# 2006 Publications Resulting from the Use of NERSC Resources

On their Allocation Year 2007 ERCAP Request Forms Principal Investigators reported 1,437 refereed publications (published or submitted) for the preceding 12 months, based on using, at least in part, NERSC resources.

## A

**PI Mowfak Al-Jassim**

Y. Yan, M.M. Al-Jassim, and S.-H. Wei Doping of ZnO with group-IB elements Appl. Phys. Lett. In press (2006)

Y. Yan, R. Noufi, and M.M. Al-Jassim Grain-Boundary Physics in Polycrystalline CuInSe2 Revisited: Experiment and Theory Phys. Rev. Lett. 96, 205501 (2006)

G. M. Dalpian, Y. Yan, and S.-H. Wei Impurity-induced phase stabilization of semiconductors Appl. Phys. Lett. 89, 011907 (2006)

Y. Yan, M.M. Al-Jassim, and S.-H. Wei, Oxygen vacancy-mediated adsorption of molecular oxygen on ZnO (1-100) surfaces Phys. Rev. B 72, 161307 (R) (2005).

Y. Yan and M.M. Al-Jassim Energetics and structure of water adsorption on ZnO (1-100) surfaces Phys. Rev. B 72, 235406 (2005).

**PI Greg Aldering**

Nearby Supernova Factory Observations of SN2005gj: Another Type Ia Supernova in a Massive Circumstellar Envelope, Aldering, G., Antilogus, P., Bailey, S., Baltay, C., Bauer, A., Blanc, N., Bongard, S., Copin, Y., Gangler, E., Gilles, S., Kessler, R., Kocevski, D., Lee, B. C., Loken, S., Nugent, P., Pain, R., Pecontal, E., Pereira, R., Perlmutter, S., Rabinowitz, D., Rigaudier, G., Scalzo, R., Smadja, G., Thomas, R. C., Wang, L., Weaver, B. A. (2006), Astrophysical Journal, 650, 510.

The Supernova Legacy Survey: measurement of Omega_M, Lambda, w from the first year data set, Astier, P., Guy, J., Regnault, N., Pain, R., Aubourg, E., Balam, D., Basa, S., Carlberg, R.~G., Fabbro, S., Fouchez, D., Hook, I.~M., Howell, D. A., Lafoux, H., Neill, J. D., Palanque-Delabrouille, N., Perrett, K., Pritchet, C. J., Rich, J., Sullivan, M., Taillet, R., Aldering, G., Antilogus, P., Arsenijevic, V., Balland, C., Baumont, S., Bronder, J., Courtois, H., Ellis, R. S., Filiol, M., Goncalves, A. C., Goobar, A., Guide, D., Hardin, D., Lusset, V., Lidman, C., McMahon, R., Mouchet, M., Mourao, A., Perlmutter, S., Ripoche, P., Tao, C., and Walton, N. (2006), Astronomy & Astrophysics, 447, 31.

Exploring dark energy with SNAP, Aldering, G. (2005), New Astronomy Review, 49, 346.

Improvements to the Image Processing of Hubble Space Telescope NICMOS Observations with Multiple Readouts, Fadeyev, V., Aldering, G., and Perlmutter, S. (2006), Publications of the Astronomical Society of the Pacific, 118, 907.

Measurement of Omega_M, Lambda from a Blind Analysis of Type Ia Supernovae with CMAGIC: Using Color Information to Verify the Acceleration of the Universe, Conley, A., et al, (2006), Astrophysical Journal, 644, 1.

Spectra of High-Redshift Type Ia Supernovae and a Comparison with Their Low-Redshift Counterparts, Hook, I. M., Howell, D. A., Aldering, G., Amanullah, R., Burns, M. S., Conley, A. and Deustua, S. E., Ellis, R., Fabbro, S., Fadeyev, V., Folatelli, G., Garavini, G., Gibbons, R., Goldhaber, G. and Goobar, A., Groom, D. E., Kim, A. G., Knop, R. A., Kowalski, M., Lidman, C., Nobili, S., Nugent, P. E., Pain, R., Pennypacker, C. R., Perlmutter, S., Ruiz-Lapuente, P., Sainton, G., Schaefer, B. E., Smith, E., Spadafora, A. L., Stanishev, V., Thomas, R. C., Walton, N. A. and Wang, L. and Wood-Vasey, W. M. (2005), Astronomical Journal, 130, 2788.

Photometric Selection of High-Redshift Type Ia Supernova Candidates, Sullivan, M., Howell, D. A., Perrett, K., Nugent, P. E., Astier, P., Aubourg, E., Balam, D., Basa, S., Carlberg, R. G., Conley, A., Fabbro, S., Fouchez, D., Guy, J., Hook, I., Lafoux, H., Neill, J. D., Pain, R., Palanque-Delabrouille, N., Pritchet, C. J., Regnault, N., Rich, J., Taillet, R., Aldering, G., Baumont, S., Bronder, J., Filiol, M., Knop, R. A., Perlmutter, S., and Tao, C., (2006), Astronomical Journal, 131, 960.

GRB 050408: A Bright Gamma-Ray Burst Probing an Atypical Galactic Environment, Foley R. J., Perley D. A., Pooley D., Prochaska J. X., Bloom J. S., Li W., Cobb B., Chen H.-W., Aldering G., Bailyn C., Blake C. H., Falco E. E., Green P. J., Kowalski M. P., Perlmutter S., Roth K., and Volk K. (2006), Astrophysical Journal, 645, 450.

The,Type Ia Supernova Rate at z ~0.5 from the Supernova Legacy Survey, Neill, J. D., et al (2006), Astronomical Journal, 132, 1126.

Spectrophotometry of the Deep Impact Ejecta of Comet 9P/Tempel~1, Hodapp, K. W., Aldering, G., Meech, K. J., & Cochran, A. L. (2006), Icarus, in press.

Snapping Supernovae at z > 1.7, Aldering, G, Kim, A. G., Kowalski, M., Linder, E. V., and Perlmutter, S. (2006), Particle Astrophysics, submitted.

**PI Yoram Alhassid**

"The nuclear moment of inertia and spin distribution of nuclear levels," Y. Alhassid, G.F. Bertsch, L. Fang, and S. Liu, Phys. Rev. C 72, 064326 (2005).

"Effective quadrupole-quadrupole interaction from density functional theory," Y. Alhassid, G.F. Bertsch, L. Fang, B. Sabbey, Phys. Rev. C 74, 034301 (2006).

"Spin projection in the shell model Monte Carlo method and the spin distribution of nuclear level densities," Y. Alhassid, S. Liu, and H. Nakada, nucl-th/0607062, submitted to Phys. Rev. Lett. (2006).

"Scrambling of Hartree-Fock Levels as a universal Brownian-Motion Process," Y. Alhassid, H. A. Weidenmueller, A. Wobst, cond-mat/0604599.

**PI Paul Alivisatos**

S. Y. Quek, J. B. Neaton, M. S. Hybertsen, E. Kaxiras, and S. G. Louie, First-principles studies of the electronic structure of cyclopentene on Si(001): density functional theory and GW calculations, Phys. Stat. Sol. (b) 243, 2048 (2006).

J. B. Neaton, M. S. Hybertsen, and S. G. Louie, Renormalization of Molecular Electronic Levels at Metal-Molecule Interfaces, Physical Review Letters, in press.

K. H. Khoo, J. B. Neaton, and S. G. Louie, First-principles study of the conductance of hydrogen-decorated nanojunctions, submitted to Nano Letters.

R. Yamachika, M. Grobis, A. Wachiowiak, J. B. Neaton, N. Bray-Ali, J. E. Moore, S. G. Louie, and M. F. Crommie, Controlled atomic doping of a single C60 molecule, submitted to Physical Review Letters.

**PI Jonathan Arons**

A. Spitkovsky, "Simulations of relativistic collisionless shocks: shock structure and particle acceleration," AIPC, 801, 345, astro-ph/0603211

E. Amato & J. Arons, 2006, "Heating and Non-thermal Particle Acceleration in Relativistic, Transverse Magnetosonic Shock Waves in Proton-Electron-Positron Plasmas", ApJ in press, astro-ph/0609034

A. Spitkovsky, 2006, "Acceleration of Particles in Unmagnetized Electron-Positron Collisionless Shocks," ApJ Lett, submitted

M. Miloslavljevic, E. Nakar, A. Spitkovsky, 2006, "Steady State Electrostatic Layers from Weibel Instability in Relativistic Collisionless Shocks," ApJ, 637, 765

O. Skjaeraasen, A. Melatos, A. Spitkovsky, 2005, "Particle In Cell Simulations of a Nonlinear Transverse Electromagnetic Wave in a Pulsar Wind Termination Shock," ApJ, 634, 542

Spitkovsky A. 2006, "Time-dependent Force-free Pulsar Magnetospheres: Axisymmetric and Oblique Rotators," ApJ, 648, L51

A. Spitkovsky, J. Arons, 2004, "Time Dependence in Relativistic Collisionless Shocks: Theory of the Variable ``Wisps'' in the Crab Nebula," ApJ, 603, 669

**PI Cynthia Atherton**

F. Dentener, D. Stevenson, K. Ellingsen, T. van Noije, M. Schultz, M. Amann, C. Atherthon, N. Bell, D. Bergmann, I. Bey, T. Butler, L. Bouwman, J. Cofala, B. Collins, J. Drevet, B. Eickhout, H. Eskes, A. Fiore, M. Gauss, D. Hauglustaine, L. Horowitz, I. Isaksen, B. Josse, M. Lawrence, M. Krol, J.F. Lamarque, V. Montanero, J.F. Muller, V.H. Peuch, J. Pyle, S. Rast, , G. Pitari, J. Rodriguez, M. Sanderson, N. Savage, S. Strahan, D. Shindell S. Szopa, K. Sudo, Oliver Wild, G. Zeng, 2006: The global atmospheric environment for the next generation, Environ. Sci. Tech., 40,.3586-3594, doi:10.1021/es0523845.

Stevenson, D.S., F.J. Dentener, M. Schultz, K. Ellingsen, T. van Noije, G. Zeng, M. Amann, C. Atherton, N. Bell, D. Bergmann, I. Bey, T. Butler, J. Cofala, W.J. Collins, R.G. Derwent, R.M. Doherty, J. Drevet, H. Eskes, A. Fiore, M. Gauss, D. Hauglustaine, L. Horowitz, I. Isaksen, M. Krol, J.F. Lamarque, M. Lawrence, V. Montanero, J.F. Muller, G. Pitari, M.J. Prather, J. Pyle, S. Fast, J. Rodriguez, M. Sanderon, N. Savage, D. Shindell, S. Strahan, K. Sudo, S. Szopa, and O. Wild, 2006: Multi-model ensemble simulations of present-day and near-future tropospheric ozone, J. Geophys. Res., 111 doi:10.1029/2005JD00638.

Van Noije, T.P.C., H.J. Eskes, F.J. Dentener, D.S. Stevenson, K. Ellingsen, M.G. Schultz, O. Wild, M. Amann, C.S. Atherton, D.J. Bergmann, I. Bey, K.F. Boersma, T. Butler, J. Cofala, J. Drevet, A.M. Fiore, M. Gauss, D.A. Hauglustaine, L.W. Horowitz, I.S. A. Isaksen, M.C. Krol, J.F. Lamarque, M. G. Lawrence, R.V. Martin, V. Montanaro, J.F. Muller, G. Pitari, M.J. Prather, J.A. Pyle, A. Richter, J.M. Rodriguez, N.H. Savage, S.E. Strahan, K. Sudo, and S. Szopa, 2006: Multi-model ensemble simulations of tropospheric NO2 compared with GOME retrievals for the year 2000, Atmospheric Chemistry and Physics Discussions, 6, 2943-2979.

Shindell, D., G. Faluvegi, D.S. Stevenson, L. K. Emmons, J.-F. Lamarque, G. Pitron, F.J. Dentener, K. Ellingsen, M. Amann, C.S. Atherton, N. Bell, D.J. Bergmann, I. Bey, T. Butler, J. Cofala, W.J. Collins, R.G. Derwent, R.M. Doherty, J. Drevet, H.J. Eskes, A.M. Fiore, M. Gauss, D.A. Hauglustaine, L.W. Horowitz, I.S.A. Isaksen, M.C. Krol, M.G. Lawrence, V. Montanaro, J.-F. Muller, G. Pitari, M.J. Prather, J.A. Pyle, S. Rast, J.M. Rodriguez, M.G. Sanderson, N.H. Savage, M.G. Schultz, S.E. Strahan, K. Sudo, S. Szopa, T.P.C. van Noije, O. Wild, and G. Zeng, 2006: Multi-model simulations of carbon monoxide: Comparison with observations and projected near-future changes, J. Geophys. Res., 111, doi:10.1029/2006JD007100.

Dentener, F., J. Drevet, J.F. Lamarque, I. Bey, B. Eickhout, A.M. Fiore, D. Hauglustaine, L.W. Horowitz, M. Krol, U.C. Kulshrestha, M. Lawrence, C. Galy-Lacaus, S. Rasta, D. Shindell, D. Stevenson, T. Van Noije, C. Atherton, N. Bell, D. Bergmann, T. Butler, J. Cofala, B. Collins, R. Doherty, K. Ellingsen, J. Galloway, M. Gauss, V. Montanaro, J.F. Muller, G. Pitari, J. Rodriguez, M. Sanderson, S. Strahan, M. Schultz, K. Sudo, S. Szopa, and O. Wild, 2006: Nitrogen and sulfur deposition on regional and global scales: A multi-model evaluation, Global Biogeochem. Cycles, in press.

## B

**PI Dmitri Babikov**

D. Babikov, V. A. Mozhayskiy and A. I. Krylov, "The photoelectron spectrum of elusive cyclic-N3 and characterization of the potential energy surface and vibrational states of the ion", J. Chem. Phys. 125, 84306 (15 pages), 2006.

M. Zhao and D. Babikov, "Phase control in the vibrational qubit", J. Chem. Phys. 125, 24105 (6 pages), 2006.

E. Vetoshkin and D. Babikov, "Semi-classical wave-packet study of ozone forming reaction", J. Chem. Phys.125, 24302 (11 pages), 2006.

V. A. Mozhayskiy, D. Babikov and A. I. Krylov, "Conical and glancing Jahn-Teller intersections in the cyclic trinitrogen cation", J. Chem. Phys. 124, 224309 (10 pages), 2006.

**PI Maria Babiuc**

Mohammad Motamed, Maria C. Babiuc, Bela Szilagyi, H-O. Kreiss, Jeffrey Winicour: "Finite Difference Schemes for Second Order Systems Describing Black Holes"" Physical Review D, (June 2006) volume 73, issue 12, page 124008, gr-qc/0604010

**PI Ferdinand Baer**

Baer, F., H. Wang, J. J. Tribbia, A. Fournier, 2006: Climate Modeling With Spectral Elements. Mon. Wea. Rev., in press.

Wang, H., J. J. Tribbia, F. Baer, A. Fournier, M. Taylor, 2006: A Spectral Element Version of CAM2. Submitted to Monthly Weather Review, October 2006.

D. Rosenberg, A. Fournier, P. Fischer & A. Pouquet, 2006: Geophysical-astrophysical spectral-element adaptive refinement (GASpAR): Object-oriented h-adaptive fluid dynamics simulation. J. Comp. Phys., 215(1), 59-80. http://dx.doi.org/10.1016/j.jcp.2005.10.031

A. Fournier, 2006: Exact calculation of Fourier series in nonconforming spectral-element methods. J. Comp. Phys., 215(1), 1-5. http://dx.doi.org/10.1016/j.jcp.2005.11.023

Christopher D. Blakely, 2006: "A Hybrid Meshless-Collocation/Spectral-Element Method for Elliptic Partial Differential Equations". International Journal of Comp. Math., submitted July 2006.

Christopher D. Blakely, 2006: "A Hybrid Meshless/Spectral-Element Method for the Shallow Water Equations on the Sphere", Computational Methods in Applied Sciences, Bookseries, Springer-Verlag, in press.

**PI David Bailey**

David H. Bailey, Jonathan M. Borwein and Richard E. Crandall, "Box Integrals," Journal of Computational and Applied Mathematics, to appear, Jun 2006; LBNL-59962.

David H. Bailey, Jonathan M. Borwein and Richard E. Crandall, "Integrals of the Ising Class," Journal of Physics A: Mathematical and General, to appear, Jun 2006; LBNL-59963.

David H. Bailey, David Borwein, Jonathan M. Borwein and Richard Crandall, "Hypergeometric Forms for Ising-Class Integrals," Experimental Mathematics, to appear, Jul 2006; LBNL-61037.

Hongzhang Shan, Erich Strohmaier, Ji Qiang, David H. Bailey, and Kathy Yelick, "Performance Modeling and Optimization of a High Energy Colliding Beam Simulation Code," Proceedings of SC2006, to appear, Nov. 2006.

Hongzhang Shan, Erich Strohmaier, Ji Qiang, Kathy Yelick, "Performance Analysis of a High Energy Colliding Beam Simulation Code on Four HPC Architectures," 2006 International Conference on Parallel Processing, Aug, 2006, Columbus, Ohio.

Hongzhang Shan, Erich Strohmaier, Ji Qiang, "Performance Analysis of a High Energy Colliding Beam Simulation Code on leading HPC Architectures", accepted for International Journal of High-Performance Computing.

S. Alam, R. Barrett, M. Fahey, O. Messer, R. Mills, P. Roth, J. Vetter and P. Worley, "An Evaluation of the ORNL Cray XT3," International Journal for High Performance Computer Applications, to appear. [This paper compared the XT3 with computations done on Bassi.]

**PI Perla Balbuena**

F. Tarazona-Vasquez and P. B. Balbuena, "Dendrimer-Tetrachloroplatinate Precursor Interactions. 3. Ligand Exchange Reaction in PAMAM Outer Pockets," J Am. Chem. Soc., submitted, October 2006.

Yuguang Ma and Perla B. Balbuena, "Enlightenment from Metalloenzymes: New Insights for Designing Oxygen Reduction Catalysts," J.Phys. Chem. B, submitted, October 2006.

F. Tarazona-Vasquez and P. B. Balbuena, "Dendrimer-Tetrachloroplatinate Precursor Interactions. 2. Non Covalent Binding in PAMAM Outer Pockets," J. Phys. Chem. A, submitted, August 2006.

F. Tarazona-Vasquez and P. B. Balbuena, "Dendrimer-Tetrachloroplatinate Precursor Interactions. 1. Hydration of Pt(II) Species and PAMAM Outer Pockets," J. Phys. Chem. A, submitted, August 2006.

L. R. Saenz, P. B. Balbuena, and J. M. Seminario, "Platinum testbeds: Interaction with oxygen," J. Phys. Chem., in press.

S. R. Calvo and P. B. Balbuena, "Density functional theory analysis of reactivity of PtxPdy alloy clusters," Surf. Sci., in press.

E. J. Lamas and P. B. Balbuena, "Oxygen Reduction on Pd0.75Co0.25 (111) and Pt0.75Co0.25 (111) Surfaces: an Ab Initio Comparative Study," J. Chem. Theory and Comp.,2, 1388-1394, (2006).

Z. Gu and P. B. Balbuena, "Dissolution of oxygen reduction electrocatalysts in acidic environment: Density functional theory study," J. Phys. Chem. A, 110, 9783-9787, (2006).

P. B. Balbuena, S. R. Calvo, E. J. Lamas, P. F. Salazar, and J. M. Seminario, "Adsorption and dissociation of H2O2 on Pt and Pt alloy clusters and surfaces," J. Phys. Chem. B, 110, 17452-17459, (2006).

E. J. Lamas and P. B. Balbuena " Molecular Dynamics Studies of a Model Polymer-Catalyst-Carbon Interface," Electrochim. Acta, 51, 5904-5911, (2006).

Gustavo E. Ramirez Caballero and Perla B. Balbuena, "Surface segregation phenomena in Pt-Pd nanoparticles: Dependence on nanocluster size," Mol. Simulation, 32, 297-303, (2006).

L. Yan, P. B. Balbuena, and J. M. Seminario, "Perfluorobutane Sulfonic Acid Hydration and Interactions with O2 Adsorbed on Pt3," J. Phys. Chem. A., 110, 4574-4581, (2006).

Y. Wang and P. B. Balbuena, "Design of Oxygen Reduction Bimetallic Catalysts: Ab initio-Derived Thermodynamic Guidelines," J. Phys. Chem. B., 109, 18902-18906, (2005).

Y. Wang and P. B. Balbuena, "Potential Energy Surface Profile of the Oxygen Reduction Reaction on a Pt Cluster: Adsorption and Decomposition of OOH and H2O2," J. Chem. Theory and Comp.,1, 935-943, (2005).

J. Zhao and P. B. Balbuena, "Structural and reactivity properties of finite length cap-ended single-wall carbon nanotubes," J. Phys. Chem. A., 110, 2771-2775, (2006).

Perla B. Balbuena, Jin Zhao, Shiping Huang, Yixuan Wang, Nataphan Sakulchaicharoen, and Daniel E. Resasco, "Role of the catalyst in the growth of single-wall carbon nanotubes," J. of Nanoscience and Nanotechnology, 6, 1247-1258, (2006).

J. Zhao, A. Martinez-Limia, and P. B. Balbuena, "Understanding catalysed growth of single-wall carbon nanotubes," Nanotechnology, 16, S575-S581, (2005).

**PI Arun Bansil**

S.W.H. Eijt, A. van Veen, H. Schut, P. E. Mijnarends, A. B. Denison, B. Barbiellini and A. Bansil, "Study of colloidal quantum dot surfaces using an innovative thin-film positron 2D-ACAR method", Nature Materials 5, 23 (2006).

Hsin Lin, S. Sahrakorpi, R.S. Markiewicz, and A. Bansil, "The 'Bi-O Pocket Problem' and the Effect of Hole-doping on the Fermi Surface of Bi2Sr2CaCu2O8+delta and Other Cuprates", Physical Review Letters 96, 097001 (2006).

R.S. Markiewicz and A. Bansil, "Probing Magnetic Gap Collapse within a Three-band Model of Resonant Inelastic X-ray Scattering (RIXS) in the Cuprates", Physical Review Letters 96, 107005 (2006).

J. Kwiatkowska, B. Barbiellini, S. Kaprzyk, A. Bansil, H. Kawata, and N. Shiotani, "Anomalous Electronic Correlations in the Ground State Momentum Density of Al2Li3", Physical Review Letters 96, 186403 (2006).

S. Sahrakorpi, M. Lindroos, R.S. Markiewicz, and A. Bansil, "Evolution of Mid-gap States and Residual 3-Dimensionality in La2-xSrxCuO4", Physical Review Letters 95, 157601 (2005).

A. Bansil, M. Lindroos, S. Sahrakorpi, and R.S. Markiewicz, "Role of Site Selectivity, Dimensionality, and Strong Correlations in Angle-resolved Photoemission from Cuprate Superconductors", Focus Issue: "Focus on Photoemission and Electronic Structure", commemorating Einstein's 1905 explanation of the Photoelectric Effect, New Journal of Physics 7, 140 (2005).

B. Barbiellini and P.M. Platzman, "The healing mechanism for excited molecules near metallic surfaces ", New Journal of Physics 8, 20 (2006).

T. Das, R.S. Markiewicz, and A. Bansil, "Nonmonotonic dx2-y2 superconducting gap in electron-doped Pr0.89LaCe0.11CuO4: Evidence of coexisting antiferromagnetism and superconductivity", Physical Review B 74, 020506 (2006).

R.S. Markiewicz, S. Sahrakorpi, M. Lindroos, Hsin Lin, and A. Bansil, "One-band Tight-binding Model Parametrization of the High-Tc Cuprates, Including the Effect of kz -dispersion", Physical Review B 72, 054519 (2005).

R.S. Markiewicz, "STM checkerboards from crossed stripes: A static stripe model", Physical Review B 71, 220504 (2005).

A. Bansil, M. Lindroos, S. Sahrakorpi, and R.S. Markiewicz, "Influence of the Third Dimension of Quasi-two-dimensional Cuprate Superconductors on Angle-resolved Photoemission Spectra", Physical Review B 71, Brief Reports, 012503 (2005).

Xu Zuo, Shaolin Yana, Bernardo Barbiellini, Vincent G. Harris and Carmine Vittoria, "A Computational Study of Nickel Ferrite", Journal of Magnetism and Magnetic Materials 303, e432 (2006).

S. Sahrakorpi, M. Lindroos, and A. Bansil, "Site and Orbital Selectivity Properties of Angle-resolved Photoemission from the Cuprates", J. Phys. Chem. Solids 67, 208 (2006).

M. Lindroos, S. Sahrakorpi, V. Arpiainen, R.S. Markiewicz, and A. Bansil, "Role of kz -dispersion in Photoemission from Quasi-2D Cuprates", J. Phys. Chem. Solids 67, 244 (2006).

B. Barbiellini, P. E. Mijnarends, S. Kaprzyk, A. Bansil, Yinwan Li, J.F. Mitchell, and P. A. Montano, "Extracting d-orbital occupancy from magnetic Compton scattering in bilayer manganites", J. Phys. Chem. Solids 66, 2197 (2005).

B. Barbiellini and A. Bansil, "A spin-polarizedi scheme for obtaining quasi-particle energies within the density functional theory", J. Phys. Chem. Solids 66, 2192 (2005).

Xu Zuo, Yongxue He, Aria Yang, B. Barbiellini, V. G. Harris, and C. Vittoria, "Calculation of exchange constants in spinel ferrites with magnetic S-state ions", J. App. Phys. 97, 10F104 (2005).

**PI Edward Baron**

D. Casebeer, K. Leighly, & E. Baron, FUSE Observations of the Narrow Line Seyfert 1 Galaxy RE 1034+39: Dependence of Broad Emission Line Strengths on the Shape of the Photoionizing Spectrum, Ap. J., (2006), 637, 157-182.

P. Hauschildt & E. Baron, A 3D Radiative Transfer Framework: I. Non-local Operator Splitting and Continuum Scattering Problems, A and A, (2006), 451, 273--284.

D. Branch, L. C. Dang, N. Hall, W. Ketchum, M. Melakayil, J. Parrent, M. A. Troxel, D. Casebeer, D. Jeffery, & E. Baron, Comparative Direct Analysis of Type Ia Supernova Spectra. II. Maximum Light, PASP, (2006), 118, 560--571.

E. Baron, S. Bongard, D. Branch, & P. Hauschildt, Spectral Modeling of SNe Ia Near Maximum Light: Probing the Characteristics of Hydrodynamical Models, ApJ, (2006), 647, 480--487.

S. Bongard, E. Baron, G. Smadja, D. Branch, & P. Hauschildt, Type Ia Supernova Spectral Line Ratios as Luminosity Indicators, ApJ, (2006), 647, 513

S. Knop, P. Hauschildt, & E. Baron, General Relativistic Radiative Transfer, A and A, (2006), submitted.

B. Chen, R. Kantowski, E. Baron, S. Knop, & P. Hauschildt, Solving the Transfer Equation for Arbitrary Flows in Stationary Spacetimes, PRD15, (2006), submitted.

D. Casebeer, E. Baron, K. Leighly, D. Jevremovic, and D. Branch, A Self-Consistent NLTE-Spectra Synthesis Model of FeLoBAL QSOs, ApJ, (2006), submitted.

E. Baron, D. Branch, and P. Hauschildt, Reddening, Abundances, and Line Formation in SNe II, ApJ, (2006), submitted.

**PI Don Batchelor**

Quasilinear evolution of non-thermal distributions in ion cyclotron resonance heating of tokamak plasmas, E. F. Jaeger, R. W. Harvey, V. E. Lynch, et al., to be published in Journal of Physics: Conference Series (2006).

Self-Consistent Full-Wave and Fokker-Planck Calculations for Ion Cyclotron Heating in Non-Maxwellian Plasmas, E. F. Jaeger, L. A. Berry, S. D. Ahern, et al., Phys. Plasmas 13, 056101 (2006).

Global wave solutions with self-consistent velocity distributions in ion cyclotron heated plasmas, E. F. Jaeger, R. W. Harvey, L. A. Berry, et al., Nucl. Fusion 46 S397 (2006).

Nonlinear ICRF-plasma interactions, J.R. Myra, D.A. D'Ippolito, D.A. Russell, L.A. Berry, E.F. Jaeger and M.D. Carter, Nucl. Fusion 46 S455 (2006).

