. N. Rescigno and C. W. McCurdy, "Three-body breakup in dissociative electron attachment to the water molecule", Phys. Rev. A (accepted).

**PI Julia Medvedeva**

J.E. Medvedeva and C.L. Hettiarachchi, "Carrier generation in transparent conductors: layered multicomponent InGaZnO4 and its constituent oxides", Submitted for publication to Physical Review B

J.E. Medvedeva, Combining optical transparency with electrical conductivity: challenges and prospects, in Transparent Electronics: From Synthesis to Applications, Editors: A. Facchetti and T. Marks, Publisher: John Wiley & Sons, Submitted in June, 2008

**PI Donghai Mei**

Y. K. Kim, R. Rousseau, B. D. Kay, J. M. White and Z. Dohnalek,"Catalytic Dehydration of 2-Propanol on (WO3)3 clusters on TiO2(100)", J. Am. Chem. Soc 130, 5059 (2008)

Y. K. Kim, R. Rousseau, B. D. Kay, and Z. Dohnalek,"Dehydration and Dehydrogenation of Alcohols by (WO3)3 clusters", J. Am. Chem. Soc. submitted. (2008)

Z. Zhang, R. Rousseau, J. Gong, S.-C. Li, B.D. Kay, Q. Ge, and Z. Dohn??lek,"Vacancy Assisted Diffusion of Alkoxy Species on Rutile TiO2(110)", Phys. Rev. Lett, in press (2008).

Kwak, J. H., D. Mei, D. H. Kim, J. Szanyi and C. H. F. Peden "The Nature of Surface Nitrates in BaO/gamma-Al2O3 NOx Storage Materials." J. Catal.: submitted. (2008)

Mei, D., N. A. Deskins and M. Dupuis "A density functional theory study of formaldehyde adsorption on ceria." Surf. Sci. 601(21): 4993-5001. (2007)

Mei, D., N. A. Deskins, M. Dupuis and Q. F. Ge "Density functional theory study of methanol decomposition on the CeO2(110) surface." J. Phys. Chem. C 112(11): 4257-4266. (2008)

Mei, D., Q. Ge, J. H. Kwak, D. H. Kim, J. Szanyi and C. H. F. Peden "Adsorption and Formation of BaO Overlayers on Gamma-alumina Surfaces." J. Phys. Chem. C: in press. (2008)

Mei, D., L. Xu and G. Henkelman "Dimer saddle point searches to determine the reactivity of formate on Cu(111)." J. Catal. 258(1): 44-51. (2008)

Mei, D., L. Xu and G. Henkelman "Potential Energy Surface of Methanol Decomposition on Cu(110)." J. Phys. Chem. C: submitted. (2008)

Du Y, Deskins NA, Zhang Z, Dohnalek Z, Dupuis M, Lyubinetsky I, "Imaging Consecutive Steps of O2 Reaction with Hydroxylated TiO2(110): Identification of HO2 and Terminal OH Intermediates", J. Phys. Chem. C: accepted. (2008)

Deskins NA, Dupuis M, "Intrinsic Hole Migration in TiO2 from Density Functional Theory", J. Phys. Chem. C: submitted. (2008)

**PI Surabi Menon**

Sednev, I., S. Menon and G. McFarquahar, 2008: Simulating mixed-phase Arctic stratus clouds: sensitivity to ice initiation mechanisms, Atmos. Chem. Phys. Discuss., 8, 11755-11819

**PI David Mikkelsen**

D. R. Mikkelsen and W. Dorland, Phys. Rev. Letters 101 (2008) 135003

T. Tala, et al., Plasma Phys. Control. Fusion 49 No 12B (2007) B291-B302

W. M. Solomon, et al., Plasma Phys. Control. Fusion 49 No 12B (2007) B313-B324

A. Casati, C. Bourdelle, X. Garbet, and F. Imbeaux , Phys. Plasmas 15 (2008) 042310

**PI Burkhard Militzer**

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", conference review article submitted for publication in Physics of Plasmas (2008).

B. Militzer and W. B. Hubbard, "Comparison of Jupiter Interior Models Derived from First-Principles Simulations", conference proceedings submitted to Astrophysics and Space Science, arXiv:astro- ph/08074266 (2008).

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, arXiv:physics/08054433.

B. Militzer, "Path Integral Monte Carlo and Density Functional Molecular Dynamics Simulations of Hot, Dense Helium", submitted to Phys. Rev. B, arXiv:cond-mat/08050317 (2008).

B. Militzer, W. B. Hubbard, J. Vorberger, I. Tamblyn, and S.A. Bonev, "A Massive Core in Jupiter Predicted From First-Principles Simulations", in press, Astrophysical Journal Letters, arXiv:astro-ph/08074264 (2008).

**PI Thomas Miller**

"Isomorphic classical molecular dynamics model for an excess electron in a supercritical fluid", Thomas F. Miller III, arXiv:0809.4522v1 [cond-mat.stat-mech] (Submitted to the Journal of Chemical Physics)

**PI William Miller**

J. Liu and W. H. Miller, Linearized Semiclassical Initial Value Time Correlation Functions Using the Thermal Gaussian Approximation: Applications to Condensed Phase Systems, J. Chem. Phys. 127, 114506.1-10 (2007).

W. H. Miller, The Initial Value Representation of Semiclassical Theory: A Practical Way for Adding Quantum Effects to Classical Molecular Dynamics Simulations of Complex Molecular Systems, in Physical Biology From Atoms to Medicine, ed. A. Zewail, Imperial College Press, London, UK, pp. 505-525 (2008).

J. Liu and W. H. Miller, Test of the Consistency of Various Linearized Semiclassical Initial Value Time Correlation Functions in Application to Inelastic Neutron Scattering from Liquid para-hydrogen, J. Chem. Phys. 128, 144511.1-15 (2008).

J. Liu and W. H. Miller, Linearized Semiclassical Initial Value Time Correlation Functions with Maximum Entropy Analytic Continuation, J. Chem. Phys. 129, 124111.1-17 (2008)

**PI Warren Mori**

[Tzoufras:2008] M. Tzoufras, W. Lu, F.S. Tsung, C. Huang, W.B. Mori, T. Katsouleas, et al., "Beam loading in the nonlinear regime of plasma-based acceleration", Phys. Rev. Lett. 101, 145002 (2008)

[Tzoufras:2009] M. Tzoufras el al., "Beam loading in nonlinear plasma wakes," submitted to Physics of Plasma.

Laser channeling in millimeter-scale underdense plasmas of fast ignition targets G. Li, R. Yan, C. Ren, T.-L. Wang, J. Tonge, and W. B. Mori, Phys. Rev. Lett. 100, 125002, 2008

Particle-in-cell simulations for fast ignition C. Ren, J. Tonge, G. Li, F. Fiuza, R. A. Fonseca, J. May, W. B. Mori, L. O. Silva, T. L. Wang, and R. Yan, Journal of Physics: Conference Series 125, 012046, 2008, url={http://stacks.iop.org/1742-6596/125/012046})

[Huang2007] C. Huang, W. Lu, M. Zhou, C. E. Clayton, C. Joshi, W. B. Mori, P. Muggli, S. Deng, E. Oz, T. Katsouleas, M. J. Hogan, I. Blumenfeld, F. J. Decker, R. Ischebeck, R. H. Iverson, N. A. Kirby, and D. Walz, "Hosing Instability in the Blow-Out Regime for Plasma-Wakefield Acceleration", Phys. Rev. Lett. 99, 255001 (2007)

[Huang2008] Huang, C.; Tsung, F. S.; Mori, W. B., "Quasi-Static Particle-In-Cell Simulation of the Plasma Wakefield Afterburner Concept," Plasma Science, IEEE Transactions on , vol.36, no.4, pp.1294-1295, Aug. 2008

[Geddes2008] 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, C Toth, F S Tsung, M Tzoufras, T Antonsen, J Vieira and W P Leemans, "Computational studies and optimization of wakefield accelerators," J. Phys.: Conf. Ser. 125 012002, 2008

[Feng2008] B. Feng, C. Huang, V. Decyk, W. B. Mori, P. Muggli, T. Katsouleas, "Enhancing quasi-static particle-in- cell simulations with a pipelining algorithm", submitted to Journal of Computational Physics.

[Fang2008] F. Fang, C. E. Clayton, K. A. Marsh, J. Ralph, A. Pak, C. Joshi, "Pump depletion limited evolution of the relativistic plasma wave-front in a forced laser-wakefield accelerator", submitted to Plasma Physics and Controlled Fusion

**PI James Morris**

C. L. Fu, Maja Krcmar, G. S. Painter, and Xing-Qiu Chen, "The vacancy mechanism of high oxygen solubility and nucleation of stable oxygen-enriched clusters in Fe", Physical Review Letters 99, 225502 (2007).

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," Shanghai Metals 30 (4), 1-6 (2008).

V.A. Levashov, T. Egami, R.S. Aga and J. R. Morris, "Equipartition theorem and the dynamics of liquids," Phys. Rev. B 78, 064205 (2008).

J. R. Morris, R. S. Aga, V. Levashov and T. Egami, "Many-body effects in BCC metals: An embedded atom model extension of the modified Johnson pair potential for iron," Phys. Rev. B 77, 174201 (2008).

V.A. Levashov et al., "Atomic bond fluctuations and crossover to potential-energy-landscape-influenced regime in supercooled liquid," submitted to Phys. Rev. E.

J. R. Morris, R.S. Aga, T. Egami and V.A. Levashov, "Simulating the Effect of Poisson Ratio on Metallic Glass Properties," submitted to Int. J. Mod. Phys. B.

J. R. Morris and Y. Y. Ye, "Phase stability and predicted stacking faults in ductile B2 intermetallics," submitted to Acta Mat.

**PI Alfred Msezane**

"Near-Threshold Electron Attachment as Regge Resonances: Cross Sections for K, Rb and Cs Atoms", A.Z. Msezane, Z. Felfli and D. Sokolovski, J. Phys. Chem. A 112, 10, 199 (2008)

"Fine-Structure Energy Levels, Oscillator Strengths and Lifetimes in Mn XIII", G. P. Gupta and A. Z. Msezane, Physica Script 76, 225 (2007).

"What can one do with Regge Poles", D. Sokolovski, A.Z. Msezane, Z. Felfli, S.Yu. Ovchinnikov and J.H. Macek, Nucl. Instr. and Meth. B 261, 133 (2007).

"Energy Levels and Radiative Rates for Transitions in Co XI", F.P. Keenan, K.M. Aggarwal and A.Z. Msezane, Astronomy & Astrophysics 473, 995 (2007).

"Octupole Contributions to the Generalized Oscillator Strengths of Discrete Dipole Transitions in Noble Gas Atoms", M. Ya. Amusia, L.V. Chernysheva, Z. Felfli and A.Z. Msezane, Phys. Rev. A75, 062703 (2007).

"Photoionization of Hydrogen-Like Ions Surrounded by Charged Spherical Shell", A. S. Baltenkov, S. T. Manson and A. Z. Msezane, Phys. Rev. A 76, 042707 (2007)

"Elastic Electron Scattering From Multicenter Potentials", A. S. Baltenkov, S. T. Manson and A.Z. Msezane, J. Phys. B 40, 769 (2007)

"Ionization of Sodium by the Impact of Alpha Particles", S. Bhattacharya, K.B. Choudhury, N.C. Deb, C. Sinha, K. Roy and A.Z. Msezane, Eur. Phys. J. D 47, 335 (2008)

"Fine-Structure Energy Levels, Oscillator Strengths and Lifetimes in Co XV", G. P. Gupta and A. Z. Msezane, European Physical Journal D, At Press (2008).

**PI James Muckerman**

Polyansky, D. E.; Cabelli, D.; Muckerman, J. T.; Fukushima, T.; Tanaka, K.; Fujita, E., Mechanism of Hydride Donor Generation Using a Ru(II) Complex Containing an NAD+ Model Ligand: Pulse and Steady-State Radiolysis Studies. Inorg. Chem. 2008; 47, 3958-3968. (cover article)

Muckerman, J. T.; Polyansky, D. E.; Wada, T.; Tanaka, K.; Fujita, E. Water Oxidation by a Ruthenium Complex with Noninnocent Quinone Ligands: Possible Formation of an OO Bond at a Low Oxidation State of the Metal. Inorg. Chem. 2008; 47, 1787-1802. (Forum on "Making Oxygen")

Jensen, L. L.; Muckerman, J. T.; Newton, M. D., First-Principles Studies of the Structural and Electronic Properties of the (Ga1-xZnx)(N1-xOx) Solid Solution Photocatalyst. J. Phys. Chem. C 2008, 112, 3439-3446.

Chaudhuri, S.; Rangan, S. S.; Veyan, J. F.; Muckerman, J. T.; Chabal, Y. J., Formation and Bonding of Alane Clusters on Al(111) Surfaces Studied by Infrared Absorption Spectroscopy and Theoretical Modeling. J. Am. Chem. Soc. 2008, 130, 10576-10587.

Cheng, T.-Y.; Szalda, D. J.; Hanson, J. C.; Muckerman, J. T.; Bullock, R. M., Four-Electron-Donor Hemilabile ??3-PPh3 Ligand that Binds through a C C Bond Rather than an Agostic CH Interaction, and Displacement of the C C by Methyl Iodide or Water. Organometallics 2008, 27, 3785-3795.

Tseng, H.-W.; Zong, R.; Muckerman, J. T.; Thummel, R., Mononuclear Ru(II) Complexes That Catalyze Water Oxidation. Inorg. Chem. 2008, in press.

Yu, H.-G.; Poggi, G.; Francisco, J.; Muckerman, J., Energetics and molecular dynamics of the reaction of HOCO with HO2 radicals. J. Chem. Phys. 2008, in press.

**PI Patric Muggli**

B. Feng, et al., "Enhancing quasi-static particle-in-cell simulations with a pipelining algorithm", submitted to Journal of Computational Physics,2008

B. Feng, et al., "Simulation of electron cloud effects on electron beam in an ERL with pipelined QuickPIC", in proceedings of AAC 2008.

X. Wang, et al., "Positron injection and acceleration on the wake driven by an electron beam in a foil and gas plasma", Phys. Rev. Lett. 101, 124801 (2008)

C. Geddes,et al., "Computational studies and optimization of wakefield accelerators",Journal of Physics,2008

B. Allen, et al.,"Simulation of Weibel Instability for LWFA and PWFA Electron Beams", in proceedings of AAC 2008.

R. "Preservation of Ultra Low Emittances Using Adiabatic Matching in Future Plasma Wakefield Accelerators", in proceedings of AAC 2008.

X. Wang,et al., "Threshold for Trapping Positrons in the Wake Driven by a Ultra-relativistic Electron Bunch", in proceedings of AAC 2008.

**PI Christopher Mundy**

C.J. Mundy, R. Rousseau, A. Curioni, S.M. Kathmann, and G.K. Schenter, "A molecular approach to understanding complex systems: computational statistical mechanics using state-of-the-art algorithms on tera-scale computational platforms," Journal of Physics Conference Series 125, 0120414, (2008).

K.A. Maerzke, G. Murdacheaw, C.J. Mundy, G.K. Schenter, and J.I. Siepmann, "Self-consistent polarization with density functional theory: Application to argon," Journal of Physical Chemistry B (submitted).

T. Ohsawa, I. Lyubinetsky, Y. Du, M.A. Henderson, R. Rousseau, V. Shutthanandan, S.A. Chambers, "Crystallographic Dependence of Visible-Light-Induced Photochemistry in Nitrogen-doped Titanium Dioxide.," Nature Materials, submitted (2008).

## N

**PI Habib Najm**

H.N. Najm, J. Ray, C. Safta, Y. Marzouk, M. Valorani, and D. Goussis, "High-Order AMR computations of reacting flow with adaptive reduction of chemical stiffness", in press, J. of Physics - Conference Series.

**PI Jeffrey Neaton**

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", Nature Nanotechnology, submitted (2008)

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, submitted (2008)

J. Sau, J. B. Neaton, H. J. Choi, S. G. Louie, and M. L. Cohen, "Electronic Energy Levels of Weakly Coupled Nanostructures: C60-Metal Interfaces", Phys. Rev. Lett, 101, 026804 (2008)

K. T. Chan, J. B. Neaton, and M. L. Cohen, "First-principles study of metal adatom adsorption on graphene", Phys. Rev. B 77, 235430 (2008)

Y. Qi, I. Ratera, J. Y. Park, P. D. Ashby, S. Y. Quek, J. B. Neaton, and M. Salmeron, "Mechanical and charge transport properties of alkanethiol self-assembled monolayers on Au(111) surfaces: The role of molecular tilt", Langmuir 24, 2219 (2007)

S. Y. Quek, L. Venkataraman, H. J. Choi, S. G. Louie, M. S. Hybertsen, and J. B. Neaton, "Amine-Au Linked Single-Molecule Junctions: Experiment and Theory", Nano Lett. 7, 3477 (2007)

**PI John Negele**

C. Alexandrou, G. Koutsou, Th. Leontiou, J.W. Negele, A. Tsapalis, "Axial Nucleon and Nucleon to Delta form fractors and the Goldberger-Treiman Relations from Lattice QCD", Phys.Rev.D76:094511, (2007) arXiv:0706.3011[hep-lat].

C. Alexandrou, Th. Leontiou, J.W. Negele, A. Tsapalis, "The Axial N to Delta transition form factors from Lattice QCD", Phys.Rev.Lett.98:052003,2007, hep-lat/0607030.

C. Alexandrou, G. Koutsou, H. Neff, J.W. Negele, W. Schroers, A. Tsapalis, "The Nucleon to Delta electromagnetic transition in full lattice QCD", Phys. Rev. D77 (2008), 085012, arXiv:0710.4621 [hep-lat].

**PI Brian Nelson**

Charlson C. Kim and the NIMROD team, "Impact of velocity space distribution on hybrid kinetic-magnetohydrodynamic simulation of the 1,1 mode", Phys. Plasmas 15, 072507 (2008)

R. D. Milroy, A. I. D. Macnab, C. C. Kim, and C. R. Sovinec, "FRC simulations using the NIMROD code,"Journal of Fusion Energy 27, 73 (2008).