Non-thermal particle and full-wave diffraction effects on heating and current drive in the ICRF and LHRF regimes, J. C. Wright, L. A. Berry, P. T. Bonoli, D. B. Batchelor, E. F. Jaeger, M. D. Carter, E. D'Azevedo, C. K. Phillips, H. Okuda, R. W. Harvey, D. N. Smithe, J. R. Myra, D. A. D'Ippolito, M. Brambilla and R. J. Dumont, Nucl. Fusion 45, 1411 (2005).

**PI Victor Batista**

J. Chem. Phys., 122, 64102, 2005 Matching-Pursuit Split Operator Fourier Transform Computations of Thermal Correlation Functions, by Xin Chen, Yinghua Wu and Victor S. Batista.

J. Chem. Phys., 122, 154709, 2005 (Also, selected for the May 2005 issue of the Virtual Journal of Ultrafast Science) Model Study of Coherent Quantum Dynamics of Hole States in Functionalized Semiconductor Nanostructures, by Luis G.C. Rego, Sabas G. Abuabara and Victor S. Batista.

Quant. Inform. Compu., 5, 318-334, 2005 Coherent Optical Control of Electronic Excitations in Functionalized Semiconductor Nanostructures, Luis G.C. Rego, Sabas G. Abuabara and Victor S. Batista.

J. Chem. Theor. Comput., 1, 674-685, 2005 QM/MM Study of the NMR Spectroscopy of the Retinylidene Chromophore in Visual Rhodopsin, by Jose A. Gascon, Eduardo M. Sproviero and Victor S. Batista.

J. Chem. Phys., 122, 114114, 2005 Matching-Pursuit Split Operator Fourier Transform Simulations of Nonadiabatic Quantum Dynamics, by Yinghua Wu, Michael Herman and Victor S. Batista.

J. Am. Chem. Soc., 127, 18234-18242, 2005. Influence of Thermal Fluctuations on Interfacial Electron Transfer in Functionalized TiO2 Semiconductors, by Sabas G. Abuabara, Luis G.C. Rego and Victor S. Batista.

J. Chem. Theor. Comput., 2, 175-186, 2006 A Self-Consistent Space-Domain Decomposition Method for QM/MM Computations of Protein Electrostatic Potentials, by Jose A. Gascon, Siegfried S.F. Leung, Enrique R. Batista and Victor S. Batista.

Photochem. Photobiol. 4, 940-949, 2005 The Mechanism of Photosynthetic Water Splitting, by James P. McEvoy, Jose A. Gascon, Victor S. Batista and Gary W. Brudvig.

Acc. Chem. Res 39, 184-193, 2006 Computational Studies of the Primary Photo-Transduction Event in Visual Rhodopsin, by Jose A. Gascon, Eduardo M. Sproviero and Victor S. Batista.

J. Inorg. Biochem. 100, 786-800, 2006 Characterization of Synthetic Oxomanganese Complexes and the Inorganic-Core of the O2-Evolving Complex in Photosystem II: Evaluation of the DFT/B3LYP Level of Theory, by Eduardo M. Sproviero, Jose A. Gascon, James P. McEvoy, Gary W. Brudvig and Victor S. Batista.

J. Chem. Theor. Comput., 4, 1119-1134, 2006 QM/MM Model 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. Am. Chem. Soc., 128, 3659-3668, 2006 Density functional theory and DFT+U study of transition metal porphine adsorbed on Au(111) surfaces and effects of applied electric fields, by Kevin Leung, Susan B. Rempe, Peter A. Schultz, Eduardo M. Sproviero, Victor S. Batista, Michael E. Chandross, and Craig J. Medforth.

J. Mod. Optics., in press, 2006 Coherent-Control of Tunneling Dynamics in Functionalized Semiconductor Nanostructures: A Quantum-Control Scenario Based on Stochastic Unitary Pulses, Luis G.C. Rego, Sabas G. Abuabara and Victor S. Batista.

J. Chem. Phys., 124, 224305, 2006 Matching-Pursuit Split Operator Fourier Transform Simulations of Excited-State Intramolecular Proton Transfer in 2-(2`-hydroxyphenyl)-oxazole, by Yinghua Wu and Victor S. Batista.

J. Chem. Phys., 125, 134313, 2006 Matching-Pursuit Split Operator Fourier Transform Simulations of Excited-State Nonadiabatic Quantum Dynamics in Pyrazine, by Xin Chen and Victor S. Batista.

Proceedings of SPIE, 6325, 63250R, 2006 Force Field Parameters for Large-Scale Computational Modeling of Sensitized TiO2 Surfaces, by Sabas G. Abuabara, Jose A. Gascon, Suet-Yee Leung and Victor S. Batista.

**PI Pat Behling**

Liu, Z., M. Notaro, J. Kutzbach and N. Liu, 2006: An observational assessment of climate-vegetation feedback: I: The global analysis. J. Clim., 19 (5), 787�

Liu, Z., S. Vavrus and F. He, 2005: The enhanced equatorial warming: a robust SST response to global warming. J. Clim., J. Clim., 18 (22), 4684-4700

Notaro, M., Z. Liu, R. Gallimore, S. Vavrus, J. Kutzbach, I.C. Prentice, and R. Jacob (2005). Simulated and Observed Pre-Industrial to Modern Vegetation and Climate Changes. Journal of Climate 18:3650-3671. CCR #854

Ruddiman, W., S. Vavrus, and J.E. Kutzbach (2005). A test of overdue-glaciation hypothesis. Quaternary Science Reviews 24(1-2), pgs. 1-10, doi: 1031016/j.quascirev.2004.07.010. CCR #852

Vavrus, S., M. Notaro, and Z. Liu, 2006: A Mechanism for Abrupt Climate Change Associated with Tropical Pacific SSTs. J. Climate, 19, 242-256.

Wen N., Z. Liu, C. Frankignoul, Q. Liu, 2005: Observations of SST, heat flux and ocean-atmosphere interaction over the North Atlantic. Geophys. Res. Lett., 32, L24619, oi:10.1029/2005GL024871

Wu, L., F. He, and Z. Liu (2005), Coupled ocean-atmosphere response to north tropical Atlantic SST: Tropical Atlantic dipole and ENSO, Geophys. Res. Lett., 32, L21712, doi:10.1029/2005GL024222.

Wu, L. and Z. Liu (2005). North Atlantic decadal variability: Air-Sea Coupling, Oceanic Memory and Potential Northern Hemisphere Resonance. Journal of Climate 18(2), pp. 331-349. doi: 10.1175/ JCLI-3264.1. CCR #844

Yang, H. and Z. Liu (2005). Tropical-Extratropical climate interaction as revealed in idealized coupled climate model experiments. Climate Dynamics, doi: 10.1007/s00382-005-0021-8. CCR #829

Yang, H., Q. Zhang, Y. Zhong, S. Varvrus, and Z. Liu (2005): How does Extratropical Warming Effect ENSO? Geophysical Research Letters 32, L01702. doi:10.1029/2004GL021624. CCR#852.

**PI John Bell**

A. S. Almgren, J. B. Bell, C. A. Rendleman, and M. Zingale, "Low Mach Number Modeling of Type Ia Supernovae. II. Energy Evolution", Astrophysical Journal, 649, 927-938, 2006.

Miniati, F. and Colella, P. "A Modified higher-Order Godunov's Scheme for Stiff Source Conservative Hydrodynamics", LBNL-59902, submitted to Journal of Computational Physics.

A. S. Almgren, J. B. Bell, C. A. Rendleman, and M. Zingale, "Low Mach Number Modeling of Type Ia Supernovae. I. Hydrodynamics", Astrophysical Journal, 637, 922-936, 2006.

Gatti-Bono, C., Colella, P., "An anelastic allspeed projection method for gravitationally stratified flows", LBNL-57158, J. Comput. Phys. Vol. 216 (2006), pp. 589-615.

J. B. Bell, M. S. Day, J. F. Grcar, M. J. Lijewski, J. F. Driscoll and S. F. Filatyev, "Numerical Simulation of a Laboratory-Scale Turbulent Slot Flame", LBNL Report LBNL-59245, in press Proc. Combust. Inst., Dec 2005.

Schwartz, P., Barad, M., Colella, P., Ligocki, T.J., "A Cartesian grid embedded boundary method for the heat equation and Poisson's equation in three dimensions", LBNL-56607, Journal of Computational Physics. Vol. 211 (2006), pp. 531-550.

J. B. Bell, M. S. Day, J. F. Grcar and M. J. Lijewski, "A Computational Study of Equivalence Ratio Effects in Turbulent, Premixed Methane-Air Flames", LBNL Report LBNL-59246, in press - Proc. ECCOMAS-CFD 2006.

Colella, P., Graves, D.T., Keen, B.J., Modiano, D., "A cartesian grid embedded boundary method for hyperbolic conservation laws", LBNL-56420, Journal of Computational Physics. Vol. 211 (2006), pp. 347-366.

J. B. Bell, R. K. Cheng, M. S. Day and I. G. Shepherd, "Numerical Simulation of Lewis Number Effects on Lean Premixed Turbulent Flames", LBNL Report LBNL-59247, in press Proc. Combust. Inst., Dec 2005.

Schwartz, P., Adalsteinsson, D., Colella, P., Arkin, A.P., Onsum, M., "Numerical computation of diffusion on a surface", Proc. Nat. Acad. Sci. Vol. 102 (2005), pp. 11151-11156.

J. B. Bell, M. S. Day, J. F. Grcar, and M. J. Lijewski, "Active Control for Statistically Stationary Turbulent Premixed Flame Simulations", LBNL Report LBNL-58751, Communications in Applied Mathematics and Computational Science, 1, 29-51, 2006.

J. Bell, M. Day, A. Almgren, M. Lijewski, C. Rendleman, R. Cheng, I. Shepherd, "Simulation of Lean Premixed Turbulent Combustion," Proceedings of the SciDAC2006 Conference, to appear.

M. Day and J. Bell, "Simulation of premixed turbulent flames," Proceedings of the SciDAC2006 Conference, to appear.

**PI Roy Benedek**

Theory of over-lithiation reaction in LiMO2 battery electrodes R. Benedek and M. M. Thackeray Chemistry of Materials 18 (5): 1296-1302 (2006)

First-principles calculations for Co-doped LiMn1.5Ni0.504 and LiMn2O4 battery electrodes R. Benedek, C. S. Johnson and M. M. Thackeray Electrochemical and Solid State Letters 9 (6): A289-A291 (2006)

Reaction energy for LiMn2O4 spinel dissolution in acid R. Benedek and M. M. Thackeray Electrochemical and Solid State Letters 9 (6): A265-A267 (2006)

**PI George Bertsch**

"Global study of quadrupole correlation effects", M.Bender, G.F.Bertsch, and P.-H. Heenen, Phys. Rev. C73 034322 (2006).

**PI Amitava Bhattacharjee**

P. Zhu, A. Bhattacharjee, and K. Germaschewski, Intermediate nonlinear evolution of the Parker instability: Formation of convection-induced discontinuities and absence of finite-time singularities, Phys. Rev. Lett. 96, 065,001, doi:10.1103/PhysRevLett.96.065001 (2006)

P. Zhu, C. C. Hegna, and C. R. Sovinec, Nonlinear growth of a line-tied g-mode near marginal stability, Phys. Plasmas 13, 102307 (2006)

P. Zhu, C. R. Sovinec, C. C. Hegna, K. Germaschewski, and A. Bhattacharjee, Nonlinear ballooning instability in the near-Earth magnetotail: Growth, structure, and possible role in substorms, submitted to J. Geophys. Res. (2006)

P. Zhu, C. C. Hegna, C. R. Sovinec, A. Bhattacharjee, and K. Germaschewski, Intermediate nonlinear regime of a line-tied g-mode, to appear in Phys. Plasmas (2007)

K. Germaschewski, A. Bhattacharjee, and C.-S. Ng The Magnetic Reconnection Code: an AMR-based fully implicit simulation suite, to appear in Numerical Modeling of Space Plasma Flows, Astronomical Society of the Pacific Conference Series

N. Bessho and A. Bhattacharjee, Collisionless Reconnection in an Electron-Positron Plasma, Phys. Rev. Lett. 95, 245001 (2005)

**PI Julian Borrill**

"Measurement of the CMB Spectrum from the 2003 Flight of BOOMERANG", Montroy et al, submitted to the Astrophysical Journal

"Instrument, Method, Brightness and Polarization Maps from the 2003 flight of BOOMERanG", Masi et al, submitted to the Astrophysical Journal

"A measurement of the polarization-temperature angular cross power spectrum of the Cosmic Microwave Background from the 2003 flight of BOOMERANG", Piacentini et al, submitted to the Astrophysical Journal

"Cosmological Parameters from the 2003 flight of BOOMERANG" MacTavish et al, submitted to the Astrophysical Journal

"A Measurement of the Angular Power Spectrum of the CMB Temperature Anisotropy from the 2003 Flight of Boomerang", Jones et al, submitted to the Astrophysical Journal

"MAXIPOL: Cosmic Microwave Background Polarimetry Using a Rotating Half-Wave Plate", Johnson et al, submitted to the Astrophysical Journal.

"MAXIPOL: Data Analysis and Results", Wu et al, submitted to the Astrophysical Journal.

"Improved Measurements of the CMB power spectrum with ACBAR", Kuo et al, submitted to the Astrophysical Journal.

"Separating Cosmological B-Modes From Foregrounds In Cosmic Microwave Background Polarization Observations", Stivoli et al, Monthly Notices of the Royal Astronomical Society, 372, 615, (2006)

"Comparison of map-making algorithms for CMB experiments", T. Poutanen et al, Astronomy & Astrophysics (in press).

"Making sky maps from Planck data", M. A. J. Ashdown et al, submitted to Astronomy & Astrophysics

**PI Marcia Branstetter**

Branstetter, M.L., David J. Erickson III, Jose Hernandez, and Robert Oglesby, "Spatial resolution and precipitation impacts on the magnitude and variability of river discharge in CCSM3", submitted to Journal of Hydrology, 2006.

**PI Eduardo Bringa**

`Simulations of carbon sputtering in fusion reactor divertor plates`, J. Marian, L.A. Zepeda-Ruiz, G.H. Gilmer, E.M. Bringa, and T. Rognlien, Physica Scripta, T 124, 65 (2006).

`Atomistic simulation of cosmic ray-induced amorphization of silicate grains`, P.R. Durham, R. Devanathan, E.M. Bringa, L.R. Corrales, A.G.G.M. Tielens, W. van Breugel, accepted in Astrophysics Letters.

`Molecular dynamics simulation of amorphization of forsterite by cosmic rays`, R. Devanathan, P. Durham, J. Du, L. R. Corrales, E. M. Bringa, accepted in Nucl. Instr. and Meth. in Phys. Res. B.

`High-Energy Ion Tracks in Thin Films`, D.M. Follstaedt, A.K. Norman, P. Rossi, B.L. Doyle, F.D. McDaniel and E.M. Bringa, Nucl. Instr. and Meth. in Phys. Res. B 242, 79 (2006).

`Simulation of ion tracks in diamond and graphite`, D. Schwen and E. Bringa, accepted in Nucl. Instr. and Meth. in Phys. Res. B.

`Implications of ab initio energetics on the thermodynamics of Fe-Cr alloys`, A. Caro, M. Caro, E.M. Lopasso, et al., Applied Physics Letters 89, 121902 (2006).

`Thermodynamics of Fe-Cu alloys as described by a classic potential`, A. Caro, M. Caro, E.M. Lopasso et al., Journal of Nuclear Materials 349, 317 (2006).

`Atomistic simulations of grain boundary pinning in CuFe alloys`, Zepeda-Ruiz LA, Gilmer GH, Sadigh B, et al., , Applied Physics Letters 87, 231904 (2005).

`Electronic effects in shock-induced melting`, L. Koci, E.M. Bringa, D. Ivanov, L. Zhigilei, A.B. Belonoshko, B. Remington, and R. Ahuja, Phys. Rev. B 74, 012101 (2006).

`Moving dislocations in disordered alloys: Connecting continuum and discrete models with atomistic simulations`, Marian J, Caro A, , Phys. Rev. B 74, 024113 (2006).

`Molecular Dynamics simulations of the Ritchmyer-Meshkov instability in shock-loaded solids`, S. V. Zybin, V. V. Zhakhovskii, E. M. Bringa, S. I. Abarzhi, and B. Remington, Shock Compression of Condensed Matter-2005, M.D. Furnish et al. eds., APS, New York, 2006, pp. 437-439.

`Pressure effects on grain boundary plasticity in nanophase metals`, E.M. Bringa, E. Leveugle and A. Caro, Applied Physics Letters 89, 023101 (2006).

`A viscoplastic micromechanical model for the yield strength of nanocrystalline materials`, R. Lebensohn, E.M. Bringa, and A. Caro, Acta Materialia, in press.

`Deforming nanocrystalline nickel at ultrahigh strain rates`, Y.M. Wang, E.M. Bringa, et al., Applied Physics Letters 88, 061917 (2006).

**PI Eric Brown**

"Ultra-Large Hyperpolarizability Twisted p-Electron System Electro-Optic Chromophores. Synthesis, Solid State and Solution Phase Structural Characteristics, Electronic Structures, Linear and Nonlinear Optical Properties, and Computational Studies." Kang, H.; Facchetti, A.; Jiang, H.; Cariati, E.; Righetto, S.; Ugo, R.; Zuccaccia, C.; Macchioni, A.; Stern, C. L.; Liu, Z.; Ho, S. T.; Brown, E. C.; Ratner, M. A.; Marks, T. J. Submitted to Journal of the American Chemical Society, 2006.

"Solvent Effects on the Potential Energy Surfaces and Nonlinear Response Properties of Twisted Chromophores." Brown, E. C.; Marks, T. J.; Ratner, M. A. Submitted to the Journal of Physical Chemistry. 2006.

**PI Virginia Brown**

Neutron-Proton Bremsstrahlung Compared to Experiment at 225 MeV, V.R.Brown et al., Bulletin American Physical Society, Session HF Topics in Nuclear Theory, October 28, 2006.

**PI David Bruhwiler**

A.V. Fedotov, I. Ben-Zvi, D.L. Bruhwiler, V.N. Litvinenko and A.O. Sidorin, "High-energy electron cooling in a collider," New J. Phys. 8 (2006), in press.

A.V. Fedotov, D.L. Bruhwiler, A.O. Sidorin, D.T. Abell, I. Ben-Zvi, R. Busby, J.R. Cary, and V.N. Litvinenko, "Numerical study of the magnetized friction force," Phys. Rev. ST Accel. Beams 9, 074401 (2006).

**PI Dmitry Budker**

A. T. Nguyen, D. Budker, S. K. Lamoreaux, and J. R. Torgerson, Sensitive search for the temporal variation of the fine structure constant using radio-frequency E1 transitions in atomic dysprosium, Phys. Rev. A 69, 022105 (2004)

D. Budker, L. Hollberg, D. F. Kimball, J. Kitching, S. Pustelny, and V. V. Yashchuk, Investigation of microwave transitions and nonlinear magneto-optical rotation in anti-relaxation-coated cells, Phys. Rev. A 71, 012903 (2005);

E. B. Alexandrov, M. Auzinsh, D. Budker, D. F. Kimball, S. M. Rochester, and V. V. Yashchuk, Dynamic effects in nonlinear magneto-optics of atoms and molecules; in a Special Issue of JOSA B on Nonlinear and Integrated Magneto-Optics; JOSA B 22(1), 7-20 (2005);

D. Budker and S. M. Rochester, A relation between electromagnetically induced absorption resonances and nonlinear magneto-optics in Lambda-systems, Phys. Rev. A 70, 025804 (2004);

M. Auzinsh, D. Budker D. F. Kimball, S. M. Rochester, J. E. Stalnaker, A. O. Sushkov, and V. V. Yashchuk, Can a quantum nondemolition measurement improve the sensitivity of an atomic magnetometer? Phys. Rev. Lett. 93(17), 173002 (2004);

## C

**PI Wei ****Cai**

A. Kanaev, V. Astratov, W. Cai, Optical Coupling at a distance between detuned spherical cavities, accepted in Applied Physics Letter, January, 2006.

W. Cai, S. Z. Deng, D. Jacobs, Extending the Fast Multipole Method to Charges Inside or Outside a Dielectric Sphere, submitted to the Journal of Computational Physics, June, 2006.

S. Deng, W. Cai, A Fourth-Order Upwinding Embedded Boundary Method (UEBM) for Maxwell's Equations in Media with Material Interfaces: Part I, the Communication in Computational Physics, Volume 1, Number 4, June 2006, pp. 744-764.

X. Ji, W. Cai, P. Zhang, High Order DGTD Methods for Dispersive Maxwell's Equations and Modelling of Silver Nanowire Coupling, the International Journal of Numerical Methods in Engineering, In Press, July, 2006

S. H. Shao, W. Cai, H. Z. Tang, Accurate Calculation of Green's Functions of Schrodinger Equations in Block Layered Potentials,the Journal of Computational Physics, Available online 9 June 2006.

M. Cho, W. Cai, T. Her, A Boundary Integral Equation Method for Photonic Crystal Fiber, accepted in the Journal of Scientific Computing, 2006.

**PI Kirk Cameron**

K.W. Cameron, R. Ge, and X.-H. Sun, "lognP and log3P: Accurate analytical models of point-to-point communication in distributed systems", to appear IEEE Transactions on Computers, 2006.

K. W. Cameron, X. Feng and R. Ge, "The Argus Prototype: Aggregate Use of Load Modules as a High density Supercomputer," Concurrency and Computation: Practice and Experience, Volume 18, Issue 1, 2006.

K. W. Cameron, R. Ge, X. Feng, "High-Performance, Power-Aware Distributed Computing for Scientific Applications," IEEE Computer, Volume 38, Issue 11, November 2005.

S. Byna, K. W. Cameron and X.-H. Sun, "Memory-Aware Communication -An Experimental Study with MPI," Parallel Processing Letters, Volume 15, Issue 4, December 2005. pp 357-365.

X. Feng, and K.W. Cameron, "High Performance, Bayesian-based Phylogenetic Inference Framework", to appear IEEE/ACM the 18th High Performance Computing, Networking and Storage Conference (SC), 2006. [Best Student Paper Nominee]

K. W. Cameron, X. Feng and R. Ge, "Performance and Energy-Conscious Distributed DVS Scheduling for Scientific Applications on Power-aware Clusters," Proceedings of the 17th IEEE/ACM High Performance Computing, Networking and Storage Conference (SC 2005), November 2005, 15 pgs. (24% accept rate)

X. Feng, R. Ge, and K. W. Cameron, "Power and Energy of Scientific Applications on Distributed Systems," to appear 19th IEEE International Parallel and Distributed Processing Symposium (IPDPS 05), April 2005, 10 pgs. (34.3% accept rate)

**PI Philip Cameron-Smith**

"Toward an Earth system model: atmospheric chemistry, coupling, and petascale computing", P Cameron-Smith, J-F Lamarque, P Connell, C Chuang and F Vitt, 2006 J. Phys.: Conf. Ser. 46 343-350, doi:10.1088/1742-6596/46/1/048

Lamarque, J.-F., P. Cameron-Smith, and 18 other authors, "Assessing Nitrogen Deposition and Carbon Cycle Feedback using a Multi-Model approach. Analysis of Nitrogen Deposition", J.G.R. Atmospheres, vol. 110, D19303, 2005.

**PI Andrew Canning**

C. Yang, J. C. Meza, and L. W. Wang. A constrained optimization algorithm for total energy minimization in electronic structure calculation. LBNL Report 57434, Lawrence Berkeley National Laboratory, to appear in Journal of Computational Physics, 2006.

Z. Zhao, L.-W. Wang, and J. Meza. Motif based hessian matrix for ab initiogeometry optimization of nanostructures. Submitted to Rapid Communication of Physical Review B, 2006

Scaling first-principles plane-wave codes to thousands of processors A. Canning and D. Raczkowski, Computer Physics Communications, Vol 169, p449, (2005) LBNL-58571

B. Lee and L.-W. Wang. Electronic structure of zinc-blende AlGaN: screened-exchange study. LBNL Report 59272, Lawrence Berkeley National Laboratory, 2006. Phys. Rev. B (in press)

Conjugate-Gradient Eigenvalue Solvers in Computing Electronic Properties of Nanostructure Architectures S. Tomov, J. Langou, A. Canning, L-W Wang and J. Dongarra, to appear in Technology Computer Aided Design: The International Journal of Computational Science and Engineering (IJCSE) Special Issue on Computational Methods and Techniques for Nanoscale (2005) LBNL-58574

Andrew Canning, Jack Dongarra, Julien Langou, Osni Marques, Stanimire Tomov, Christof Voemel, and Lin-Wang Wang, Towards bulk based preconditioning for quantum dot computations,(accepted to IEEE/ACM Proceedings of HPCNano05).

Andrew Canning, Jack Dongarra, Julien Langou, Osni Marques, Stanimire Tomov, Christof Voemel, and Lin-Wang Wang, Performance evaluation of eigensolvers in nano-structure computations,(accepted to IEEE/ACM Proceedings of HPCNano05).

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. To appear in the Journal of Computational Physics 2006

**PI John Cary**

D. A. Dimitrov, D. L. Bruhwiler, J. R. Cary, C. G. R. Geddes, R. E. Giacone, E. Esarey and W. P. Leemans, "Particle-in-cell Simulations of Laser Pulse Propagation in Plasma Channels," Phys. Plasmas, submitted (2006).

A. V. Fedotov, D. L. Bruhwiler, A. O Sidorin, D. T. Abell, I. Ben-Zvi, R. Busby, J. R. Cary, and V. N. Litvinenko, "Numerical Study of the Magnetized Friction Force," Phys. Rev. ST/AB 9, 074401 (2006).

C. G. R. Geddes, Cs. Toth, J. van Tilborg, E. Esarey, C. B. Schroeder, J. Cary, and W. P. Leemans, "Guiding of relativistic laser pulses by preformed plasma channels," Phys. Rev. Lett. 95, 145002 (2005).

C. G. R. Geddes, Cs. Tsth, J. van Tilborg, E. Esarey, C. B. Schroeder, D. Bruhwiler, C. Nieter, J. Cary, and W. P. Leemans, "Production of high-quality electron bunches by dephasing and beam loading in channeled and unchanneled laser plasma accelerators," Phys. Plasmas 12 (5), 056709 (2005).

J. R. Cary, R. Giacone, C. Nieter, D. L. Bruhwiler, "Clean beams from optical injection with a cleanup pulse," Phys. Plasmas 12 (5), 056704 (2005).

**PI Fausto Cattaneo**

Aleksandr Obabko, Fausto Cattaneo, Paul Fischer "Magneto-rotational instability and turbulent angular momentum transport", 48th Annual Meeting of the Division of Plasma Physics of American Physics Society, Philadelphia, Pennsylvania, October 30-November 3, 2006

**PI Yuen-Dat Chen**

Search for periodicities in the 8B solar neutrino flux measured by the Sudbury Neutrino Observatory Aharmim, B.et al. Phy. Rev. D72 (2005) 052010, LBNL-61065

A Search for Neutrinos from the Solar hep Reaction and the Diffuse Supernova Neutrino Background with the Sudbury Neutrino Observatory B. Aharmim, et. al. (SNO Collaboration) (to appear in ApJ) hep-ex/0607010

**PI Choong-Seock Chang**

S.H. Hahn, Seunghoe Ku and C.S. Chang, "Wall intersection of ion orbits induced by fast transport of pedestal plasma over an electrostatic potential hill in a tokamak plasma edge," Physics of Plasmas 12, 102501 (2005)

Hoyul Baek, Seunghoe Ku and C.S. Chang, "Neoclassical polarization drift of collisionless single ions in a sheared radial electric field in a tokamak magnetic geometry," Phys. Plasmas, 13, 012503 (2006)

C. S. Chang and S. Ku, Particle simulation of neoclassical transport in the plasma edge, Contrib. Plasma Phys. 46, 496 (2006).

S. Ku, C.S. Chang, M. Adams, et al., Gyrokinetic particle simulation of neoclassical transport in the pedestal/scrape-off region of a tokamak plasma, Journal of Physics, in press

S.E. Parker, J.J. Kahut, Y. Chen, Z. Lin, F.L. Hinton and W.W. Lee, "Fine-Scale zonal flow suppression of electron temperature gradient turbulence," submitted.

W. Wan, Y. Chen and S.E. Parker, "Gyrokinetic deltaf simulation of the collisionless and semicollisional tearing mode instability," Physics of Plasmas 12, 012311 (2005)

W. Wan, Y. Chen and S. Parker, "delta-f simulation of the collisionless tearing mode instability with a ion gyrokinetic responce," IEEE Trans. Plasma Sci., Vol 33 No 2, April (2005).

**PI James Chelikowski**

M.L. Tiago and J.R. Chelikowsky: "First-principles GW-BSE excitations in organic molecules," Solid State Comm. 136, 333 (2005).

X. Huang, A. Makmal, J. R. Chelikowsky and L. Kronik: "Size dependent spintronic properties of dilute magnetic semiconductor nanocrystals," Phys. Rev. Lett. 94, 236801 (2005).

K.S. Nakayama, M.M.G. Alemany, H. Kwak, T. Sugano, K. Ohmori, J.R. Chelikowsky and J.H. Weaver: "Electronic structure of Si(001)-c(4x2) analyzed by scanning tunneling spectroscopy and ab initio simulations," Phys. Rev. B 73, 035330 (2006).

C. Bekas, Y. Saad, M.L. Tiago and J.R. Chelikowsky: "Computing charge densities with partially reorthogonalized Lanczos," Comp. Phys. Comm. 171, 175 (2005).

M. Lopez del Puerto, M.L. Tiago, I. Vasiliev and J.R. Chelikowsky: "Real space pseudopotential calculations of the ground state and excited state properties of the water molecule," Phys. Rev. A 72, 052504 (2005).

M.M.G. Alemany and J.R. Chelikowsky: "Ab initio calculations for the interconversion of optically active defects in amorphous silica," Phys. Rev. B 73, 235211 (2006).

M.L. Tiago and J.R. Chelikowsky: "Optical excitations in organic molecules, clusters and defects from first Principles Green's function methods," Phys. Rev. B 73, 205334 (2006).

L. Kronik, A. Makmal, M.L. Tiago, M.M.G. Alemany, M. Jain, X. Huang, Y. Saad and J.R. Chelikowsky: "PARSEC-the pseudopotential algorithm for real space electronic structure calculations: recent advances and novel applications to nano-structures," phys. stat. sol. (b) 243, 1063 (2006).

G. Dalpian, M.L. Tiago, M. Lopez del Puerto and J.R. Chelikowsky: "Symmetry considerations for semiconductor nanocrystals," Nano Lett. 6, 501 (2006).

L. Kong, M. L. Tiago and J. R. Chelikowsky: "Real-space pseudopotential method for electron transport properties of nano-scale junctions," Phys. Rev. B 73, 195118 (2006).

G. Dalpian and J.R. Chelikowsky: "Self-Purification in Semiconductor Nanocrystals," Phys. Rev. Lett. 96, 226802 (2006).

S. Li, M.M.G. Alemany and J. R. Chelikowsky: "Real-space Ab initio pseudopotential calculations for anion clusters: Fe_n^- (n=3-6)," Phys. Rev. B 73, 233404 (2006).

S. Li, M.M.G. Alemany and J. R. Chelikowsky: "Real space pseudopotential calculations for copper clusters," J. Chem. Phys. 125, 034311(2006).

Y. Saad, Y. Zhou, C. Bekas and J.R. Chelikowsky: "Diagonalization Methods in PARSEC," phys. stat. sol. (b) 243, 2188 (2006).

J.R. Chelikowsky, E. Kaxiras and R.M. Wentzcovitch: "Theory of Spintronic Materials," phys. stat. sol. (b) 243, 2133 (2006).

M. Lopez del Puerto, M.L. Tiago, and J.R. Chelikowsky: "Excitonic effects and optical properties of passivated CdSe clusters," Phys. Rev. Lett. 97, 096401 (2006).

M.L. Tiago and J.R. Chelikowsky: "Confinement effects in the optical properties of semiconductor nanocrystals," phys. stat. sol. (b) 243, 2151 (2006).

M.L. Tiago, Y. Zhou, M.M.G. Alemany, Y. Saad, J.R. Chelikowsky: "The Evolution of Magnetism in Iron from the Atom to the Bulk," Phys. Rev. Lett. (in press).

N.S. Norberg, G.M. Dalpian, J.R. Chelikowsky, and D.R. Gamelin: "Vacuum Pinning of Magnetic Impurity Levels in Quantum Confined Semiconductors," Nano Letters (in press).

S. Beckman, J. Han, and J.R. Chelikowsky: "Role of Quantum Confinement in Ge Nanowires," Phys. Rev. B 74, 165314 (2006).

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," Phys. Rev. Lett. (submitted).

**PI Jacqueline Chen**

E. R. Hawkes and J. H. Chen, "Comparison of Direct Numerical Simulations of Lean Premixed Methane-Air Flames with Strained Laminar Flame Calculations", Combust. Flame, 144: 112-125. (2005).

J. C. Sutherland, P. J. Smith, and J. H. Chen, "Quantification of Differential Diffusion in Nonpremixed Systems," Combust. Theory and Modeling, 9:2, pp. 365-383. (2005).

J. H. Chen, E. R. Hawkes, R. Sankaran, S. D. Mason, and H. G. Im, "Direct Numerical Simulation of Ignition Front Propagation in a Constant Volume With Temperature Inhomogeneities, Part I: Fundamental Analysis and Diagnostics", Combust. Flame, 145: 128-144. (2006).

E. R. Hawkes, R. Sankaran, P. Pebay, and J. H. Chen, "Direct Numerical Simulation of Ignition Front Propagation in a Constant Volume With Temperature Inhomogeneities, Part II: Parametric Study", Combust. Flame, 145: 145-159. (2006).

E. R. Hawkes, R. Sankaran, J. Sutherland, and J. H. Chen, "Scalar Mixing in Direct Numerical Simulations of Temporally-Evolving Plane Jet Flames with Detailed CO/H2 Kinetics," to appear Proceedings of the Combustion Institute, 31. (2006).

J. C. Sutherland, P. J. Smith, and J. H. Chen, "A Quantitative Method for Apriori Evaluation of Combustion Reaction Models," to appear in Combustion Theory and Modelling, 2006.

**PI Liu Chen**

"Dynamics of Turbulence Spreading in Magnetically Confined Plasmas", O. D. Gurcan, P. H. Diamond, T. S. Hahm, and Z. Lin, Phys. Plasmas 12, 032303 (2005).

"A Gyrokinetic Electron and Fully Kinetic Ion Plasma Simulation Model", Yu Lin, Xueyi Wang, Zhihong Lin, and Liu Chen, Plasma Phys. Contr. Fusion 47, 657-669 (2005).

"Role of Nonlinear Toroidal Coupling in Electron Temperature Gradient Turbulence", Z. Lin, L. Chen, and F. Zonca, Phys. Plasmas 12, 056125 (2005).

"On the Dynamics of Edge-Core Coupling", T. S. Hahm, P. H. Diamond, Z. Lin, G. Rewoldt, O. Gurcan, and S. Ethier, Phys. Plasmas 12, 090903 (2005).

"Nonlinear Toroidal Mode coupling: A New Paradigm for Drift Wave Turbulence in Toroidal Plasmas", L. Chen, F. Zonca, and Z. Lin, Plasma Phys. Contr. Fusion 47, B71-B81 (2005).

"A Finite Element Poisson Solver for Global Gyrokinetic Particle Simulations", Y. Nishimura, Z. Lin, J. L. V. Lewandowski, and S. Ethier, J. Comput. Phys. 214, 657-671 (2006).

"Global particle-in-cell simulations of microturbulence with kinetic electrons", J. L. V. Lewandowski, G. Rewoldt, S. Ethier, and W. W. Lee, and Z. Lin, Phys. Plasmas 13, 072306 (2006).

"A Finite Element Mesh in a Tokamak Edge Geometry", Y. Nishimura and Z. Lin, Contributions Plasma Phys. 7-9, 551-556 (2006).

"Gyro-kinetic simulation of global turbulent transport properties in tokamak Experiments", W. X. Wang, Z. Lin, W. M. Tang, W. W. Lee, S. Ethier, J. L. V. Lewandowski, G. Rewoldt, T. S. Hahm, and J. Manickam, Phys. Plasmas 13, 092505 (2006).

"Comparative studies of nonlinear ITG and ETG dynamics", F. Zonca, L. Chen, Z. Lin and R.B. White, in Proceedings of the Second IAEA Technical Meeting on the Theory of Plasma Instabilities: Transport, Stability and their Interaction (Trieste, Italy, 2005).

"Particle-in-Cell Simulations of Electron Transport from Plasma Turbulence: Recent Progress in Gyrokinetic Particle Simulations of Turbulent Plasmas", Z. Lin, G. Rewoldt, S. Ethier, T. S. Hahm, W. W. Lee, J. L. V. Lewandowski, Y. Nishimura, and W. X. Wang, in SciDAC2005, Journal of Physics: Conference Series 16, 16-24 (2005).

"Gyrokinetic particle-in-cell simulations of plasma microturbulence on advanced computing platforms", S. Ethier, W. M. Tang, and Z. Lin, in SciDAC2005, Journal of Physics: Conference Series 16, 1-15 (2005).

"Global Gyrokinetic Particle Simulation of Turbulence and Transport in Realistic Tokamak Geometry", W. X. Wang, Z. Lin, W. M. Tang, W. W. Lee, S. Ethier, J. L. V. Lewandowski, G. Rewoldt, T. S. Hahm, and J. Manickam, in SciDAC2005, Journal of Physics: Conference Series 16, 59-64 (2005).

"Fine-Scale Zonal Flow Suppression of Electron Temperature Gradient Turbulence", S. E. Parker, J. J. Kohut, Y. Chen, Z. Lin, F. L. Hinton, and W. W. Lee, In Proceedings of Joint Varenna-Lausanne International Workshop on Theory of Fusion Plasmas, Varenna, Italy, 2006.

"Gyrokinetic particle simulation of neoclassical transport in the pedestal/scrape-off region of a tokamak plasma", S. Ku, C.-S. Chang, M. Adams, J. Cummings, F. Hinton, D. Keyes, S. Klasky, W. Lee, Z. Lin, S. Parker, and the CPES team, in SciDAC2006, Journal of Physics: Conference Series 46, 87-91 (2006).

"Calculating the Thermal Structure of Solar Active Region in Three Dimension", Y. Mok, Z. Mikic, R. Lionello, and J. Linker, Astrophys. J., 621 (2005).

**PI Yang Chen**

Y. Chen and S. E. Parker, "Electromagnetic gyrokinetic delta-f particle-in-cell turbulence simulation with realistic equilibrium profiles and geometry," Journal of Computational Physics, in press.

S.E. Parker, J.J. Kahut, Y. Chen, Z. Lin, F.L. Hinton and W.W. Lee, "Fine-Scale zonal flow suppression of electron temperature gradient turbulence," Published Proceedings of the Joint Varenna-Lausanne International Workshop on the Theory of Fusion Plasmas, Varenna,Italy, Aug. 28-Sept. 1, 2006.

Y. Chen, S.E. Parker and J-Y. Lang, "Arbitrary plasma shape and trapped electron modes in the GEM gyrokinetic electromagnetic turbulence simulation code", J. Phys.: Conf. Ser. 46 92-96 doi:10.1088/1742-6596/46/1/013, 2006

J. Candy, R. E. Waltz, S. E. Parker, and Y. Chen, "Relevance of the parallel nonlinearity in gyrokinetic simulations of tokamak plasmas", Phys. Plasmas 13, 074501 (2006)

W. Wan, Y. Chen and S.E. Parker, "Gyrokinetic deltaf simulation of the collisionless and semicollisional tearing mode instability," Physics of Plasmas 12, 012311 (2005)

Su, Y., S. T. Jones, R. E. Ergun, F. Bagenal, S. E. Parker, P. A. Delamere, and R. L. Lysak (2006), "Io-Jupiter interaction: Alfven wave propagation and ionospheric AlfvYang Chen0 7Yang Chen0_7Yang Chen0_5n resonator," J. Geophys. Res., 111, A06211, doi:10.1029/2005JA011252.

Y-J. Su, R.E. Ergun, S.T. Jones et al., "Generation of short-burst radiation through Alfvenic acceleration of auroral electrons," to be submitted to Journal of Geophysical Research-Space Physics.

W. Wan, Y. Chen and S. Parker, "delta-f simulation of the collisionless tearing mode instability with a ion gyrokinetic responce," IEEE Trans. Plasma Sci., Vol 33 No 2, April (2005).

**PI Hai-Ping Cheng**

K-doped self-assembly of C60 monolayer: Where are electrons? Jingguang Che and Hai-Ping Cheng. submitted PRB, 2006.

Simulation of anomalous Hall effect in Fe-C60 monolayer thin film, Zhang, J.W., A.F. Hebard, and H.-P. Cheng, submitted PRB, 2006.

A perspective on multi-scale simulation: Toward understanding water-silica, Trickey SB, Yip S, Cheng HP, et al., J. COMPUTER-AIDED MATERIALS DESIGN 13 (1-3): 1-12 OCT 2006.

Procedure for building a consistent embedding at the QM-CM interface, Mallik A, Taylor DE, Runge K, et al., J. COMPUTER-AIDED MATERIALS DESIGN 13 (1-3): 1-12 OCT 2006.

Quantum, classical, and multi-scale simulation of silica-water interaction: molecules, clusters, and extended systems, Cheng HP, Wang LL, Du MH, et al., J. COMPUTER-AIDED MATERIALS DESIGN 13 (1-3): 1-12 OCT 2006.

Stability and structure of cationic sodium hydroxide clusters, Feiden P, Cheng HP, Leygnier J, et al. CHEMICAL PHYSICS LETTERS 425 (4-6): 283-288 JUL 10 2006.

Local electronic structure of Bi2Sr2CaCu2O8 near oxygen dopants: A window on the high-T-c pairing mechanism, He Y, Nunner TS, Hirschfeld PJ, et al., PHYSICAL REVIEW LETTERS 96 (19): Art. No. 197002 MAY 19 2006.

From cluster to bulk: Size dependent energetics of silica and silica-water interaction, He Y, Cao C, Wan YX, et al., JOURNAL OF CHEMICAL PHYSICS 124 (2): Art. No. 024722 JAN 14 2006

Elena Dolghih, Adrian E. Roitberg and Jeffrey L. Krause, "Fluorescence resonance energy transfer in dye-labeled DNA," Journal of Photochemistry and Photobiology A: Chemistry, submitted.

Calculation of energy-transfer rates between the 2-ring and 3-ring chromophores in a phenylacetylene dendrimer using the transition density cube method, W. Ortiz, A. E. Roitberg, J. L. Krause and B. P. Krueger, submitted to JCP.

Molecular dynamics study of azobenzene containing alkanethiol monolayer on gold surfaces, Sabri Alkis, Ping Jiang, Lin-Lin Wang, Adrian E. Roitberg, Jeffrey L. Krause and Hai-Ping Cheng, (submitted).

**PI Wai-Yim Ching**

Jun Chen, Yong-Nian Xu, Paul Rulis, Lizhi Ouyang, and W.Y. Ching "Ab-initio tensor experiments on Y-doped S=3 grain boundary in a-Al2O3", Acta Materialia, 53 [2], 403-410 (2005).

Paul Rulis, Jun Chen, Lizhi Ouyang and W.Y. Ching, Xiaotao Su, S.H. Garofalini, "Electronic structure and bonding of the intergranular glassy films (IGF) in polycrystalline Si3N4: Ab-initio studies and classical MD simulations", Phys. Rev. B71, 235317-1-10 (2005).

Jun Chen, L. Ouyang, and W.Y. Ching, "Molecular dynamic simulation of Y doped S=37 grain boundary in a-Al2O3", Acta Materialia, 53 [15], 4111-4120 (2005)

W.Y. Ching, Lizhi Ouyang , Paul Rulis and I. Tanaka, "Prediction of the x-ray absorption near-edge edge spectra of the new high-density phase of SiO2", Phys. Stat. Sol. (b): Rapid Research Letters, 242 (11), R94-R96 (2005).

Y.-N. Xu, P. Rulis and W.Y. Ching, "Electronic structure and bonding in a new quaternary Y3Si5N9O", Phys. Rev. B72, 113101-04 (2005).

J. Chen, P. Rulis, L. Ouyang, A. Misra, and W.Y. Ching, "Complex nonlinear deformation of a nanometer intergranular glassy films in silicon nitride ceramics", Phys. Rev. Lett. 95, 256103-07 (2005).

J. Buban, K. Matsunaga, J. Chen, N. Shibata, W.Y. Ching, T. Yamamoto, Y. Ikuhara, "Grain Boundary Strengthening in Alumina by Rare Earth Impurities", Science, 311, 212-215 (2006).

W.Y Ching and Paul Rulis, "Ab-initio calculation of the electronic and spectroscopic properties of spinel c-Sn3N4", Phys. Rev. B73, 045202-1-9 (2006).

W.Y. Ching, Paul Rulis, Yong-Nian Xu and L. Ouyang, "The electronic structure and spectroscopic properties of 3C, 2H, 4H, 6H, 15R, 21R polymorphs of SiC", Materials Science and Engineering A, 422 C1-2, 147-156 (2006).

A. Zerr, R. Riedel, T. Sikine, T. Lowther, W.Y. Ching, and I. Tanaka, "Recent Advances in New Nitrides", Advanced Materials, 18, 1-17 (2006).

**PI Mei-Yin Chou**

"Hydrogenation-Induced Insulating State in the Intermetallic Compound LaMg2Ni," K. Yvon, G. Renaudin, C. M. Wei and M. Y. Chou, Phys. Rev. Lett. 94, 066403 (2005).

"Persistent Superconductivity in Ultrathin Pb Films: A Scanning Tunneling Spectroscopy Study," D. Eom, S. Qin, M. Y. Chou, and C.K. Shih, Phys. Rev. Lett. 96, 027005 (2006).

"Lattice Dynamics and Thermodynamic Properties of NaAlH4," A. Peles and M. Y. Chou, Phys. Rev. B. 73, 184302 (2006).

"Beyond the Local Approximation to the Exchange-Correlation Energy: the Role of the Laplacian of the Density," A. C. Cancio and M. Y. Chou, Phys. Rev. B 74, 081202(R) (2006).

"Exchange-correlation energy in molecules: A variational quantum Monte Carlo study," C.R. Hsing, M. Y. Chou, and T. K. Lee, Phys. Rev. A 74, 032507 (2006).

"Enhanced Electron-Hole Interaction and Optical Absorption in a Silicon Nanowire," L. Yang, C. D. Spataru, S. G. Louie, and M. Y. Chou, submitted to Phys. Rev. Lett.

"Band-Structure Contribution to the Quantum Size Effect in Pb(100) Films, " C. M. Wei and M. Y. Chou, submitted to Phys. Rev. Lett.

**PI Daryl Chrzan**

C. Kisielowski, B. Freitag, X. Xu, S.P. Beckman and D.C. Chrzan, "Sub-angstrom imaging of dislocation core structure: how well are experiments comparable with theory?" Philosophical Magazine 86 (2006) 4575-4588.

S.P. Beckman and D.C. Chrzan, "Structure and energy of the partial dislocation cores in GaAs," Phys. Stat. Sol. B 243 (2006) 2122-2132.

S.P. Beckman and D.C. Chrzan, "The reconstruction energies of partial dislocations in cubic semiconductors," submitted to Physical Review B.

**PI Catherine Chuang**

Cameron-Smith, P, J-F Lamarque, P Connell, C Chuang, and F Vitt, 2006: Toward an Earth system model: atmospheric chemistry, coupling, and petascale computing, J. Phys.: Conf. Ser. 46 343-350, doi:10.1088/1742-6596/46/1/048

Kelly, JT, C.C. Chuang, and A.S. Wexler, 2006: Influence of Dust Composition on Cloud Droplet Formation, submitted to Atmospheric Environment.

Considine, D.B., D.J. Bergmann, and H. Liu, 2005: Sensitivity of Global Modeling Initiative chemistry and transport model simulations of radon-222 and lead-210 to input meteorological data, Atmospheric Chemistry and Physics Discussions, 5, 3389-3406.

Van Noije, T.P.C., H.J. Eskes, F.J. Dentener, D.S. Stevenson, K. Ellingsen, M.G. Schultz, O. Wild, M. Amann, C.S. Atherton, D.J. Bergmann, et al, 2006: Multi-model ensemble simulations of tropospheric NO2 compared with GOME retrievals for the year 2000, Atmospheric Chemistry and Physics Discussions, 6, 2965-3047.

Stevenson, D.S., F.J. Dentener, M. Schultz, K. Ellingsen, T. van Noije, G. Zeng, M. Amann, C. Atherton, D. Bergmann, et al, 2006: Multi-model ensemble simulations of present-day and near-future tropospheric ozone, J. Geophys. Res., 111, Art. No. D08301.

Dentener, F., D. Stevenson, C. Atherton, D. Bergmann, et al., 2006: Global Atmospheric Environment for the next Generation, Environmental Science and Technology, es0523845.

**PI Bruce Cohen**

Snyder, P.B., Wilson, H.R, Xu, and X.Q, "Progress in the peeling-ballooning model of edge localized modes: Numerical studies of nonlinear dynamics", Phys. Plasmas 12, 056115 (2005)

Nevins, W.M., Hammett, G.W., Dimits, A.M., Dorland, W., and Shumaker, D.E., Discrete Particle Noise in Particle-in-Cell Simulations of Plasma Microturbulence, Phys. Plasmas, 12, 122305, (Nov. 2005).

J. Candy and R.E. Waltz, "Velocity Space Resolution, entropy production, upwind dissipation in gyrokinetic simulations" Phys. Plasmas 13, 032310 (2006)

J. Candy, R.E. Waltz, S.E. Parker, and Y. Chen, "Relevance of the parallel nonlinearity in gyrokinetic simulation of tokamak plasmas", Phys. Plasmas 13, 0743501 (2006)

C. Estrada-Mila, J. Candy, R.E. Waltz, "Density peaking and turbulent pinch in DIIID", Phys.Plasmas 13, 074505 (2006)

C. Estrada-Mila, J. Candy, R.E. Waltz, "Turbulent transport of alpha particles in reactor plasma" General Atomics Report GA-A23514 accepted by Phys.Plasmas (2006)

J.E. Kinsey, R.E. Waltz, and J. Candy, "Effect of Shear and Safety Factor on Turbulent Transport in Nonlinear Gyrokinetic Simulations", Phys. Plasmas 13, 22305 (2006)

J.E. Kinsey "The GYRO nonlinear gyrokinetic simulation database" (2006), GYRO website: http://Fusion.gat.com/comp/parallel/

W. M. Nevins, J. Candy, S. Cowley, T. Dannert, A. Dimits, W. Dorland, C.Estrada-Mila, G.W. Hammett, F. Jenko, and D. E. Shumaker, "Characterizing electron gradient temperature via numerical simulations", submitted to Phys. Plasmas (2006)

R. E. Waltz, J. Candy, and C.C. Petty, " Projected profile similarity in gyrokinetic simulations of Bohm and gyroBohm scaled DIII-D L- and H-modes " Phys. Plasmas 13 , 072304 (2006)

R. E. Waltz, M.E. Austin, K.H. Burrell, and J. Candy, " Gyrokinetic simulations of off-axis minimum-q profile corrugations" General Atomics Report Phys. Plasmas 13, 052301 (2006)

R. E. Waltz, J, Candy, and M. Fahey, "Coupled ITG/TEM-ETG gyrokinetic simulations", GA-A25609 Oct 2006 to be submitted to Phys. Plasmas APS06 Edition.

Hooper, T.A. Kopriva, B.I. Cohen, D.N. Hill, H.S. McLean, R.D. Wood, S. Woodruff, C.R. Sovinec, "A Magnetic Reconnection Event in a Driven Spheromak," Phys. Plasmas 12, 092503 (2005), UCRL-JRNL-208364

"Gyrokinetic Simulations of ETG and ITG Turbulence", 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 , C. Estrada-Mila, Paper TH/P2-3, in the Proceedings of the 21st IAEA Fusion Conference, Chengdu, China, Oct. 18-21, 2006.

**PI Marvin Cohen**

Kevin T. Chan, Jay D. Sau, Peihong Zhang, Marvin L. Cohen, "Ab Initio Calculations of Phonon Splittings in Antiferromagnetic ZnCr2O4", submitted to Physical Review B.

Masa Ishigami, Jay Deep Sau, Shaul Aloni, Marvin L Cohen, and Alex Zettl, "Symmetry breaking in Boron Nitride nanotubes", Phys Rev B (in press).

Jay Deep Sau and Marvin L. Cohen, "Possibility of increased mobility in Ge-Sn alloys", submitted to Phys. Rev. B.

Y.-W. Son, J. Ihm, M.L. Cohen, S.G. Louie, and H.J. Choi, "Electrical switching in metallic carbon nanotubes," Phys. Rev. Lett. 95, 216602 (2005).

S.-H. Jhi, S.G. Louie, and M.L. Cohen, "Reentrant semiconducting behavior of zigzag carbon nanotubes at substitutional doping by oxygen dimers," Phys. Rev. Lett. 95, 226403 (2005).

Y.-W. Son, M. L. Cohen, and S. G. Louie, "Electrically tunable spin transport in single-wall nanotubes", submitted to Phys. Rev. Lett.

Y.-W. Son, M. L. Cohen, and S. G. Louie, "Half-metallic graphene nanoribbons", Nature (in press).

Y.-W. Son, M. L. Cohen, and S. G. Louie, "Energy gaps in graphene nanoribbons", submitted to Phys. Rev. Lett.

**PI Peter Cummings**

Ionescu, T. C., Qi, F., McCabe, C., Striolo, A., Kieffer A., and Cummings, P. T., Evaluation of Force Fields for Molecular Simulation of Polyhedral Oligomeric Silsesquioxanes, Journal of Physical Chemistry B, 110 (2006) 2502-2510.

Leng, Y. S., and Cummings, P. T., Hydration structure of water confined between mica surfaces, Journal of Chemical Physics 124 (2006) Art. No. 074711.

Zhao, X. C., Leng, Y. S. and Cummings, P. T., Self-assembly of 1,4-benzenedithiolate/ tetrahydrofuran on a gold surface: A Monte Carlo simulation study, Langmuir 22 (2006) 4116-4124.

Zhao, X. G. and Cummings, P. T., Molecular dynamics study of carbon nanotube oscillators revisited, Journal of Chemical Physics 124 (2006) Art. No. 134705.

Leng, Y. S., and Cummings, P. T., Shear dynamics of hydration layers, Journal of Chemical Physics, 125 (2006) Art. No. 104701.

Striolo, A., McCabe, C., and Cummings, P. T., Organic-Inorganic Telechelic Molecules: Solution Properties from Simulations, Journal of Chemical Physics, 125 (2006) Art. No. 104904.

Rivera, J. L., Starr, F. W., Paricaud, P., Cummings, P. T., Polarizable contributions to the surface tension of liquid water, Journal of Chemical Physics 125 (2006) Art. No. 094712.

Dyer, P. J. and Cummings, P. T., Hydrogen bonding and induced dipole moments in water: Predictions from the Gaussian charge polarizable model and Car-Parrinello molecular dynamics, Journal of Chemical Physics 125 (2006) Art. No. 144519.

Zhao, X. G., Cummings, P. T., and Lee, J. W., Single stranded DNA molecules translocation through nanoelectrode gaps, Biophysical J., submitted (2006).

Leng, Y.S., Dyer, P. J., Krstic;, P. S., Harrison, R. J., and Cumming, P. T., Calibration of chemical bonding between benzenedithiolate and gold: the effects of geometry and size of gold clusters, Molecular Simulation, accepted for publication (2006).

Predota, M., Cummings, P. T., Wesolowski, D. J., Electric double layer at the rutile (110) surface. 3. Inhomogeneous viscosity and diffusivity measurement by computer simulations, J. Phys. Chem. B, submitted (2006).

Payne, C. M., Zhao, X., Cummings, P. T., Molecular simulations of DNA transport in solution, Molecular Simulation, accepted for publication (2006).

Vlcek, L., Zhang, Z., Machesky, M. L., Fenter, P., Rosenqvist, J., Wesolowski, D. J., Anovitz, L. M., Cummings, P. T., Electric Double Layer at Metal Oxide Surfaces: Static Properties of the Cassiterite - Water Interface, Langmuir, submitted (2006).