A. I. D. Macnab, R. D. Milroy, C. C. Kim, and C. R. Sovinec, "Hall Magneto-hydrodynamics Simulations of End-Shorting Induced Rotation in Field-Reversed Configurations," Physics of Plasmas 14, 092503 (2007).

**PI Karoly Nemeth**

K. Nemeth, et.al., "Laser-Driven Coherent Betatron Oscillation in a Laser-Wakefield Cavity", Physical Review Letters, 100, 095002 (2008).

K. Nemeth, et.al., "Laser-Driven Coherent Betatron Oscillation in a Laser-Wakefield Cavity: Formation of Sinusoid Beam-Shapes and Coherent Trajectories", submitted to the Proceedings of the Advanced Acelerator Concepts 2008 Workshop, to be published by the Americal Institute of Physics, Editors: Wim Leemans (LBNL), et.al.; oral and poster presentation of the same results have been contributed at the same conference.

Baifei Shen, et.al., "Bubble Regime for Ion Acceleration in a Laser-Driven Plasma.", Physical Review E (R) 76 (5-2):055402 18233710

**PI Gregory Newman**

Commer M., and Newman G.A., 2007, New advances in three-dimensional controlled-source electromagnetic inversion, Geophysical Journal International, 172, 513-535.

Commer M., Newman G.A., Carazzone J.J., Dickens T.A., Green K.E., Wahrmund L.A., Willen D.E., and Shiu J., 2008, Massively-parallel electrical-conductivity imaging of hydrocarbons using the Blue Gene/L supercomputer, IBM Journal of Research and Development, 52-1/2, 93-103.

Commer M., Newman G.A., Carazzone J.J., Dickens T.A., Green K.E., Wahrmund L.A., Willen D.E., and Shiu J., 2008, Massively-parallel electrical-conductivity imaging of hydrocarbons using the Blue Gene/L supercomputer, First Break, 26, 93-102 (Reprint of 2).

**PI Cheuk-Yiu Ng**

Xi Xing, Beth Reed, Kai-Chung Lau, Sun-Jong Baek, Mi-Kyung Bahng, and C. Y. Ng, "Assignment of rovibrational transitions of propyne in the region of 2934-2952 cm-1 measured by two-color IR-vacuum ultraviolet laser photoion-photoelectron methods" J. Chem. Phys., 2007, 127, 044313 (2007).

Xi Xing, Mi-Kyung Bahng, Beth Reed, C. S. Lam, Kai-Chung Lau, and C. Y. Ng, "Rovibrationally selected and resolved pulsed field ionization photoelectron study of propyne: Ionization energy and spin-orbit interaction in the propyne cation", J. Chem. Phys. 128, 094311 (2008).

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, in press.

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**

J. Demmel, Y. Hida, X.S. Li, and E.J. Riedy, "Extra-precise Iterative Refinement For Overdetermined Least Squares Problems", ACM Trans. Math. Software. (to appear)

W. Gao, X.S. Li, C. Yang, and Z. Bai, "An Implementation and Evaluation of the AMLS Method for Sparse Eigenvalue Problems", ACM Trans. on Math. Software, Vol. 34, No. 4, July 2008.

L. Grigori, J.W. Demmel, and X.S. Li, "Parallel Symbolic Factorization for Sparse LU with Static Pivoting", SIAM J. Scientific Computing, Vol. 29, Issue 3, 1289-1314, 2007.

X. S. Li, "Evaluation of sparse LU factorization and triangular solution on multicore architectures", Proceedings of VECPAR'08, 8th International Meeting High Performance Computing for Computational Science, June 24-27, 2008, Toulouse, France. (to appear)

K. Nakajima, "Parallel multigrid method based on a hierarchical graph decomposition", IPSJ Proceedings of HPCS2008, pp. 115-122, 2008.

Philip Sternberg, Pieter Maris, Esmond Ng, Masha Sosonkina, Hung Viet Le, James Vary, and Chao Yang, "Accelerating Full Configuration Interaction Calculations for Nuclear Structure". To appear in SC08 Proceedings (2008).

**PI Jerry Nolen**

Superconducting Accelerating Structures for Very Low Velocity Ion Beams; J.Xu, K.W. Shepard, P. N. Ostroumov, J. D. Fuerst, G. Waldschmidt, and I. V. Gonin; Phys. Rev. ST Accel. Beams 11, 032001/1-8 (2008)

A Parallel 3D Poisson Solver for Space Charge Simulation in Cylindrical Coordinates; J. Xu, P. N. Ostroumov, and J. Nolen; Comp. Phy. Comm. 178, 290-300 (2008)

**PI Arthur Nozik**

J. L. Blackburn, D. Svedruzic, T. J. McDonald, Y.-H. Kim, P. W. King, and M. J. Heben, Raman spectroscopy of charge transfer interactions between single wall carbon nanotubes and [FeFe] hydrogenase, Dalton Trans., In Press (2008).

S.-H. Lee, Y.-H. Kim, R. Deshpande, P. A. Parilla, E. Whitney, D. T. Gillaspie, K. M. Jones, A. H. Mahan, S. B. Zhang, and A. C. Dillon, Reversible Lithium-Ion Insertion in Molybdenum Oxide Nanoparticles, Adv. Mater., In Press (2008).

J. L. Blackburn, T. M. Barnes, M. C. Beard, Y.-H. Kim, R. C. Tenent, T. J. McDonald, B. To, T. Coutts, M. J. Heben, Transparent Conductive Single-walled Carbon Nanotube Networks with Precisely Tunable Ratios of Semiconducting and Metallic Nanotubes, ACS Nano 2, 1266 (2008).

**PI Peter Nugent**

The Sixth Data Release of the Sloan Digital Sky Survey, David Schlegel at al, The Astrophysical Journal Supplement Series, Volume 175, Issue 2, pp. 297-313, 2008ApJS..175..297A

An Improved Photometric Calibration of the Sloan Digital Sky Survey Imaging Data, David Schlegel at al, The Astrophysical Journal, Volume 674, Issue 2, pp. 1217-1233, 2008ApJ...674.1217P

## O

**PI Robert Odette**

Formation of Y-Ti-O nanoclusters in nanostructured ferritic alloys: A first-principles study, Yong Jiang, John R. Smith, and G. R. Odette, PHYSICAL REVIEW B 79, 064103 (2009)

**PI Grazyna Odyniec**

B. I. Abelev, et al. [STAR Collaboration], ``Spin alignment measurements of the K*0(892) and phi(1020) vector mesons in heavy ion collisions at sqrt{s}{NN} = 200 GeV,'' Phys. Rev. C 77 (2008) 061902.

B. I. Abelev, et al. [STAR Collaboration], ``Forward Neutral Pion Transverse Single Spin Asymmetries in p+p Collisions at \sqrt{s}=200 GeV,'' arXiv:0801.2990 - accepted for publication in Physical Review Letters.

Y. Chen, Z.T. Liang, E. Sichtermann, Q.H. Xu and S.S. Zhou, ``Anti-Hyperon polarization in high energy pp collisions with polarized beams,'' Phys. Rev. D 78 (2008) 054007.

B. I. Abelev, et al. "Centrality dependence of charged hadron and strange hadron elliptic flow from sqrt{s}{NN}} = 200 GeV Au+Au collisions" Phys. Rev. C 77 (2008) 54901

B. I. Abelev, et al. "Spin alignment measurements of the K* and phi vector meson at RHIC" Phys. Rev. C 77 (2008) 61902

B. I. Abelev, et al. "rho0 Photoproduction in Ultra-Peripheral Relativistic Heavy Ion Collisions with STAR " Phys. Rev. C 77 (2008) 34910

B. I. Abelev, et al. "Longitudinal double-spin asymmetry for inclusive jet production in p+p collisions at sqrt{s}=200 GeV" Phys. Rev. Lett. 100 (2008) 232003

B. I. Abelev, et al. "Forward Lambda Production and Nuclear Stopping Power in d+Au Collisions at sqrt{s}{NN} = 200GeV " Phys. Rev. C 76 (2007) 64904

B. I. Abelev, et al. "Measurement of Transverse Single-Spin Asymmetries for Di-Jet Production in Proton-Proton Collisions at sqrt{s} = 200 GeV " Phys. Rev. Lett. 99 (2007) 142003

**PI Joseph Oefelein**

R.C. Knaus, C. Pantano and J.C. Oefelein (2009). Statistical analysis and modeling of scalar dissipation and its relation to the filtered mixture fraction. Physics of Fluids. Submitted (8/08).

T.G. Drozda, G. Wang, V. Sankaran, J.R. Mayo, J.C. Oefelein and R.S. Barlow (2008). Scalar filtered mass density functions in nonpremixed turbulent jet flames. Combustion & Flame. Accepted.

V. Sankaran, T.G. Drozda and J.C. Oefelein (2008). A tabulated closure for turbulent nonpremixed combustion based on the linear eddy model. Proceedings of the Combustion Institute, 32nd International Symposium on Combustion, August 3-8, Montreal, Canada. Accepted.

J.H. Chen, J.C. Oefelein and R. Sankaran (2008). High-fidelity simulations for clean and efficient combustion of alternative fuels. Journal of Physics, SciDAC 2008, July 13-17, Seattle, WA. Accepted.

**PI Serdar Ogut**

Juan C. Idrobo, Weronika Walkosz, Shing F. Yip, Serdar Ogut, Jinlan Wang, and Julius Jellinek, "Static Polarizabilities and Optical Absorption Spectra of Gold Clusters (Au_n, n = 2 - 14 and 20) from First Principles", Phys. Rev. B 76, 205422 (Nov. 2007).

Kopinjol Baishya, Juan C. Idrobo, Serdar Ogut, Mingli Yang, Koblar Jackson, and Julius Jellinek, "Optical Absorption Spectra of Intermediate Size Silver Clusters from First Principles", Phys. Rev. B 78, 075439 (2008).

Weronika Walkosz, Juan C. Idrobo, Robert F. Klie, and Serdar Ogut, "Reconstructions and Non-Stoichiometry on Oxygenated beta-Si3N4 (10-10) Surfaces", accepted for publication in Phys. Rev. B (2008).

Murilo L. Tiago, Juan C. Idrobo, Serdar Ogut, Julius Jellinek, and James R. Chelikowsky, "Comparison of Time-Dependent Density Functional Theory and GW-Bethe-Salpeter-Equation Methods for Optical Excitations in Ag_n (n=1-8) Clusters", submitted to Phys. Rev. B (2008).

**PI Leonid Oliker**

M. Wehner, L. Oliker, J. Shalf, "Towards Ultra-High Resolution Models of Climate and Weather", International Journal of High Performance Computing Applications (IJHPCA), April, 2008. LBNL-60799

L. Oliker, A. Canning, J. Carter, J. Shalf, S. Ethier, "Scientific Application Performance on Leading Scalar and Vector Supercomputing Platforms", International Journal of High Performance Computing Applications, Feb 2008, LBNL 60800.

S. Williams, L. Oliker, R. Vuduc, J. Shalf, K. Yelick, J. Demmel, "Optimization of Sparse Matrix-Vector Multiplication on Emerging Multicore Platforms", SC07: International Conference for High-Performance Computing, Networking, Storage, and Analysis, Nov. 2007 LBNL-63296.

K. Datta, S. Kamil, S. Williams, L. Oliker, J. Shalf, K. Yelick, "Optimization and Performance Modeling of Stencil Computations on Modern Microprocessors", SIAM Review, 2008 (in press). LBNL-63192

L. Oliker, J. Shalf, J. Carter, A. Canning, S. Kamil, M. Lijewski, S. Ethier "Performance Characteristics of Potential Petascale Scientific Applications ", Petascale Computing: Algorithms and Applications, Chapman & Hall / CRC Press, Nov 2007, LBNL # pending.

J. Borrill, L. Oliker. J. Shalf, H. Shan, Andrew Uselton "HPC Global File System Performance Analysis Using A Scienti"c-Application Derived Benchmark", Parallel Computing Journal, under review.

S. Ethier, W. M. Tang, R. Walkup, L. Oliker, "Large-Scale Gyrokenetic particle simulation of Microturbulence in Magnetically Confined Fusion Plasmas" , IBM Journal of Research and Development, March 2008. LBNL pending

**PI Kostas Orginos**

Finite Volume Study of the Delta Magnetic Moments Using Dynamical Clover Fermions C. Aubin, K. Orginos, V. Pascalutsa, M. Vanderhaeghen. JLAB-THY-08-872, e-Print: arXiv:0809.1629 POS(Lattice 2008) 146 2008.

Computing and deflating eigenvalues while solving multiple right hand side linear systems in quantum chromodynamics. Andreas Stathopoulos, Kostas Orginos (William-Mary Coll.) e-Print: arXiv:0707.0131 under review SIAM Journal of Numerical Analysis.

## P

**PI Bahram Parvin**

Chang, DeFilippis, Tlsty, and Parvin, "Graphical Methods for Quantifying Macromolecules through Bright Field Imaging," /Bioinformatics/, August 14, 2008.

McLendon, et al. "Comprehensive genomic characterization defines human glioblastoma genes and core pathways," /Nature/, September 2008.

Maxwell, Fleisch, Costes, Erikson, Boissiere, Gupta, Ravani, Parvin, and Barcellos-Hoff, "Targeted and non-targeted effects of ionizing radiation that impact genomic instability," Cancer Research, in press

**PI Joyce Penner**

Ito, A., S. Sillman, and J.E. Penner, 2008: Global CTM study of ozone response to temperature changes in chemical kinetics and BVOC emissions: Sensitivities to isoprene nitrate chemistry and grid resolution, J. Geophys. Res., submitted.

Wang, M., J.E. Penner, and X. Liu, The Coupled IMPACT Aerosol and NCAR CAM3 Model: Evaluation of Predicted Aerosol Number and Size Distribution, J. Geophys. Res., submitted, 2008.

Wang, M. and J. E. Penner, 2008: Aerosol indirect forcing in a global model with particle nucleation, Atmos. Chem. Phys. Disc., Vol. 8, 13943-13998, SRef-ID: 1680-7375/acpd/2008-8-13943.

Lee, S. S., J.E. Penner, and S.M. Saleeby, 2008: Aerosol effects on liquid-water path of thin stratocumulus clouds, submitted to J. Geophys. Res.

Guo, H., Y. Liu, and J. E. Penner, 2008: Does the threshold representation associated with the autoconversion process matter?, Atmos. Chem. Phys., 8, 1225-1230.

Ito, A., K. Sudo, H. Akimoto, S. Sillman, J.E. Penner, 2007: Global modeling analysis of tropospheric ozone and its radiative forcing from biomass burning emissions in the twentieth century, J. Geophys. Res., 112, D24307, doi:10.1029/2007JD008745.

Ito, A., S. Sillman, and J.E. Penner, 2008: Global CTM study of ozone response to temperature changes in chemical kinetics and BVOC emissions: Sensitivities to isoprene nitrate chemistry and grid resolution, J. Geophys. Res., submitted.

**PI Stephen Pennycook**

Sang Ho Oh, Klaus van Benthem, Sergio I. Molina, Albina Y. Borisevich, Weidong Luo, Peter Werner, Nikolai D. Zakharov, Dhananjay Kumar, Sokrates T. Pantelides, and Stephen J. Pennycook, "Point Defect Configurations of Supersaturated Au Atoms Inside Si Nanowires", Nano Letters 8, 1016 (2008).

Weidong Luo, Stephen J. Pennycook, and Sokrates T. Pantelides, "Magnetic dead-layer at a complex oxide interface", submitted to Physical Review Letters (2008).

M. Varela, W. Luo, J. Tao, M. P. Oxley, M. Watanabe, A. R. Lupini, W. Tian, D. G. Mandrus, S. T. Pantelides, S. J. Pennycook, "Atomic resolution imaging of oxidation states in manganites", submitted to Physical Review B (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 LaxCa1_xMnO3", submitted to Physical Review Letters (2008).

J.C. Idrobo, A. Halabica, R.H. Magruder III, R.F. Haglund Jr. S.J. Pennycook, and S.T. Pantelides, "Universal optical response of Si-Si bonds and its evolution from nanoparticles to bulk crystal", submitted to Phys. Rev. Lett., (2008).

**PI Saul Perlmutter**

Improved Cosmological Constraints from New, Old and Combined Supernova Datasets, Kowalski, M., et al., arXiv, arXiv:0804.4142 (2008).

Looking Beyond Lambda with the Union Supernova Compilation, Rubin, D., et al., arXiv, arXiv:0807.1108 (2008).

Discovery of an Unusual Optical Transient with the Hubble Space Telescope, Barbary, K., et al., arXiv, arXiv:0809.1648 (2008).

**PI Steven Pieper**

`Dependence of two-nucleon momentum densities on total pair momentum', R. B. Wiringa, J. Carlson, Steven C. Pieper, and J. Carlson, Phys. Rev. C78, 021001(R).

`Simulating nonlinear neutrino flavor evolution', Huaiyu Duan, George M. Fuller, and J. Carlson, accepted for publication in Computational Science and Discovery (2008).

`Strongly Paired Fermions: Cold Atoms and Neutron Matter', Alexandros Gezerlis and J. Carlson, Phys. Rev. C77, 032801(R) (2008).

`Flavor Evolution of the Neutronization Neutrino Burst from an O-Ne-Mg Core-Collapse Supernovae', Huaiyu Duan, George M. Fuller, J. Carlson, and Yong-Zong Qian, Phys. Rev. Lett. 100, 021101 (2008).