Mamontov, E., Vlcek, L., Wesolowski, D. J., Cummings, P. T., Wang, W., Anovitz, L. M., Rosenqvist, J., Brown, C. M., Sakai, V. G., Diffusion dynamics of hydration water in nano-powder rutile and cassiterite on pico- to nano-second time scale studied by quasielastic neutron scattering and molecular dynamics simulations, J. Phys. Chem. B, submitted (2006).

Jingguang Che and Hai-Ping Cheng, K-doped self-assembly of C60 monolayer: Where are electrons? submitted Physical Review B, 2006.

R. Zikic, P. S. Krstic, X. G. Zhang, M. Fuentes Cabrera, J. Wells, X. Zhao, Characterization of the Tunneling Conductance Across DNA Bases, PHYSICAL REVIEW E 74 (1): Art. No. 011919 Part 1 JUL 2006. (This paper was selected by AIP for the August 14, 2006 issue of Virtual Journal of Nanoscale Science & Technology http://www.vjnano.org, as well as for the August 1, 2006 issue of Virtual Journal of Biological Physics Research http://www.vjbio.org).

X. G. Zhang, P. S. Krstic, R. Zikic, J. C. Wells, M. Fuentes Cabrera, First-principles transversal DNA conductance deconstructed, BIOPHYSICAL JOURNAL Letters 91 (1): L4-L6 JUL 2006.

He Y., Nunner T. S., Hirschfeld P. J., Local electronic structure of Bi2Sr2CaCu2O8 near oxygen dopants: A window on the high-Tc pairing mechanism, PHYSICAL REVIEW LETTERS 96 (19): Art. No. 197002 MAY 19 2006.

M. Fuentes-Cabrera, B. G. Sumpter, J. E. Sponer, J. Sponer, L. Petit, and J. C. Wells, heoretical Study on the Structure, Stability and Electronic Properties of the Guanine-Zn-Cytosine base-pair in M-DNA, submitted Journal of Physical Chemistry B (2006).

Zhang, J.W., Hebard, A. F., and Cheng, H.-P. , Simulation of anomalous Hall effect in Fe-C60 monolayer thin film, submitted Physical Review B, 2006.

Molecular dynamics study of azobenzene containing alkanethiol monolayer on gold surfaces, Sabri Alkis, Ping Jiang, Lin-Lin Wang, Adrian E. Roitberg, Jeffrey L. Krause and Hai-Ping Cheng, submitted 2006.

Non-equilibrium quantum transport properties of organic molecules on silicon, W. Lu, V. Meunier, and J. Bernholc, Phys. Rev. Lett. 95, 206805 (2005).

Surface reconstructions of TiO2 (110) driven by suboxides, K. Park, M. H. Pan, V. Meunier, and E.W. Plummer, Phys. Rev. Lett., 96, 226105 (2006)

Scanning Frequency Mixing Microscopy of High Frequency Transport Behavior at Electroactive Interfaces, Brian J. Rodriguez, Stephen Jesse, Vincent Meunier, and S. Kalinin , Appl. Phys. Lett. 88 (14), 143128 (2006)

Adsorption, desorption, and dissociation of benzene on TiO2 (110) and Pd/TiO2_(110): Experimental characterization and first-principles calculations, J. Zhou, S. Dag, S. D. Senanayake, B. C. Hathorn, S. V. Kalinin, V. Meunier, D. R. Mullins, S. H. Overbury, and A. P. Baddorf, Phys. Rev. B, in press (2006)

Optimizing the Electronic Properties of carbon nanotubes using Amphoteric Doping, B. G. Sumpter and V. Meunier, Taylor & Francis , in press (2006)

Density Functional Theory Studies of Quantum Transport in Molecular Systems, V. Meunier, W. Lu, B.G. Sumpter, and J Bernholc, Int. J. Quantum Chem., in press (2006)

Atomic Scale Design of Nanostructures, J. Bernholc, W. Lu, S. M. Nakhmanson, P. H. Hahn, V. Meunier, M. Buongiorno Nardelli, and W. G. Schmidt, Molecular Physics, in press (2006)

Structural Characterization of Carbon Nanotubes, Ph. Lambin, J.F. Colomer, L. Henrard, A. Lucas, and V. Meunier, Microscopy and Microanalysis Vol 12, Suppl 2 (2006) 570-571

Covalent 2D and 3D Networks from 1D Nanostructures: Designing New Materials, Jose Romo-Herrera, Mauricio Terrones, Humberto Terrones, Sefa Dag , and Vincent Meunier, submitted (2006)

A new class of self-assembled molecular wires, B. G. Sumpter, V. Meunier, E. F. Valeev, A. J. Lampkins, L. Hengfeng, and R.C. Castellano, submitted (2006)

Nonvolatile memory element based on carbon nanotubes intercalated with organic molecules, V. Meunier, S. K. Kalinin, B.G. Sumpter, submitted (2006)

**PI Larry Curtiss**

"Quantum Chemical Study of Mechanisms for Oxidative Dehydrogenation of Propane on Vanadium Oxide", P. C. Redfern, P. Zapol, M. Sternberg, S. P. Adiga, S. A. Zygmunt, and L. A. Curtiss, Journal of Physical Chemistry, B 110 8363 (2006).

"Atomistic simulations of amorphous alumina surfaces", S. P. Adiga, P. Zapol, L. A. Curtiss, Phys. Rev. B 74 064204 (2006).

"Atomistic simulations of nanoporous anodic alumina surfaces", S. P. Adiga, P. A. Curtiss, Mater. Res. Soc. Symp. Proc. Vol. 900E 0900-O12-17.1 (2006).

## D

**PI Ronald Davidson**

"Collective Temperature Anisotropy Instabilities in Intense Charged Particle Beams", E. A. Startsev, APS-DPP06 invited talk, in preparation for submission to Physics of Plasmas (2006).

"Two-Stream Instability for a Longitudinally-Compressing Charged Particle Beam", E. A. Startsev and R. C. Davidson, Physics of Plasmas 13, submitted for publication (2006).

"Multspecies Weibel Instability for Intense Charged Particle Beam Propagation Through Background Plasma", R. C. Davidson, M. Dorf, I. D. Kaganovich, H. Qin, A. B. Sefkow and E. A. Startsev, D. R. Welch, D. V. Rose and S. M. Lund, Nuclear Instruments and Methods in Physics Research A, in press (2006).

"Optimized Simultaneous Transverse and Longitudinal Focusing of Intense Ion Beam Pulses for Warm Dense Matter Applications", A. Sefkow, R.C. Davidson, I.D. Kaganovich, E.P. Gilson (PPPL), P.K. Roy, S.S. Yu, P.A. Seidl, D.R. Welch D.V. Rose, J.J. Barnard, Nuclear Instruments and Methods in Physics Research A, submitted for publication (2006).

"Nonlinear Delta-f Particle Simulations of Collective Effects in High-Intensity Bunched Beams", H. Qin, R. C. Davidson and E. A. Startsev, Nuclear Instruments and Methods in Physics Research A, submitted for publication (2006).

"Dynamic Stabilization of the Two-Stream Instability During Longitudinal Compression of Intense Charged Particle Beam Propagation Through Background Plasma", E. A. Startsev and R. C. Davidson, Nuclear Instruments and Methods in Physics Research A, submitted for publication (2006).

"Effects of Finite Pulse Length, Magnetic Field, and Gas Ionization on Ion Beam Pulse Neutralization by Background Plasma", I. D. Kaganovich, A. B. Sefkow, E.A. Startsev, R. C. Davidson and D. R. Welch, Nuclear Instruments and Methods in Physics Research A, submitted for publication (2006).

E. V. Belova, R. C. Davidson, H. Ji, M. Yamada, Advances in the numerical modeling of field-reversed configurations, Phys. Plasmas 13, 056115 (2006).

E. V. Belova, R. C. Davidson, H. Ji, M. Yamada, C. D. Cothran, M. R. Brown, M. J. Schaffer, Numerical study of the formation, ion spin-up and nonlinear stability properties of field-reversed configurations, Nuclear Fusion 46, 162 (2006).

Belova, E.V.; Davidson, R.C.; Ji, H.; Yamada, M.; Gerhardt, S.P., "Effects of energetic beam ions on stability properties of field reversed configuration", Proceedings of the 21th Int. Conf. Chengdu, 2006, paper IAEA-TH/P3-16 (International Atomic Energy Agency, Vienna, 2006).

S.P. Gerhardt, E. Belova, M. Inomoto, M. Yamada, H. Ji, Y. Ren and A. Kuritsyn, Equilibrium and stability studies of oblate field reversed configurations in the Magnetic Reconnection Experiment, Phys. Plasmas, in press (2006).

S. P. Gerhardt, M. Inomoto, E. Belova, M. Yamada, H. Ji, Y. Ren, Improved stability for oblate field reversed configurations through passive stabilization and plasma shaping, submitted to Phys. Rev. Lett. (2006).

S. P. Gerhardt, M. Inomoto, E. Belova, M. Yamada, H. Ji, Y. Ren, Studies of free-boundary field-reversed configurations with improved stability in the Magnetic Reconnection Experiment, Proceedings of the 21th Int. Conf. Chengdu, 2006, paper IAEA-IC/P7-13 (International Atomic Energy Agency, Vienna, 2006).

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, submitted to J. Fusion Energy (2006).

M. Inomoto, S. P. Gerhardt, M. Yamada, H. Ji, E. Belova, Y. Ren, and A. Kuritsyn, Hall effect on magnetic reconnection during counter-helicity spheromak merging experiment, Phys. Rev. Lett. 97, 135002 (2006).

M. Yamada, H. Ji, E. Belova, S. P. Gerhardt, R. C. Davidson, and D. Mikkelsen, A Self-organized Plasma with Induction, Reconnection, and Injection Techniques: the SPIRIT concept for Field Reversed Configuration Research, submitted to Plasma and Fusion Research in Japanese Society of Plasma Fusion (2006).

M. R. Brown, C. D. Cothran, J. Fung, M. Schaffer, E. Belova, M. Chang, and J. Horwitz, Dipole trapped shperomak in a prolate flux conserver, submitted to Phys. Plasmas (2006).

**PI Eric DeWeaver**

DeWeaver, E., and C. M. Bitz, 2004: Atmospheric circulation and Arctic sea ice in CCSM3 at medium and high resolution. J. Climate, 19, 2415-2436.

Lorenz, D. J., and E. T. DeWeaver, 2006: Tropopause height and the zonal-mean zonal wind response to global warming in IPCC scenario integrations. J. Geophys. Res., submitted.

Lorenz, D. J., and E. T. DeWeaver, 2006: The response of the extratropical hydrological cycle to global warming. J. Climate, accepted.

**PI David Dean**

Ab initio coupled-cluster study of 16O, M. Wloch, D.J. Dean, J.R. Gour, M. Hjorth-Jensen, K. Kowalski, T.Papenbrock, and P. Piecuch, Phys. Rev. Lett. 94, 212501 (2005).

Thermal properties of N=40 isotopes, K. Langanke, D.J. Dean, and W. Nazarewicz, Nucl. Phys A 757, 360 (2005).

Quadrupole deformation of the self-conjugate nucleus 72Kr, A. Gade, D. Bazin, A. Becerril, C.M. Cambell, J.M. Cook, D.J. Dean, D.-C. Dinca, T. Glasmacher, G.W. Hitt, M.E. Howard, W.F. Mueller, H. Olliver, J.R. Terry, and K. Yoneda, Phys. Rev. Lett. 95, 022502 (2005); and Erratum, Phys. Rev. Lett. 96, 189901 (2006).

Coupled-cluster calculations for valence systems around 16O, J.R. Gour, P. Piecuch, M. Hjorth-Jensen, M. Wloch, and D.J. Dean, Phys. Rev. C 74, 024310 (2006).

Shell model Monte Carlo method in the pn-formalism and applications to the Zr and Mo isotopes, C. Ozen and D.J. Dean, Phys. Rev. C73, 014302 (2006).

High-spin intruder states in the fp-shell nuclei and isoscalar proton-neutron correlations, G. Stoitcheva, W. Satula, W. Nazarewicz, D.J. Dean, M. Zalewski, and H. Zdunczuk, Phys. Rev. C 73, 061304 (2006).

Correlations and effective interactions in nuclear matter, P. Bozek, D.J. Dean, and H. Muther, Phys. Rev. C 74, 014303 (2006)

Complex coupled-cluster approach to an ab initio description of open quantum systems, G. Hagen, D.J. Dean, M. Hjorth-Jensen, and T. Papenbrock, submitted to Phys. Rev. Lett. (2006).

**PI James Demmel**

Demmel, J., Hida, Y., Kahan, W., Li, X. S., Mukherjee, S., and Riedy, E. J. Error bounds from extra-precise iterative refinement. ACM Transactions on Mathematical Software. 32, 2 (Jun. 2006), 325-351. DOI:10.1145/1141885.1141894

Marques, O., Riedy, E. J., and Voemel, C. Benefits of IEEE-754 Features in Modern Symmetric Tridiagonal Eigensolvers. SIAM Journal on Scientific Computing. 28, 5 (2006), 1613-1633. DOI:10.1137/050641624

**PI Dimitre Dimitrov**

D. A. Dimitrov, R. E. Giacone, D. L. Bruhwiler, R. Busby, J. R. Cary, C. G. R. Geddes, E. Esarey, and W. P. Leemans, "Coupling of Laser Energy into Plasma Channels", submitted for publication to the Physics of Plasmas Journal.

**PI Chris Ding**

Y. He and C. Ding, Coupling Multi-Component Models with MPH on Distributed Memory Computer Architectures., International Journal of High Performance Computing Applications, to appear in August 2005.

A.P. Craig, R.L. Jacob, B. Kauffman, T. Bettge, J. Larson, E. Ong, C. Ding, and Y. He, CPL6: The New Extensible, High-Performance Parallel Coupler for the Community Climate System Model, International Journal of High Performance Computing Applications, to appear in August 2005.

**PI Sebastian Doniach**

Jan Lipfert and Sebastian Doniach "Unzipping the Polar Zipper": Molecular Dynamics Simulations of Force-Induced Beta-Amyloid Disassembly and Implications for Future Experiments. submitted

Jan Lipfert, Joel Franklin, Fang Wu and Sebastian Doniach Protein Misfolding and Amyloid Formation for the Peptide GNNQQNY from Yeast Prion Protein Sup35: Simulation by Reaction Path Annealing. J. Mol. Biol. 349:648-658 (2005)

Chu, V.B., Y. Bai, J. Lipfert, D. Herschlag, and S. Doniach. Evaluation of Ion Binding to DNA Duplexes Using a Size-Modified Poisson-Boltzmann Theory. 2006. Submitted to Biophysical Journal.

Bai, Y., K. Travers, V. Chu, J. Lipfert, S. Doniach, D. Herschlag. Quantitative and comprehensive decomposition of the ion atmosphere around nucleic acids. 2006. Submitted to Journal of the American Chemical Society.

**PI William Dorland**

A Macnab, G Vahala, L Vahala, J Carter, M Soe and W Dorland, "Non-local closures and parallel performance of lattice Boltzmann models for some plasma physics problems", Physica A, Vol 326, p 48, 2006.

C M Roach, et al., "Microstability physics as illuminated in the spherical tokamak", Plasma Phys. Controll. Fusion, Vol 47, p B323 (2005).

N F Loureiro, S C Cowley, W Dorland, M G Haines, and A A Schekochihin, "X-point collapse and saturation in the nonlinear tearing mode reconnection", PRL, Vol 95, p 235005, (2005).

W M Nevins, G W Hammett, A M Dimits, W Dorland, and D E Shumaker, "Discrete particle noise in particle-in-cell simulations of plasma microturbulence", PoP, Vol 12, p 122305 (2005).

M H Redi, W Dorland, et al., "Microturbulent drift mode stability before internal transport barrier formation in the Alcator C-Mod radio frequency heated H-mode", PoP, Vol 12, p 072519 (2005).

B N Rogers and W Dorland, "Noncurvature-driven modes in a transport barrier", PoP, Vol 12, 062511 (2005).

M. A. Shay, J. F. Drake and W. Dorland, Equation Free Projective Integration: A Multiscale Method applied to an Ion Acoustic Wave, J. Comp. Phys., submitted (2006).

P. Cassak, M. A. Shay and J. F. Drake, A catastrophe model for the onset of fast magnetic reconnection, Phys. Rev. Lett. 95, 235002, 2005 (A Physical Review Focus article was written on this paper).

J. F. Drake and M. A. Shay, The fundamentals of collisionless reconnection, in Reconnection of Magnetic Fields: Magnetohydrodynamics and Collisionless Theory and Observations, J. Birn and E. R. Priest, editors, Cambridge University Press (Cambridge, UK), 2005 (book chapter).

J. F. Drake, H. Che, M. A. Shay and M. Swisdak, Electron acceleration from contracting magnetic islands during reconnection, Nature 443, 553, 2006.

J. F. Drake, M. Swisdak, K. M. Schoeffler, B. N. Rogers and S. Kobayashi, Formation of secondary islands during magnetic reconnection, Geophys. Res. Lett. 33, L13105, 2006.

P. Cassak, J. F. Drake and M. A. Shay, A model for spontaneous onset of fast reconnection, Astrophys. J. Lett. 644, L145, 2006.

Edge localized modes and edge transport in spherical tokamaks R. G. Kleva and P. N. Guzdar, Phys. Plasmas 12, 052518 (2005)

Repetitive transport bursts in simulations of edge localized modes R. G. Kleva and P. N. Guzdar, Phys. Plasmas 13, 072509 (2006)

Zonal flow, sawteeth and the time period between edge localized transport bursts in tokamaks, R. G. Kleva and P. N. Guzdar, submitted to Phys. Plasmas.

**PI John Drake**

Cameron-Smith, J. Taylor, P. Jones, D. Erickson, R. Jacob, and J.-F. Lamarque, ``Science Requirements for Coupling Tracers in CCSM3,'' Technical report UCRL-MI-220728, 2005

J.-F. Lamarque, J. Kiehl, G. Brasseur, T. Butler, P. Cameron-Smith, W. D. Collins, W. J. Collins, C. Granier, D. Hauglustaine, P. Hess, E. Holland, L. Horowitz, M. Lawrence, D. McKenna, P. Merilees, M. Prather, P. Rasch, D. Rotman, D. Schindell, and P. Thornton, ``Assessing future nitrogen deposition and carbon cycle feedback using a multi-model approach: Analysis of nitrogen deposition'', J. Geophys. Res., vol 10, D19303, doi:10.1029/2005JD005825, 2005.

Lamarque, J.-F., J. T. Kiehl, P. G. Hess, W. D. Collins, L. K. Emmons, P.Ginoux, C. Luo, and X. X. Tie, Response of a coupled chemistry-climate model to changes in aerosol emissions: Global impact on the hydrological cycle and the tropospheric burdens of OH, ozone and NOx. Geophys. Res. Lett., Vol. 32, No.16, L16809, 2005.

**PI German Drazer**

Zhigang Li and German Drazer, Fluid Enhancement of Particle Transport in Nanochannels, Physics of Fluids, 2006 (in press).

Zhigang Li and German Drazer, Separation of suspended Particles by Arrays of Obstacles in Microfluidic Devices, Physical Review Letters 2006 (submitted). (arXiv:cond-mat/0606732)

**PI Barry Dunietz**

Corneliu Buda and Barry D Dunietz: Hydrogen physisorption on the organic linker in metal organic framworks: Ab initio computational study JPCB, 2006, 110, 10479.

## E

**PI Charlotte Elster**

Three-Body Scattering at Intermediate Energies, H. Liu, Ch. Elster, W. Gloeckle, Phys. Rev. C72, 054003 (2005).

Three-Body Elastic and Inelastic Scattering at Intermediate Energies, H. Liu, Ch. Elster, W. Gl\"ockle, nucl-th/0610006, to appear in Nuclear Physics A.

**PI Eric Esarey**

D.A. Dimitrov, R.E. Giacone, D.L. Bruhwiler, R. Busby, J.R. Cary, C.G.R. Geddes, E. Esarey and W.P. Leemans, "Coupling of Laser Energy into Plasma Channels," Phys. Plasmas (2006), submitted.

E. Esarey, C.B. Schroeder, E. Michel, B.A. Shadwick, C.G.R. Geddes, and W.P. Leemans, "Thermal effects in plasma-based accelerators", Physics of Plasmas (2006), submitted.

G. Fubiani, E. Esarey, C. B. Schroeder, and W. P. Leemans, "Improvement of electron beam quality in optical injection schemes using negative plasma density gradients," Phys. Rev. E 73, 026402 (2006).

G. Fubiani, J. Qiang, E. Esarey, W. P. Leemans, and G. Dugan, "Space charge modeling of dense electron beams with large energy spreads," Phys. Rev. ST Accel. Beams 9, 064402 (2006).

P. Messmer and D.L. Bruhwiler, "Simulating laser pulse propagation and low-frequency wave emission in capillary plasma channel systems with a ponderomotive guiding center model," Phys. Rev. ST Accel. Beams 9, 031302 (2006).

W. P. Leemans, B. Nagler, A. J. Gonsalves, Cs. Toth, K. Nakamura, C. G. R. Geddes, E. Esarey, C. B. Schroeder, S. M. Hooker, "GeV electron beams from a centimetre-scale accelerator," Nature Physics, V 2 (2006), p. 696.

C. G. R. Geddes, Cs. Toth, J. van Tilborg, E. Esarey, C. B. Schroeder, J. Cary, and W. P. Leemans, "Guiding of relativistic laser pulses by preformed plasma channels, "Phys. Rev. Lett. 95, 145002 (2005).

R.M.G.M. Trines, L.P.J. Kamp, T.J. Schep, F.W. Sluijter, W.P. Leemans, E.H. Esarey, "On the effect of laser and plasma parameters on stimulated Raman scattering and fast-electron generation," J. Plasma Phys. 71, 411-433 (2005).

## F

**PI Roland Faller**

Jayeeta Ghosh, Brian Y. Wong, Qi Sun, Florence R.Pon, and Roland Faller: Simulations of Glasses: Multiscale Modeling and Density of States Monte Carlo Simulations Molecular Simulation 32(3-4) 175-184 (2006)

Jayeeta Ghosh, and Roland Faller: A comparative molecular simulation study of the glass former ortho-terphenyl in bulk and free standing films J Chem Phys 125(4) 044506 (2006)

Jayeeta Ghosh and Roland Faller Modelling of the Glass Transition of Ortho-terphenyl in Bulk and Thin Films in Mechanics of Nanoscale Materials and Devices, Mater. Res. Soc. Symp. Proc. 924E (Warrendale, PA, 2006, Editors A. Misra, J.P. Sullivan, H. Huang, K. Lu, S. Asif) paper 0924-Z03-21

Qi Sun, and Roland Faller: Phase Separation in Polyisoprene/Polystyrene Blends by a Systematically Coarse-Grained Model submitted

**PI William Fawley**

"Optimization Studies of the FERMI at ELETTRA FEL Design" (with G. DeNinno, W.S. Graves, and G.E.Penn). 2005, Proceedings 2005 International FEL Conference, pp. 59-62.

"LCLS X-Ray FEL Output Performance in the Presence of Highly Time-Dependent Undulator Wakefields" (with K.L.F. Bane and 5 others), 2005, Proceedings 2005 International FEL Conference, pp. 510-513.

**PI Andrew Felmy**

Eric .J. Bylaska (2006) Estimating the Thermodynamics and Kinetics of Chlorinated Hydrocarbon Degradation, submitted to a special issue of Theoretical Chemistry Accounts, Ed. C.J. Cramer. This issue is devoted to perspective articles and entitled "New Perspectives in Theoretical Chemistry". 35 young scientists were asked to contribute, mainly those whose publications began to appear in earnest in the ~1995-1999 time frame, vol. 116 (1-3): 281-296 AUG 2006

Eric. J. Bylaska, Kiril Tsemekhman, and Fei Gao (2005) New Development of Self-Interaction Corrected DFT for Extended Systems Applied to the Calculation of Native Defects in 3C-SiC, submitted for publication in the Topical Issue of the Physica Scripta titled New Directions of Advanced Computer Simulations and Experiments in Fusion-Related Plasma-Surface Interactions (PSIF), T124: 86-90 MAY 2006

Eric J. Bylaska, Michel Dupuis, and Paul G. Tratnyek (2006), Electron Transfer Reactions of Polychlorinated Ethylenes: Concerted Versus Stepwise Cleavages, Journal of Physical Chemistry, A. submitted.

James R. Rustad, J. Wang, and E.J Bylaska (2006) The Effect of Solvation on Isotopic Fractionation Between B(OH)3 and B(OH)4- in Aqueous Solution, submitted to Journal of Chemical Physics.

**PI Charlotte Fischer**

"Relativistic energy levels, lifetimes, and transition probabilities for the Na-like to Ar-like sequences". C. Froese Fischer, G. Tachiev, and A., Irimia Atom. Data Nucl. Data Tables 92, 607-812 (2006).

**PI Graham Fleming**

Evidence for wavelike energy transfer: Quantum coherence in photosynthetic complexes, G.S. Engel, T.R. Calhoun, E.L. Read, T.K. Ahn, T. Mancal, Y.C. Cheng, R.E. Blankenship, G.R. Fleming. Nature. Submitted (2006).

**PI Michael Fox-Rabinovitz**

Fox-Rabinovitz, M. S., E. H. Berbery, L.L. Takacs, and R.C. Govindaraju, 2005: A multiyear ensemble simulation of the U.S. climate with a stretched-grid general circulation model, Mon. Wea. Rev., Vol. 133, No. 9, pp. 2505-2525.

Fox-Rabinovitz, M.S., J. Cote, M. Deque, B. Dugas, J. McGregor, 2006: International SGMIP Stretched-Grid Model Intercomparison Project): Multi-model ensemble results for prognostic fields and precipitation, J. Geophys. Res., 111, D16104, doi:10.1029/2005JD006520..

Krasnopolsky, V.M., M.S. Fox-Rabinovitz, and D.V. Chalikov, 2005: New Approach to Calculation of Atmospheric Model Physics: Accurate and Fast Neural Network Emulation of Long Wave Radiation in a Climate Model, Mon. Wea. Rev., vol. 133, No. 5, pp. 1370-1383.

Krasnopolsky, V.M., and M.S. Fox-Rabinovitz, 2006a: A New Synergetic Paradigm in Environmental Numerical Modeling: Hybrid Models Combining Deterministic and Machine Learning Components, Ecological Modeling, 191, pp. 5-18.

Krasnopolsky, V.M., and M.S. Fox-Rabinovitz, 2006b: Complex hybrid models combining deterministic and machine learning components for numerical climate modeling and weather prediction, Neural Networks 19, 122-134.

**PI Alberto Franceschetti**

A. Franceschetti and M.C. Troparevsky, "Screening of Point Charges in Si Quantum Dots", Phys. Rev. B 72, 165311 (2005).

M.C. Troparevsky and A. Franceschetti, "Radiative Recombination of Charged Excitons and Multiexcitons in CdSe Quantum Dots", Appl. Phys. Lett. 87, 263115 (2005).

M. Califano, A. Franceschetti and A. Zunger, "Temperature Dependence of Excitonic Radiative Decay in CdSe Quantum Dots: The Role of Surface Hole Traps", Nano Letters 5, 2360 (2005).

A. Zunger, A. Franceschetti, G. Bester, W. B. Jones, K. Kim, P.A. Graf, L.W. Wang, A. Canning, O. Marques, C. Voemel, J. Dongarra, J. Langou and S. Tomov, "Predicting the Electronic Properties of 3D, Million-Atom Semiconductor Nanostructure Architectures", J. Phys. Conf. Ser. 46, 292 (2006).

A. Franceschetti, J.M. An, and A. Zunger, "Impact Ionization Can Explain Carrier Multiplication in PbSe Quantum Dots", Nano Letters 6, 2191 (2006).

G.A. Narvaez, G. Bester, A. Franceschetti and A. Zunger, "Excitonic Exchange Effects on the Radiative Decay Time of Monoexcitons and Biexcitons in Quantum Dots", Phys. Rev. B (in press).

M. Califano, A. Franceschetti and A. Zunger, "Lifetime and polarization of the radiative decay of excitons, biexcitons and trions in CdSe nanocrystal quantum dots" (submitted).

M.C. Troparevsky and A. Franceschetti, "The Optimized Configuration Interaction Method for Electronic Excitations in Semiconductor Nanostructures" (submitted).