**PI Michael Pindzola**

The evolution of the triple differential cross sections for the double photoionization of He and H_2, J. Colgan, M. Foster, M. S. Pindzola, and F. Robicheaux, Journal of Physics B 40, 4391 (November 2007)

Electron-impact excitation of Fe+4: an intermediate-coupling R-matrix calculation, C. P. Ballance, D. C. Griffin, and B. M. McLaughlin, Journal of Physics B 40, F327 (December 2007)

Electron-impact excitation of Ar+: an improved determination of Ar impurity influx in tokamaks, D. C. Griffin, C. P. Ballance, S. D. Loch, and M. S. Pindzola, Journal of Physics B 40, 4537 (December 2007)

Fully correlated electronic dynamics for anti-proton impact ionization of helium, M. Foster, J. Colgan, and M. S. Pindzola, Physical Review Letters 100, 033201 (January 2008)

Time-dependent lattice methods for ion-atom collisions in Cartesian and cylindrical coordinates, M. S. Pindzola and D. R. Schultz, Physical Review A 77, 014701 (January 2008)

An R-matrix with pseudo states calculation of electron-impact excitation in Ar, C P Ballance and D C Griffin, Journal of Physics B 41, 065201 (March 2008)

Internuclear separation dependence of the angular distributions from the photoionization of H+_2, J. Colgan, A. Huetz, T. J. Reddish, and M. S. Pindzola, Journal of Physics B 41, 085202 (April 2008)

Physical interpretation of the KER effect in the photodouble ionization of H_2, T. J. Reddish, J. P. Colgan, P. Bolognesi, L. Avaldi, M. Gisselbrecht, M. Lavollee, M. S. Pindzola, and A. Huetz, Physical Review Letters 100, 193001 (May 2008)

Doubly differential cross sections for proton-impact double ionization of He, M. Foster, J. Colgan, and M. S. Pindzola, Journal of Physics B 41, 111002 (June 2008)

Two-photon double ionization of the Hydrogen molecule, J. Colgan, M. S. Pindzola, and F. Robicheaux, Journal of Physics B 41, 121002 (June 2008)

Collisions of Bose-Einstein condensates in both ground and excited states, B. Sun and M. S. Pindzola, Journal of Physics B 41, 155302 (August 2008)

**PI Ruth Pordes**

Publication and Protection of Sensitive Site Information in a Grid Infrastructure, Shreyas Cholia and R. Jefferson Porter, Proceedings of the 2008 Eighth IEEE International Symposium on Cluster Computing and the Grid (CCGRID) - Volume 00, Pages 639-644

**PI Larry Pratt**

Lawrence M. Pratt, Son C. Nguyen, Bui T. Thanh A Computational Study of Lithium Ketone Enolate Aggregation in the Gas Phase and in THF Solution J. Org. Chem. 2008, 73, 6086

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, In press

Lawrence M. Pratt. Ohyun Kwon, Thanh Chi Ho, Ngan Van Nguyen A Computational Study of Lithium Methoxide Mixed Aggregates with Alkyllithiums Tetrahedron 2008, 64, 5314.

Lawrence M. Pratt, Shin-ichi Fujiwara, Nobuaki Kambe Structure, bonding, and Aggregation of Selenium-Containing Organolithium Species Tetrahedron, 2009, In press

Lawrence M. Pratt, Phuong Thao Thi 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, In Revision

**PI Joel Primack**

Ceverino, Daniel, and Klypin, Anatoly 2007, The role of stellar feedback in the formation of galaxies, arXiv0712.3285

Ceverino, D., and Klypin, A., 2007, Resonances in barred galaxies, MNRAS, 379, 1155.

**PI Fritz Prinz**

submitted to Nature Materials: Y. Zhou, R. Pasquarelli, J. Berry, D. Ginley, T. Holme, R. O'Hayre, "Improving PEM Fuel Cell Catalyst Activity and Durability Using Nitrogen-Doped Carbon Supports"

submitted to Nano Letters: T. Holme, Y. Zhou, R. Pasquarelli, R. O'Hayre, "First principles study of doped carbon supports for platinum catalysts"

**PI Philip Pritchett**

P.L. Pritchett, "Collisionless Magnetic Reconnection in an Asymmetric Current Sheet", J. Geophys. Res., 113, A06210, doi:10.1029/2007JA012930, 2008.

P.L. Pritchett, "Energetic Electron Acceleration During Multi-Island Coalescence," Phys. Plasmas, 15, in press, 2008.

## Q

**PI Ji Qiang**

J. Qiang, J. M. Byrd, J. Feng, G. Huang, X-ray streak camera temporal resolution improvement using a longitudinal time-dependent field, Nuclear Instruments & Methods in Physics Research A 598, 465 (2009).

J. Qiang, R. D. Ryne, M. Venturini, A. A. Zholents, Billion particle linac simulations for future light sources, to appear in Proc. of Linac08 conference, Sep. 29 - Oct. 3, Victoria, British Columbia, Canada, 2008.

J. Qiang, M. Borland, A. Kabel, R. Li, R. Ryne, E. Stern, Y. Wang, H. Wasserman, Y. Zhang, SciDAC advances in beam dynamics simulation: from light sources to colliders, Journal of Physics: proceedings of SciDAC 2008, July 14-17, Seattle, 012004, 2008.

## R

**PI Abhay Ram**

"Role of Zonal Flows in TEM Turbulence through Nonlinear Gyrokinetic Particle and Continuum Simulation," D. R. Ernst, J. Lang, W. Nevins, M. Hoffman, Y. Chen, W. Dorland, S. Parker, 22nd IAEA Fusion Energy Conference Geneva, Switzerland, 13 - 18 October 2008, paper IAEA-CN-165/TH/P8-39.

"Observation of trapped electron mode turbulence in tokamak plasmas through direct comparison of nonlinear gyrokinetic simulations with density fluctuation measurements," D. R. Ernst, N. P. Basse, W. Dorland, C. L. Fiore, L. Lin, A. Long, E. S. Marmar, M. Porkolab, and K. Zhurovich, submitted to Physical Review Letters.

Plasma Science: Advancing Knowledge in the National Interest, Plasma 2010 Committee, Plasma Science Committee, National Research Council , ISBN-10: 0-309-10943-4, ISBN-13: 978-0-309-10943-7, pub. National Academies, 2007. (features our work comparing TEM spectrum of fluctuations with experiments, using NERSC resources).

"Linearized model Fokker-Planck collision operators for gyrokinetic simulations. II. Numerical implementation and tests," M. Barnes, I. G. Abel, W. Dorland, D. R. Ernst, G. W. Hammett, P. Ricci, B. N. Rogers, A. A. Schekochihin, and T. Tatsuno, submitted to Phys. Plasmas (2008).

"Microturbulent drift mode suppression as a trigger mechanism for internal transport barriers on Alcator C-Mod," K. Zhurovich, C.L. Fiore, D.R. Ernst, P.T. Bonoli, M.J. Greenwald, A.E. Hubbard, J.W. Hughes, E.S. Marmar, D.R. Mikkelsen, P. Phillips and J.E. Rice, Nucl. Fusion 47 (9) (September 2007) 1220-1231.

C. L. Fiore, D. R. Ernst, J. E. Rice, K. Zhurovich, N. Basse, P. T. Bonoli, M. J. Greenwald, E. S. Marmar, S. J. Wukitch, "Internal transport barriers in Alcator C-Mod," Fusion Science and Technology, 51 (3), April 2007, p 303-16.

"Identification of TEM Turbulence through Direct Comparison of Nonlinear Gyrokinetic Simulations with Phase Contrast Imaging Density Fluctuation Measurements," D. R. Ernst, N. Basse, W. Dorland, C. L. Fiore, L. Lin, A. Long, M. Porkolab, K. Zeller, and K. Zhurovich, IAEA Fusion Energy Conference Chengdu, China, 16-21 October (2006), oral paper IAEA-CN-149/TH/1-3.

**PI David Randall**

Khairoutdinov, M., C. A. DeMott, and D. A. Randall, 2008: Evaluation of the simulated interannual and subseasonal variability in an AMIP-style simulation using the CSU Multiscale Modeling Framework. J. Climate, 21, 413- 431.

Toy, M. D., and D. A. Randall, 2009: Design of a non-hydrostatic atmospheric model based on a generalized vertical coordinate. Submitted to Mon. Wea. Rev.

Benedict, J., and D. A. Randall, 2009: MJO Structure in the Superparameterized CAM. Submitted to J. Atmos. Sci.

Thayer-Calder, K., and D. A. Randall, 2009: The Role of Convective Moistening in the Formation and Progression of the MJO. Submitted to J. Atmos. Sci.

DeMott, C., and D. A. Randall, 2009: Implied ocean heat transports in the standard and super- parameterized Community Atmosphere Models. Submitted to J. Climate.

**PI Sergey Rashkeev**

M.M.Kuklja and S.N.Rashkeev. Molecular instability at shear-strain interface. Appl. Phys. Lett. (submitted 08/27/2008).

I.G.Batyrev, D.Hughart, R.Durand, M.Bounasser, B.R.Tuttle, D.M.Fleetwood, R.D.Schrimpf, S.N.Rashkeev, G.W.Dunham, M.Law, and S.T.Pantelides. Effects of hydrogen on the radiation response of bipolar transistors: Experiment and modeling. IEEE Trans. Nucl. Sci. (submitted 07/11/2008).

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 (2008), doi:10.10.16/j.cattod.2008.03.029.

K.Griffin Roberts, M.Varela, S.Rashkeev, S.T.Pantelides, S.J.Pennycook, and Kannan M. Krishnan. Defect-mediated ferromagnetism in insulating Co-doped anatase TiO2 thin films. Phys. Rev. B 78, 014409 (2008).

A.G.Marinopoulos, K.van Benthem, S.N.Rashkeev, S.J.Pennycook, and S.T.Pantelides. Impurity segregation and ordering in Si/SiO2/HfO2 structures. Phys. Rev. B 77, 195317 (2008).

S.T.Pantelides, Z.-Y. Lu, C.Nicklaw, T.Bakos, S.N.Rashkeev, D.M.Fleetwood, and R.D.Schrimpf. The E prime center and oxygen vacancies in SiO2. J. of Non-Crystalline Solids 354, N2-9, 217-223 (2008).

**PI Lawrence Rauchwerger**

G. Tanase, C. Raman, M. Bianco, N. Amato and L. Rauchwerger, ``Associative Parallel Containers in STAPL'', in Proc. of the 20-th Workshop on Languages and Compilers for Parallel Computing (LCPC), Urbana-Champaign, IL, Oct 2007, to appear.

G. Tanase, M. Bianco, N. Amato and L. Rauchwerger, ``The STAPL pArray'', inProc. of the 8-th MEmory Performance: DEaling with Applications, Systems and Architecture Workshop (MEDEA), (held in conjunction with PACT'07), Brasov, Sept. 2007.

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, to appear.

Antal Buss, Timmie Smith, Gabriel Tanase, Nathan Thomas, Mauro Bianco, Nancy Amato and Lawrence Rauchwerger, "Design for Interoperability in STAPL", Proc. of the 21-th Workshop on Languages and Compilers for Parallel Computing (LCPC), Edmonton, Canada, Aug. 2008, to appear.

**PI Asok Ray**

"Atomic Adsorption on the (020) Surface of ?? " Pu " A Density Functional Study," (with R. Atta-Fynn), Physical Review B, 77, 085105-1-11(2008).

"A Density Functional Study of Atomic Hydrogen and Oxygen Chemisorption on the Relaxed (0001) Surface of Double Hexagonal Close Packed Americium," (with P. Dholabhai and R. Atta-Fynn), European Physical Journal B, 61, 261-270 (2008).

"An Ab Initio Study of the Adsorption and Dissociation of Molecular Oxygen on the (0001) Surface of Double Hexagonal Close Packed Americium," (with P. Dholabhai and R. Atta-Fynn), Physica B, accepted for publication.

"A First Principles Study of the Adsorption and Dissociation of CO2 on the ??-Pu (111) Surface," (with R. Atta-Fynn), Physical Review B, submitted for publication.

"Adsorption and Dissociation of Molecular Hydrogen on the (0001) Surface of Double Hexagonal Close Packed Americium," (with P. P. Dholabhai), European Physical Journal B, submitted for publication.

"Interplay between Spin Polarization, Orbital Polarization, and Spin-Orbit Coupling in Actinides from Pa to Cm," (with F. Islam), Physical Review B , submitted for publication.

"Atomic Hydrogen Adsorption on the (020) Surface of ?? " Pu " A Computational Study," (with F. Islam), Modeling and Simulation in Materials Science and Engineering, submitted for publication.

"Does Hybrid Density Functional Theory Predict a Non-Magnetic Ground State for ?? " Pu," (with R. Atta-Fynn), Europhysics Letters, submitted for publication.

"Adsorption and Dissociation of Water on the (0001) Surface of Double-Hexagonal-Close-Packed Americium," (with P. Dholabhai), Physica Status Solidi (b),submitted for publication.

**PI Fernando Reboredo**

D. Jiang, W. Luo, M.L. Tiago and S. Dai, "In search of a structural model for a thiolate-protected Au38 cluster", J. Phys. Chem. C 112, 13905 (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(R) (2008).

D. Jiang, M.L. Tiago, W. Luo and S. Dai, "The Staple motif: a key to stability of thiolate-protected gold nanoclusters", J. Am. Chem. Soc., 130, 2777 (2008).

M.M.G. Alemany, R.C. Longo, L.J. Gallego, D.J. Gonzalez, L.E. Gonzalez, M.L. Tiago, and J.R. Chelikowsky, "Ab initio molecular dynamics simulations of the static, dynamic, and electronic properties of liquid Pb using real-space pseudopotentials", Phys. Rev. B 76, 214203 (2007)

**PI John Rehr**

J. J. Kas, A. P. Sorini, M. P. Prange, L. W. Cambell, and J. A. Soininen, and J. J. Rehr, "Many-pole model of inelastic losses in x-ray absorption spectra," J Phys. Rev. B 76, 195116 (2007).

J. J. Rehr, J. J. Kas, M. P. Prange, A. P. Sorini, Y. Takimoto, and F. D. Vila, "Ab initio Theory and Calculations of X-ray Spectra, Theoretical Optical Spectra, L. Reining, ed., Compte Rend. in press (2008).

H. M. Lawler, J. J. Rehr, F. Vila, S. D. Dalosto, E. L. Shirley and Z. H. Levine, "Optical to UV spectra and birefringence of SiO_2 and TiO_2: "First-principles calculations with excitonic effects," submitted to PRB (July, 2008); arXiv:0807.1920.

F. Vila, J.J. Rehr, J. Kas, R.G. Nuzzo, A.I. Frenkel, "Dynamic structure in supported Pt nanoclusters: Real-time density functional theory and x-ray spectroscopy simulations," Phys. Rev. B 78, 121404(R), 2008.

Y. Takimoto, F. D. Vila and J. J. Rehr, "Real time time-dependent density functional theory approach for frequency-dependent non-linear optical response in photonic molecules," J. Chem. Phys. 127, 154114 (2007).

**PI Thomas Reichler**

Austin, J. and T. Reichler (2008): Long-term evolution of the cold point tropical tropopause: simulation results and attribution analysis J. Geophys. Res., , (in press).

Reichler, T., and J. Kim (2008): Uncertainties in the climate mean state of global observations, reanalyses, and the GFDL climate model, J. Geophys. Res., 113, D05106, doi:10.1029/2007JD009278.

Reichler, T., and J. Kim (2008): How Well do Coupled Models Simulate Today's Climate? Bull. Amer. Meteor. Soc, 89, 303-311.

**PI Chuang Ren**

Laser channeling in millimeter-scale underdense plasmas of fast ignition targets G. Li, R. Yan, C. Ren, T.-L. Wang, J. Tonge, and W. B. Mori, Phys. Rev. Lett. 100, 125002, 2008

**PI Barrett Rogers**

``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, submitteed to Phys Plasmas (2008)

``The scaling of forced magnetic reconnection in three dimensions'', B. Sullivan and B. N. Rogers, submitted to Phys. of Plasmas (2008) ``Nonlinear finite-Larmor-radius effects in reduced fluid models'', A. Brizard, R. Denton, B. Rogers, W. Lotko, submitted to Phys. of Plasmas (2008)

``High and low confinement modes in simple magnetized toroidal plasmas'', P. Ricci, B. Rogers, S. Brunner, Phys. Rev. Lett. {\bf 100}, 225002 (2008)

``Gyrokinetic simulations of collisionless magnetic reconnection'', B. N. Rogers, S. Kobayashi, W. Dorland, T. Tatsuno, J. Drake, Phys. Plasmas 14, 092110, DOI: 10.1063/1.2774003 (2007)

**PI Tony Rollett**

J. R. Morris, R. S. Aga, V. Levashov and T. Egami, "Many-body effects in BCC metals: An embedded atom model extension of the modified Johnson pair potential for iron," Phys. Rev. B 77, 174201 (2008).

L. J. Peng, J. R. Morris and Y. C. Lo, "Temperature-dependent mechanisms of homogeneous crystal nucleation in quenched Lennard-Jones liquids," Phys. Rev. B 78, 012201 (2008).

S. Namilae, B. Radhakrishnan and J. R. Morris, "Atomistic Simulation of the Effect of Ga on Crack Tip Opening in Al Bicrystals," Modelling and Simulation in Materials Science and Engineering 16, 075001 (2008).

J. R. Morris, U. Dahlborg and M. Calvo-Dahlborg, "Recent developments and outstanding challenges in theory and modeling of liquid metals," J. Non-cryst. Sol 353, 3444-3453 (2007).

J. R. Morris, M. I. Mendelev and D. J. Srolovitz, "A comparison of crystal-melt interfacial free energies using different Al potentials," J. Non-cryst. Sol 353, 3565-3569 (2007).

D. Buta, M. Asta and J. J. Hoyt, "Atomistic Simulation Study of the Structure and Dynamics of a Faceted Crystal-Melt Interface," Phys. Rev. E (in press)

V. A. Ivanov and Y. Mishin: Dynamics of grain boundary motion coupled to shear deformation. An analytical model and its verification by molecular dynamics. Phys. Rev. B 78, 064106 (2008).

**PI Barbara Romanowicz**

Romanowicz, B., M. Panning, Y. Gung and Y. Capdeville (2008)On the computation of long period seismograms in a 3D earth using normal mode based approximations, Geophys. J. Int, in press.

Panning, M., Y. Capdeville and B. Romanowicz (2008). Do first order 3D Born finite-frequency kernels improve modeling of surface waveforms?, Geophys. J. Int., in revision.