**PI Joachim Frank**

Wen Li, Jayati Sengupta, Bimal K. Rath, and Joachim Frank (2006) Functional Conformations of the L11-Ribosomal RNA Complex Revealed by Correlative Analysis of Cryo-EM and Molecular Dynamics Simulations. RNA.12(7):1240-53.

**PI Stuart Freedman**

"Search for the Invisible Decay of Neutrons with KamLAND", KamLAND Collaboration, Phys. Rev. Lett. 96, 101802 (2006).

"Experimental Investigation of Geologically Produced Antineutrinos with KamLAND", KamLAND Collaboration, Nature 436, 499 (2005).

**PI Arthur Freeman**

Charge compensation and mixed valency in LaAlO3/SrTiO3 heterointerfaces determined by the FLAPW method, Min Sik Park, S. H. Rhim, and Arthur J. Freeman, Phys. Rev. B, accepted for publication.

**PI Alex Friedman**

R. H. Cohen, A. Friedman, M. Kireeff Covo, S. M. Lund, A. W. Molvik, F. M. Bieniosek, P. A. Seidl, J.-L. Vay, P. Stoltz, S. Veitzer, "Simulating Electron Clouds in Heavy-Ion Accelerators," Phys. Plasmas 12, 056708 (2005).

A. Friedman, "Overview of Theory and Simulation in the Heavy Ion Fusion Science Virtual National Laboratory," Nuclear Instruments and Methods in Physics Research A (to be published), LBNL-60935.

D. P. Grote, "Design and Modeling of the Multi-Beamlet Injector," Nuclear Instruments and Methods in Physics Research A (to be published), LBNL-59923.

D. P. Grote, "Simulation of Integrated Beam Experiment Design," Nuclear Instruments and Methods in Physics Research A 544, 360 (2005).

S. M. Lund, D. P. Grote, E. P. Lee, R. C. Davidson, "Simulations of Beam Emittance Growth from the Collective Relaxation of Space-Charge Non-uniformities," Nuclear Instruments and Methods in Physics Research A 544, 472 (2005).

S. M. Lund, S. H. Chilton, E. P. Lee, "Efficient Computation of Matched Solutions of the Kv Envelope Equation for Periodic Focusing Lattices," Phys. Rev. ST Accel. Beams 9, 064201 (2006).

S. M. Lund,J. J. Barnard, B. Bukh, S. R. Chawla, S. H. Chilton, "Space-Charge Transport Limits of Ion Beams in Periodic Quadrupole Focusing Channels," Nuclear Instruments and Methods in Physics Research A (to be published), LBNL-59927.

W. M. Sharp, R. H. Cohen, A. Friedman, D. P. Grote, J.-L. Vay, and I. Haber, "Simulating Electron Clouds in High-Current Ion Accelerators with Solenoid Focusing," Nuclear Instruments and Methods in Physics Research A (to be published), LBNL-61683.

W. M. Sharp, J. J. Barnard, D. P. Grote, C. M. Celata, S. S. Yu, D. V. Rose, D. R. Welch, "Simulation of Drift-Compression for Heavy-Ion-Fusion," Nuclear Instruments and Methods in Physics Research A 544, 398 (2005).

J.-L. Vay, P. Colella, J. W. Kwan, P. McCorqudale. D. Serafini, A. Friedman, D. P. Grote, G. A. Westenskow, J.-C. Adam, A. Heron, and I. Haber, "Application of Adaptive Mesh Refinement to PIC Simulation in Heavy Ion Fusion," Nuclear Instruments and Methods in Physics Research A 544, 347 (2005).

**PI Inez Fung**

Fung, I., S.C. Doney, K. Lindsay, and J. John (2005). Evolution of carbon sinks in a changing climate. Proc. Nat. Acad. Sci. (USA), 102, 11201-11206.

Doney, S.C., K. Lindsay, I. Fung and J. John (2006). Natural Variability in a Stable, 1000 Year Global Coupled Climate-Carbon Cycle Simulation. J Climate, 19(13), 3033-3054

Friedlingstein, P.,P. Cox, R. Betts, L. Bopp, W. von Bloh, V. Brovkin, S. Doney, M. Eby, I. Fung, B. Govindasamy, J. John, C. Jones, F. Joos, T. Kato, M. Kawamiya, W. Knorr, K. Lindsay, H. D. Matthews, T. Raddatz, P. Rayner, C. Reick, E. Roeckner, K.-G. Schnitzler, R. Schnur, K. Strassmann, S. Thompson, A. J.Weaver, C. Yoshikawa, and N. Zeng (2006) Climate carbon cycle feedback analysis, results from the C4MIP model intercomparison. J. Climate 19(14): 3337-3353.

Lee, J.-E., R. Oliviera, T. Dawson and I. Fung (2006). Root functioning modifies seasonal climate. Proc. Nat. Acad. Sci. (USA), 102, 17576-17581.

Koven C. D., I. Fung (2006), Inferring dust composition from wavelength-dependent absorption in Aerosol Robotic Network (AERONET) data, J. Geophys. Res., 111, D14205, doi:10.1029/2005JD006678.

Lam, P.J., J.K.B. Bishop, C. C. Henning, M. A. Marcus, G. Waychunas, and I. Fung (2006). Wintertime phytoplankton bloom in the Subarctic Pacific supported by continental margin iron. Global Biogeochem Cycles, 20(1), GB1006, doi: 10.1029/2005GB002557.

**PI Miguel Furman**

M. A. Furman and V. H. Chaplin, "Update on electron-cloud power deposition for the LHC arc dipoles," LBNL-59062/CBP Note 723, January 30, 2006; PRST-AB 9, 034403 (2006). http://prst-ab.aps.org/pdf/PRSTAB/v9/i3/e034403

M. A. Furman, "A preliminary assessment of the electron cloud effect for the FNAL main injector upgrade," LBNL-57634-JArt/CBP Note-737, June 22, 2006; to be published by invitation in the Focus Issue "Accelerator and Beam Physics" of the New Journal of Physics.

## G

**PI Giulia Galli-Gygi**

"Adhesion of single functional groups to individual carbon nanotubes: Electronic effects probed by ab-initio calculations", G.Cicero, J.C.Grossman and G.Galli Phys. Rev. B 74, 035425 (2006).

"First principles simulations of the structural and electronic properties of silicon nanowires", T.Vo, A.J.Williamson and G.Galli , Phys. Rev. B 74, 045116 (2006).

"Surface structure of CdSe rods revealed by combined X-ray absorption fine structure measurements and ab-initio calculations", D.Aruguete, M.A. Marcus, L-Shi. Li, A.J.Williamson, S.Fakra, F.Gygi,G. Galli, A.P.Alivisatos (submitted).

**PI Alan Garfinkel**

Sato D, Shiferaw Y, Garfinkel A, Weiss JN, Qu Z, Karma A.Spatially discordant alternans in cardiac tissue: role of calcium cycling. Circ Res. 2006 Sep 1;99(5):520-7.

Baher A, Qu Z, Hayatdavoudi A, Lamp ST, Yang MJ, Xie F, Turner S, Garfinkel A, Weiss JN. Short-term Cardiac Memory and Mother Rotor Fibrillation. Am J Physiol Heart Circ Physiol. 2006 Aug 4.

Weiss JN, Karma A, Shiferaw Y, Chen PS, Garfinkel A, Qu Z. From pulsus to pulseless: the saga of cardiac alternans. Circ Res. 2006 May 26;98(10):1244-53.

Qu Z, Garfinkel A, Weiss JN. Vulnerable window for conduction block in a one-dimensional cable of cardiac cells, 1: single extrasystoles. Biophys J. 2006 Aug 1;91(3):793-804.

Qu Z, Garfinkel A, Weiss JN. Vulnerable window for conduction block in a one-dimensional cable of cardiac cells, 2: multiple extrasystoles. Biophys J. 2006 Aug 1;91(3):805-15.

Weiss JN, Qu Z, Chen PS, Lin SF, Karagueuzian HS, Hayashi H, Garfinkel A, Karma The dynamics of cardiac fibrillation. Circulation. 2005 Aug 23;112(8):1232-40.

**PI Bruce Garrett**

S. Du and J. S. Francisco, G. K. Schenter, T. D. Iordanov, B. C. Garrett, M. Dupuis, and J. Li, "The OH radical-H2O molecular interaction potential", J. Chem. Phys. 124, 224318 (2006)

K. A. Ramazan, L. M. Wingen, Y. Miller, G. M. Chaban, R. B. Gerber, S. S. Xantheas and B. J. Finlayson-Pitts, "New Experimental and Theoretical Approach to the Heterogeneous Hydrolysis of NO2: Key Role of Molecular Nitric Acid and Its Complexes", Journal of Physical Chemistry A 110, 6886 (2006)

S. S. Xantheas, T. A. Blake, "The Structure, Anharmonic Spectra and Puckering Barrier of Cyclobutane: A Theoretical Study", Journal of Physical Chemistry A 110, 10487 (2006)

S .S. Xantheas, "Anharmonic vibrational spectra of hydrogen bonded clusters: Comparison between higher energy derivative and mean-field grid based methods", Roger E. Miller memorial issue (invited), International Reviews of Physical Chemistry 25, 719 (2006)

S. Bulusu, S. Yoo, E. Apr`, S. S. Xantheas, X. C. Zeng, "The lowest energy structures of water clusters (H2O)11 and (H2O)13", Journal of Physical Chemistry A 110, 11781 (2006)

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. Published online July 13, 2006. DOI: 10.1007/s00214-006 -0145-x

G. S. Fanourgakis and S. S. Xantheas, "The flexible, polarizable, Thole-type interaction potetnial for water (TTM2-F) revisited", J. Phys. Chem. A 110, 4100 (2006)

G. S. Fanourgakis and S. S. Xantheas, "The bend angle of water in ice Ih and liquid water: The significance of implementing the non-linear monomer dipole moment surface in classical interaction potentials", Journal of Chemical Physics 124, 174504 (2006)

G. S. Fanourgakis, G. K. Schenter and S. S. Xantheas, "A quantitative account of quantum effects in liquid water", Journal of Chemical Physics 125, 141102 (2006)

**PI Jose Gascon**

J. Chem. Theor. Comput., 2, 175-186, 2006 A Self-Consistent Space-Domain Decomposition Method for QM/MM Computations of Protein Electrostatic Potentials, by Jose A. Gascon, Siegfried S.F. Leung, Enrique R. Batista and Victor S. Batista.

**PI Cameron Geddes**

W. P. Leemans, B. Nagler, A. J. Gonsalves, Cs. Toth, K. Nakamura, C. G. R. Geddes, E. Esarey, C. B. Schroeder, S. M. Hooker, "GeV electron beams from a centimetre-scale accelerator," Nature Physics, V 2 (2006), p. 696.

D.A. Dimitrov, R.E. Giacone, D.L. Bruhwiler, R. Busby, J.R. Cary, C.G.R. Geddes, E. Esarey and W.P. Leemans, "Coupling of Laser Energy into Plasma Channels," Phys. Plasmas (2006), submitted.

E. Esarey, C.B. Schroeder, E. Michel, B.A. Shadwick, C.G.R. Geddes, and W.P. Leemans, "Thermal effects in plasma-based accelerators", Physics of Plasmas (2006), submitted.

G. Fubiani, E. Esarey, C. B. Schroeder, and W. P. Leemans, "Improvement of electron beam quality in optical injection schemes using negative plasma density gradients," Phys. Rev. E 73, 026402 (2006).

G. Fubiani, J. Qiang, E. Esarey, W. P. Leemans, and G. Dugan, "Space charge modeling of dense electron beams with large energy spreads," Phys. Rev. ST Accel. Beams 9, 064402 (2006).

P. Messmer and D.L. Bruhwiler, "Simulating laser pulse propagation and low-frequency wave emission in capillary plasma channel systems with a ponderomotive guiding center model," Phys. Rev. ST Accel. Beams 9, 031302 (2006).

C. G. R. Geddes, Cs. Toth, J. van Tilborg, E. Esarey, C. B. Schroeder, J. Cary, and W. P. Leemans, "Guiding of relativistic laser pulses by preformed plasma channels, "Phys. Rev. Lett. 95, 145002 (2005).

R.M.G.M. Trines, L.P.J. Kamp, T.J. Schep, F.W. Sluijter, W.P. Leemans, E.H. Esarey, "On the effect of laser and plasma parameters on stimulated Raman scattering and fast-electron generation," J. Plasma Phys. 71, 411-433 (2005).

**PI Ahmed Ghoniem**

Y. M. Marzouk and A. F. Ghoniem. Vorticity structure and evolution in a transverse jet. Journal of Fluid Mechanics (in print).

D. Wee and A. F. Ghoniem. Modified interpolation kernels for treating diffusion and remeshing in vortex methods. Journal of Computational Physics, 213:239-263 (2006).

Y. M. Marzouk and A. F. Ghoniem. Actuating transverse jets via nozzle-edge vortical perturbations. AIAA-2006-1492. 44th AIAA Aerospace Sciences Meeting and Exhibit (2006).

**PI James Glimm**

A Simple Package for Front Tracking, Jian Du, Brian Fix, James Glimm, Xiaolin Li, Yunhua Li, Lingling Wu, accepted by J. Comp. Phys., 2005, in Press.

The Influence of Scale Breaking Phenomena on Turbulent Mixing Rates, E. George, J. Glimm, X. L. Li, Y. H. Li and X. F. Liu, Phys. Rev. Lett., Submitted, 2005.

Errors in Numerical Solutions of Spherically Symmetric Shock Physics Problems J. Glimm, J. W. Grove, Y. Kang, T. Lee, X. Li, D. H. Sharp, Y. Yu, K. Ye and M. Zhao, Contemporary Mathematics, 371, pp. 163--179, 2005.

Self similarity of Rayleigh-Taylor mixing rates, E. George and J. Glimm, Phys. Fluids, 17, pp. 054101-1--154101-13, 2005.

Rayleigh-Taylor Mixing Rates for Compressible Flow, H. Jin, X. F. Liu, T. Lu, B. Cheng, J. Glimm and D. H. Sharp, Phys. Fluids, 17, pp. 1-10, 2005.

Statistical Riemann Problems and a Composition Law for Errors in Numerical Solutions of Shock Physics Problems, SISC, 26, pp. 666-697, 2004.

Spherical Richtmyer-Meshkov Instability for Axisymmetric Flow, S. Dutta, J. Glimm, J. W. Grove, D. H. Sharp and Y. Zhang, Mathematics and Computers in Simulations, 65, pp. 417--430, 2004.

A multiphase Flow Model for the Unstable Mixing of Layered Incompressible Materials, B. Cheng, J. Glimm, D. H. Sharp and Y. Yu, Phys. of Fluids, 17, 2005.

S. Dutta, J. Glimm, J. W. Grove, D. H. Sharp, and Y. Zhang, Error Comparison in Tracked and Untracked Spherical Simulations, Computers and Mathematics with Applications, 2004, 48, 1733--1747.

W. Bo, B. Cheng, J. Du, B. Fix, E. George , J. Glimm, J. Grove, X. Jia, H. Jin, H. Lee , Y. Li, X. Li, X. Liu, D. H. Sharp, L. Wu, and Yan Yu, Recent Progress in the Stochastic Analysis of Turbulent Mixing, Contemporary Mathematics, 2005, Submitted.

S. Dutta, J. Glimm, and Y. Zhang, LES Simulations of Turbulent Combustion in a Type Ia Supernovae, Astrophysical Journal, 2005, submitted.

E. George, J. Glimm, X. L. Li, Y. H. Li, and X. F. Liu, The Influence of Surface Tension on Turbulent Mixing Rates of Immiscible Fluids, Phys. Rev. Lett., 2005, submitted.

E. George, J. Glimm, and X. F. Liu, Turbulent Mixing with Physical Mass Diffusion, Phys. Rev. E, 2005 submitted.

H. Jin, J. Glimm, and D. H. Sharp, Two-Pressure Two-Phase Flow Models, Appl. Math. Lett., 2005, Submitted.

Y. Yu, M. Zhao, T. Lee, N. Pestieau, W. Bo, J. Glimm, and J. W. Grove, Uncertainty Quantification for Chaotic Computational Fluid Dynamics, J. Comp. Phys., 2005, submitted.

**PI Yousry Gohar**

Yousry Gohar, "Fusion Shield Design and Optimization Demonstration," Proceedings of The American Nuclear Society 14th Biennial Topical Meeting of the Radiation Protection and Shielding Division, Carlsbad New Mexico, USA. April 2-6, 2006.

**PI Stephen Gray**

Quantum dynamics study of the dissociative phototodetachment of HOCO-; S. Zhang, D. M. Medvedev, E. M. Goldfield, and S. K. Gray., J. Chem. Phys., in press (2006).

Methyl radical: ab initio global potential energy surface, vibrational levels, and partition function; D. M. Medvedev, L. B. Harding, and S. K. Gray, Mol. Phys. 104, 73-82 (2006).

Quantitative multispectral biosensing and 1D imaging using quasi-3D plasmonic crystals; M. E. Stewart, N. H. Mack, V. Malyarchuk, J. A. N. T. Soares, T.-W. Lee, S. K. Gray, R. G. Nuzzo, and J. A. Rogers, Proc. Nat. Acad. Sci. (USA), in press (2006).

Theoretical study of the complex-forming CH + H2 --> CH2 + H reaction; J. Mayneris, A. Saracibar, E. M. Goldfield, M. Gonzalez, E. Garcia, and S. K. Gray, J. Phys. Chem. A 110, 5542-5548 (2006).

**PI Chris Greene**

"Theoretical study of dissociative recombination of C_2v triatomic ions: application to H2D and D2H" V. Kokoouline and C.H. Greene Phys. Rev. A 72, 022712 (2005)

"Renner-Teller effects in HCO+ dissociative recombination" I. Mikhaylov, V. Kokoouline, A. Larson, S. Tonzani and C. H. Greene Phys. Rev. A, 74, 032707 (2006)

"Low energy electron scattering from DNA and RNA bases: shape resonances and radiation damage" S. Tonzani and C. H. Greene J. Chem. Phys., 124, 054312 (2006)

"Radiation damage to DNA: electron scattering from the backbone subunits" S. Tonzani and C. H. Greene J. Chem. Phys., 125, 094504 (2006)

"Near-threshold rotational excitation of molecular ions by electron impact" A. Faure, V. Kokoouline, C. H. Greene, and J. Tennyson, J. Phys. B, 39, 4261 (2006)

"Theoretical progress and challenges in H3+ dissociative recombination" C. H. Greene and V. Kokoouline Phil. Trans. R. Soc. A, 364, 2965 (2006)

**PI Maciej Gutowski**

M. Haranczyk, J. Rak, M. Gutowski, D. Rasisic, S.T. Stokes, K.H. Bowen, Intermolecular Proton Transfer in Anionic Complexes of Uracil with Alcohols, J. Phys. Chem. B, 109, 13383, (2005).

M. Haranczyk, M. Gutowski, Finding Adiabatically Bound Anions of Guanine through Combinatorial-Computational Approach, Angew. Chem. Int. Ed., 44, 6585, (2005).

M. Haranczyk, J. Rak, M. Gutowski, Stabilization of Very Rare Tautomers of 1-methylcytosine by an Excess Electron, J. Phys. Chem. A. (Jack Simons Festschrift), 109, 11495, (2005).

J.E. Jaffe, R.A. Bachorz, M. Gutowski, Low-temperature Polymorphs of ZrO2 and HfO2. A Density Functional Theory Study, Phys. Rev. B, 72, 144107, (2005).

W. Zheng, K.H. Bowen, Jr., J. Li, I. Dabkowska, M. Gutowski, Electronic Structure Differences in ZrO2 vs. HfO2, J. Phys. Chem. A. (Jack Simons Festschrift), 109, 11521, (2005).

K. Mazurkiewicz, R.A. Bachorz, M. Gutowski, J. Rak, On the unusual stability of valence anions of thymine based on very rare tautomers. A computational study, J. Phys. Chem. B, DOI: 10.1021/jp065666f.

M.Haran'czyk, M. Gutowski, Quantum Mechanical Energy -Based Screening of Combinatorially Generated Library of Tautomers. TauTGen: A Tautomer Generator Program, J. Chem. Inf. Model., accepted for publication.

I.N. Yakovkin, M. Gutowski, Driving Force for the WO3(001) Surface Relaxation, Surface Science, submitted for publication.

J.E. Jaffe, R.A. Bachorz, M. Gutowski, Band offset and magnetic property engineering for epitaxial interfaces: a monolayer of M2O3 (M = Al, Ga, Sc, Ti, Ni) at the alpha-Fe2O3/alpha-Cr2O3 (0001) interface, Phys. Rev. B, submitted for publication.

## H

**PI Stephan Haas**

Phys. Rev. Lett. (to be submitted), cond-mat/0605200

Phys. Rev. B 74, 144418 (2006)

Phys. Rev. B 74, 073103 (2006)

Phys. Rev. B 73, 064406 (2006)

J. Phys. B 39, S153 (2006)

Phys. Rev. Lett. 95, 207206 (2005)

Phys. Rev. Lett. 95, 227201 (2005)

**PI Edward Hamilton**

Seideman T and Hamilton E, "Nonadiabatic alignment by intense pulses. Concepts, theory, and directions." Advances in Atomic, Molecular, and Optical Physics 52, 289 (2005).

Hamilton E, Seideman T, Poulsen M, et al., "Alignment of symmetric top molecules by short laser pulses" Phys. Rev. A 72, 043402 (2005).

S. Vifrup, Ch. Bisgaard, V. Kumarappan, et al., "Three Dimensional Alignment of Molecules Using a Long and a Short Laser Pulse" in (extended) preparation, intended PRL

**PI Bruce Harmon**

Add-drop filters in 3-dimensional layer-by-layer photonic crystals using waveguides and resonant cavities, P Kohli, C. Christensen, J. Muehlmeier, R. Biswas, G. Tuttle, and K.-M. Ho, Appl. Phys. Lett. to be published (2006).

Theory of subwavelength hole arrays coupled with photonic crystals for extraordinary thermal emission, R. Biswas, C.G. Ding , I. Puscasu, M. Pralle, M. McNeal, J. Daly, A. Greenwald, E. Johnson, Phys. Rev. B. 74, 045107 (2006). Virtual Journal of Nanoscale Science & Technology July 24, 2006.

R. Biswas J. Ahn, T. Lee, J.-H. Lee, Y.S. Kim, C.H. Kim, W. Leung, C.H. Oh, K. Constant, K.-M. Ho, "Photonic gaps of conformally coated structures". J. Optical Society of America B 22, 2728 (2005).

"Quantum size effect on the diffusion barriers and growth morphology of Pb/Si(111)", T. L. Chan, C. Z. Wang, M. Hupalo, M. C. Tringides, and K. M. Ho, Phys. Rev. Lett. 96, 226102, (2006).

"Magic structures of H-passivated <110>silicon nanowires" T. L. Chan, C. V. Ciobanu, F.-C. Chuang, N. Lu, C. Z. Wang, and K. M. Ho, Nanolett. 6, 277-281 (2006).

"Undissociated screw dislocation in Si: glide or shuffle-set?" C. Z. Wang, Ju Li, K. M. Ho, and S. Yip Appl. Phys. Lett. 89, 051910 (2006).

"Diffusion, coalescence and reconstruction of vacancy defects in graphene layers" Gun-Do Lee, C. Z. Wang, Euijoon Yoon, Nong-Moon Hwang, Doh-Yeon Kim, and K. M. Ho Phys. Rev. Lett. 95, 205501 (2005).

"Impact of Interface Relaxation on Nanoscale corrugation in Pb/Si(111) Islands", Z. L. Chan, C. Z. Wang, M. Hupalo, M. C. Tringides, W. C. Lu, and K. M. Ho, Surf. Sci. Lett. 600, L179-L183, (2006).

"Diffusion of Pb Adatom and Ad-dimer on Si(100) From ab initio Studies" T. L. Chan, Y. Y. Ye, C. Z. Wang, and K. M. Ho, Surf. Sci. Lett. 600, L159-L163, (2006).

"Global structure optimization of Si magic clusters on the Si(111)7x7 surface", F-C. Chuang, B. Liu, C. Z. Wang, T L. Chan, and K. M. Ho, Surf. Sci. Lett. 598, L339-L346 (2005).

"Model reconstructions for the Si(337) orientation", F. C. Chuang, C. V. Ciobanu, C. Z. Wang, and K. M. Ho, J. Appl. Phys. 98, 073507 (2005).

"Transferability of the Slater-Koster Tight-Binding Scheme from a First-Principles Perspective", W.C. Lu, C.Z. Wang, K. Ruedenberg, and K. M. Ho, Phys. Rev. B, 72, 205123 (2005).

"Structures of neutral aluminum clusters Aln ( n=2-23)" Feng-chuan Chuang, C. Z. Wang, and K. H. Ho Phys. Rev. B 73, 125431 (2006).

"Structures of Si7H2m (m=1-7) clusters by global optimization", Mingsheng Tang, C.Z. Wang, W. C. Lu, and K.M. Ho, Phys. Rev. B (in press)

"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, Phys. Rev. Lett. (submitted).

"Highly localized quasiatomic minimal basis orbitals for Mo from ab-initio calculations" T.-L. Chan, Y. X. Yao, C. Z. Wang, W. C. Lu, J. Li, X. F. Qian,S. Yip, K. M. Ho, Phys. Rev. B (submitted).

"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. Lett. (submitted)

"Formation of local haeckelite structures induced by vacancy defects in a graphene layer", Gun-Do Lee, C. Z. Wang, Euijoon Yoon, Nong-Moon Hwang, and K. M. Ho, Phys. Rev. B (accepted)

**PI Charles Harris**

"19-Electron Intermediates in the Ligand Substitution of CpW(CO)3 with a Lewis Base" J.F. Cahoon, M.F Kling, K.R. Sawyer, H. Frei, C.B. Harris, J. Am. Chem. Soc. 128, 3152-3153 (2006).

"Ligand Rearrangement Reactions of Cr(CO)6 in Alcohol Solutions: Experiment and Theory" J.E. Shanoski, E.A. Glascoe, and C.B. Harris, J. Phys. Chem. B. 110, 996 (2006).

"Nature and Role of Bridged Carbonyl Intermediates in the Ultrafast Photoinduced Rearrangement of Ru3(CO)12" E.A. Glascoe, M.F. Kling, J.E. Shanoski, and C.B. Harris, Organometallics 25, 775, (2006).

"Photo-induced beta-Hydrogen Elimination and Radical Formation with CpW(CO)3(CH2CH3): Ultrafast IR and DFT Studies" E.A. Glascoe, M.F. Kling, J.E. Shanoski, C.K. Payne, B.V. Mork, T.D. Tilley and C.B. Harris, Organometallics, accepted with revisions.

"Disproportionation of [CpW(CO)3]2 with Lewis bases: electron transfer between 17- and 19-electron radicals" J.F. Cahoon, M.F. Kling, K.R. Sawyer and C.B. Harris, J. Am. Chem. Soc., submitted.

"The influence of the metal spin state in iron assisted alkene isomerization studied with ultrafast infrared spectroscopy" E.A. Glascoe, K.R. Sawyer, J.E. Shanoski and C.B. Harris, J. Am. Chem. Soc., submission anticipated in ca. 1 week.

"Ultrafast Infrard Studies of Doublet Reactivity in the Photochemical Formation of 3Co(CO)3(NO)" K.R. Sawyer, E.A. Glascoe, J.F. Cahoon, J.P. Schlegel, R.P. Steele and C.B. Harris, J. Am. Chem. Soc., submission anticipated in ca. 1 month.

**PI Martin Head-Gordon**

Chandler, D., J.P. Garrahan, R.L. Jack, L. Maibaum and A.C. Pan, "Lengthscale dependence of dynamic four-point susceptibilities in glass formers," cond-mat/0605084, accepted by Phys. Rev. E (2006).

Hagan, M.F., Chandler D., " Dynamic pathways for viral capsid assembly," Biophys. J. 91, 42-54 (2006).

Miller, T.F, Predescu, C., cond-mat/0610597 (2006)

Herbert JM, Head-Gordon M, "First-principles, quantum-mechanical simulations of electron solvation by a water cluster," PNAS 103 (39): 14282-14287 (2006)

Subotnik JE, Sodt A, Head-Gordon M, "A near linear-scaling smooth local coupled cluster algorithm for electronic structure," J. Chem. Phys. 125 (7) (2006)

Steele RP, DiStasio RA, Shao Y, et al. "Dual-basis second-order Moller-Plesset perturbation theory: A reduced-cost reference for correlation calculations," J. Chem. Phys. 125 (7) (2006)

**PI Teresa Head-Gordon**

M. E. Johnson, T. Head-Gordon, A. A. Louis (2006). Representability problems for coarse-grained water models. J. Chem. Phys., Submitted.

T. Head-Gordon and S. Rick (2006). Consequences of chain networks on thermodynamic, dielectric and structural properties for liquid water. Phys. Chem. Chem. Phys. submitted.

N. Lux Fawzi, Y. Okabe, E.-H. Yap & T. Head-Gordon (2006). Fibril stability and elongation studies of the Alzheimer's ab1-40 peptide. J. Mol. Biol., In press.

R. M. Lynden-Bell and T. Head-Gordon (2006). Solvation in modified water models: toward understanding hydrophobic solvation. Mol. Phys. In press.

T. Head-Gordon & M. E. Johnson (2006). Tetrahedral structure or chains for liquid water? Proc. Natl. Acad. Sci. 103, 7973-7977.

I. Lotan & T. Head-Gordon (2006). An analytical electrostatic model for salt screened interactions between multiple proteins J. Comp. Theo. Chem. 2, 541-555.

N. Marianayagam, N. Fawzi & T. Head-Gordon (2005). Protein folding by distributed computing and the denatured state ensemble, Proc. Natl. Acad. Sci. 102, 16684-16689.

**PI Eric Held**

"Computational modeling of fully ionized magnetized plasmas using the fluid approximation," D. D. Schnack, D. C. Barnes, D. P. Brennan, C. C. Hegna, E. Held, C. C. Kim, S. E. Kruger, A. Y. Pankin, and C. R. Sovinec Phys. Plasmas 13, 058103 (2006)

"Exact linearized Coulomb collision operator in the moment expansion," Jeong-Young Ji and Eric D. Held, Phys. Plasmas 13, 102103 (2006)

**PI Brian Hingerty**

Durandin A, Jia L, Crean C, Kolbanovskiy A, Ding S, Shafirovich V, Broyde S, Geacintov NE. Assignment of absolute configurations of the enantiomeric spiroiminodihydantoin nucleobases by experimental and computational optical rotatory dispersion methods. Chem Res Toxicol. 2006 Jul;19(7):908-13.

Wang L, Broyde S. A new anti conformation for N-(deoxyguanosin-8-yl)-2-acetylaminofluorene (AAF-dG) allows Watson-Crick pairing in the Sulfolobus solfataricus P2 DNA polymerase IV (Dpo4). Nucleic Acids Res. 2006 Feb 1;34(3):785-95. Print 2006.

Jia L, Shafirovich V, Shapiro R, Geacintov NE, Broyde S. Structural and thermodynamic features of spiroiminodihydantoin damaged DNA duplexes. Biochemistry. 2005 Oct 11;44(40):13342-53.

Zhang L, Shapiro R, Broyde S. Molecular dynamics of a food carcinogen-DNA adduct in a replicative DNA polymerase suggest hindered nucleotide incorporation and extension. Chem Res Toxicol. 2005 Sep;18(9):1347-63.

Jia L, Shafirovich V, Shapiro R, Geacintov NE, Broyde S. Spiroiminodihydantoin lesions derived from guanine oxidation: structures, energetics, and functional implications. Biochemistry. 2005 Apr 26;44(16):6043-51.

Zhang N, Lin C, Huang X, Kolbanovskiy A, Hingerty BE, Amin S, Broyde S, Geacintov NE, Patel DJ. Methylation of cytosine at C5 in a CpG sequence context causes a conformational switch of a benzo[a]pyrene diol epoxide-N2-guanine adduct in DNA from a minor groove alignment to intercalation with base displacement. J Mol Biol. 2005 Mar 4;346(4):951-65. Epub 2004 Dec 31.

Wang L, Wu M, Yan SF, Patel DJ, Geacintov NE, Broyde S. Accommodation of a 1S-(-)-benzo[c]phenanthrenyl-N6-dA adduct in the Y-family Dpo4 DNA polymerase active site: structural insights through molecular dynamics simulations. Chem Res Toxicol. 2005 Mar;18(3):441-56.

Perlow-Poehnelt RA, Zharkov DO, Grollman AP, Broyde S. Substrate discrimination by formamidopyrimidine-DNA glycosylase: distinguishing interactions within the active site. Biochemistry. 2004 Dec 28;43(51):16092-105.

Wu M, Yan SF, Tan J, Patel DJ, Geacintov NE, Broyde S. Conformational searches elucidate effects of stereochemistry on structures of deoxyadenosine covalently bound to tumorigenic metabolites of benzo[C] phenanthrene. Front Biosci. 2004 Sep 1;9:2807-18.

Perlow-Poehnelt RA, Likhterov I, Scicchitano DA, Geacintov NE, Broyde S. The spacious active site of a Y-family DNA polymerase facilitates promiscuous nucleotide incorporation opposite a bulky carcinogen-DNA adduct: elucidating the structure-function relationship through experimental and computational approaches. J Biol Chem. 2004 Aug 27;279(35):36951-61. Epub 2004 Jun 21.

**PI Kai-Ming Ho**

"Quantum size effect on the diffusion barriers and growth morphology of Pb/Si(111)" T. L. Chan, C. Z. Wang, M. Hupalo, M. C. Tringides, and K. M. Ho Phys. Rev. Lett. 96, 226102, (2006).

"Persistent Superconductivity in Ultrathin Pb Films: A Scanning Tunneling Spectroscopy Study," D. Eom, S. Qin, M. Y. Chou, and C.K. Shih, Phys. Rev. Lett. 96, 027005/1-4 (2006).

"Theoretical Analysis of Mound Slope Selection during Unstable Multilayer Growth" Maozhi Li and J.W. Evans, Phys. Rev. Lett. 95 (2005) 256101.

"Impact of Interface Relaxation on Nanoscale corrugation in Pb/Si(111) Islands" Z. L. Chan, C. Z. Wang, M. Hupalo, M. C. Tringides, W. C. Lu, and K. M. Ho, Surf. Sci. Lett. 600, L179-L183, (2006).

"Correlations in Nano-Scale Step Fluctuations: Comparison of Simulation and Experiments" F. Szalma, D.B. Dougherty, Ellen D. Williams, Michael I. Haftel, and T.L. Einstein Phys. Rev. B 73, 115413 (2006).

"Formation of monatomic Fe chains on vicinal Cu(111) surfaces: An atomistic view" J. Guo, Y. Mo, E. Kaxiras, Z. Zhang, and H. H. Weitering Phys. Rev. B 73, 193405 (2006)

"Quantum size effects in Pb films from first principles: The role of the substrate" Y. Jia, B. Wu, H. H. Weitering, and Z. Zhang Phys. Rev. B 74, 035433 (2006).

"Nanomechanical Architecture of Strained Bilayer Thin Films: from design principles to experimental fabrication", Minghuang Huang, C. Boone, M. Roberts, D. E. Savage, M. G. Lagally, N. Shaji, H. Qin, R. Blick, J. A. Nairn and Feng Liu, Adv. Mater. 17, 2860 (2005).

"Nanotube Formation from Self-Bending Nanofilms Driven by Atomic-scale Surface Stress Imbalance", Ji Zang, Minghuang Huang and Feng Liu, Phys. Rev. Lett. (Submitted).

"Optimal dopant control in dilute magnetic semiconductors via subsurfactant epitaxy" C. G. Zeng, Z. Y. Zhang, H. Weitering, et al., submitted to Nature.

"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, Phys. Rev. Lett. (submitted).

"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. (submitted) [cond-mat/0609237].

**PI Steve Holbrook**

Transitive Closure and Metric Inequality of Weighted Graphs-Detecting Protein Interaction Modules Using Cliques; Chris H.Q. Ding, Xiaofeng He, and Stephen R. Holbrook International Journal of Data Mining and Bioinformatics September, 2006: Volume 1, Number 2

Anatomy of the Yeast Protein Interaction Network by Hierarchical Decomposition; (2006) submitted, Nature Biotechnology Chunlin Wang, Chris H.Q. Ding & Stephen R. Holbrook

Biclustering Protein Complex Interactions with a Biclique Finding Algorithm; 2006 IEEE International Conference on Data Mining, IEEE Computer Society Press, Chris Ding, Ya Zhang, and Stephen Holbrook

Simultaneously Relating Domains and Protein complexes through Biclique Discovery; (2006) submitted to Bioinformatics, Ya Zhang, Chris Ding and Stephen Holbrook

## I

**PI Hong Im**

Wang, Y. and Rutland, C.J. (2006), "Direct numerical simulation of ignition in turbulent n-heptane liquid fuel spray jets", Comb. and Flame, accepted.

Yoo, C. S. and Im, H. G. (2006), "Characteristic boundary conditions for simulations of compressible reacting flows with multi-dimensional, viscous, and reaction effects," Combust. Theory Modelling, in press.

Cook, D. J., Pitsch, H., Chen, J. H., and Hawkes, E. R. (2006), "Flamelet-based modeling of H2/Air Auto-ignition with thermal inhomogeneities," Proc. Combust. Inst., 31, in press.

Hawkes, E. R., Sankaran, R., Sutherland, J., and Chen, J. H. (2006), "Scalar mixing in direct numerical simulations of temporally-evolving plane jet flames with detailed CO/H2 kinetics," Proc. Combust. Inst., 31, in press.

Sankaran, R., Hawkes, E. R., Chen, J. H., Lu, T., and Law, C. K. (2006), "Structure of a spatially-developing lean methane-air turbulent bunsen flame," Proc. Combust. Inst., 31, in press.

Yoo, C. S. and Im, H. G. (2006), "Transient soot dynamics in turbulent nonpremixed ethylene-air counterflow flames," Proc. Combust. Inst., 31, in press.

Chen, J. H., Hawkes, E. Sankaran, R., Mason, S. D., and Im, H. G. (2006), "Direct numerical simulation of ignition front propagation in a constant volume with temperature inhomogeneities, Part I: Fundamental analysis and diagnostics," Combustion and Flame, 145:128-144.

Hawkes, E., Sankaran, R., Pibay, P. P., and Chen, J. H. (2006), "Direct numerical simulation of ignition front propagation in a constant volume with temperature inhomogeneities, Part II: Parametric Study," Combustion and Flame, 145:145-159.

Wang, Y. and Trouvi A. (2006), "Direct numerical simulation of non-premixed flame-wall interactions", Combustion and Flame, Combust. Flame, 144:461-475.

Yoo, C. S., Wang, Y., Trouvi A. and Im, H. G. (2005), "Characteristic boundary conditions for direct simulations of turbulent counterflow flames", Combust. Theory Modelling, 9:617-646.

Sankaran, R., Im, H. G., Hawkes, E. R. and Chen, J. H. (2005), "The effects of nonuniform temperature distribution on the ignition of a lean homogeneous hydrogen-air mixture," Proc. Combust. Inst., 30:875-882.

Yoo, C. S. and Im, H. G. (2005), "Transient dynamics of edge flames in a laminar nonpremixed hydrogen-air counterflow," Proc. Combust. Inst., 30:349-356.

Wang, Y. and Rutland, C. J. (2005), "Effects of temperature and equivalence ratio on the ignition of n-heptane fuel droplets in turbulent flow," Proc. Combust. Inst., 30:893-900.

**PI Marc Ingber**

Ingber, M. S., Tanski, J. A., and Alsing, P., "A domain decomposition tool for boundary element methods,'' submitted for publication.

**PI Valerie Izzo**

V.A. Izzo, Nuclear Fusion 46 (2006) 541.

R.S Granetz, et. al. "Gas Jet Disruption Mitigation Studies on Alcator C-Mod," accepted by Nuclear Fusion, Oct. 2006.

## J

**PI Bing Jap**

B.-G. Han, A.B. Guliaev, P.J. Walian and B.K. Jap. Water Transport in AQP0 Aquaporin: Molecular Dynamics Studies. J. Mol. Biol. 360, 285-296, 2006.

**PI Stephen Jardin**

D. Reynolds, R. Samtaney, C. Woodward, "A fully implicit numerical method for single fluid resistive magnetohydrodynamics", J. Comp. Physics, 2006, to appear.

H.R. Strauss, L. Sugiyama, C.S. Chang, G. Park, S. Ku, W. Park3, J. Breslau, S. Jardin, "ELM Simulations with M3D," paper TH/P8-6, IAEA Fusion Energy Conference, Hengdu, China, 2006 (to appear in proceedings)

G. Y. Fu, J. A. Breslau, W. Park, S. C. Jardin, J. Chen, "Nonlinear Simulations of Fishbone Instability and Sawteeth in Tokamaks and Spherical Torus", paper EX/7-4Rb, IAEA Fusion Energy Conference, Hengdu, China, 2006 (to appear in proceedings)

J A Breslau, W Park and S C Jardin, "Massively parallel modeling of the sawtooth instability in tokamaks", 2006 J. Phys.: Conf. Ser. 46 97-101

Kramer GJ, Fu GY "Reversed shear Alfven eigenmodes associated with the ellipticity and triangularity Alfven gaps" ,PLASMA PHYSICS AND CONTROLLED FUSION 48 (9): 1285-1295 SEP 2006

Brennan DP, Sugiyama LE "Tearing mode stability in a low-beta plasma with sawteeth", PHYSICS OF PLASMAS 13 (5): Art. No. 052515 MAY 2006

Ferraro NM, Jardin SC "Finite element implementation of Braginskii's gyroviscous stress with application to the gravitational instability" PHYSICS OF PLASMAS 13 (9): Art. No. 092101 SEP 2006

Fu GY, Park W, Strauss HR, Breslau J, Chen J, Jardin S, Sugiyama LE, "Global hybrid simulations of energetic particle effects on the n=1 mode in tokamaks: Internal kink and fishbone instability" PHYSICS OF PLASMAS 13 (5): Art. No. 052517 MAY 2006

Kramer GJ, Nazikian R, Alper B, de Baar M, Berk HL, Fu GY, Gorelenkov NN, McKee G, Pinches SD, Rhodes TL, Sharapov SE, Solomon WM, van Zeeland MA. "Interpretation of core localized Alfven eigenmodes in DIII-D and Joint European Torus reversed magnetic shear plasmas", PHYSICS OF PLASMAS 13 (5): Art. No. 056104 MAY 2006

Jardin SC, Kessel CE, Mau TK, et al. "Physics basis for the advanced tokamak fusion power plant, ARIES-AT" FUSION ENGINEERING AND DESIGN 80 (1-4): 25-62 JAN 2006

Fredrickson ED, Bell RE, Darrow DS, Fu GY, Gorelenkov NN, LeBlanc BP, Medley SS, Menard JE, Park H, Roquemore AL, Heidbrink WW, Sabbagh SA, Stutman D, Tritz K, Crocker NA, Kubota S, Peebles W, Lee KC, Levinton FM, "Collective fast ion instability-induced losses in national spherical tokamak experiment" PHYSICS OF PLASMAS 13 (5): Art. No. 056109 MAY 2006

Kessel CE, Mau TK, Jardin SC, et al. "Plasma profile and shape optimization for the advanced tokamak power plant, ARIES-AT" , FUSION ENGINEERING AND DESIGN 80 (1-4): 63-77 JAN 2006

Jardin, S.C; Breslau, J.A. , 2005, Implicit solution of the four-field extended-magnetohydrodynamic equations using high-order high-continuity finite elements. PHYSICS OF PLASMAS 12, 10 pages

J. Chen, S. C. Jardin, and H.R. Strauss, "Solving Anisotropic Transport Equations on Misaligned Grids", Springer-Verlag, Lecture Notes in Computer Science, 3516, pp. 1076-1079, 2005

Paccagnella R, Cavinato M, Bolzonella T, Ortolani S, Pautasso G, Schneider W, Lukash V, Khayrutdinov R, Strauss HR , "Vertical displacement events simulations for tokamak plasmas" Paccagnella R, Cavinato M, Bolzonella T, Ortolani S, Pautasso G, Schneider W, Lukash V, Khayrutdinov R, Strauss HR Source: FUSION ENGINEERING AND DESIGN 75-9: 589-593 NOV 2005

Yamada M, Ren Y, Ji H, Breslau J, Gerhardt S, Kulsrud R, Kuritsyn A "Experimental study of two-fluid effects on magnetic reconnection in a laboratory plasma with variable collisionality," PHYSICS OF PLASMAS 13 (5): Art. No. 052119 MAY 2006

L. P. Ku and P. R. Garabedian, "New classes of qusi-axially symmetric stellarator configurations," Fusion Science & Technology, 50(2), 207, 2006.

L. P. Ku and the ARIES Team, "Configuration optimization and physics basis for ARIES-CS," Proc. 17th Topical Meeting on the Technology of Fusion Energy, Albuquerque, NM, Nov 13-15, 2006.

H. Mynick, A. Boozer, L. P. Ku, "Improving confinement in quasi-axisymmetric stellarators," Physics of Plasmas, 13, 064505, 2006.

J. F. Lyon, L. P. Ku, L. El-Guebaly, L. Bromberg and the ARIES Team, "Optimization of the ARIES-CS compact stellarator power plant parameters," Proc. 17th Topical Meeting on the Technology of Fusion Energy, Albuquerque, NM, Nov 13-15, 2006.

J. F. Lyon, L.P. Ku, L. El-Guebaly, T. K. Mau, L. Bromberg, "Optimizing compact stellarator performance," 33rd European Physical Society Conference on Controlled Fusion and Plasma Physics, Rome, Italy, June 19-23 2006.

**PI Julius Jellinek**

THE SIZE DEPENDENCE OF STATIC POLARIZABILITIES AND ADSORPTION SPECTRA OF Ag CLUSTERS J. C. Idrobo, S. Ogut, and J. Jellinek Phys. Rev. B 72, 085445(1-8) (2005)

HOLLOW CAGES VERSUS SPACE-FILLED STRUCTURES FOR MEDIUM-SIZED GOLD CLUSTERS: THE SPHERICAL AROMATICITY OF THE Au50 CAGE J. Wang, J. Jellinek, J. Zhao, Z. Chen, R. B. King, and P. v. R. Schleyer J. Phys. Chem. A 109, 9265-9269 (2005)

INFRARED SPECTRA OF V_nBz_n+1 SANDWICH CLUSTERS J. Wang and J. Jellinek J. Phys. Chem. A 109, 10180-10182 (2005)

COMPUTATIONAL ELECTRON SPECTROSCOPY - APPLICATION TO MAGNESIUM CLUSTERS J. Jellinek and P. H. Acioli Lecture Series in Computer and Computational Sciences, Vol. 3, G. Maroulis and T.Simos, Eds., VSP, Leiden, 2005, pp. 59-74

STRUCTURAL EVOLUTION OF ANIONIC SILICON CLUSTERS Si_N- (20*N*45) J. Bai, L.-F. Cui, J. Wang, S. Yoo, X. Li, J. Jellinek, C. Koehler, T. Frauenheim, L.-S. Wang, and X. C. Zeng J. Phys. Chem. A 110, 908-912 (2006)

Mn_n- CLUSTERS: THE SIZE-INDUCED TRANSITION TO HALF-METALLICITY J. Jellinek, P. H. Acioli, J. Garcia-Rodeja, W. Zheng, O. C. Thomas, and K. H. Bowen Phys. Rev.B 74, 153401(1-4) (2006) This paper has been selected for reprinting in the Virtual Journal of Nanoscale Science and Technology, Vol. 14, Issue 16 (2006)

STRUCTURE AND SHAPE VARIATIONS IN INTERMEDIATE SIZE COPPER CLUSTERS M. Yang, K. A. Jackson, C. Koehler, T. Frauenheim, and J. Jellinek J. Chem. Phys. 124, 024308(1-6) (2006)

DENSITY-FUNCTIONAL STUDY OF SMALL AND MEDIUM-SIZED As_n CLUSTERS UP TO n=28 J. Zhao, X. Zhou, X. Chen, J. Wang, and J. Jellinek Phys. Rev. B 73, 115418((1-10) (2006)

DIPOLE POLARIZABILITIES OF MEDIUM-SIZED Au_N, N=32, 38, 44, 50, 56, CLUSTERS J. Wang, M. Yang, J. Jellinek, and G. Wang Phys. Rev. A 74, 023202(1-5) (2006)

STRUCTURAL, ELECTRONIC, AND OPTICAL PROPERTIES OF NOBLE METAL CLUSTERS FROM FIRST PRINCIPLES S. Ogut, J. C. Idrobo, J. Jellinek, and J. Wang J. Clust. Sci. (submitted)

**PI Chueng-Ryong Ji**

PQCD analysis of exclusive e+ e- --> D(/s)+ D(/s)- cross section at s**(1/2) = 10.6-GeV, H.M. Choi and C.R. Ji, Phys. Rev. D 73, 114020 (2006)

Higher Fock state contributions to the generalized parton distribution of pion, C.R Ji, Y. Mishchenko and A. Radyushkin, Phys. Rev. D 73, 114013 (2006)

Real and virtual nucleon Compton scattering in the perturbative limit, R. Thomson, A. Pang and C.R. Ji, Phys. Rev. D 73, 054023 (2006)

Instanton-inspired model of QCD phase transition and bubble dynamics, C.R. Ji, G. Kang and J. Lee, Phys. Rev. D 73, 085003 (2006)

Restoring The Equivalence Between The Light-Front And Manifestly Covariant Formalisms,B.L.G. Bakker, M.A. DeWitt, C.R. Ji and Y. Mishchenko, Phys. Rev. D 72, 076005 (2005).

Light-front wavefunction dependence of quark recombination,B. Hong, C.R. Ji and D.P. Min, Phys. Rev. C 73, 054901 (2006)

The parity determination of the pentaquark Theta+ from photoproduction near threshold, B.G. Yu, T.K. Choi and C.R. Ji, J. Phys. G 32, 387 (2006)

**PI Donald Johnson**

Pierce, R. B., J. Al-Saadi, C. Kittaka, D. Fairlie, T. K. Schaack, D. R. Johnson, T. H. Zapotocny, M. Avery, A. Thompson, R. Cohen, J. Dibb, J. Crawford, D. Rault, Jim Szykman, Randall Martin, 2006: Chemical data assimilation based estimates of Continental US Ozone and Nitrogen budgets during INTEX-A. Submitted to J. Geophys. Res.

## K

**PI Martin Karplus**

Electrostatic Energies and Forces Computed Without Explicit Interparticle Interactions: A Linear Time Complexity Formulation, J. Comput. Chem. 26, 755-787 (2005), by R. J. Petrella and M. Karplus.

Structure of a Repair Enzyme Interrogating Undamaged DNA Elucidates Recognition of Damaged DNA, Nature 434, 612-618 (2005), by A. Banerjee, W. Yang, M. Karplus and G. Verdine.

Simulation of Conformational Transitions by the Restricted Perturbation-Targeted Molecular Dynamics (RP-TMD) Method, J. Chem. Phys. 122, 114903.1-114903.6 (2005), by A. van der Vaart and M. Karplus.

Normal Mode Calculations of Icosahedral Viruses with Full Dihedral Flexibility by Use of Molecular Symmetry, J. Mol. Biol. 350, 528-542 (2005), by H. W. T. van Vlijmen and M. Karplus.

Role of Conformational Heterogeneity in Domain Swapping and Adapter Function of the Cks Proteins, J. Biol. Chem. 280, 30448-30459 (2005), by M. A. Seeliger, M. Spichty, S. E. Kelly, M. Bycroft, S.M.F. Freund, M. Karplus, and L. S. Itzhaki.

Large Amplitude Conformational Change in Proteins Explored with a Plastic Network Model: Adenylate Kinase, J. Mol. Biol. 352, 807-822 (2005), by P. Maragakis and M. Karplus.

The Allosteric Mechanism of Yeast Chorismate Mutase: A Dynamic Analysis, J. Mol. Biol. 356, 237-247 (2005), by Y. Kong, J. Ma, M. Karplus, and W. N. Lipscomb.

A Structure-Based Model for Synthesis and Hydrolysis of ATP by F1ATPase, Cell 123, 195-205 (2005), by Y. Q. Gao, W. Yang, and M. Karplus.

Optimal Estimate of Free Energies from Multistate Nonequilibrium Work Data, Phys. Rev. Lett. 96, 100602/1-4 (2006), by P. Maragakis, M. Spichty and M. Karplus

Probing Polar Solvation Dynamics in Proteins: A Molecular Dynamics Simulation Analysis, J. Phys. Chem., submitted, by A. A. Golosov and M. Karplus

**PI Thomas Katsouleas**

T. Katsouleas, "Plasma accelerators race to 10 GeV and beyond", Physics of Plasma, 2006

S. Deng, C.D. Barnes, C.E. Clayton, C. Oonnell, F.J. Decker, R.A. Fonseca, C. Huang, M.J. Hogan, R. Iverson, D.K. Johnson, C. Joshi, T. katsouleas, P. Krejcik, W. Lu, W.B. Mori, P. Muggli, E. Oz, F. Tsung, D. Walz, M. Zhou, "Hose Instability and Wake Generation by an Intense Electron," submitted Phys. Rev. Lett. 2005.

W. Lu, C. Huang, M. Zhou, M. Tzoufras, F. S. Tsung, W. B. Mori, and T. Katsouleas, "A nonlinear theory for multidimensional relativistic plasma wave wakefields", Physics of Plasma, 2006

A. Z. Ghalam, T. Katsouleas, V. K. Decyk, C. K. Huang, W. B. Mori, G. Rumolo, E. Benedetto, and F. Zimmermann, "Three-dimensional continuous modeling of beam-electron cloud interaction:Comparison with analytic models and predictions for the present and future circular machines", Physics of Plasma, 2006

I. Blumenfeld, C. E. Clayton, F. Decker, M. J. Hogan, C. Huang, R. Ischebeck, R. Iverson, C. Joshi, T. Katsouleas, N. Kirby, W. Lu, K. A. Marsh, W. B. Mori, P. Muggli, E. OZ, R. H. Siemann, D. Walz, M. Zhou, "Energy Doubling of 42 Gev Electrons in a Meter Scale Plasma Wakefield Accelerator", submitted to Nature, 2006

C. Huang et al., "QUICKPIC: A highly efficient particle-in-cell code for modeling wakefield acceleration in plasmas", Journal Comp. Phys. 2006.

**PI Kwiseon Kim**

A. Zunger, A. Franceschetti, G. Bester, W. B. Jones, Kwiseon Kim, P. A. Graf, L.-W. Wang, A. Canning, O. Marques, C. Voemel, J. Dongarra, J. Langou and S. Tomov, Predicting the electronic properties of 3D, million-atom semiconductor nanostructure architectures. J. Phys.: Conf. Ser. 2006 46 292-298 doi:10.1088/1742-6596/46/1/040

P. A. Graf, K. Kim, W. B. Jones, L.-W. Wang, Surface passivation optimization using DIRECT, Journal of Computational Physics. (Accepted).

P. A. Graf and W. B. Jones, A Projection Based Multiscale Optimization Method for Eigenvalue Problems, Journal of Global optimization (Submitted).

P. A. Graf, K. Kim, W. B. Jones, G. L. W. Hart (2005). Direct Enumeration of Alloy Configurations for Electronic Structural Properties. Article No. 243111. Applied Physics Letters. Vol. 87(24), 2005; 3 pp.; NREL Report No. JA-530-39127.

**PI Richard Klein**

"The Formation of Massive Stars" Beuther, H., Churchwell, E. B., McKee, C. F., Tan, J. C., 2007, in Protostars and Planets V, ed. B. Reipurth, (Tucson: Univ. of Arizona Press), in press.

"Current Advances in the Methodology and Computational Simulation of the Formation of Low-Mass Stars" Klein, R. I., Inutsuka, S. I., Padoan, P., & Tomisaka, K., 2007, in Protostars and Planets V, ed. B. Reipurth, (Tucson: Univ. of Arizona Press), in press.

"Radiation Feedback and Fragmentation in Massive Protostellar Cores" Krumholz, M. R. 2006, ApJ, 641, 45.

"Simulations of Collapse and Fragmentation in Massive Protostellar Cores" Krumholz, M. R., Klein, R. I., & McKee, C. F., 2007a, ApJ, submitted, astro-ph/0609798.

"Equations and Algorithms for Astrophysical Radiation Hydrodynamics in All Non-Relativistic Regimes, from Dense Accretion Disks to Diffuse Circumstellar Envelopes" Krumholz, M. R., Klein, R. I., & McKee, C. F. 2007b, ApJ, submitted.