**PI Edward Rubin**

Kalyuzhnaya, MG; Lapidus, A; Ivanova, N; et al. High-resolution metagenomics targets specific functional types in complex microbial communities NATURE BIOTECHNOLOGY, 26 (9): 1029-1034 SEP 2008

Prabhakar, S; Visel, A; Akiyama, JA; et al. Human-specific gain of function in a developmental enhancer SCIENCE, 321 (5894): 1346-1350 SEP 5 2008

Wilson, A; Punginelli, C; Gall, A; et al. A photoactive carotenoid protein acting as light intensity sensor PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 105 (33): 12075-12080 AUG 19 2008

Srivastava, M; Begovic, E; Chapman, J; et al. The Trichoplax genome and the nature of placozoans NATURE, 454 (7207): 955-U19 AUG 21 2008

Dalevi, D; Ivanova, NN; Mavromatis, K; et al. Annotation of metagenome short reads using proxygenes BIOINFORMATICS, 24 (16): I7-I13 AUG 15 2008

Hwang, JS; Takaku, Y; Chapman, J; et al. Cilium evolution: Identification of a novel protein, nematocilin, in the mechanosensory cilium of Hydra nematocytes MOLECULAR BIOLOGY AND EVOLUTION, 25 (9): 2009-2017 SEP 2008

Rubin, EM Genomics of cellulosic biofuels NATURE, 454 (7206): 841-845 AUG 14 2008

Ishoey, T; Woyke, T; Stepanauskas, R; et al. Genomic sequencing of single microbial cells from environmental samples CURRENT OPINION IN MICROBIOLOGY, 11 (3): 198-204 JUN 2008

Van Brabant, B; Gray, T; Verslyppe, B; et al. Laying the foundation for a genomic rosetta stone: Creating information hubs through the use of consensus identifiers OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY, 12 (2): 123-127 JUN 2008

Hirschman, L; Clark, C; Cohen, KB; et al. Habitat-Lite: A GSC case study based on free text terms for environmental metadata OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY, 12 (2): 129-136 JUN 2008

Angiuoli, SV; Gussman, A; Klimke, W; et al. Toward an online repository of Standard Operating Procedures (SOPs) for (Meta) genomic annotation OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY, 12 (2): 137-141 JUN 2008

Mackelprang, R; Rubin, EM Paleontology - New tricks with old bones SCIENCE, 321 (5886): 211-212 JUL 11 2008

Kraaijeveld, K; Denniff, M; Baker, RH; et al. The evolution of sperm and non-sperm producing organs in male Drosophila BIOLOGICAL JOURNAL OF THE LINNEAN SOCIETY, 94 (3): 505-512 JUL 2008

Hendrix, DA; Hong, JW; Zeitlinger, J; et al. Promoter elements associated with RNA Pol 11 stalling in the Drosophila embryo PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 105 (22): 7762-7767 JUN 3 2008

Kyrpides, N Genomics, evolution and evolution of genomics FEBS JOURNAL, 275: 9-9 Suppl. 1 JUN 2008

Katsaveli, K; Tsiamis, G; Ntougias, S; et al. Microbial community shifts during the annual operation of Messolonghi solar saltern, Greece FEBS JOURNAL, 275: 282-282 Suppl. 1 JUN 2008

Kallimanis, A; Kavakiotis, K; Kyrpides, NC; et al. Identification of two 1-hydroxy-2-naphthoate dioxygenase genes in Arthrobacter sp strain Sphe3 FEBS JOURNAL, 275: 409-409 Suppl. 1 JUN 2008

Putnam, NH; Butts, T; Ferrier, DEK; et al. The amphioxus genome and the evolution of the chordate karyotype NATURE, 453 (7198): 1064-U3 JUN 19 2008

Mccoy, SR; Kuehl, JV; Boore, JL; et al. The complete plastid genome sequence of Welwitschia mirabilis: an unusually compact plastome with accelerated divergence rates BMC EVOLUTIONARY BIOLOGY, 8: Art. No. 130 MAY 1 2008

Norton, JM; Klotz, MG; Stein, LY; et al. Complete genome sequence of Nitrosospira multiformis, an ammonia-oxidizing bacterium from the soil environment APPLIED AND ENVIRONMENTAL MICROBIOLOGY, 74 (11): 3559-3572 JUN 2008

Mueller, RL; Gregory, TR; Gregory, SM; et al. Genome size, cell size, and the evolution of enucleated erythrocytes in attenuate salamanders ZOOLOGY, 111 (3): 218-230 2008

## S

**PI Yousef Saad**

H.R. Fang & Y. Saad, "Two Classes of Multisecant Methods for NonLinear Acceleration", Numerical Linear Algebra with Applications, August 2008, available online at http://www3.interscience.wiley.com/journal/121387552/abstract

**PI Martin Savage**

Color Screening by Pions, William Detmold & Martin J. Savage, e-Print: arXiv:0809.0892 [hep-lat], submitted to Phys. Rev. Lett.

Kaon Condensation with Lattice QCD, William Detmold, Kostas Orginos, Martin J. Savage & Andre Walker-Loud e-Print: arXiv:0807.1856 [hep-lat], accepted for publication ibn Phys Rev D

Multi-Pion States in Lattice QCD and the Charged-Pion Condensate. William Detmold, Martin J. Savage, Aaron Torok, Silas R. Beane, Thomas C. Luu , Kostas Orginos, Assumpta Parreno e-Print: arXiv:0803.2728 [hep-lat] Phys Rev D 78, 014507 (2008).

**PI Richard Saykally**

J. Uejio, C. Schwartz, R. Saykally, D. Prendergast; Manuscript submitted and under review with Chemical Physics Letters, Ms. No.: CPLETT-08-1815

**PI Henry Schaefer**

Jeremiah J. Wilke, Wesley D. Allen, and Henry F. Schaefer III, "Establishment of the C2H5+O2 reaction mechanism: A combustion archetype", J. Chem. Phys., 128, 074308 (2008).

Gabor Czako, Edit Matyus, Andrew C. Simmonett, Attila G. Csaszar, Henry F. Schaefer III, and Wesley D. Allen, "Anchoring the Absolute Proton Affinity Scale", J. Chem. Theory Comput., 4, 1220 (2008).

Andrew C. Simmonett, Henry. F. Schaefer III and Wesley D. Allen, "The Enthalpy of Formation and Anharmonic Force Field of Diacetylene", J. Chem. Phys., (submitted).

Andrew C. Simmonett, Francesco A. Evangelista, Wesley D. Allen and Henry F. Schaefer III, "In Search of the Definitive IR Signatures of the Elusive NCCO Radical", J. Chem. Phys., 127, 014306 (2007).

Raj K. Sreeruttun, Ponnadurai Ramasami, Chaitanya S. Wannere, Andrew C. Simmonett, and Henry F. Schaefer, III, "?? and ??-Phenylethynyl Radicals and Their Isomers o-, m-, and p-Ethynylphenyl: Structures, Energetics, and Electron Affinities", J. Phys. Chem. A, 112, 2838 (2008).

Jacqueline C. Hargis, Francesco A. Evangelista, Justin B. Ingels and Henry F. Schaefer III, "Short Intramolecular Hydrogen Bonds: Derivatives of Malonaldehyde with Symmetrical Substituents", J. Am. Chem. Soc. (accepted).

**PI Rocco Schiavilla**

"Dependence of Two-Nucleon Momentum Densities on Total Pair Momentum," R.B. Wiringa, R. Schiavilla, S.C. Pieper, and J.Carlson, Phys. Rev. C78, 021001 (2008).

"Neutron Spin Rotation in n-d Scattering," R. Schiavilla, M. Viviani, L. Girlanda, A. Kievsky, and L.E Marcucci, Phys. Rev. C78, 014002 (2008).

"Quantum Monte Carlo Calculations of Magnetic Moents and M1 Transitions in A \leq 7 Nuclei Including Meson-Exchange Currents," L.E. Marcucci, M. Pervin, S.C. Pieper, R. Schiavilla, and R.B. Wiringa, submitted to Phys.\ Rev.\ C.

**PI David Schultz**

Electron-impact ionization of the boron atom, J. C. Berengut, S. D. Loch, M. S. Pindzola, C. P. Ballance, and D. C. Griffin, Physical Review A 76, 042704 (October 2007)

Dielectronic recombination data for dynamic finite-density plasmas: XIII. The magnesium isoelectronic sequence, Z. Altun, A. Yumak, N. R. Badnell, S. D. Loch, and M. S. Pindzola, Astronomy and Astrophysics 474, 1051 (November 2007)

Feasibility studies of a charge exchange recombination diagnostic for measurement of impurity flows in the divertor of the DIII-D tokamak, N. H. Brooks, N. S. Wolf, W. P. West, S. Loch, M. O'Mullane, R. E. Olson, T. E. Evans, and R. L. Boivin, Atomic and Plasma-Material Interaction Data for Fusion {\bf 13}, 1 (November 2007)

Generalized collisional-radiative model for light elements: B: Data for the Be isonuclear sequence, S. D. Loch, M. S. Pindzola, C. P. Ballance, D. C. Griffin, J. P. Colgan, N. R. Badnell, M. G. O'Mullane, and H. P. Summers, Atomic Data and Nuclear Data Tables 94, 257 (March 2008)

Electron-impact ionization of atomic ions in the Sn and Xe isonuclear sequences, S. D. Loch, M. S. Pindzola, C. P. Ballance, and D. C. Griffin, International Journal of Mass Spectrometry 271, 68 (April 2008).

Electron-impact ionization of Be-like C, N, and O, M. Fogle, E. M. Bahati, M. E. Bannister, C. R. Vane, S. D. Loch, M. S. Pindzola, C. P. Ballance, R. D. Thomas, V. Zhaunerchyk, P. Bryans, W. Mitthumsiri, and D. W. Savin, Astrophysics Journal Supplemental Series 175, 543 (April 2008)

Electron-impact ionization of atoms in high temperature dense plasmas, M. S. Pindzola, S. D. Loch, J. Colgan, and C. J. Fontes, Physical Review A 77, 062707 (June 2008)

Electron-impact ionization of B+, J. C. Berengut, S. D. Loch, M. S. Pindzola, C. P. Ballance, D. C. Griffin, M. Fogle, and M. E. Bannister, Physical Review A 78, 012704 (July 2008)

Total and state-selective charge transfer in He+2 + H collisions, T. Minami, T-G Lee, M. S. Pindzola, and D. R. Schultz, Journal of Physics B 41, 135201 (July 2008)

Electron-impact ionization of atomic ions in the Na-like isoelectronic sequence, Z. Altun, A. Yumak, U. Golcek, S. D. Loch, M. S. Pindzola, and D. C. Griffin, Physica Scripta 78, 025304 (August 2008)

**PI Annabella Selloni**

C. Sbraccia, F. Zipoli, R. Car, M. H. Cohen, G. C. Dismukes and A. Selloni, "Mechanism of H2 Production by the [FeFe]H Subcluster of Di-Iron Hydrogenases: Implications for Abiotic Catalysts", J. Phys. Chem. B, in press (2008). Available on-line http://pubs.acs.org/cgi-bin/abstract.cgi/jpcbfk/asap/abs/jp803657b.html

Abstract of the American Chemical Society National Meeting August 2008 Authors: C. Sbraccia, F. Zipoli, R. Car, M. H. Cohen, G. C. Dismukes and A. Selloni PAPER ID: 1201679 86-INORG PAPER TITLE: "Mechanism of H2 production by the [FeFe]H subcluster of di-iron hydrogenases"

**PI John Shalf**

H. Shan, J. Shalf, K. Antypas, "Characterizing and Predicting the I/O Performance of HPC Applications using a Parameterized Synthetic Benchmark,", Proceedings of SC2008, Austin Texas, 2008.

S. Kamil, A. Jain, M. Mohiyuddin, J. Shalf, J. Kubiatowicz, "Performance and Energy Comparison of Electrical and Hybrid Photonic Networks for CMPs," Proceedings of the High Performance Embedded COmputing Conference, MIT Campus, Cambridge Mass, September 2008.

K. Datta, M. Murphy, V. Volkov, S. Williams, J. Carter, L. Oliker, D. Patterson, J. Shalf, K. Yelick, "Stencil Computation Optimizations and Autotuning on State-of-the-art Multicore Architectures," Proceedings of SC2008, Austin Texas, 2008.

**PI Shunli Shang**

S. L. Shang, A. J. Bottger, and Z. K. Liu. The influence of interstitial distribution on phase stability and properties of hexagonal epsilon-Fe6Cx, epsilon-Fe6Ny, and spsilon-Fe6CxNy phases: a first-principles calculation. Acta Mater., Vol. 56 (2008) 719-725. http://dx.doi.org/10.1016/j.actamat.2007.10.018

M. Nikolussi, S. L. Shang, T. Gressmann, A. Leineweber, E. J. Mittemeijer, Y. Wang, and Z. K. Liu. Extreme elastic anisotropy of cementite, Fe3C: first-principles calculations and experimental evidence by X-ray diffraction stress measurements. Script Mater., Vol. 59 (2008) 814-817. http://dx.doi.org/10.1016/j.scriptamat.2008.06.015

S. L. Shang, Y. Wang, Z. K. Liu, C. E. Yang, and S. Z. Yin. Band structure of FeBO3: implications for tailoring the band gap of nanoparticles. Appl. Phys. Lett., Vol. 91 (2007) 253115. http://dx.doi.org/10.63/1.2824869

D. E. Kim, S. L. Shang, and Z. K. Liu. The prediction of alloying effects on elastic properties on Ni by first-principles calculations. Acta Mater. (2008) submitted.

**PI Marjorie Shapiro**

First Observation of B-bar0_s --> D+/-_s K-/+ and Measurement of the Ratio of Branching Fractions B(B-bar0_s --> D+/-_s K-/+)/B(B-bar0_s --> D+_s pi+-) T. Aaltonen et al., The CDF Collaboration, Fermilab-Pub-08-330-E. Submitted to Phys. Rev. Lett. August 28, 2008.

CHECK: Precise Measurement of the Top Quark Mass in the Lepton+Jets Topology at CDF II

A. Abulencia et al., The CDF CollaboratiSearch for Standard Model Higgs Boson Production in Association with a W Boson at CDF T. Aaltonen et al., The CDF Collaboration, Phys. Rev. D78, 032008 (2008).on, Phys. Rev. Lett. 99, 182002 (2007).

**PI Michael Shay**

Malakit, K., P. A. Cassak, M. A. Shay, J. F. Drake, "The Hall effect in magnetic reconnection: Hybrid vs. Hall-less hybrid simulations," Geophysical Research Letters, submitted, 2008.

Cassak, P. A. and M. A. Shay, "The scaling of asymmetric hall magnetic reconnection," Geophysical Research Letters, In Press, 2008.

Drake, J. F., M. A. Shay, and M. Swisdak, "The Hall fields and fast magnetic reconnection, "Physics of Plasmas, Vol. 15, 042306, 2008.

Cassak, P. A., D. J. Mullan, and M. A. Shay, "From Solar and Stellar Flares to Coronal Heating: Theory and Observations of How Magnetic Reconnection Regulates Coronal Conditions," The Astrophysical Journal, Vol. 676, L69, 2008.

Phan, T. D., J. F. Drake, M. A. Shay, F. S.Mozer, and J. P. Eastwood, "Evidence for an elongated (> 60 ion skin depths) electron diffusion region during fast magnetic reconnection," Physical Review Letters, Vol. 99, 255002, 2007.

Cassak, P. A. and M. A. Shay," Scaling of Asymmetric Magnetic Reconnection: General Theory and Collisional Simulations," Physics of Plasmas, Vol. 14, 102114, 2007.

**PI Junko Shigemitsu**

``Highly-Improved Staggered Quarks on the Lattice with Applications to Charm Physics''; \\ E.Follana, Q.Mason, C.Davies, K.Hornbostel, P.Lepage, J.Shigemitsu, H.Trottier and K.Wong; Phys. Rev. D\underbar{75}:054502 (2007).

``$B^0_s - \overline{B^0_s}$ Mixing Parameters from Unquenched Lattice QCD''; \\ E.Dalgic, A.Gray, E.Gamiz, C.Davies, P.Lepage, J.Shigemitsu, H.Trottier and M.Wingate; Phys. Rev. D\underbar{76}:011501(R) (2007).

``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, J.Shigemitsu, H.Trottier, R.Woloshyn, K.Chetyrkin, J.Kuehn, M.Steinhauser and C.Sturm; \\ to appear in Phys.Rev.D, arXiv:0805.2999 [hep-lat].

**PI Donald Sinclair**

D.K.Sinclair, ``Separating the scales of confinement and chiral-symmetry breaking in lattice QCD with fundamental quarks,'' arXiv:0805.4627 [hep-lat].

J.B.Kogut and D.K.Sinclair, ``Lattice QCD at finite temperature and density in the phase-quenched approximation,'' Phys. Rev. D 77, 114503 (2008) [arXiv:0712.2625 [hep-lat]].

C.Strouthos and J.B.Kogut, ``Chiral Symmetry breaking in Three Dimensional QED,'' arXiv:0808.2714 [cond-mat.supr-con].

A.Bazavov, P.Petreczky and A.Velytsky, ``Static quark anti-quark pair in SU(2) gauge theory,'' arXiv:0809.2062 [hep-lat].

A.Denbleyker, D.Du, Y.Liu, Y.Meurice and A.Velytsky, ``Series expansions of the density of states in SU(2) lattice gauge theory,'' arXiv:0807.0185 [hep-lat].

A.Velytsky, ``Equilibrium criterion and effective spin models for finite temperature gauge theories,'' Phys. Rev. D 78, 034505 (2008) [arXiv:0805.4450 [hep-lat]].

A.Velytsky, ``Entanglement entropy in d+1 SU(N) gauge theory,'' Phys. Rev. D 77, 085021 (2008) [arXiv:0801.4111 [hep-th]].

A.Velytsky, ``Finite temperature SU(2) gauge theory: critical coupling and universality class,'' arXiv:0711.0748 [hep-lat].

**PI George Smoot**

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**

Sung, C.; Broadbelt, L.J.; Snurr, R.Q., "A DFT Study of Adsorption Intermediates in the NOx Reduction Pathway over BaNaY Zeolites", Catalysis Today, 2008, 136, 64-75.

Ryan, P., Broadbelt, L.J., and R.Q. Snurr. "Is Catenation Beneficial for Hydrogen Storage in Metal-Organic Frameworks?" Chemical Communications. 2008. 4132-4134.

**PI Masha Sosonkina**

M. Sosonkina, A. Sharda, A. Negoita and J.P. Vary, "Integration of ab initio nuclear physics calculations with optimization techniques", In proc. 8th International Conference, Krakow, Poland, June 23-25, 2008, Lecture Notes in Computer Science , Vol. 5101, Bubak, M.; Albada, G.D.v.; Dongarra, J.; Sloot, P.M.A. (Eds.) pp. 833 - 842 (2008).

Masha Sosonkina, Fang Liu, and Randall Bramley, "Usability levels for sparse linear algebra components", Concurrency and Computation: Practice and Experience, 20 (2008) pp. 1439--1454.

**PI Carl Sovinec**

P. Zhu and C.C. Hegna, "Ballooning filament growth in the intermediate nonlinear regime," Phys. Plasmas 15, 092306 (2008).

P. Zhu, D.D. Schnack, F. Ebrahimi, E.G. Zweibel, M.Suzuki, C.C. Hegna, and C.R. Sovinec, "Absence of complete finite-Larmor-radius stabilization in extended MHD," Phys. Rev. Lett. 101, 085005 (2008).

J. M. Reynolds, C. R. Sovinec, and S. C. Prager, "Nonlinear Magnetohydrodynamics of Pulsed Parallel Current Drive in Reversed-field Pinches," Physics of Plasmas 15, 062512 (2008).

E. B. Hooper, B. I. Cohen, H. S. McLean, R. D. Wood, C. A. Romero-Talamas, and C. R. Sovinec, "NIMROD Resistive Magnetohydrodynamic Simulations of Spheromak Physics," Physics of Plasmas 15, 032502 (2008).

R. D. Milroy, A. I. D. Macnab, C. C. Kim, and C. R. Sovinec, "FRC simulations using the NIMROD code," Journal of Fusion Energy 27, 73 (2008).

J. A. Breslau, C. R. Sovinec and S. C. Jardin, "An improved tokamak sawtooth benchmark for 3D nonlinear MHD," Commun. Comput. Phys. 4, 647 (2008).

A. I. D. Macnab, R. D. Milroy, C. C. Kim, and C. R. Sovinec, "Hall Magneto-hydrodynamics Simulations of End-Shorting Induced Rotation in Field-Reversed Configurations," Physics of Plasmas 14, 092503 (2007).

**PI Panagiotis Spentzouris**

Journal of Physics: Conference Series, Volume 125, 2008, 012001 Multiscale, multiphysics beam dynamics framework design and applications J F Amundson, D Dechow, L McInnes, B Norris, P Spentzouris and P Stoltz

Journal of Physics: Conference Series, Volume 125, 2008, 012002 Computational studies and optimization of wakefield accelerators 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, C Toth, F S Tsung, M Tzoufras, T Antonsen, J Vieira and W P Leemans

Journal of Physics: Conference Series, Volume 125, 2008, 012003 Design and optimization of large accelerator systems through high-fidelity electromagnetic simulations C Ng, V Akcelik, A Candel, S Chen, L Ge, A Kabel, Lie-Quan Lee, Z Li, E Prudencio, G Schussman, R Uplenchwar, L Xiao, K Ko, T Austin, J R Cary, S Ovtchinnikov, D N Smith, G R Werner and L Bellantoni

Journal of Physics: Conference Series, Volume 125, 2008, 012004 SciDAC advances in beam dynamics simulation: from light sources to colliders J Qiang, M Borland, A Kabel, R Li, R Ryne, E Stern, Y Wang, H Wasserman and Y Zhang

Journal of Physics: Conference Series, Volume 125, 2008, 012005 Community petascale project for accelerator science and simulation: advancing computational science for future accelerators and accelerator technologies P Spentzouris, J Cary, L C McInnes, W Mori, C Ng, E Ng and R Ryne

**PI Frank Spera**

Nevins, D., Spera, F.J.(2008) Shear viscosity and diffusion in liquid MgSiO3: Implications for magma ocean Stratification, American Mineralogist (submitted august 2008)

Martin,B, Spera, F.J., Nevins,D., Ghiorso, M. (2008), Structure, thermodynamic and transport properties of molten Mg2SiO4: Part I Molecular Dynamics Simulations, American Mineralogist, (submitted august 2008)

Spera, F.J., Nevins, D., Cutler, I., Ghiorso, M (2008) Structure, thermodynamics and transport properties of CaAl2Si2O8 liquid: Part I. Molecular Dynamics Simulations, Geochimica Cosomochimica Acta (sub september 2008)

Pertermann,M., Whittington,A., Hofmeister,A., Spera, F.J. (2008) Transport properties of low-sanidine single crystals, glasses and melts at high temperature, Contributions to Mineralogy and Petrology,155,689-702

D. Nevins, F.J. Spera, , (2007), "Accurate computation of shear viscosity from equilibrium molecular dynamics simulations" Molecular Simulation, Volume 33, Issue 15 December 2007 , pages 1261 - 1266.

F.J. Spera, Bohrson, W. A., Till, C.B., Ghiorso, M.S., (2007), "Partitioning of trace elements among coexisting crystals, melt, and supercritial fluid during isobaric crystallization and melting" American Mineralogist, Vol 92, pages 1881-1898.

Bohrson, W. A., and F. J. Spera (2007), Energy-Constrained echarge, Assimilation, and Fractional Crystallization (EC-RAFC): A Visual Basic computer code for calculating trace element and isotope variations of open-system magmatic systems, Geochem. Geophys. Geosyst., 8, Q11003, doi:10.1029/2007GC001781.

**PI Don Spong**

Neoclassical Viscosities in NCSX and QPS with Few Toroidal Periods and Low Aspect Ratios, Shin NISHIMURA, David R. MIKKELSEN, Donald A. SPONG, Steven P. HIRSHMAN, Long-Poe KU, Henry E. MYNICK and Michael C. ZARNSTORFF, Plasma Fusion Research, Vol. 3, S1059 (2008).

L. Chacon, "Scalable solvers for 3D magnetohydrodynamics," J. Physics: Conf. Series, 125, 012041 (2008)

L. Chacon, "An optimal, parallel, fully implicit Newton-Krylov solver for three-dimensional visco- resistive magnetohydrodynamics," Phys. Plasmas, 15, 056103 (2008)

"Proper Orthogonal Decomposition methods for noise reduction in particle-based transport calculations," D. del-Castillo-Negrete, D. A. Spong, S. P. Hirshman, accepted for publication in Physics of Plasmas (2008).

"Recent advances in design and R&D for the quasi-poloidal stellarator experiment," Lyon, J.F. (Oak Ridge Nat. Lab., Oak Ridge, USA); Nelson, B.E.; Benson, R.D.; Berry, L.A.; Cole, M.J.; Fogart, P.J.; Freudenberg, K.D.; Goranson, P.L.; Harris, J.H.; Heitzenroeder, P.; Lumsdaine, A.D.; Madhukar, M.A.; Neilson, G.H.; Shannon, T.E.; Spong, D.A. Source: Fusion Engineering and Design, v 82, n 5-14, Oct. 2007, p 575-82

"Neoclassical Viscosities in NCSX and QPS with Few Toroidal Periods and Low Aspect Ratios," Shin Nishimura, David R. Mikkelsen, Donald A. Spong, Steven P. Hirshman, Long-Poe Ku, Henry E. Mynick and Michael C. Zarnstorff, Plasma Fusion Research, Vol. 3, S1059 (2008).

"Simulation Study of Energetic Ion Transport due to Alfv??n Eigenmodes in LHD Plasma," Yasushi Todo, Noriyoshi Nakajima, Masaki Osakabe, Satoshi Yamamoto and Donald A. Spong, Plasma Fusion Research, Vol. 3, S1074 (2008).

**PI Garrison Sposito**

Kwon, K.D., Refson, K., Sposito, G. (2008) Zinc surface complexes on birnessite: A density functional theory study, Geochimica et Cosmochimica Acta (submitted).

Kwon, K.D., Refson, K., Sposito, G. (2008) Defect-induced photoconductivity in layered manganese oxides: A density functional theory study, Physical Review Letters, 100, 146601.

Bourg, I.C. (2008) Comment on "Modeling sulfur isotope fractionation and differential diffusion during sulfate reduction in sediments of the Cariaco Basin" by M.A. Donahue, J.P. Werne, C. Meile and T.W. Lyons, Geochimica et Cosmochimica Acta (in press).

Bourg, I.C., Sposito, G. (2008) Isotopic fractionation of noble gases by diffusion in liquid water: Molecular dynamics simulations and hydrologic applications, Geochimica et Cosmochimica Acta, 72, 2237-2247 (#4 "Hottest" article in Geochim. Cosmochim. Acta, April-June 2008).

**PI Philip Sprangle**

D. Kaganovich, D. F. Gordon, A. Ting, "Observation of large-angle quasi-monoenergetic electrons from a laser wakefield," Phys. Rev. Lett. 100, 215002 (2008)

D. F. Gordon, B. Hafizi, D. Kaganovich, and A. Ting, "Electro-optic shocks from ultraintense laser- plasma interactions," Phys. Rev. Lett. 101, 045004 (2008)

D.F. Gordon, "Improved Ponderomotive Guiding Center Algorithm," IEEE Trans. Plasma Sci. 35, 1486 (2007)

**PI Malcolm Stocks**

Frank W. Averill and Gayle S. Painter, "Embedded-cluster self-consistent partial-wave method: Extending the spatial scale of electronic structure calculations" Phys. Rev. B 77, 155109 (2008).

C. L. Fu, Maja Krcmar, G. S. Painter, and Xing-Qiu Chen, "The vacancy mechanism of high oxygen solubility and nucleation of stable oxygen-enriched clusters in Fe", Physical Review Letters 99, 225502 (2007).

Xing-Qiu Chen, C. L. Fu, and R. Podloucky, "Bonding and strength of the cubic gauche structure of nitrogen (cg-N)", Physical Review B77, 064103 (2008).

Xing-Qiu Chen, C L. Fu, M. Krcmar, and G. S. Painter, "Electronic and structural origin of ultra-incompressibility of 5d transition-metal diborides MB2 (M= W, Re, Os)", Physical Review Letters 100, 196403 (2008).

M. Eisenbach, B. Ujfalussy, B. L. Gyorffy, G. M. Stocks, "Exchange Mediated Magnetic Anisotropy", submitted to Phys. Rev. Lett. (August 2008).

M. Eisenbach, G. M. Stocks, "Invar effect and non-collinear magnetism in FeCu alloys", submitted to J. Appl. Phys. (September 2008).

R. S. Fishman, S. Okamoto, and F. A. Reboredo "Inverse Jahn-Teller Transition in Bimetallic Oxalates " Phys. Rev. Lett. 101, 116402 (2008).

Y. Lei, S. A. Shevlin, W. G. Zhu, and Z. X. Guo "Hydrogen-induced magnetization and tunable hydrogen storage in graphitic structures" Phys. Rev. B 77, 134114 (2008.

I. I. Mazin, D. J. Singh, M. D. Johannes, and M. -H. Du, Phys. Rev. Lett., 101, 057003 (2008).

D. J. Singh and M. -H. Du, Phys. Rev. Lett. 100, 237003 (2008).

Alaska Subedi, D. J. Singh, and M. -H. Du, Phys. Rev. B, 78, 060506(R) (2008).

M.L. Tiago, P.R.C. Kent, R.Q. Hood, and F.A. Reboredo, "Neutral and charged excitations in carbon fullerenes from first-principles many-body theories", J. Chem. Phys. 129, 084311 (2008).

Shenyuan Yang, Mina Yoon, Enge Wang, and Zhenyu Zhang, "Electron Transfer and Localization in Endohedral Metallofullerenes", Phys. Rev. B 78, 115435 (2008).

Shenyuan Yang, Mina Yoon, Enge Wang, and Zhenyu Zhang, "Energetics and Kinetics of Ti clustering on neutral and charged C60 surfaces", J of Chem. Phys. 129, 1 (2008).

Mina Yoon, Shenyuan Yang, Christian Hicke, David Geohegan, Enge Wang, and Zhenyu Zhang, "Calcium as a superior coating metal in functionalization of carbon fullerenes for high-capacity hydrogen storage", Phys. Rev. Lett. 100, 206806(2008).

W. G. Zhu, Z. Y. Zhang, and E. Kaxiras "Dopant-assisted concentration enhancement of substitutional Mn in Si and Ge" Phys. Rev. Lett. 100, 027205 (2008).

**PI David Strauss**

Kirtman, B. P., D. M. Straus, D. Min, E. K. Schneider, and L. Siqueira, 2009: Understanding the Link Between Weather and Climate in CCSM3.0. Geophys. Res. Lett, submitted.

**PI Alberto Striolo**

D. Konatham and A. Striolo, Molecular Design of Stable Graphene Nano-Sheets Dispersions, Nano Letters (2008) submitted.

B.H. Morrow and A. Striolo, Platinum Nanoparticles on Carbonaceous Materials: Effect of Support Geometry on Nanoparticle Mobility, Morphology, and Melting, Nanotechnology, 19 (2008) 195711.

B.H. Morrow and A. Striolo, Morphology and Diffusion Mechanism of Platinum Nanoparticles Supported on Carbon Nanotube Bundles, Journal of Physical Chemistry C, 111 (2007) 17905.

A. Striolo, On the Solution Self-Assembly of Colloidal Brushes: Insights from Simulations, Nanotechnology (2008) in Press.

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. Journal cover.

N.R. Tummala and A. Striolo, Hydrogen-Bond Dynamics for Water Confined in Carbon Tetrachloride-Acetone Mixtures, Journal of Physical Chemistry B, 112 (2008) 10675-10683.

N.R. Tummala and A. Striolo, Role of Counter-Ion Condensation on the Self-Assembly of SDS Surfactants at the Water-Graphite Interface, Journal of Physical Chemistry B, 112 (2008) 1987.

A. Striolo and D. Konatham, Graphene Sheets-Oil Nanocomposites: Equilibrium and Transport Properties from Molecular Simulation, MRS Fall Meeting, Boston, MA, December 1st-5th, 2008.

D. Argyris, N.R. Tummala, and A. Striolo, Structural and Dynamic Properties of Water on Hydrophobic and Hydrophilic, Solid and Fluid Interfaces, Gordon Research Conference on Water & Aqueous Solutions, Holderness School, Holderness, NH, July 27th - August 1st, 2008

A. Striolo, Emerging Structures for Colloidal Brushes: from Dispersions and Agglomerates to Spherulites, Wires, and Beyond, APS March Meeting, New Orleans, LA, March 9th-14th 2008.

**PI Erich Strohmaier**

H. Shan, E. Strohmaier, and J. Qiang, "Performance Analysis of leading HPC Architectures with BeamBeam3D International Journal of High Performance Computing Applications (IJHPCA), 22:1:21-32 (2008), LBNL-61134

E. Strohmaier, "Performance and it"s Complexity on Petascale Systems", Book chapter in Petascale Computing: Algorithms and Applications, D.A. Bader editor.

M. M. Tikir, L. Carrington, E. Strohmaier, A. Snavely , "A Genetic Algorithms Approach to Modeling the Performance of Memory-bound Computations" Proceedings of SC2007, Reno, November 2007.

S. Kamil, J. Shalf, and E. Strohmaier, "Power Efficiency in High Performance Computing" to appear in IPDPS 2008

E. Strohmaier, "Generalized Utility Metrics for Supercomputers", submitted to SC08

## T

**PI Xianzhu Tang**

A.N. Simakov and L. Chacon, A quantitative analytical model for fast magnetic reconnection in Hall magnetohydrodynamics, accepted to Phys. Rev. Lett. (2008);

L. Chacon, A.N. Simakov, V. Lukin, and A. Zocco, On fast reconnection in non-relativistic 2D electron-positron (pair) plasmas, Phys. Rev. Lett. 101, 025003 (2008);

L. Chacon, A.N. Simakov, and A. Zocco, Steady-state properties of driven magnetic reconnection in 2D electron MHD, Phys. Rev. Lett. 99, 235001 (2007);

W. Wan and G. Lapenta, "Micro-Macro Coupling in Plasma Self-Organization Processes during Island Coalescence", PRL 100, 035004 (2008)

W. Wan and G. Lapenta, "Electron Self-Reinforcing Process of Magnetic Reconnection", PRL 101, 015001 (2008)

W. Wan and G. Lapenta and G. L. Delzanno and J. Egedal, "Electron acceleration during guide field magnetic reconnection", PoP 15, "032903" (2008)

G. L. Delzanno, J. M. Finn, The effect of line-tying on tearing modes, Phys. Plasmas 15, 032904 (2008)

G.L. Delzanno, L. Chac??n, J.M. Finn, Y. Chung, G. Lapenta, An optimal robust equidistribution method for two-dimensional grid generation based on Monge-Kantorovich optimization, submitted to Journal of Computational Physics (2008).

X.Z. Tang and A.H. Boozer, "Scale-up of spherical tokamak solenoid-free startup by co-axial helicity injection," Phys. Plasmas Vol. 14, 100704 (2007).

X.Z. Tang and A.H. Boozer, "Reactor prospect of spheromak concept by electrostatic helicity injection," Phys. Plasmas Vol. 15, 072510 (2008).

X.Z. Tang, "Self-organization of radio lobe magnetic fields by driven relaxation," Astrophysical Journal, Vol.679, 1000 (2008).

**PI Bhupender Thakur**

B. Thakur, S. Pittel, N. Sandulecsu, "Density Matrix Renormalization Group study of $^{48}$Cr and $^{56}$Ni", Accepted for publication in Physical Review C, http://arxiv.org/abs/0808.1277

**PI Dave Thirumalai**

D. L. Pincus, C. Hyeon and D. Thirumalai, J. Am. Chem. Soc., Effects of trimethylamine n-oxide (tmao) and crowding agents on the stability of rna hairpins. J. Am. Chem. Soc., 130(23):7364-7372, (2008).