"Bondi-Hoyle Accretion in a Turbulent Medium" Krumholz, M. R., McKee, C. F., & Klein, R. I. 2006, ApJ, 638, 369.

"The Heavy-Ion Approximation for Ambipolar Diffusion Calculations for Weakly Ionized Plasmas" Li, P. S., McKee, C. F., & Klein, R. I. 2006, ApJ, in press.

"A Multigroup Diffusion Solver Using Pseudo Transient Continuation for a Radiation-Hydrodynamic Code with Patch-Based AMR" Shestakov, A. I. & Offner, S. S. R. 2006, JCP, submitted.

**PI Spencer Klein**

"First year performance of the IceCube neutrino telescope," A. Achterberg et al., Astropart. Phys. 26, 155 (2006)

"Limits on the high-energy gamma and neutrino fluxes from the SGR 1806-20 giant flare of December 27, 2004 with the AMANDA=II detector. A Achterberg et al, preprint astro-ph/0607233, submitted to Physical Review Letters.

**PI Kwok Ko**

K. Ko, N. Folwell, L.Ge, A. Guetz, L. Lee, Z. Li, C. Ng, E. Prudencio, G. Schussman, R. Uplenchwar, L. Xiao, Advances in Electromagnetic Modelling Through High Performance Computing, Physica C 441 (2006) PP258-262

C. Ng, N. Folwell, A. Guetz, V. Ivanov, L. Lee, Z. Li, G. Schussman, K. Ko, Simulating dark current in NLC structures, Nuclear Instruments and Methods in Physics Research A 558 (2006), 192-195

**PI Boris Kogan**

Huffaker RB, Weiss JN, Kogan B. Ca-induced Early Afterdepolarizations and Cardiac Arrhythmias in Simulated Tissue. In submission to Biophys J.

**PI Joel Koplik**

Lattice-Boltzmann method for non-Newtonian fluid flows, Phys. Rev. E 72, 046312 (2005), S. Gabbanelli, G. Drazer and J. Koplik.

Flow channeling in a single fracture induced by shear displacement, submitted to Geothermics, (2006), H. Auradou, G. Drazer, A. Boschan, J. P. Hulin and J. Koplik.

**PI V. Rao Kotamarthi**

Modeling of trace gases from the 1998 North Central Mexico forest fire plume, as measured over Phoenix, V. R. Kotamarthi, P. V. Doskey, S. R. Springston, P. Hyde, J. S. Gaffney and N. A. Marley. Atmos. Chem. Phys. Discuss, 6, 1-38, 2006.

**PI Arnold Kritz**

A. Y. Pankin, et al., Nuclear Fusion 46, 403 (2006).

D. P. Brennan, et al., J. Phys.: Conf. Ser. 46, 63 (2006).

A. Y. Pankin, et al., Plasma Phys. Cont. Fusion (submitted for publication, 2006).

G. Bateman, et al., Plasma Phys. Control. Fusion 48, A93 (2006).

**PI Steven Krueger**

Garrett, T.J., M.A. Zulauf, and S.K. Krueger, 2006: Effects of cirrus near the tropopause on anvil cirrus dynamics. Geophys. Res. Lett., 33, L17804, doi:10.1029/2006GL027071.

Luo, Y., S.K. Krueger, and K.-M. Xu, 2006: Cloud Properties Simulated by a Single-Column Model. Part II: Evaluation of Cumulus Detrainment and Ice-phase Microphysics Using a Cloud Resolving Model. J. Atmos. Sci., accepted, Feb 2006.

Sun, R., S.K. Krueger, M.A. Jenkins, M.A. Zulauf, and J.J. Charney, 2006: The importance of fire/atmosphere coupling and boundary layer turbulence to wildfire spread, Bound.-Layer. Meteor., submitted, July 2006.

Yang, F., H.-L. Pan, S. Krueger, S. Moorthi, and S. Lord, 2006: Evaluation of NCEP Global Forecast System at the ARM SGP Site. J. Climate, accepted, Feb 2006.

**PI John Kuriyan**

Nicholas M. Levinson, Olga Kuchment, Kui Shen, Matthew A. Young, Michael Koldobskiy, Martin Karplus, Philip A. Cole and John Kuriyan (2006). A Src-Like Inactive Conformation in the Abl Tyrosine Kinase Domain. Public Library of Science, Biology (2006) Vol. 4(5): e144

## L

**PI Andrew Lacis**

Q. Ma, R. H. Tipping, and C. Boulet, Irreducible Correlation Functions of the S Matrix in the Coordinate Representation: Application in Calculating Lorentzian Half-width and Shifts. J. Chem. Phys. 124, 014109 (2006).

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, accepted for publication (2006).

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, accepted for publication (2006).

C. Boulet, J. Boissoles, R. H. Tipping, and Q. Ma, On the Temperature Dependence of the Integrated Intensity of the Collision-Induced Fundamental Band of O2 O2. Mol. Phys., accepted for publication (2006).

J. Boissoles, A. Domanskaya, C. Boulet, R. H. Tipping, and Q. Ma, New Experimental Measurements and Theoretical Analysis of the Collision-Induced Absorption in N2 H2 Pairs. J.Q.S.R.T 95, 489-498 (2005).

R. H. Tipping, Q. Ma, C. Boulet, J.-M. Hartmann, Theoretical Analysis of the Collision-Induced Electronic Absorptions in O2 N2 and O2 CO2 Pairs. J. Mol. Structure 742, 83-86 (2005).

**PI Jean-Francois Lamarque**

Lamarque, J.-F., J. T. Kiehl, C. A. Shields, B. A. Boville, and D. E. Kinnison, Modeling the response to changes in tropospheric methane concentration: application to the Permian-Triassic boundary. Paleoceanography, 21, PA3006, doi:10.1029/2006PA001276, 2006.

**PI Uzi Landman**

"Oxidative Damage to DNA: Counter-Ion Assisted Addition of Water to Ionized DNA", R. N. Barnett, A. Bongiorno, C. L. Cleveland, A. Joy, U. Landman, G. B. Schuster, J. Am. Chem. Soc. 128, 10798 (2006).

"Bonding Trends and Dimensionality Crossover of Gold Nanoclusters on Metal-supported MgO Thin Films", D. Ricci, A. Bongiorno, G. Pacchioni, U. Landman, Phys. Rev. Lett. 97, 36106 (2006).

"Structural Evolution of Au Nanoclusters: From Planar to cage to nanotube Motifs", X. Xing, B. Yoon, J. H. Parks, U. Landman, Phys. Rev. B. November (2006), in press.

"Size-dependent evolution of structures and chemical reactivity of gold anosclusters: AuN-, N=15-24", B. Yoon, P. Koshkinen, B. Huber, O. Kostki, B. von Issendorff, H. Hakkinen, M. Moleler, U. Landman, Chem. Phys. Chem. November (2006), in press.

**PI Jean-Noel Leboeuf**

P.L. Pritchett, "Onset and Saturation of Guide-Field Magnetic Reconnection", Phys. Plasmas, 12, 062301, 2005.

P.L. Pritchett, "Onset of Magnetic Reconnection", in Reconnection of Magnetic Fields, edited by J. Birn and E. Priest, in press, Cambridge Univ. Press, Cambridge, 2006.

B. Lembege, P.L. Pritchett, M.V. Goldman, and D.L. Newman, "Kinetic and Nonlinear Processes in Space Plasma", Radio Sci. Bulletin, No 314 (September, 2005), p. 16.

J. Birn, P.L. Pritchett, and 10 other authors, "Forced Magnetic Reconnection", Geophys. Res. Lett., 32, L06105, doi:10.1029/2004GL022058, 2005.

P.L. Pritchett, "The "Newton Challenge": Kinetic Aspects of Forced Magnetic Reconnection", J. Geophys. Res., 110, A10213, doi:10.1029/2005JA011228, 2005.

P.L. Pritchett, "Relativistic Electron Production During Driven Magnetic Reconnection, Geophys. Res. Lett., 33, L13104, doi:10.1029/2005GL025267, 2006.

P.L. Pritchett, "Relativistic Electron Production During Guide-Field Magnetic Reconnection, J. Geophys. Res., 111, A10212, doi:10.1029/2006JA011793, 2006.

P.-A. Gourdain, J. N. Leboeuf, and Y. Neches, "High resolution magnetohydrodynamic equilibrium code for unity beta plasmas", Accepted for Publication, Journal of Computational Physics, December 5, 2005. Available online January 19, 2006. doi:10.1016/j.jcp.2005.12.005

V. I. Sotnikov, V. V. Ivanov, T. E. Cowan, J. N. Leboeuf, B. V. Oliver, C. Coverdale, B. Jones, C. deeney, T. A. Mehlhorn, P. D. LePell, P. Hellinger, P. Travnicek, "Hybrid simulation of Z-pinches in support of wire array implosion experiments at NTF", Jour. Plasma Phys., Accepted for Publication, December 12, 2005.

Jean-Noel Leboeuf, Maha Ashour-Abdalla, Jean-Nichel Bosqued, Nicole Cornilleau-Wehrlin, David Schriver, and Vladimir Sotnikov, "Particle-in-cell guiding center models of ion velocity space shell instabilities in space and fusion plasmas", Jour. Plasma Phys., Accepted for publication, January 9, 2006.

David Schriver, Jean-Noel Leboeuf, Maha Ashour-Abdalla, Mostafa El-Alaoui, Jean-Nichel Bosqued, and Vladimir Sotnikov, "Loading experimental velocity distributions in particle-in-cell simulations of space and fusion plasmas", Jour. Plasma Phys., Accepted for publication, December 17, 2005.

M. Ashour-Abdalla, J. N. Leboeuf, D. Schriver, J.-M. Bosqued, N. Cornilleau-Wehrlin, V. Sotnikov, A. Marchaudon and A. N. Fazakerley, "Instabilities Driven by Ion Shell Distributions Observed by CLUSTER in the Mid-Altitude Plasma Sheet Boundary Layer," Journal of Geophysical Reseasrch-Space Physics, Accepted for Publication, March 7, 2006.

V. I. Sotnikov, V. V. Ivanov, T. E. Cowan, J. N. Leboeuf, B. V. Oliver, C. Coverdale, B. Jones, C. Deeney, T. A. Mehlhorn, G. S. Sarkisov and P.D. LePell, "Investigation of Electromagnetic Flute Mode Instability in a High Beta Z-pinch Plasma", IEEE Trans. Plasma Sci., Accepted for Publication, April 27, 2006.

Turbulence, magnetic fields, and plasma physics in clusters of galaxies A. A. Schekochihin and S. C. Cowley Phys. Plasmas 13, 056501 (2006)

Gyrokinetic simulations of off-axis minimum-q profile corrugations R. E. Waltz, M. E. Austin, K. H. Burrell, and J. Candy Phys. Plasmas 13, 052301 (2006)

Velocity-space resolution, entropy production, and upwind dissipation in Eulerian gyrokinetic simulations J. Candy and R. E. Waltz Phys. Plasmas 13, 032310 (2006)

The effect of safety factor and magnetic shear on turbulent transport in nonlinear gyrokinetic simulations J. E. Kinsey, R. E. Waltz, and J. Candy Phys. Plasmas 13, 022305 (2006)

Discrete particle noise in particle-in-cell simulations of plasma microturbulence W. M. Nevins, G. W. Hammett, A. M. Dimits, W. Dorland, and D. E. Shumaker Phys. Plasmas 12, 122305 (2005).

Microturbulent drift mode stability before internal transport barrier formation in the Alcator C-Mod radio frequency heated H-mode M. H. Redi, W. Dorland, C. L. Fiore, J. A. Baumgaertel, E. M. Belli, T. S. Hahm, G. W. Hammett, and G. Rewoldt Phys. Plasmas 12, 072519 (2005)

Noncurvature-driven modes in a transport barrier B. N. Rogers and W. Dorland Phys. Plasmas 12, 062511 (2005

Erratum: "Gyrokinetic simulations of ion and impurity transport" [Phys. Plasmas 12, 022305 (2005)] C. Estrada-Mila, J. Candy, and R. E. Waltz Phys. Plasmas 12, 049902 (2005

Gyrokinetic simulations of ion and impurity transport C. Estrada-Mila, J. Candy, and R. E. Waltz Phys. Plasmas 12, 022305 (2005)

Determination of long-range correlations by quiet-time statistics, V.E. Lynch, B.A. Carreras, R. Sanchez, B. LaBombard, B.Ph. van Milligen and D.E. Newman , Physics of Plasmas 12 052304 (2005)

On the Idenfification of SOC dynamics in the Sun-Earth system, R.A. Woodard, D.E. Newman, R. Sanchez and B.A. Carreras , capmtulo aparecido en Multiscale Coupling of Sun-Earth Processes, edited by A.T.Y. Lui, Y. Kamide and G. Consolini, Elsevier Publishing Company (2005) - ISBN: 0-444-51881-9

Quiet-time statistics of electrostatic turbulent fluxes from the JET tokamak and the W7-AS and TJ-II stellarators , R. Sanchez, B.Ph. van Milligen, D.E. Newman and B .A. Carreras, Physical Review Letters, 90 185005 (2003)

Local particle flux reversal under strongly sheared flow, P. W. Terry, D. E. Newman, and A. S. Ware, Phys. Plasmas 10, 1066 (2003).

Modelling of ELM-like phenomena via SOC-diffusive dynamics, R. Sanchez, D.E. Newman, B.A. Carreras, R. Woodard, W. Ferenbaugh and H.R. Hicks Nuclear Fusion , 43 1031 (2003)

A Transition in the Dynamics of a Diffusive Running Sandpile, D. E. Newman, R. Sanchez and B. A. Carreras, Phys Rev Lett., 204304, (2002)

A self-organized critical transport model based on critical-gradient fluctuation dynamics, L. Garcia, B. A. Carreras and D. E. Newman, Phys. Plasmas 9, 841 (2002)

Waiting-time statistics of self-organized critical systems, R. Sanchez, D. E. Newman, and B. A. Carreras,Phys. Rev. Lett. 88, 068302 (2002)

SOC-diffusive dynamics as a paradigm of plasma turbulent transport, R. Sanchez, D.E. Newman and B.A. Carreras, Nuclear Fusion, 41, 247 (2001)

**PI Frank Lee**

"Magnetic Polarizability of Hadrons from Lattice QCD in the Background Field Method", F.X. Lee, L. Zhou, W. Wilcox, J. Christensen, Phys. Rev. D 73, 034503 (2006), hep-lat/0509065

"Spin-3/2 baryons from an anisotropic lattice QCD action", L. Zhou and F.X. Lee, Phys. Rev. D (in press). hep-lat/0604023

"Excited decuplet baryons from QCD sum rules", F.X. Lee, submitted to Phys. Rev. D. nucl-th/0605065

"Spectroscopy of light hadrons in anisotropic lattice QCD", F.X. Lee, submitted to Int. J. Mod. Phys.

"Charmonium Spectrum from Quenched QCD with Overlap Fermions", S. Tamhankar, A. Alexandru, Y. Chen, S. J. Dong, T. Draper, I. Horvath, F. X. Lee, K. F. Liu, N. Mathur and J. B. Zhang, Phys. Lett. B 638, 55 (2006), hep-lat/0507027.

"Scalar mesons a0(1450) and s(600) from lattice QCD", N. Mathur, A. Alexandru, Y. Chen, S.J. Dong, T. Draper, I.Horvath, F.X. Lee, K.F. Liu, S. Tamhankar, and J.B. Zhang, submitted to Phys. Rev. Lett. hep-ph/0607110

"The Sequential Empirical Bayes Method: An Adaptive Constrained-Cuve Fitting Algorithm for Lattice QCD", Y. Chen, S.J. Dong, T. Draper, I. Horvath, F.X. Lee, K.F. Liu, N. Mathur, C. Srinivasan, J.B. Zhang, submitted to Phys. Rev. D, hep-lat/0405001.

"Glueball Spectrum and Matrix Elements on Anisotropic Lattices" Y. Chen, S.J. Dong, T. Draper, I. Horvath, F.X. Lee, K.F. Liu, N. Mathur, C. Morningstar, M. Peardon, B.L. Young, J.B. Zhang, Phys. Rev. D 73, 014516 (2006), hep-lat/0510074.

**PI T. S. Harry Lee**

Study of Nucleon Resonances with Electromagnetic Interactions T.-S. H. Lee and L. C. Smith, Submitted to Journal of Physics G.

Extraction and Interpretations of $\gamma N \rightarrow \Delta$ Form Factors at EBAC B. Julia-Diaz, T.-S. H. Lee, T. Sato, and L.C. Smith, Submitted to Phys. Rev. C

**PI Wei-li Lee**

W. X. Wang et. al, Nonlocal Neoclassical Transport in Tokamak and Spherical Torus Experiments, Phys. Plasmas <13>, 082501 (2006).

W. X. Wang et. al, Gyrokinetic Simulation of Global Turbulent Transport Properties in Tokamak Experiments, Phy. Plasmas <13>, 092505 (2006).

J. L. V. Lewandowski et al. Global particle-in-cell simulations of microturbulence with kinetic electrons, Phys. Plasmas <13>, 072306 (2006).

Y. Chen and S.E. Parker, "Electromagnetic gyrokinetic delta-f particle-in-cell turbulence simulation with realistic equilibrium profiles and geometry", J. Comput. Phys. (in press, 2006).

Y. Nishimura, Z. Lin, J. L. V. Lewandowski, and S. Ethier, A Finite Element Poisson Solver for Global Gyrokinetic Particle Simulations, J. Comput. Phys. <214>, 657 (2006).

Y. Nishimura and Z. Lin, A Finite Element Mesh in a Tokamak Edge Geometry, Contributions Plasma Phys. 7-9, 551-556 (August 2006).

W. W. Lee, Gyrokinetic particle simulation of fusion plasmas: path to petascale computing, invited talk, Second Annual DoE SciDAC Conference, Denver, CO (2006); to appear in Journal of Physics: Conference Series (SciDAC 2006).

W. W. Lee, Long time simulations of microturbulence, invited talk, Annual Sherwood Theory Conference, Dallas, TX; Bull. Am. Phys. Soc. 51-2, 111, (2006).

W. X. Wang et al., Gyrokinetic Studies of Nonlocal Properties of Turbulence-Driven and Neoclassical Transport, invited talk, IAEA Fusion Energy Conference, Chengdu, China (2006).

S. E. Parker, Zonal Flow Suppression of Electron Temperature Gradient Turbulence, invited talk, Joint Varenna-Lausance International Workshop, Varrena, Italy (2006).

S. Ethier, Gyrokinetic Particle Simulation of Fusion Plasma, invited talk, Fall Creek Falls Conference, Fall Creek Falls, TN (2006).

**PI William Lester**

A. Aspuru-Guzik, A. C. Kollias, R. Salomon-Ferrer, and W. A. Lester, Jr. "Quantum Monte Carlo: Theory and Applications to Atomic, Molecular and Nano Systems," in the Handbook of Theoretical and Computational Nanotechnology, eds. M. Rieth and W. Schommers, American Scientific Publishers (2005).

A. C. Kollias, D. Domin, G. Hill, M. Frenklach, D. M. Golden, and W. A. Lester, Jr., "Quantum Monte Carlo Study of Heats of Formation and Bond Dissociation Energies of Small Hydrocarbons," Int. J. Chem. Kinetics 37, 583 (2005).

A. C. Kollias, D. Domin, G. Hill, M. Frenklach, and W. A. Lester, Jr., "Quantum Monte Carlo Study of Small Hydrocarbon Atomization Energies," Mol. Phys. 104, 467 (2006).

A. Aspuru-Guzik and W. A. Lester, Jr., "Quantum Monte Carlo: Theory and Application to Molecular Systems," Adv. Quant. Chem. 49, 209 (2005).

R. Whitesides, A.C. Kollias, D. Domin, W.A. Lester, Jr., and M. Frenklach, "Graphene Layer Growth: Collision of Migrating 5-Member Rings," Fall Meeting of the Western States Section of the Combustion Institute, Stanford, CA, October 17-18, 2005, paper 05F-62.

R. Whitesides, A. C. Kollias, D. Domin, W. A. Lester, Jr., and M. Frenklach, "Graphene Layer Growth: Collision of Migrating Five-Member Rings," submitted to the 31st International Symposium on Combustion, University of Heidelberg, Germany, August 6-11, 2006.

W. A. Lester, Jr. and R. Salomon-Ferrer, "Some Developments in Quantum Monte Carlo for Electronic Structure: Methods and Application to a Bio System," THEOCHEM 771, 51 (2006).

B. Austin, A. Aspuru-Guzik, R. Salomon-Ferrer, and W. A. Lester, Jr., "Linear Scaling Evaluation of the Local Energy in Quantum Monte Carlo," to appear in Proceedings of the Pacifichem Symposium on Advances in Quantum Monte Carlo, Oxford University Press.

**PI Mary Ann Leung**

Mahmud, K. W., Leung, M.A., Reinhardt, W. P., Phase engineering of squeezed states and controlled entangled number states of Bose-Einstein Condensates in multiple wells, submitted to Phys. Rev. A., 2004, under review

**PI Rui Li**

"Curvature-Induced Bunch Self-Interaction for an Energy-Chirped Bunch in Bends", Jefferson Lab tech note Jlab-TN-05-046, under preparation for publication.

**PI Yu Lin**

Sun, X., Y. Lin, and X. Wang, Reversal of Magnetic Field Rotation in the Reconnection Layer Due to Shear Flow Effects, Journal of Geophysical Research, in press, 2006.

Lin, Y. and X. Y. Wang, Formation of Dayside Low-Latitude Boundary Layer Under Northward Interplanetary Magnetic Field, Geophysical Research Letters, in press, 2006.

**PI Feng Liu**

R. Pala and Feng Liu, Nature of reactive O2 and slow CO2 evolution kinetics in CO oxidation by TiO2 supported Au cluste, J. Chem. Phys. 125, 144714 (2006).

Li Huang, Feng Liu, Guang-Hong Lu and X. G. Gong, Surface Mobility Difference between Si and Ge and its Effect on Growth of SiGe Alloy Films and Islands, Phys. Rev. Lett 96, 016103 (2006).

G.H. Lu, Y. Zhang, S. Deng, T. Wang, M. Kohyama, R. Yamamoto, Feng Liu, K. Horikawa, and M. Kanno, Origin of intergranular embrittlement of Al alloys induced by Na and Ca segregation: Grain boundary weakening, Phys. Rev. B 73, 224115 (2006).

Raj Ganesh S. Pala and Feng Liu, Critical Epi-Nucleation on Reconstructed Surfaces and a Model Study of Si(001) Homoepitaxy, Phys. Rev. Lett 95, 136106 (2005).

**PI Keh-Fei Liu**

[UK/05-06] S. Tamhankar, A. Alexandru, Y. Chen, S.J. Dong, T. Draper, I. Horvath, F.X. Lee, K.F. Liu, N. Mathur, and J.B. Zhang, `Charmonium Spectrum from Quenched QCD with Overlap Fermions', Phys. Lett. B638, 55-60, (2006), [hep-lat/0507027].

[UK/05-07] A. Alexandru, M. Faber, I. Horvath, K.F. Liu, `Lattice QCD at finite density via a new canonical approach', Phys. Rev. D72, 114513 (2005), [hep-lat/0507020].

[UK/05-09] Y. Chen, A. Alexandru, S.J. Dong, T. Draper, I. Horvath, F.X. Lee, K.F. Liu, N. Mathur, C. Morningstar, M. Peardon, S. Tamhankar, B.L. Young, and Z.B. Zhang, Glueball Spectrum and Matrix Elements on Anisotropic Lattices', Phys. Rev. D73, 014516 (2006), [hep-lat/0510074].

[UK/05-12] I. Horvath, A. Alexandru, J.B. Zhang, Y. Chen, S.J. Dong, T. Draper, F.X. Lee, K.F. Liu, N. Mathur, S. Tamhankar, H.B. Thacker, `Inherently Global Nature of Topological Charge Fluctuations in QCD', Phys. Lett., B612 21-28, (2005), [hep-lat/0501025].

[UK/05-13] I. Horvath, A. Alexandru, J.B. Zhang, Y. Chen, S.J. Dong, T. Draper, K.F. Liu, N. Mathur, S. Tamhankar, H.B. Thacker, `The Negativity of the Overlap-Based Topological Charge Density Correlator in Pure-Glue QCD and the Non-Integrable Nature of its Contact Part', Phys. Lett., B617, 49-59, (2005), [hep-lat/0504005].

[UK/05-14] K.F. Liu and N. Mathur, `A Review of Pentaquark Calculations on the Lattice', Int. J. Mod. Phys., A21, 851-858 (2006), [hep-lat/0510036].

[UK/05-17] A. Alexandru, I. Horvath, J.B. Zhang, `The reality of the fundamental topological structure in the QCD vacuum', Phys. Rev. D72, 034506 (2005), [hep-lat/0506018].

[UK/06-06] N. Mathur, A. Alexandru, Y. Chen, S.J. Dong, T. Draper, I. Horvath, F.X. Lee, K.F. Liu, S. Tamhankar, and J.B. Zhang, `a_0(1450) and \sigma(600) Mesons from Lattice QCD', submitted for publication in Phys. Rev. D, [hep-ph/0607110].

[UK/06-07] H.Y. Cheng, C.K. Chua, and K.F. Liu, `Scalar Glueball, Scalar Quarkonia, and their Mixing, accepted for publication in Phys. Rev. D, [hep-ph/0607206].

[UK/06-09] I. Horvath, `A Framework for systematic study of QCD vacuum structure I:, Kolmogorov entropy and the principle of chiral ordering', submitted for publication, [hep-lat/0605008].

[UK/06-10] I. Horvath, `A Framework for Systematic Study of QCD Vacuum Structure II: Coherent Lattice QCD', submitted for publication, [hep-lat/0607031].

[UK/06-11] Terrence Draper, Nilmani Mathur, Andrei Alexandru, Ying Chen, Shao-Jing Dong, Ivan Horvath, Frank X. Lee, Keh-Fei Liu, Sonali Tamhankar, Jianbo Zhang, `On the Locality and Scaling of Overlap Fermions at Coarse Lattice spacings', submitted for publication, [hep-lat/0609034].

**PI Stewart Loken**

A Consistent prescription for the production involving massive quarks in hadron collisions. Borut Paul Kersevan (Stefan Inst., Ljubljana & Ljubljana U.) , Ian Hinchliffe (LBL, Berkeley) . Mar 2006. 22pp. Published in JHEP 0609:033,2006 e-Print Archive: hep-ph/0603068

Supersymmetry parameter analysis: SPA convention and project. J.A. Aguilar-Saavedra et al. SLAC-PUB-11579, CERN-PH-TH-2005-232, DESY-05-242, FERMILAB-PUB-05-524-T, KEK-TH-1054, Nov 2005. 19pp. Published in Eur.Phys.J.C46:43-60,2006 e-Print Archive: hep-ph/0511344

**PI Steven Louie**

Yayu Wang, X.H. Lu, E. Kioupakis, R. Yamachika, D. Wegner, S.G.Louie, M.F. Crommie, J. E. Dahl, S. G. Liu and R. M. K. Carlson, "Spatially resolved electronic and vibronic characteristics of tetramantane diamondoid", submitted.

P.T. Tangney, R.B. Capaz, C.D. Spataru, M.L. Cohen, and S.G. Louie, "Structural transformations of carbon nanotubes under hydrostatic pressure," Nano Lett. 5, 2268 (2005).

C.D. Spataru, S. Ismail-Beigi, R.B. Capaz, and S.G. Louie, "Theory and Ab Initio Calculation of Radiative Lifetime of Excitons in Semiconducting Carbon Nanotubes," Phys. Rev. Lett. 95, 247402 (2005).

C.-H. Park, C.D. Spataru, and S.G. Louie, "Excitons and Many-Electron Effects in the Optical Response of Single-Walled Boron Nitride Nanotubes", Phys. Rev. Lett. 96, 126105 (2006).

Y.Z. Ma, C.D. Spataru, L. Valkunas, S.G. Louie, and G.R. Fleming, "Spectroscopy of Zigzag Single-Walled Carbon Nanotubes: Comparing Femtosecond Transient Absorption Spectra with Ab Initio Calculations," Phys. Rev. B 74, 085402 (2006).

K.H. Khoo, J.B. Neaton, and S.G. Louie, "Conductance of hydrogen across Pt and Pd leads", submitted to NanoLett.