D. L. Pincus and D. Thirumalai. Crowding effects on the mechanical stability and unfolding pathways of ubiquitin. J. Phys. Chem. B, 2009, 113 (1), 359-368

Minimal Models for Proteins and RNA: From Folding to Function David L. Pincus*, Samuel S. Cho*, Changbong Hyeon, and D. Thirumalai, Progress in Molecular Biology, vol84, p203 (2008)

**PI Doug Toussaint**

"The B -> D* l nu form factor at zero recoil from three-flavor lattice QCD: A model independent determination of |V_cb|", 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, ArXiv:0808.2519, submitted to Phys. Rev. D.

"QCD equation of state with 2+1 flavors of improved staggered quarks," C. Bernard, T. Burch, C. DeTar, Steven Gottlieb, L. Levkova, U.M. Heller, J.E. Hetrick, R. Sugar, D. Toussaint, Phys. Rev. D75 (2007) 094505.

**PI Trevor Tyson**

"Local Structure of Multiferroic RMn2O5: Important Role of theR site", T. A. Tyson, Z. Chen1, M. Deleon, S. Yoong, and S.-W. Cheong, submitted to the Journal of Magnetism and Magnetic Materials

"Local Structure of Thermoelectric Ca3Co4O9" T. A. Tyson, Z. Chen, Q. Jie, Q. Li, J. J. Tu, Phys. Rev. B 79, 024109 (2009)

**U**

**V**

**PI George Vahala**

G. Vahala, B. Keating, M. Soe, J. Yepez, L. Vahala and S. Ziegeler, "Entropic, LES and Boundary Conditions in Lattice Boltzmann Simulations of Turbulence", Euro Phys. J (accepted for publication)

J. Yepez, G. Vahala and L. Vahala, "Vortex-antiVortex pair in a Bose-Einstein Condensate", Euro Phys. J. (accepted for publication)

G. Vahala, B. Keating, M. Soe, J. Yepez, L. Vahala, J. Carter and S. Ziegeler,"MHD Turbulence Studies using Lattice Botlzmann Algorithms", Commun in Computat. Physics. 4, 624-646 (2008)

G. Vahala, J. Yepez and L. Vahala, "Quantum Lattice Gas Algorithm for Quantum Turbulence and Vortex Reconnection in the Gross-Pitaevskii Equation", Proc. SPIE, 6976, 69760U1-10 (2008)

J. Yepez, G. Vahala and L. Vahala, "Twisting of Filamentary Vortex Solitons Demarcated by Fast Poincare Recurrence", submitted for publication

**PI David Vanderbilt**

"Ideal barriers to polarization reversal and domain-wall motion in strained ferroelectric thin films", S. P. Beckman, Xinjie Wang, Karin M. Rabe, and David Vanderbilt, submitted to Phys. Rev. B.

**PI James Vary**

M. Sosonkina, A. Sharda, A. Negoita and J.P. Vary, "Integration of ab initio nuclear physics calculations with optimization techniques", In proc. 8th International Conference, Krakow, Poland, June 23-25, 2008, Lecture Notes in Computer Science , Vol. 5101, Bubak, M.; Albada, G.D.v.; Dongarra, J.; Sloot, P.M.A. (Eds.) pp. 833 - 842 (2008).

T. Dytrych, K.D. Sviratcheva, C. Bahri, J.P. Draayer and J.P. Vary, "Highly deformed modes in the ab initio symplectic no-core shell model," J. Phys. G. 35, 095101 (2008).

P. Sternberg, E.G. Ng, C. Yang, P. Maris, J.P. Vary, M. Sosonkina and H. V. Le, "Accelerating Configuration Interaction Calculations for Nuclear Structure", accepted for publication in Proceedings of Super Computing 2008.

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," Submitted to Phys. Rev. C, arXiv 0806.4018

P. Maris, J.P. Vary and A. M. Shirokov, "Ab Initio no-core full configuration calculations of light nuclei," Submitted for publication to Phys. Rev. C., arXiv 0808.3420.

**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", submitted to Phys. Plasmas

[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, R. E. Waltz,2 J. Candy, G. R. McKee, M. W. Shafer, A. E. White, L. Schmitz, G. R. Tynan, "Validation of gyrokinetic transport simulations using DIIID core turbulence measurements", submitted to Phys Plasmas

[Izzo 2008a] V. A. Izzo, D. G. Whyte, R. S. Granetz, P. B. Parks, E. M. Hollmann, L. L. Lao, and J. C. Wesley, "Magnetohydrodynamic simulations of massive gas injection into Alcator C-Mod and DIII-D plasmas" PHYSICS OF PLASMAS 15, 056109 (2008)

[Izzo 2008b] V.A. Izzo, I. Joseph, "RMP enhanced transport and rotational screening in simulations of DIII-D plasmas", Nucl. Fusion 46 (2008). In Press.

**PI Cai-Zhuang Wang**

Structure of Zr_x Pt_100-x (73<=x<=77) metallic glasses, D.J. Sordelet, R.T. Ott, M.Z. Li, S.Y. Wang, C.Z. Wang, , M.F. Besser, A.C.Y. Liu and M.J. Kramer, Metallurgical and Materials Transaction A 39, 1908 (2008).

Molecular dynamics investigation of dynamical heterogeneity and local structure in the supercooled liquid and glass states of Al, Maozhi Li, C. Z. Wang, M. I. Mendelev, and K. M. Ho, Phys. Rev. B, 77, 184202 (2008).

"Cluster-in-jellium model and icosahedral ordering tendencies in liquid Al alloys", Y. X. Yao, C. Z. Wang and K. M. Ho, Phys. Rev. B 76, 174209 (2007).

Short- and medium-range order in a Zr73Pt27 glass: experimental and simulation Studies, S. Y. Wang, C. Z. Wang, M. Z. Li, L. Huang, R. T. Ott, M. J. Kramer, D. J. Sordelet, and K. M. Ho, Phys. Rev. B 78, 184204 (2008).

Structure and dynamics of liquid Al1-xSix alloys by Ab initio molecular dynamics Simulations, Songyou Wang, C. Z. Wang, C. X. Zheng, and K. M. Ho, J. Non-Crys. Sol. (in press).

Experimental and ab Initio structural studies of liquid Zr2Ni, 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, Phys. Rev. B (submitted).

Experimental and ab initio molecular dynamics simulation studies of liquid Al60Cu40 alloy, S. Y. Wang, M. J. Kramer, M. Xu, S. Wu, S. G. Hao, D. J. Sordelet, K. M. Ho, and C. Z. Wang, Phys. Rev. B (submitted).

Icosahedral Two-Phase Structure and Medium-Range Order in ZrxCu1-x Metallic Glasses, M. Li, C. Z. Wang, S. G. Hao, M. J. Kramer, and K. M. Ho, Phys. Rev. Lett. (submitted).

**PI Haobin Wang**

M. Thoss, I. Kondov, and H. Wang, ``Correlated electron-nuclear dynamics in ultrafast photoinduced electron-transfer reactions at dye-semiconductor interfaces'', Phys. Rev. B, 76, 153313 (2007).

H. Wang and M. Thoss, ``Nonperturbative quantum simulation of time-resolved nonlinear spectra: Methodology and application to electron transfer reactions in the condensed phase'', Chem. Phys., 347, 139 (2008).

I. Nieto, F. Ding, R. P. Bontchev, H. Wang, and J. M. Smith, ``Thermodynamics of Hydrogen Atom Transfer to a High-Valent Iron Imido Complex'', J. Am. Chem. Soc. 130, 2716 (2008).

I. Kondov, V. Vallet, H. Wang, and M. Thoss, "Ground and excited state properties of the mixed-valence complex [(NH_3)_5Ru^{III}NCRu^{II}(CN)_5]^-", J. Phys. Chem. A, 112, 5467 (2008).

K. A. Velizhanin, H. Wang and M. Thoss, ``Heat transport through model molecular junctions: A multilayer multiconfiguration time-dependent Hartree approach'', Chem. Phys. Lett., 460, 325, (2008).

W. Chen, S. Chen, F. Ding, H. Wang, L. E. Brown, and J. P. Konopelski, ``Nanoparticle-Mediated Intervalence Transfer'', J. Am. Chem. Soc., 130, 12156, (2008).

J. Li, M. Nilsing, I. Kondov, H. Wang, P. persson, S. Lunell, and M. Thoss, ``Dynamical Simulation of Photoinduced Electron Transfer Reactions in Dye-Semiconductor Systems with Different Anchor Groups'', J. Phys. Chem. C 112, 12326 (2008).

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., accepted.

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., accepted.

Z. G. Yu, M. A. Berding, and H. Wang, ``Spatially correlated fluctuations and coherence dynamics in phototsynthesis'', Phys. Rev. E, accepted.

X. G. Song, H. Wang, and T. Van Voorhis, ``A Langevin equation approach to electron transfer reqctions in the diabatic basis'', J. Chem. Phys., accepted.

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., accepted.

**PI Jun Wang**

Peng Gu, Jun Wang, Yifeng Zhu, Hong Jiang, Nexus: A Novel Weighted-Graph-Based Prefetching Algorithm for Metadata Servers in Large Scale Storage Systems, submitted to IEEE transactions on computer.

**PI Lin-Wang Wang**

F. Wang, H. Yu, J. Li, Q. Hang, D. Zemlyanov, P. C. Gibbons, L.W. Wang, D. B. Janes, W. E. Buhro, "Spectroscopic properties of colloidal indium phosphide quantum wires", J. Am. Chem. Soc. 129, 14327 (2007).

C. Voemel, S.Z. Tomov, O.A. Marques, A. Canning, L.W. Wang, J.J. Dongarra, "State-of-the-art eigensolvers for electronic structure calculations of large scale nano-systems", J. Comp. Phys. 223, 774 (2007).

B. Lee, A. Canning, L.W. Wang, "Effects of d-electrons in pseudopotential screened-exchange density functional calculations", J. Appl. Phys. 103, 113713 (2008).

J. Schrier, B. Lee, L.W. Wang, "Mechanical and electronic structure properties of compressed CdSe tetrapod nanocrystals", J. Nanosci. Nanotech. 8, 1994 (2008).

L.W. Wang, Z. Zhao, J. Meza, "A linear scaling three dimensional fragment method for large scale electronic structure calculations", Phys. Rev. B 77, 165113 (2008).

D.O. Demchenko, R.D. Robinson, B. Sadtler, C.K. Erdonmez, A.P. Alivisatos, L.W. Wang, "Formation mechanism and properties of CdS/Ag2S nanorod superlattices", ACS Nano. 2, 627 (2008).

Z. Zhao, J. Meza, L.W. Wang, "A divide-and-conquer linear scaling three dimensional fragment method for large scale electronic structure calculations", J. Phys.: Conds. Matt. 20, 294203 (2008).

N. Vulmirovic, L.W. Wang, "Charge patching method for electronic structure of organic systems", J. Chem. Phys. 128, 121102 (2008).

J. Sun, L.W. Wang, W.E. Buhro, "Synthesis of cadmium telluride quantum wires and the similarity of their effective band gaps to those of equidiameter cadmium telluride quantum dots", J. Am. Chem, Soc. 130, 7997 (2008).

J. Schrier, L.W. Wang, "Shape dependence of resonant energy tranfer between semiconductor nanocrystals", J. Phys. Chem. (in press).

C. Yang, J. Meza, B. Lee, L.W. Wang, "A MATLAB toolbox for solving the Kohn-Sham equations", ACM Trans. on Math. Software (in press).

Y, Zhang, A. Mascarenhas, L.W. Wang, "Non-Bloch nature of alloy states in a conventional semiconductor alloy Ga_xIn_(1-x)P as an example", Phys. Rev. Lett. (in press).

D.O. Demchenko, G.M. Sacha, M. Salmeron, L.W. Wang, "Interactions of oxygen and hydrogen on Pd(111) surface", Surf. Sci. (in press).

J. Sun, W.E. Buhro, L.W. Wang, J. Schrier, "Electronic structure and spectroscopy of cadmium telluride quantum wires" nanoletter (in press).

A. Garcia-Lekue, L.W. Wang, "Self-consistent non-equilibrium transport using planewaves" (submitted).

S. Dag, L.W. Wang, "Modelling of Nanoscale morphology of regioregular poly(3-hexylthiophene) on ZnO (10-10) surface" (submitted).

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" (submitted).

L.W. Wang, "Ab initio calculation of shallow acceptor levels in Si" (submitted).

L.W. Wang, "Large scale ab initio nanostructure electronic structure calculations for energy applications" (submitted).

N. Vukmirovic, L.W. Wang, "Electronic structure of disordered conjugated polymers: the example of polythiophenes" (submitted).

**PI Warren Washington**

Alexander L.V. and J.M. Arblaster, 2008: Assessing trends in observed and modelled climate extremes over Australia in relation to future projections, Int. J. Climatol., doi: 10.1002/joc.1730, early view online.

Deser, C. and H. Teng, 2008: Evolution of Arctic sea ice concentration trends and the role of atmospheric circulation forcing, 1979-2007, Geophysical Research Letters, 35, doi: 10.1029/2007GL032023.

Lawrence, D.M., A.G. Slater, R.A. Tomas, M.M. Holland and C. Deser, 2008: Accelerated Arctic land warming and permafrost degradation during rapid sea ice loss. Geophys. Res. Lett., 35, L11506, doi: 10.1029/2008GL033985.

Lawrence, D.M. and A.G. Slater, 2007: Incorporating organic soil into a global climate model. Clim. Dyn., doi: 10.1007/s00382-007-0278-1.

Meehl G.A., J.M. Arblaster, G.W. Branstator and H. van Loon, 2008a: A coupled air-sea response mechanism to solar forcing in the Pacific region, J. Climate, 21, 2883-2897.

Meehl ,G.A., J.M. Arblaster and W.D. Collins 2008b: Effects of black carbon aerosols on the Indian monsoon, J. Climate, 21, 2869-2882.

Meehl ,G.A., J.M. Arblaster and C. Tebaldi, 2007a: Contributions of natural and anthropogenic forcing to changes in temperature extremes over the United States, Geophys. Res. Letts., 34, L19709, doi: 10.1029/2007GL030948.

Meehl, G.A., C. Tebaldi and H. Teng, 2007b: Current and future US weather extremes and El Nino. Geophysical Research Letters, 34, doi: 10.1029/2007GL031027

Meehl , G.A. and J.M. Arblaster, 2008c: A lagged warm event-like response to peaks in solar forcing in the Pacific region, J. Climate, accepted.

Oleson, K.W., G.-Y. Niu, Z.-L. Yang, D.M. Lawrence, P. E. Thornton, P.J. Lawrence, R. St??ckli, R.E. Dickinson, G.B. Bonan, S. Levis, A. Dai and T. Qian, 2008: Improvements to the Community Land Model and their impact on the hydrological cycle. J. Geophys. Res., 113, G01021, doi: 10.1029/2007JG000563.

Stott, P. A., J. F. B. Mitchell, M. R. Allen, T. L. Delworth, J. M. Gregory, G. A. Meehl, and B. D. Santer, 2006: Observational constraints on past attributable warming and predictions of future global warming. Journal of Climate, 19, 3055-3069.

Teng, H., W.M. Washington and G.A. Meehl, 2008: Interannual variations and future change of wintertime extratropical cyclone activity over North America, Climate Dynamics, doi: 10.1007/s00382-007-0314-1.

**PI William Weber**

R. Devanathan and W. J. Weber, "Dynamic Annealing of Defects in Irradiated Zirconia-Based Ceramics", Journal of Materials Research 23 (2008) 593-597.

R. Devanathan and W. J. Weber, "Radiation Effects in a Model Ceramic for Nuclear Waste Disposal", JOM 59(4) (2007) 32-35.

**PI Suhai Wei**

"Nature of the Band Gap of In2O3 Revealed by First-Principles Calculations and X-Ray Spectroscopy", A. Walsh, J. L. F. Da Silva, S.-H. Wei et al., Physical Review Letters 100, 167402 (2008).

"Rules of structure formation for the homologous InMO3(ZnO)n compounds", J. L. F. Da Silva, Y. Yan and S.-H. Wei, Physical Review Letters 100, 255501 (2008).

"Origins of band-gap renormalization in degenerately doped semiconductors", A. Walsh, J. L. F. Da Silva and S.-H. Wei, Physical Review B 78, 075211 (2008).

"Electronic structure and phase stability of MgO, ZnO, CdO, and related ternary alloys", Y. Z. Zhu, G. D. Chen, H. Ye, A. Walsh, C. Y. Moon and S.-H. Wei, Physical Review B 77, 245209 (2008).

"Theoretical Description of Carrier Mediated Magnetism in Cobalt Doped ZnO", A. Walsh, J. L. F. Da Silva an S.-H. Wei, Physical Review Letters 100, 256401 (2008).

"Effect of Co-Passivation of Cl and Cu on CdTe Grain Boundaries", Lixin Zhang, Juarez L. F. Da Silva, Jingbo Li, Yanfa Yan, T.A. Gessert, and Su-Huai Wei, Phys. Rev. Lett. (in press).

"Enhanced Ferromagnetic Stability in Cu Doped Passivated GaN Nanowires", H. J. Xiang and Su-Huai Wei, Nano Lett. 7, 1825 (2008).

"Accurate and Efficient van der Waals Interactions within Density Functional Theory by Local Atomic Potential Approximation", Y. Y. Sun, Y.-H. Kim, K. Lee, and S. B. Zhang, J. Chem. Phys. (in press).

**PI Michael Weinert**

Atomistic view of the autosurfactant effect during GaN epitaxy. S. T. King, M. Weinert, and L. Li, Phys. Rev. Lett. 98, 206106 (2007).

YCo_2: Intrinsic Magnetic Surface of a Paramagnetic Bulk Material. Yu. S. Dedkov, C. Laubschat, S. Khmelevskyi, J. Redinger, P. Mohn, and M. Weinert, Phys. Lett. 99, 047204 (2007).

Incorporation of Ge on GaN(0001). Y. Qi, S. T. King, S. H. Cheung, M. Weinert, and L. Li, Appl. Phys. Lett. 92, 111918 (2008).

Effects of Unreconstructed and Reconstructed Polar Surface Terminations on Growth, Structure, and Magnetic Properties of Hematite Films. S. H. Cheung, A. Celik-Aktas1, P. Dey, M. Weinert, B. Kabius, D. J. Keavney, V. K. Lazarov, S. A. Chambers, and M. Gajdardziska-Josifovska, Phys. Rev. B (in press)

Spin-polarized STM study of MnxGa{1-x} on GaN(0001), Y. Qi, G. F. Sun, M. Weinert, and L. Li, Appl. Phys. Lett. (submitted).

**PI Harold Weitzner**

H. R. Strauss, B. Hientzsch, J. Chen, A spectral element implementation for the M3D extended MHD code, Commun. Comput. Physics 4, 506 (2008).

J. Cummings, A. Pankin, N. Podhorszki, et. al, Plasma Edge Kinetic-MHD Modeling in Tokamaks Using Kepler Workflow for Code Coupling, Data Management and Visualization, Commun. Comput. Physics, 4, 675 (2008)

C.S. Chang, S. Klasky, J. Cummings, R. Samtaney, et. al., Toward a first-principles integrated simulation of tokamak edge plasmas, J. of Physics: Conference Series, 125, 012042, (2008)

Y. Chen, S. E. Parker, G. Rewoldt, S. Ku, G.Y. Park, C.S. Chang, Coarse-graining the electron distribution in gyrokinetic simulations, Phys. Plasmas, 15, 055905 (2008)

C.S. Chang, S. Ku, Spontaneous rotation sources in a quiescent tokamak edge plasma, Phys. Plasmas, 15, 062510 (2008)

**PI Gerhard Wellein**

Zeiser, Thomas ; Hager, Georg ; Wellein, Gerhard: "Vector Computers in a World of Commodity Clusters, Massively Parallel Systems and Many-Core Many-Threaded CPUs: Recent Experience Based on an Advanced Lattice Boltzmann Flow Solver". In: Nagel, Wolfgang E. ; Kröner, Dietmar B. ; Resch, Michael M. (Hrsg.) : High Performance Computing in Science and Engineering '08: Transactions of the High Performance Computing Center, Stuttgart (HLRS) 2008. Bd. 5. Berlin Heidelberg : Springer, 2009, (Mathematics and Statistics), S. 333-347. - ISBN 978-3-540-88301-2. Received the HLRS Golden Spike Award 2008.

**PI Zhaofang Wen**

"Initial Experiences with BEC Parallel Programming Environment," Mike Heroux, Zhaofang Wen, Junfeng Wu, Yuesheng Xu. 7th International Symposium on Parallel and Distributed Computing ISPDC 2008, Krakow, Poland.

**PI Don Werthimer**

Resolving Structure at the Innermost Stable Circular Orbit of the Super Massive Black Hole candidate SgrA, Doeleman et al, Nature, v455, p78-80, 4 September 2008

**PI Martin White**

Brown, M. J. I., et al., `Red Galaxy Growth and the Halo Occupation Distribution', ApJ, 682, 963 (2008)

Percival, W. J, White, M., `Testing cosmological structure formation using redshift-space distortions', submitted to MNRAS

Padmanabhan, N., White, M., `Constraining anisotropic baryon oscillations', Physical Review D, 77, (2008)

Seo, H.-J., et al., `Non-linear structure formation and the acoustic scale', ApJ, in press.

Cohn, J. D., White, M., `Dark matter halo abundances, clustering and assembly histories at high redshift', MNRAS, 385, 2033 (2008)

Dalal, N., et al., `Halo Assembly Bias in Hierarchical Structure Formation', ApJ, in press.

Padmanabhan, N., et al., `The real-space clustering of luminous red galaxies around z

**PI John Wilkins**

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).

From compact point defects to extended structures in silicon. Y. A. Du, R. G. Hennig, T. J. Lenosky and J. W. Wilkins. Eur. Phys. J. B 57 229 (2007).

Alleviation of the Fermion-Sign Problem by Optimization of Many-Body Wave Functions. C. J. Umrigar, J. Toulouse, C. Filippi, S. Sorella and R. G. Hennig. Phys. Rev. Lett. 98, 110201 (2007).

Questioning the existence of a unique ground-state structure for Si clusters. W. Hellmann, R. G. Hennig, S. Goedecker, C. J. Umrigar, B. Delley and T. Lenosky. Phys. Rev. B 75, 085411 (2007).

**PI Brian Wirth**

Y. Jiang, J.R. Smith, and G.R. Odette, "Formation of Y-Ti-O Nanoclusters in Nanostructured Ferritic Alloys: A First Principles Study", submitted to Phys. Review B.

**PI Simon Woodruff**

Woodruff, S. Technical survey of simply connected compact tori (CTs): spheromaks, FRCs and compression schemes Journal of Fusion Energy, v 27, n 1, June 2008, p 134-48

Macnab, Angus I.D. (Woodruff Scientific, LLC); Woodruff, Simon Simulations of the supersonic translation, collision, and merging of two field-reversed configurations for plasma heating IEEE Transactions on Plasma Science, v 36, n 4 PART 1, August, 2008, Images in Plasma Science, p 1208-1209

**PI Stan Woosley**

"Radiation-Hydrodynamic Simulations of Collapse and Fragmentation in Massive Protostellar Cores," Krumholz, M.P., Klein, R.I., & McKee, C.F., ApJ, 656, 959, 2007

"Simulations of Magnetically-Driven Supernova and Hypernova Explosions in the Context of Rapid Rotation," (A. Burrows, L. Dessart, E. Livne, C.D. Ott, & J. Murphy), ApJ, 664, 416, 2007

"The Protoneutron Star Phase of the Collapsar Model and the Route to Long-Soft Gamma-ray Bursts and Hypernovae," (Luc Dessart, Adam Burrows, Eli Livne, and Christian Ott), ApJ Letters, 673, L43, 2008

"2D Multi-Angle, Multi-Group Neutrino Radiation-Hydrodynamic Simulations of Postbounce Supernova Cores," (C.D. Ott, A. Burrows, L. Dessart, & E. Livne), ApJ, 685, 1069, 2008

Tchekhovskoi, A.D., McKinney, J.C., & Narayan, R., Simulations of Ultrarelativistic Magnetodynamic Jets from Gamma-ray Burst Engines, 2008, MNRAS, 388, 551

Komissarov, S.S. & McKinney, J.C., "Meissner effect" and Blandford-Znajek mechanism in conductive black hole magnetospheres, 2007, MNRAS LETTERS, 377, L49

Riquelme, M. & Spitkovsky, A. 2008, "Non-Linear Study of Bell's Cosmic Ray Current-Driven Instability," ApJ, submitted

Medvedev, M. & Spitkovsky, A. 2008, "Radiative Cooling in Relativistic Collisionless Shocks: Can Simulations and Experiments Probe Relevant GRB Physics?" ApJ, submitted

Spitkovsky, A. 2008, "Particle Acceleration in Relativistic Collisionless Shocks: Fermi Process at last?" ApJ Lett., 682, L5

Spitkovsky, A. 2008, "On the Structure of Relativistic Collisionless Shocks in Electron-Ion Plasmas," ApJ Lett., 673, L39.

H. Dimmelmeier, C. D. Ott, A. Marek, and H.-T. Janka, "The Gravitational Wave Burst Signal from Core Collapse of Rotating Stars," accepted for publication in Phys. Rev. D.

Offner, S. S. R., Krumholz, M. K., Klein, R. I., & McKee,\ C. F. 2008, `The Kinematics of Molecular Cloud Cores in the Presence\ of Driven and Decaying Turbulence: Comparisons with Observations'',\ AJ, 136, 4040.

"Magnetically-Driven Explosions of Rapidly-Rotating White Dwarfs Following Accretion-Induced Collapse," (L. Dessart, A. Burrows, E. Livne, & C.D. Ott), ApJ, 669, 585, 2007

T. Z. Summerscales, A. Burrows, C. D. Ott, and L. S. Finn, "Maximum Entropy for Gravitational Wave Data Analysis: Inferring the Physical Parameters of Core-Collapse Supernovae," ApJ 678, 1142, 2008.

"Optimizing Type Ia supernova follow-up in future dark energy surveys" Authors: P Nugent, R Thomas and G Aldering 2008 Journal: J. Phys.: Conf. Ser. 125 012011

"Verifying the Cosmological Utility of Type Ia Supernovae: Implications of a Dispersion in the Ultraviolet Spectra," Ellis, R. S.; Sullivan, M.; Nugent, P. E.; Howell, D. A.; Gal-Yam, A.; Astier, P.; Balam, D.; Balland, C.; Basa, S.; Carlberg, R. G.; Conley, A.; Fouchez, D.; Guy, J.; Hardin, D.; Hook, I.; Pain, R.; Perrett, K.; Pritchet, C. J.; Regnault, N., Ap.J., Volume 674, Issue 1, pp. 51-69.

"Towards a real-time transient classification engine," Bloom, J. S.; Starr, D. L.; Butler, N. R.; Nugent, P.; Rischard, M.; Eads, D.; Poznanski, D. Journal: Astronomische Nachrichten, Vol.329, Issue 3, p.284

**PI Jianzhong Wu**

"Structure and swelling of grafted polyelectrolytes: Predictions from a non-local density functional theory,'' T. Jiang, Z. Li and J. Wu, Macromolecules, 40(2), 334-343 (2007).

"Molecular dynamics for surfactant-assisted protein refolding", D. Lu, Z. Liu, and J. Wu, Journal of Chemical Physics 126, Article# 064906 (2007).

"Potential distribution theorem for the polymer-induced depletion between colloidal particles," Z. Li and J. Wu, Journal of Chemical Physics, 126, Article# 144904 (2007) (Appeared also in April 15, 2007 issue of Virtual Journal of Biological Physics Research).

"Density functional theory for a primitive model of nanoparticle-block copolymer mixtures", D. Cao and J. Wu, Journal of Chemical Physics 126, Article# 144912 (2007).

''Protein refolding assisted by periodic mesoporous organosilicas,'' X. Wang, D. Lu, R. Austin, A. Agarwal, L. J. Mueller, Z. Liu, J. Wu, P. Feng, Langmuir, 23(10), 5735-9, 2007.

"Density functional theory for complex fluids", J. Wu and Z. Li, Annual Review of Physical Chemistry, 58:85-112, 2007.

''Isotropic"nematic phase transition in athermal solutions of rod"coil diblock copolymers,'' J. Jiang, J. Wu, Journal of Chemical Physics, 127, Article# 034902, 2007.

"Surface-facilitated separation of long DNA molecules,'' L. Gao, J. Wu, D. Gao, J. Wu, Applied Physics Letters, 91, Article # 113902, 2007. (Also appeared in September 15, 2007 issue of Virtual Journal of Biological Physics Research and featured in Nature Nanotechnology, Published online: 21 September 2007).

''Dynamic control of protein folding pathway with a polymer of tunable hydrophobicity,'' D. Lu, J. Wu, Z. Liu, The Journal of Physical Chemistry B, 111 (42), 12303 -12309, 2007.

''Density functional theory for liquid structure and thermodynamics,'' J. Wu, Molecular Thermodynamics of Complex Systems, Springer, X. Lu, Y. Hu (Eds), 106 m.s. pages, 2007. (Invited contribution)

''Melting kinetics of thermally responsive microgel crystals,'' S. Tang, Z. Hu, B. Zhou, Z. Cheng J. Wu, M. Marquez, Macromolecules, 40, 9544-9548, 2007.

''Osmotic pressure and packaging structure of caged DNA,'' Z. Li, J. Wu, Z. G. Wang, Biophysical Journal, 94: 737-746, 2008.

''Towards a quantitative theory of ultra"small liquid droplets and vapor"liquid nucleation,'' Z. Li, J. Wu, Industrial & Engineering Chemistry Research, 47 (15): 4988"4995, 2008. (Invited contribution)

"A theoretical study for nanoparticle partitioning in the lamellae of diblock copolymers", J. Jin and J. Wu, Journal of Chemical Physics, 128, 074901, 2008. (Also appeared in the March 1, 2008 issue of Virtual Journal of Biological Physics Research and in the March 3, 2008 issue of Virtual Journal of Nanoscale Science & Technology).

"Pairwise additive hydrophobic effect for alkanes in water", J. Wu and J. M. Prausnitz, PNAS, accepted, 2008.

"Ionic Effects in Collapse of Polyelectrolyte Brushes", J. Tao and J. Wu, The Journal of Physical Chemistry B, accepted, 2008.

**PI Meng-Shiou Wu**

M.-S. Wu, H. Mori, J. Bentz, T. Windus, H. Netzloff, M. Sosonkina and M. S. Gordon, "Constructing a Performance Database for Large-Scale Quantum Chemistry Packages", in High Performance Computing and Simulation Symposium (HPCS 2008), Ottawa, Canada, April 14-16, 2008.

F. Peng, M.-S. Wu, M. Sosonkina, J. Bentz, T.Windus, M.S. Gordon, J. Kenny, C. Janssen. "Tackling Component Interoperability in Quantum Chemistry Software," in the Workshop on Component and Framework Technology in High-Performance and Scientific Computing, held in conjunction with ooPLSA 2007, Montreal, Canada, October 21-22, 2007.

"Components for Integral Evaluation in Quantum Chemistry", J.P. Kenny, C.L. Janssen, E.F. Valeev, and T.L. Windus, J. Comp. Chem., in press, 10.1002/jcc.20815.

**PI Ruqian Wu**

S.C. Hong. J.I. Lee and R.Q. Wu, "Ferromagnetism in Pd thin films induced by quantum well states", Phys. Rev. B 75, 172402 (2007).

J.X. Cao, X.G. Gong, and R.Q. Wu, "Giant piezoresistance and its origin in Si(111) nanowires: First-principles calculations", Phys. Rev. B 75, 233302 (2007).

J.H. Wang, C.S. Jo, R.Q. Wu, "Magnetic Properties of Fe-5d (Os, Ir, and Pt) Nanowires Encapsulated in Carbon Nanotubes", Appl. Phys. Lett. 92, 032507 (2008).

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).

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).

J. X. Cao, Y. Zhu, Z. Q. Yang, and R. Q. Wu, "What produces magnetism in CaB6", Phys. Rev. Lett. Submitted.

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. Lett. Submitted.

D.W. Yuan, X.G. Gong, and R.Q. Wu, "Atomic configurations of Pd atoms in PdAu(111) bimetallic surfaces investigated using the first-principles pseudopotential plane wave approach", Phys. Rev. B 75, 085428 (2007).

D.L. Mills, J.X. Cao and R.Q. Wu, "Interaction of adsorbates with electric-field fluctuations near surfaces: Nonradiative lifetimes and energy-level shifts", Phys. Rev. B 75, 205439 (2007).

D.W. Yuan, X.G. Gong, and R.Q. Wu, "Ensemble effects on ethylene dehydrogenation on PdAu(001) surfaces investigated with first-principles calculations and nudged-elastic-band simulations," Phys. Rev. B 75, 233401 (2007).

D.W. Yuan, X.G. Gong, and R.Q. Wu, "Origin of high activity and selectivity of PdAu(001) bimetallic surfaces toward vinyl acetate synthesis", J. Phys. Chem. 112, 1539-1543 (2008).

D.W. Yuan, X.G. Gong, and R.Q. Wu, "Methanol dehydrogenation on PtAu(111) bimetallic surfaces", J. Chem. Phys. 128, 064706 (2008).

C.S. Jo, A.A. Shinde, J.X. Cao, R. Ragan, and R.Q. Wu, "First Principles Studies of Adsorption of Pd, Ag, Pt, and Au on YSi2 Nanowires", Chem. Phys. Lett., 454, 327 (2008).

D.W. Yuan, X.G. Gong, and R.Q. Wu, "The peculiar distribution pattern of Pd on PdAu bimetallic nanoclusters", Phys. Rev. B 78, 035441 (2008)

**PI Donald Wuebbles**

Holloway, T. S. N. Spak, D. Barker, M. Bretl1, K. Hayhoe, J. Van Dorn, and D. Wuebbles, 2008: Change in ozone air pollution over Chicago associated with global climate change. J. Geophys. Res., 113, D22306, doi:10.1029/2007JD009775.

Kunkel, K. E., H.-C. Huang, X.-Z. Liang, J.-T. Lin, D. Wuebbles, Z. Tao, A. Williams, M. Caughey, J. Zhu, and K. Hayhoe, 2008: Sensitivity of future ozone concentrations in the Northeast U.S. to regional climate change. Mitigation and Adaptation Strategies for Global Change, 13, 597-606.

Huang, H.-C., J. Lin, Z. Tao, H. Choi, K. Patten, K. E. Kunkel, M. Xu, J. Zhu, X.-Z. Liang, A. Williams, M. Caughey, D. J. Wuebbles, and J. Wang, 2008: Impacts of long-range transport of global pollutants and precursor gases on US air quality under future climatic conditions. J. Geophys. Res., 113, D19307, doi:10.1029/2007JD009469.

Lin, J.-T., K. O. Patten, X.-Z. Liang, and D. J. Wuebbles, 2008: Climate change effects on ozone air quality in the United States and China with constant precursor emissions. J. Appl. Meteor., 47, 1888-1909.

Lin, J.-T., D. Youn, X.-Z. Liang, D. J. Wuebbles 2008: Global model simulation of summertime U.S. ozone diurnal cycle and its sensitivity to PBL mixing, spatial resolution, and emissions. Atmos. Environ., 42, 8470-8483.

United Nations Economic Commission for Europe (coauthor), 2007: Hemispheric Transport of Air Pollution 2007. Air Pollution Studies report No. 16, United Nations, New York and Geneva (published in 2008).

## X

**PI Nong Xiang**

J. R. Cary and N. Xiang, "Wave excitation in inhomogeneous dielectric media," Phys. Rev. E 76, 055401(R) (2007), http://link.aps.org/doi/10.1103/PhysRevE.76.055401.

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; http://link.aps.org/abstract/PRL/v100/e0850023

J. R. Cary, "EBW harmonic generation in heating and current drive," Ann. Meeting of the Division of Plasma Physics JI1.00006 (Orlando, FL, 2007).

## Y

**PI Yanfa Yan**

Muhammad N. Huda, Yanfa Yan, Su-Huai Wei and Mowafak Al-Jassim Group-IIIA vs. IIIB delafossites: the Origin of Contrary Band Gap Trends To be submitted

Aron Walsh, Yanfa Yan, M. M. Al-Jassim, and Su-Huai Wei Electronic, Energetic, and Chemical Effects of Intrinsic Defects and Fe-Doping of CoAl2O4: A DFT+U Study J. Phys. Chem. C 112; 12044 (2208)

Muhammad N. Huda, Yanfa Yan, Chang-Yoon Moon, Su-Huai Wei, and Mowafak M. Al-Jassim Density-functional theory study of the effects of atomic impurity on the band edges of monoclinic WO3 Phys. Rev B 77, 195102 (2008).

A. Walsh, S.-H. Wei, Y. Yan, M.M. Al-Jassim, J. Turner, M. Woodhouse, and B.A. Parkinson Structural, magnetic, and electronic properties of the Co-Fe-Al oxide spinel system: Density-functional theory calculations Phys. Rev. B 76, 165119 (2007)

**PI Chao Yang**

J. Chung, P. Sternberg and C. Yang, High Performance 3-D Image Reconstruction for Molecular Structure Determination, submitted to International Journal of High Performance Computing Applications, 2008

C. Yang, W. Jiang, D. Chen, U. Adiga, E. Ng and W. Chiu, Estimating Contrast Transfer Function and Associated Parameters by Constrained Nonlinear Optimization, submitted to Journal of Microscopy, 2008

**PI Katherine Yelick**

Jimmy Su and Katherine Yelick, "Automatic Performance Debugging in Partitioned Global Address Space Programs" 20th International Workshop on Languages and Compilers for Parallel Computing (LCPC), Urbana, Illinois, October 2007. Lecture Notes in Computer Science 5234 Springer 2008, ISBN 978-3-540-85260-5

Parry Husbands and Katherine Yelick, "Multithreading and One-Sided Communication in Parallel LU Factorization." Proceedings of Supercomputing (SC07), Reno, NV, November, 2007.

Tong Wen, Jimmy Su, Phillip Colella, Katherine Yelick and Noel Keen, "An Adaptive Mesh Refinement Benchmark for Modern Parallel Programming Languages." Proceedings of Supercomputing (SC07), Reno, NV, November 2007.

Paul H. Hargrove, Dan Bonachea, Christian Bell, "Experiences Implementing Partitioned Global Address Space (PGAS) Languages on InfiniBand," " "OpenFabrics Alliance 2008 International Sonoma Workshop, April 2008. (Presentation only.)

Rajesh Nishtala, George Almasi, Calin Cascaval, "Performance without Pain = Productivity, Data layouts and Collectives in UPC," Principles and Practice of Parallel Programming (PPoPP) 2008, Salt Lake City, USA, February 2008.

Costin Iancu, Wei Chen, and Katherine Yelick, "Performance Portable Optimizations for Loops Containing Communication Operations," International Conference on Supercomputing (ICS).

Costin Iancu, Wei Chen, Katherine A. Yelick: Performance portable optimizations for loops containing communication operations. International Conference on Supercomputing, Island of Kos, Greece, June 7-12, 2008, pages 266-276.

J. Demmel, M. Hoemmen, M. Mohiyuddin, K. Yelick, "Avoiding Communication in Sparse Matrix Computations," IEEE Intern. Parallel and Distributed Processing Symposium (IPDPS"08), April 2008.

John Mellor-Crummey, Peter Beckman, Jack Dongarra, Ken Kennedy, Barton Miller, Katherine Yelick. "Software for leadership-class computing," SciDAC Review. Fall 2007, pages 36-45.

**PI Hua-Gen Yu**

H.-G. Yu, J.S. Francisco and J.T. Muckerman, "Energetics and molecular dynamics of the reaction of HOCO with HO2 radicals," J. Chem. Phys. (submitted, 2008).

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.

## Z

**PI Peter Zapol**

D. A. Horner, P. C. Redfern, M. Sternberg, P. Zapol, L. A. Curtiss, Increased reactivity of single wall carbon nanotubes at carbon ad-dimer defect sites Chem. Phys. Lett., 450, 71, 2007.

**PI Bin Zhang**

Bin Zhang, Lie-Wen Chen, and Che Ming Ko "Evolution of the bulk properties of the hot dense matter in relativistic heavy ion collisions" Journal of Physics G: Nuclear and Particle Physics, vol. 35, (2008), 065103.

Ruipeng Li, Hai Jiang, Hung-Chi Su, Bin Zhang, and Jeff Jenness "Speculative and distributed simulation of many-particle collisions systems" Proceedings of ICPADS 2007, the 13th international conference on parallel and distributed systems, Dec 5-7, 2007, Hsinchu, Taiwan

Ruipeng Li, Hai Jiang, Hung-Chi Su, Bin Zhang, and Jeff Jenness "Coordination Schemes in Distributed Simulation of Relativistic Particle Transport" Proceedings of the 23rd ACM Symposium on Applied Computing 2008, Special Track on Advances in Computer Simulation. March 16-20, 2008, Cear Fortaleza, Brazil.

Ruipeng Li, Hai Jiang, Hung-Chi Su, Bin Zhang, and Jeff Jenness "Parallel and Distributed Particle Collision Simulation with Decentralized Control" Proceedings of GPC 2008, the 3rd International Conference on Grid and Pervasive Computing. May 25 - 28, 2008, Kunming, China., (2008). Lecture Notes in Computer Science, Volume 5036/2008, pp244-255.

Ruipeng Li, Hai Jiang, Hung-Chi Su, Jeff Jenness, Bin Zhang "On Load Balancing Distributed Simulation of Relativistic Particle Transport" Proceedings of PDPTA'08 - The 2008 International Conference on Parallel and Distributed Processing Techniques and Applications, Monte Carlo Resort, Las Vegas, Nevada, USA (July 14-17, 2008)

Ruipeng Li, Hai Jiang, Hung-Chi Su, Bin Zhang, Jeff Jenness "Adaptive and Fault Tolerant Simulation of Relativistic Particle Transport with Data-level Checkpointing" Proceedings of 2008 IEEE 11th International Conference on Computational Science and Engineering. July 16-18, 2008 - Sao Paulo - Brazil

**PI Guoping Zhang**

Understanding laser-induced ultrafast magnetization in ferromagnets: First-principles investigation, G. P. Zhanga, Yihua Bai, W. H??bner, Georg Lefkidis and T. F. George, JOURNAL OF APPLIED PHYSICS 103, 07B113 2008

Total angular momentum conservation in laser-induced femtosecond magnetism, G. P. Zhang and T. F. George, PHYSICAL REVIEW B 78, 052407 2008

Nonlinear optical response and ultrafast dynamics in C60, G. P. Zhang and T. F. George, J. Phys. Chem. A (2008, invited review)

Time-resolved and energy-dispersed spin excitation in ferromagnets and clusters under influence of femtosecond laser pulses, T. Hartenstein, G. Lefkidis, W. H\"ubner, G. P. Zhang and Y. Bai, submitted to Journal of Applied Physics

Laser-induced orbital and spin excitations in ferromagnets:\\ Insights from a two-level system, G. P. Zhang, submitted to Physical Review Letters (2008)

**PI Zhenyu Zhang**

W. G. Zhu, Z. Y. Zhang, and E. Kaxiras Dopant-assisted concentration enhancement of substitutional Mn in Si and Ge Phys. Rev. Lett. 100, 027205 (2008).

C. G. Zeng, Z. Y. Zhang, K. van Benthem, M. F. Chisholm, and H. H. Weitering Optimal Doping Control of Magnetic Semiconductors via Subsurfactant Epitaxy Phys. Rev. Lett. 100, 066101 (2008).

S. Q. Hao and Z. Y. Zhang Concerted Diffusion, Clustering, and Magnetic Properties of Mn Dopants on a 2??2-T4 GaN(0001) Substrate Phys. Rev. Lett. 99, 166101 (2007).

Y. Lei, S. A. Shevlin, W. G. Zhu, and Z. X. Guo Hydrogen-induced magnetization and tunable hydrogen storage in graphitic structures Phys. Rev. B 77, 134114 (2008)

J. Ma, E. G. Wang, Z. Y. Zhang, and B. Wu Theory of the excitation of the vibrational mode of an adatom-substrate system under a resonant laser field Phys. Rev. B 78, 125303 (2008).

S. Yang, L. Zhang, H. Chen, E. G. Wang, and Z. Y. Zhang Generic guiding principle for the prediction of metal-induced reconstructions of compound semiconductor surfaces Phys. Rev. B 78, 075305 (2008).

B. Wu and Z. Y. Zhang, Stability of metallic thin films studied with a free electron model Phys. Rev. B 77, 035410 (2008).

B. N. J. Persson, I. M. Sivebaek, V. N. Samoilov, K. Zhao, A. I. Volokitin, and Z. Y. Zhang On the origin of Amonton's friction law J. Phys.: Condens. Matter 20, 395006 (2008).

W. Hong, Z. Suo, and Z. Y. Zhang Dynamics of terraces on a silicon surface due to the combined action of strain and electric current J. Mech. Phys. Solids 56, 267 (2008).

A. Khajetoorians, W. Zhu, S. Y. Qin, H. Eisele, Z. Y. Zhang, and C.-K. Shih Adsorbate-induced restructuring of Pb nanomesas grown on vicinal Si(111) in the quantum regime Submitted to Phys. Rev. Lett.

Y. Mo, W. G. Zhu, E. Kaxiras, and Z. Y. Zhang Electronic nature of step-edge barriers against adatom descent on transition-metal surfaces Submitted to Phys. Rev. Lett.

W. G. Zhu, X. F. Qiu, H. Pan, W. Wang, M. Parans Paranthaman, V. Iancu, H. Weitering, N. Dimitrijevic, T. Rajh, H. M. Meyer, G. Eres, B. H. Gu, and Z. Y. Zhang Bandgap Narrowing of TiO2 by Non-Compensated Doping Using Cationic and Anionic Elements Submitted to Nature Materials.

M. Yoon, S. Yang, C. Hicke, E. Wang, D. Geohegan, and Z. Zhang, Calcium as the Superior Coating Metal in Functionalization of Carbon Fullerenesfor High-Capacity Hydrogen Storage, Phys. Rev. Lett. 100, 206806 (2008).

**PI Linjin Zheng**

E. Asp, J.-H. Kim, W. Horton, L. Porte, S. Alberti, A. Karpushov, Y. Martin, O. Sauter, G. Turi and the TCV TEAM, Electron Transport analysis in the Tokamak Configuration Variable, Physics of Plasmas, 15, 0821317 (2008).

F. Militello, F. L. Waelbroeck, R. Fitzpatrick, and W. Horton, Interaction between turbulence and a nonlinear tearing mode in low beta regime, Physics of Plasmas, 15, 050701 (2008).

W. Horton, J. Pratt, H. L. Berk and E. Spencer, Global Energy Confinement Scaling Predictions for Tandem Mirrors, Journal of Fusion Energy, 2007.

W. Horton, J.-H. Kim, F. Militello, M. Ottaviani, Turbulent Impulsive Magnetic Energy Releases from Electron scale reconnection, Phys. of Plasmas 14, 012902 (2007).

E. Spencer, W. Horton, M. L. Mays, I. Doxas, and J. Kozyra (2007), Analysis of the 3-7 October 2000 and 15-24 April 2002 geomagnetic storms with an optimized nonlinear dynamical model, J. Geophys. Res., 112, A04S90, (2007).

S.M. Kaye, F.M. Levinton, D. Stutman, K. Tritz, H. Yuh, M.G. Bell, R.E. Bell, C.W. Domier, D. Gates, W. Horton, J. Kim, B.P. LeBlanc, N.C. Luhmann Jr, R. Maingi, E. Mazzucato, J.E. Menard, D. Mikkelsen, D. Mueller, H. Park, G. Rewoldt, S.A. Sabbagh, D.R. Smith and W. Wang, ``Confinement and local transport in the National Spherical Torus Experiment (NSTX)'' Nuclear Fusion 47(7), 499 (2007).

W. Horton, J.-H. Kim, F. Militello and M. Ottaviani, ``Turbulent Impulsive Magnetic Energy Release from Electron Scale Reconnection'' Physics of Plasma 14, 012902 (2007).

T.-H. Watanabe, Y. Todo, and W. Horton, "Benchmark Tests of Fusion Plasma Simulation Codes for Studying Microturbulence and Energetic-Particle Dynamics", Plasma Fusion Res., Vol. 3, 061-1-061-6 (2008).

P. Valanju, M. Kotschenreuther, S. Mahajan, Super X Divertors for solving heat and neutron flux problems of fusion devices", Submitted to Fusion Engineering Design, Sept. 2008

L. J. Zheng, H. Takahashi, E.D. Fredrickson, Edge-localized modes explained as the amplification of scrape-off-layer current coupling, Phys. Rev. Lett. 100, 115001 (2008).

L.-J. Zheng, B. Li, R. D. Hazeltine, Bifurcated states of the error-field-induced magnetic islands, Physics Letters A, 372, 17 (2008).

L. J. Zheng, M. Kotschenreuther, and J. W. Van Dam, Kinetic Analysis of the Resistive Wall Modes in ITER Advanced Tokamak Scenario, Submitted to Nucl. Fusion, 2008.

**PI Ping Zhu**

P. Zhu and C.C. Hegna, Ballooning filament growth in the intermediate nonlinear regime, Phys. Plasmas 15, 092306 (2008).

P. Zhu, D.D. Schnack, F. Ebrahimi, E.G. Zweibel, M.Suzuki, C.C. Hegna, and C.R. Sovinec, Absence of complete finite-Larmor-radius stabilization in extended MHD, Phys. Rev. Lett. 101, 085005 (2008).

P. Zhu, J. Raeder, K. Germaschewski, and C. C. Hegna, Initiation of ballooning instability by reconnection

**PI Alex Zunger**

H. Raebiger, S. Lany, A. Zunger, "Control of ferromagnetism via electron-doping in In2O3:Cr", Phys. Rev. Lett. 101, 027203 (2008).

H. Raebiger, S. Lany, and A. Zunger, "Charge self-regulation upon changing the oxidation state of transition metals in insulators", Nature 453, 763 (2008).

J.Z. Liu and A. Zunger, "Thermodynamic states and phase diagrams for bulk-incoherent, bulk-coherent, and epitaxially-coherent semiconductor alloys: Application to cubic (Ga,In)N", Phys. Rev. B 77, 205201 (2008).

P. Piquini, A. Zunger, and R. Magri, "Pseudopotential calculations of band gaps and band edges of short-period (InAs)(n)/(GaSb)(m) superlattices with different substrates, layer orientations, and interfacial bonds", Phys. Rev. B 77, 115314 (2008).

P. Piquini, P. Graf, and A. Zunger, "Band-gap design of quaternary (In,Ga)(As,Sb) semiconductors via the inverse-band-structure approach", Phys. Rev. Lett. 100, 186403 (2008).

G. Trimarchi and A. Zunger, "Finding the lowest-energy crystal structure starting from randomly selected lattice vectors and atomic positions: first-principles evolutionary study of the Au-Pd, Cd-Pt, Al-Sc, Cu-Pd, Pd-Ti, and Ir-N binary systems", J. Phys. Cond. Matt. 20, 295212 (2008).

M. d'Avezac and A. Zunger, "Identifying the minimum-energy atomic configuration on a lattice: Lamarckian twist on Darwinian evolution", Phys. Rev. B 78, 064102 (2008).

A. Zunger, "New insights on chalcopyrites from solid-state theory", Thin Solid Films 515, 6160 (2007).

S. Lany and A. Zunger, "Intrinsic DX centers in ternary chalcopyrite semiconductors", Phys. Rev. Lett. 100, 016401 (2008). (listed as "submitted" in ERCAP-request of last year)

S. Lany, H Raebiger, and A. Zunger, "Magnetic interactions of Cr-Cr and Co-Co impurity pairs in ZnO within a band-gap corrected density-functional approach", Phys. Rev. B 77, 241201(R) (2008).

S. Lany and A. Zunger, "Assessment of correction methods for the band gap problem and for finite-size effects in supercell defect calculations: Case studies for ZnO and GaAs" Phys. Rev. B, submitted.

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 (in press).

J.W. Luo, G. Bester, and A. Zunger, "Atomistic Pseudopotential Calculations of Thickness Fluctuation GaAs Quantum Dots", Phys. Rev. B (submitted).

V. Popescu, G. Bester, M.C. Hanna, A.G. Norman, and A. Zunger, "Theoretical and Experimental Examination of the Intermediate-Band Concept for Strain-Balnced (In,Ga)As/Ga(As,P) Quantum-Dot Solar Cells", Phys. Rev. B (submitted).

L. He, G. Bester, Z. Su, and A. Zunger, "Calculation of Near-field Scanning Optical Images of Exciton, Charged-exciton, and Multiexciton Wave Functions in Self-assembled InAs/GaAs Quantum Dots", Phys. Rev. B 76, 035313 (2007)

G. Bester, D. Reuter, Lixin He, A. Zunger, P. Kailuweit, A. D. Wieck, U. Zeitler, J. C. Maan, O. Wibbelhoff, and A. Lorke, "Experimental Imaging and Atomistic Modeling of Electron and Hole Quasiparticle Wave Functions in InAs/GaAs Quantum Dots", Phys. Rev. B 76, 075338 (2007).

J.M. An, M. Califano, A. Franceschetti, and A. Zunger, "Excited-state relaxation in PbSe quantum dots", J. Chem. Phys. 128, 164720 (2008).

J.W. Luo, A. Franceschetti, and A. Zunger, "Quantum-Size-Induced Electronic Transitions in Quantum Dots: Indirect Band-Gap GaAs", Phys. Rev. B 78, 035306 (2008).

J.W. Luo, G. Bester, and A. Zunger, "Full-Zone Spin-Splitting for Electrons and Holes in Bulk GaAs and GaSb", Phys. Rev. Lett. (submitted).

C. Curutchet, A. Franceschetti, A. Zunger, G.D. Scholes, "Examining Forster Energy Transfer for Semiconductor Nanocrystalline Quantum Dot Donors and Acceptors", J. Phys. Chem. C. (Letter) 112, 13336 (2008).

**PI Piotr Zyla**

"Review of Particle Physics", C. Amsler et al. (PDG Collaboration), Physics Letters B667, 1-1340