**PI Walter Loveland**

G.L. Malli,(Communication) "Dissociation energy of Ekaplutonium fluoride E126F", J. Chem. Phys. 124,071102(2006). The first study of a molecular system with g spinors/orbitals occupied in one of its atoms in the ground state.

G.L. Malli,(Communication) "Electronic structure and prediction of atomization energy of naked homoleptic uranium hexacarbonyl U(CO)6", J. Chem. Phys. 124,021102(2006). U(CO)6 so far has not been synthesized so far despite numerous attempts dating back to Manhattan Project. My prediction of its very large binding energy should goad chemists to devise novel ingenious methods for its synthesis.

R. Arratia-Perez and G.L. Malli, "Relativistic molecular orbital study of the optical and magnetic properties of hexachloro protoactinate (IV): PaCl6-2, J. Chem.Phys. 124,074321(2006).

R. Arratia-Perez, L. Hernadez-Acevedo and G.L. Malli, "Calculated optical and magnetic properties of hexafluorouranate(V)anion:UF6-", J .Chem. Phys. 121,7743 (2004)

G.L. Malli, M. Siegert and D.P. Turner, "Relativistic and Electron correlation Effects for Molecules of Heavy Elements: Ab Initio Fully Relativistic Coupled-Cluster Calculations for PbH4", Int. J. Quantum Chem. 99,940(2004)

G.L. Malli, "Relativistic Quantum Chemistry of Heavy and Superheavy Elements: Fully Relativistic Coupled-Cluster Calculatiions for Molecules of Heavy and Transactinide Superheavy Elemens", in Fundamental World of Quantum Chemistry, E.J. Brandas and E.S. Kryachko (eds), Kluwer Academic,Vol III,323 (2004).

W. Loveland, D.J.Morrissey and G.T.Seaborg, "Modern Nuclear Chemistry", Wiley, New York, 671 pages (2006).

R.W. Stoenner, R.L. Klobucher, P.E. Haustein, G.J. Virtes, J.B. Cumming and W. Loveland, "Angular distribution in multifragmentation", Phys. Rev. C 73,047602(2006).

K.E. Gregorich and W. Loveland et al. "Attempts to confirm superheavy element production in the 48Ca+ 238U reaction", Phys. Rev. C 72, 014605(2005).

W. Loveland, A. Gallant and C. Joiner, J. Radioanal. Nucl. Chem. 263,151(2005).

J.F. Liang, D. Shapira,...,W. Loveland et al, "Sub-barrier fusion induced by neutron-rich radioactive 132Sn", Eur. Phys. J, A25, Suppl 1,239(2005)

W.Loveland, "Fusion Studies with RIBS", Eur. Phys. J A25, Supll 1,233 (2005)

K.E. Gregorich, W. Loveland,et al "Attempts to confirm superheavby element production in the 48 Ca+238 U reaction", Phys. Rev. C 72,014605(2005).

D. Shapira, F. Liang,....W. Loveland,et al ," Measurement of evaporation residue cross sections from reactions with radioactive nutron rich beams", Eur. Phys. JU A 25, Suppl 1,239 (2005).

W. Loveland, "Synthesis of heavy nuclei using radioactive beams", Nucl.Phys. A 746,108c(2004).

P.R. Watson, W. Loveland, P.M. Zelinski, K.E. Gregorich and H. Nitsche, Nucl. Instru. Meth. Phys. Res. B 226,543(2004).

J.F. Liang, D. Shapira, C.J. Gross, J.R. Beene, J.D. Bierman, A. Galindo-Uribarri, J. Gomez del Compo, P.A. Hausladen, Y. Larochelle, W. Loveland et. al "Sub-barrier fusion enhancement in neutron-rich 132 Sn on 64 Ni", Prog. Theoret. Physics Supplement, 154,106 (2004).

## M

**PI Chung-Pei Ma**

M. Boylan-Kolchin, C.-P. Ma, and E. Quataert (2006), Monthly Notices of Royal Astronomical Society, 369, 1081. "Red Mergers and the Assembly of Massive Elliptical Galaxies: the Fundamental Plane and its Projections"

M. Boylan-Kolchin and C.-P. Ma (2006), MNRAS, in press. "Satellite Accretion onto Massive Galaxies with Central Black Holes"

L. Desroches, E. Quataert, C.-P. Ma, and A. West (2006), submitted to MNRAS. "Luminosity Dependence in the Fundamental Plane Projections of Elliptical Galaxies"

**PI Kyoko Makino**

D.A. Ovsyannikov, K. Makino, and M. Berz (Eds.). Proceedings, 8th International Computational Accelerator Physics Conference, St. Petersburg. Elsevier, 2006.

C. J. Johnstone, M. Berz, and K. Makino. Staging acceleration and cooling in a neutrino factory. NIM-A, 258:282-291, 2006.

K. Makino. Suppression of the wrapping effect by Taylor model based verified integrators: Long-term stabilization by preconditioning. International Journal of Differential Equations and Applications, 2006.

A. Poklonskiy, D. A. Ovsyannikov, A. D. Ovsyannikov, D. Neuffer, and M. Berz. Optimization of the buncher and phase rotator for a neutrino factory. SPbSU Messenger (Vestnik), 10,1, 2006.

S. L. Manikonda and M. Berz. Multipole expansion solution of the Laplace equation using surface data. NIM-A, 258:175-183, 2006.

K. Makino, M. Berz, Y.-K. Kim, and P. Snopok. Long term stability of large accelerators. ECMI Newsletter on Result Verification, A. Frommer and B. Lang (Eds.), 39, 2006.

P. Snopok, D. A. Ovsyannikov, A. D. Ovsyannikov, M. Berz, and C. Johnstone. Modeling and optimization of muon collider interaction regions. SPbSU Messenger (Vestnik), 10,1, 2006.

M. Berz and K. Makino. Suppression of the wrapping effect by Taylor model based verified integrators: Long-term stabilization by shrink wrapping. International Journal of Differential Equations and Applications, 2006.

M. Berz, K. Makino, and Y.-K. Kim. Long-term stability of the Tevatron by validated global optimization. NIM-A, 258:1-10, 2005.

S. L. Manikonda, M. Berz, and K. Makino. A highly accurate high-order validated method to solve the Neumann boundary condition problem for the 3D Laplace equation. Transactions on Computers, 4,11:1604-1610, 2005.

P. Snopok, M. Berz, K. Makino, and C. Johnstone. Simulation and optimization of the Tevatron accelerator. Lecture Notes on Computational Science and Engineering, 50:199-209, 2005.

J. Grote, K. Makino, and M. Berz. High-order validated representation of Poincare maps. Transactions on Systems, 4:1986-1992, 2005.

A. A. Poklonskiy, D. Neuffer, C. J. Johnstone, M. Berz, K. Makino, D. A. Ovsyannikov, and A. D. Ovsyannikov. Optimizing the adiabatic buncher and phase rotator. NIM-A, 258:135-141, 2005.

J. Grote, M. Berz, and K. Makino. High-order representation of Poincare maps. Lecture Notes on Computational Science and Engineering, 50:59-66, 2005.

K. Makino and M. Berz. Range bounding for global optimization with Taylor models. Transactions on Computers, 4,11:1611-1618, 2005.

P. V. Snopok, C. J. Johnstone, M. Berz, D. A. Ovsyannikov, and A. D. Ovsyannikov. Study and optimal correction of a systematic skew quadrupole field in the Tevatron. NIM-A, 258:142-146, 2005.

S. L. Manikonda and M. Berz. A highly accurate high-order method to solve the Neumann boundary condition problem for the 3D Laplace equation. International Journal of Pure and Applied Mathematics, 23,3:365-378, 2005.

K. Makino and M. Berz. COSY INFINITY version 9. NIM-A, 258:346-350, 2005.

**PI Shaolin Mao**

Shaolin Mao, Edward Patton, Z.G. Feng, and Efstathios Michaelides, Impact of an imposed wall-jet on canopy turbulence and the net ecosystem-atmosphere exchange of carbon dioxide, submitted to Boundary-Layer Meteorology, 2006.

Shaolin Mao, Z.G. Feng, and E.E. Michaelides, Large eddy simulation of low-level jet-like flow in canopy, accepted for publication, Enviromental Fluid Mechanics, 2006.

Moniqe Leclerc, Shaolin Mao, and E.E. Michaelides, Flux footprint analysis over horizontal inhomogeneous canopies by large-eddy simulation, submitted to Q.J. Royal Meteorological Society, 2006.

**PI Osni Marques**

T. Drummond and Osni marques, The Advanced CompuTational Software (ACTS) Collection, ACM TOMS, 31:282-301, 2005.

**PI Angelo Mascarenhas**

"Novel approach to tuning the physical properties of organic-inorganic hybrid semiconductors", Y. Zhang, G. M. Dalpian, B. Fluegel, S.-H. Wei, A. Mascarenhas, X.-Y. Huang, J. Li, and L. W. Wang, Phys. Rev. Lett. 96, 026405 (2006).

"Study of phase selectivity of organic-inorganic hybrid semiconductors", C.-Y. Moon, G. M. Dalpian, Y. Zhang, S.-H. Wei, X.-Y. Huang, and J. Li, Chem. Mater. 18, 2805 (2006).

"Systematic approach to distinguishing a perturbed host state from an impurity state in a supercell calculation for a doped semiconductor: using GaP:N as an example", Y. Zhang, A. Mascarenhas, and L.-W. Wang, Phys. Rev. B(Rapid Commun) 74, 41201 (2006).

"Ordering induced direct/indirect transitions in semiconductor alloys", C.-Y. Moon, J. Li, S.-H. Wei, A. T.-L. Lim and Y. P. Feng, Phys. Rev. B (in press).

"Band gap of Hg chalcogenides: Symmetry-reduction-induced band gap opening of materials with inverted band structures", C.-Y. Moon and S.-H. Wei, Phys. Rev. B 74, 045205 (2006).

"Impurity-induced phase stabilization of semiconductors", G. M. Dalpian, Y. Yan, and S.-H. Wei, Appl. Phys. Lett. 89, 011907 (2006).

"Photoluminescence from the nitrogen-perturbed above bandgap states in dilute GaAsN alloys probed by micro-PL", 6. P. H. Tan, X. D. Luo, Z. Y. Xu, Y. Zhang, A. Mascarenhas , H. P. Xin, C. W. Tu, and W. K. Ge, Phys. Rev. B 73, 205205 (2006).

**PI Manos Mavrikakis**

N. Schumacher, A. Boisen, S. Dahl, A. A. Gokhale, S. Kandoi, L. C. Grabow, J. A. Dumesic, M. Mavrikakis and I. Chorkendorff, "Trends in low-temperature water-gas shift reactivity on transition metals." Journal of Catalysis, 2005. 229(2): p. 265.

J. Greeley and M. Mavrikakis, "Surface and subsurface hydrogen: Adsorption properties on transition metals and near-surface alloys." Journal of Physical Chemistry B, 2005. 109(8): p. 3460.

J. L. Zhang, M. B. Vukmirovic, Y. Xu, M. Mavrikakis and R. R. Adzic, "Controlling the catalytic activity of platinum-monolayer electrocatalysts for oxygen reduction with different substrates." Angewandte Chemie-International Edition, 2005. 44(14): p. 2132.

J. L. Zhang, M. B. Vukmirovic, K. Sasaki, A. U. Nilekar, M. Mavrikakis and R. R. Adzic, "Mixed-metal Pt monolayer electrocatalysts for enhanced oxygen reduction kinetics." Journal of the American Chemical Society, 2005. 127(36): p. 12480.

Y. Xu, J. Greeley and M. Mavrikakis, "Effect of subsurface oxygen on the reactivity of the Ag(111) surface." Journal of the American Chemical Society, 2005. 127(37): p. 12823.

J. Greeley and M. Mavrikakis, "Near-surface alloys for hydrogen fuel cell applications." Catalysis Today, 2006. 111(1-2): p. 52.

S. Kandoi, J. Greeley, M. A. Sanchez-Castillo, S. T. Evans, A. A. Gokhale, J. A. Dumesic and M. Mavrikakis, "Prediction of experimental methanol decomposition rates on platinum from first principles." Topics in Catalysis, 2006. 37(1): p. 17.

L. Grabow, Y. Xu and M. Mavrikakis, "Lattice strain effects on CO oxidation on Pt(111)." Physical Chemistry Chemical Physics, 2006. 8(29): p. 3369. - including cover page image.

J. Zhang, M.B. Vukmirovic, K. Sasaki, A.U. Nilekar, F. Uribe, M. Mavrikakis and R.R. Adzic, "Platinum Monolayer Electrocatalysts for Oxygen Reduction." Electrochimica Acta (in press).

A. U. Nilekar, J. Greeley and M. Mavrikakis, "A simple rule of thumb for diffusion on transition metal surfaces." Angewandte Chemie International Edition (in press).

M. Mavrikakis, "Computational Approaches: A search engine for catalysts." Nature Materials, (in press).

T. Mitsui, E. Fomin, F. Ogletree, M. Salmeron, A. U. Nilekar and M. Mavrikakis, "Manipulation and patterning of the surface concentration of hydrogen on Pd(111) by electric fields." (submitted).

**PI William McCurdy**

C. S. Trevisan, A. E. Orel and T. N. Rescigno, Resonant Electron-CF Collision Processes, Phys. Rev. A 72, 062720 (2005).

Wim Vanroose, F. Martin, T. N. Rescigno and C. W. McCurdy, Complete Photofragmentation of the H2 Molecule as a Probe of Molecular Electron Correlation, Science 310, 1787 (2005).

K. Houfek, T. N. Rescigno and C. W. McCurdy, A Numerically Solvable Model for Resonant Collisions of Electrons with Diatomic Molecules, Phys. Rev. A 73, 032721 (2006).

T. N. Rescigno, C. S. Trevisan and A. E. Orel, Dynamics of Low-Energy Electron Attachment to Formic Acid , Phys. Rev. Lett. 96, 213201 (2006).

D. J. Haxton, C. W. McCurdy and T. N. Rescigno, Angular Dependence of Dissociative Electron Attachment to Polyatomic Molecules: Application to the 2B1 Metastable State of the H2O and H2S Anions, Phys. Rev. A 73, 062724 (2006).

C. S. Trevisan. A. E. Orel and T. N. RescignoElastic scattering of low-energy electrons by tetrahydrofuran, J. Phys. B 39, L255 (2006).

Wim Vanroose, D. A. Horner, F. Martmn, T. N. Rescigno and C. W. McCurdy, Double Photoionization of Aligned Molecular Hydrogen, Phys. Rev. A 74, xxxx (2006).

T. N. Rescigno, Wim Vanroose, D. A. Horner, F. Martin and C. W. McCurdy, First Principles Study of Double Photoionization of H2 Using Exterior Complex Scaling, Elec. Spectros., Rel. Phenom. (submitted).

**PI William McMahon**

"5-7-5 line defects on As/Si(100): A general stress-relief mechanism for V/IV surfaces"; W. E. McMahon, Iskander G. Batyrev, T. Hannappel J. M. Olson, and S. B. Zhang; Phys. Rev. B 74, 033304 (2006).

**PI Anthony Mezzacappa**

"On the Performance of SPAI and ADI-like Preconditioners for Core Collapse Supernova Simulations in One Spatial Dimension", by Dennis Smolarski, Ramesh Balakrishnan, Eduardo D'Azevedo, John W. Fettig, Bronson Messer, Anthony Mezzacappa, Faisal Saied, Paul E. Saylor, and F. Douglas Swesty, Computer Physics Communications, vol. 175 pgs. 330-338 (Sept. 2006)

"A Numerical Algorithm for Modeling Multigroup Neutrino-Radiation Hydrodynamics in Two Spatial Dimension", F.D. Swesty and Eric S. Myra, submitted to The Astrophysical Journal (August 2006)

"The Spherical Accretion Shock Instability in the Linear Regime", J. M. Blondin and A. Mezzacappa, The Astrophysical Journal, vol 642, 401 (Sept. 2006)

"Composition of the Innermost Core-Collapse Supernova Ejecta", C. Frvhlich, P. Hauser, M. Liebendvrfer, G. Martmnez-Pinedo, F.-K. Thielemann, E. Bravo, N. T. Zinner, W. R. Hix, K. Langanke, and A. Mezzacappa, The Astrophysical Journal, vol. 637, p. 415, (Jan. 2006)

"Simultaneous flavor transformation of neutrinos and antineutrinos with dominant potentials from neutrino-neutrino forward scattering", G.M. Fuller and Y.-Z. Qian, Phys. Rev. D, vol. 73, p. 023004 (Jan 2006)

"Dark matter sterile neutrinos in stellar collapse: alteration of energy/lepton number transport and a mechanism for supernova explosion enhancement", J. Hidaka, and G. M. Fuller, submitted (astro-ph/0609425)

"Light Element Signatures of Sterile Neutrinos and Cosmological Lepton Numbers", C. J. Smith, G. M. Fuller, C. T. Kishimoto, and K. N. Abazajian, Phys. Rev. D., vol. 74, p. 085008 (2006)

"Coherent Development of Neutrino Flavor in the Supernova Environment", H. Duan, G. M. Fuller, J. Carlson, and Y.-Z. Qian, submitted (astro-ph/0608050)

"Stellar Collapse Dynamics With Neutrino Flavor Changing Neutral Currents" P. Amanik and G. M. Fuller, submitted (astro-ph/0606607)

**PI David Mikkelsen**

"Confinement and Transport Research in Alcator C-Mod", M. Greenwald, et al., accepted by Fusion Sci. Tech. (2006).

**PI Norman Miller**

N. L. Miller, J. Jin, Y. He, and C.-F. Tsang, Analyzing the Local Climate Impacts due to the Three Gorges Dam. American Meteorological Society 16th Symposium on Global Change & Climate Variations, January 9-13, 2005, San Diego, CA.

**PI William Miller**

J. Vanicek, W. H. Miller, J. F. Castillo and F. J. Aoiz, Quantum Instanton Evaluation of the Kinetic Isotope Effects, J. Chem. Phys. 123, 054108.1-14 (2005).

Y. Li and W. H. Miller, Using a Family of Dividing Surfaces Normal to the Minimum Energy Path for Quantum Instanton Rate Constants, J. Chem. Phys. 125, 064104.1-8 (2006).

J. Liu and W. H. Miller, Using the Thermal Gaussian Approximation for the Boltzmann Operator in Semiclassical Initial Value Time Correlation Functions, J. Chem. Phys. 125, 224104.1-13 (2006).

**PI Warren Mori**

W. Lu, M. Tzoufras, C. Joshi, F.S. Tsung, W.B. Mori, J. Vieira, R.A. Fonseca, and L.O. Silva, "Generating multi-GeV electron bunches using single stage laser wakefield acceleration in the blowout regime,"submitted to Nature Physics.

M. J. Hogan, C. D. Barnes, C. E. Clayton, F. J. Decker, S. Deng, P. Emma, C. Huang, R. H. Iverson, D. K. Johnson, C. Joshi, T. Katsouleas, P. Krejcik, W. Lu, K. A. Marsh, W. B. Mori, P. Muggli, C. L. O. Connell, E. Oz, R. H. Siemann, and D. Walz, "Multi-GeV Energy Gain in a Plasma-Wakefield Accelerator", Phys. Rev. Lett., 95, 054802 (2005).

S. Deng, C. D. Barnes, C. E. Clayton, C. Oonnell, F. J. Decker, R. A. Fonseca, C. Huang, M. J. Hogan, R. Iverson, D. K. Johnson, C. Joshi, T. Katsouleas, P. Krejcik, W. Lu, W. B. Mori, P. Muggli, E. Oz, F. Tsung, D. Walz, and M. Zhou, "Hose Instability and Wake Generated by an Intense Electron Beam in a Self-Ionized Gas", Phys. Rev. Lett., 96, 045001 (2006).

S. P. D. Mangles, A. G. R. Thomas, M. C. Kaluza, O. Lundh, F. Lindau, A. Persson, F. S. Tsung, Z. Najmudin, W. B. Mori, C.-G. Wahlstrvm, and K. Krushelnick, "Laser-Wakefield Acceleration of Monoenergetic Electron Beams in the First Plasma-Wave Period", Phys. Rev. Lett., 96, 215001 (2006).

S.P.D. Mangles, K. Krushelnick, Z. Najmudin, M.S. Wei, B. Walton, A. Gopal, A.E. Dangor, S. Fritzler, C.D. Murphy, A.G.R. Thomas, W.B. Mori, J. Gallacher, D. Jaroszynski, P.A. Norreys, R. Viskup, "The generation of mono-energetic electron beams from ultrashort pulse laser-plama interactions", Phil. Trans. Of the Royal Society A., 364, 663 (2006).

F. S. Tsung, W. Lu, M. Tzoufras, W. B. Mori, C. Joshi, J. M. Vieira, L. O. Silva, and R. A. Fonseca, "Simulation of monoenergetic electron generation via laser wakefield accelerators for 5_ TW lasers", Phys. Plas., 13, 056708 (2006).

W. Lu, C. Huang, M. Zhou, M. Tzoufras, F. S. Tsung, W. B. Mori, and T. Katsouleas, "A nonlinear theory for multidimensional relativistic plasma wave wakefields", Phys. Plas., 13, 056709 (2006).

W. Lu, C. Huang, M. Zhou, W. B. Mori, and T. Katsouleas, "Nonlinear Theory for Relativistic Plasma Wakefields in the Blowout Regime", Phys. Rev. Lett., 96 165002 (2006).

C. Huang, V.K. Decyk, C. Ren, M. Zhou, W. Lu, W.B. Mori, J.H. Cooley, T.M. Antonsen, Jr. and T. Katsouleas, "QUICKPIC: A highly efficient particle-in-cell code for modeling wakefield acceleration in plasmas," Journal of Computational Physics, 217(2), 658-679, 2006

A. . Z. Ghalam, T. Katsouleas, V. K. Decyk, C. K. Huang, W. B. Mori, G. Rumolo, E. Benedetto, and F. Zimmermann, "Three-dimensional continuous modeling of beam-electron cloud interaction: Comparison with analytic models and predictions for the present and future circular machines", Phys. Plas., 13, 056710 (2006).

M. Tzoufras, C. Ren, F. S. Tsung, J. W. Tonge, W. B. Mori, M. Fiore, R. A. Fonseca, and L. O. Silva, "Space-Charge Effects in the Current-Filamentation or Weibel Instability", Phys. Rev. Lett., 96, 105002 (2006).

**PI James Morris**

M. I. Mendelev, J. Schmalian, C. Z. Wang, J. R. Morris and K. M. Ho, "Interface mobility and the liquid-glass transition in a one-component system described by an EAM potential," Phys. Rev. B 74, 104206 (2006).

R. S. Aga, J. R. Morris, V. Levashov and T. Egami, "Local structural fluctuations in a supercooled liquid," to appear in Mat. Sci. Eng. A.

J. R. Morris, U. Dahlborg and M. Calvo-Dahlborg, "Recent developments and outstanding challenges in theory and modeling of liquid metals," to appear in J. Non-cryst. Sol.

Min Xu, Y. Y. Ye, J. R. Morris, D. Sordelet and M. J. Kramer, "Influence of Pd on formation of amorphous and quasicrystal phases in rapidly quenched Zr2Cu(1-x)Pdx," Phil. Mag 86, 389 (2006).

C. L. Fu and Maja Krcmar, "First-principles studies of the structural, defect, and mechanical properties of B2 FeCo alloys", Physical Review B (in press).

M. K. Miller, C. L. Fu, M. Krcmar, D. T. Hoelzer, and C. T. Liu, "Vacancies as an alloy design component", Nature Materials (submitted).

**PI Christopher Mundy**

I.F.W. Kuo, C.J. Mundy, B.L. Eggimann, M.J. McGrath, I.J. Siepmann, B. Chen, J. Vieceli, and D.J. Tobias, "Structure and Dynamics of the Aqueous Liquid-Vapor Interface: A Comprehensive Particle-Based Simulation Study", J. Phys. Chem. B, 110 (8), 3738 -3746, 2006.

N. Goldman and L. E. Fried, "A superionic phase of Hydrogen Fluoride (HF) at high pressures and temperatures," J. Chem. Phys. 125, 044501, 2006.

**PI Paul Murad**

"Closed-Form Solutions to the Transient/Steady-State Navier-Stokes Fluid Dynamic Equations", STAIF-2006, Albuquerque, New Mexico, February 2006.

## N

**PI Habib Najm**

J. Ray, C. A. Kennedy, S. Lefantzi and H. N. Najm, "Using high-order methods on adaptively refined block-structured meshes - derivatives, interpolations, and filters", SIAM Journal on Scientific Computing, 2006. In press.

**PI Farrokh Najmabadi**

T.K. Mau, H. McGuinness, A. Grossman, R. Raffray, D. Steiner, "Exploratory Divertor Heat Load Studies for Compact Stellarator Reactors" Proc. 21th IEEE/NPSS Symposium on Fusion Engineering, Knoxville, Tenessee, Sept. 26-29, 2005.

T.K. Mau, H. McGuiness, A. Grossman, R. Raffray, X. Wang, D. Steiner, "Divertor Configuration and Heat Load Distribution for a Compact Stellarator Reactor," submitted to 17th Top. Meeting on the Technology of Fusion Energy, Albuquerque, New Mexico, November 13-15, 2006. To be published in Fusion Science and Technology thereafter.

**PI Rick Nebel**

L. Chacon, D. A. Knoll, "A fully implicit 3D extended MHD algorithm," 33nd EPS Conference on Plasma Physics, June 19-23, 2006, Rome, Italy.

L. Chacon, "A fully implicit 3D extended MHD algorithm," 32nd EPS Conference on Plasma Physics, June 27th - July 1st, 2005, Tarragona, Spain.

L. Chacon, "A non-staggered, conservative, , finite-volume scheme for 3D implicit extended magnetohydrodynamics in curvilinear geometries," Comput. Phys. Comm., 163 (3), 143-171 (2004).

L. Chacon, D. A. Knoll, "A 2D high-b Hall MHD implicit nonlinear solver," J. Comput. Phys., 188 (2), 573-592 (2003).

L. Chacon, D. A. Knoll, J. M. Finn, "An implicit, nonlinear reduced resistive MHD solver," J. Comput. Phys., 178, 15-36 (2002).

**PI John Negele**

The N to Delta electromagnetic transition form-factors from lattice QCD. C. Alexandrou, Ph. de Forcrand, H. Neff, J. W. Negele, W. Schroers, A. Tsapalis, Phys.Rev.Lett.94:021601,2005. [hep-lat/0409122]

The Nucleon electromagnetic form factors from Lattice QCD. C. Alexandrou, G. Koutsou, J.W. Negele and0 A. Tsapalis Phys.Rev.D74:034508,2006. [hep-lat/0605017]

The Axial N to Delta transition form factors from Lattice QCD. C. Alexandrou, Th. Leontiou, J.W. Negele and A. Tsapalis Submitted to Phys. Rev. Lett. [hep-lat/0607030]

The Nucleon axial charge in full lattice QCD, R.G. Edwards et al. (LHP Collaboration) Phys.Rev.Lett.96:052001,2006. [hep-lat/0510062]

**PI Gregory Newman**

Commer, M. and Newman G., 2006, An accelerated time domain finite difference simulation scheme for three-dimensional transient electromagnetic modeling using geometric multigrid concepts: Radio Science, 41, 1-15.

Hoversten G. M., Newman G., Geier N., and Flanagan G., 2006, 3D modeling of a deepwater EM exploration survey: geophysics, 71, G239-G248.

**PI Cheuk-Yiu Ng**

K.-C. Lau and C. Y. Ng, Acc. Chem. Res., in press (2006). "Benchmarking state-of-the-art ab initio thermochemical predictions with accurate pulsed-field ionization photoion-photoelectron measurements".

K.-C. Lau and C. Y. Ng, J. Chem. Phys., 124, 044323 (2006). "Accurate ab initio predictions of ionization energies and heats of formation for the 2-propyl, phenyl, and benzyl radicals".

K.-C. Lau and C. Y. Ng, Chinese J. Chem. Phys., 19, 29 (2006). "Accurate ab initio predictions of ionization energies and heats of formation for the cyclopropenylidene, propargylene and propadienylidene radicals".

K.-C. Lau, H. K. Woo, P. Wang, X. Xing, and C. Y. Ng, J. Chem. Phys., 124, 224311 (2006). "Vacuum Ultraviolet Laser Pulsed Field Ionization-Photoelectron Study of Cis-Dichloroethene".

T. Zhang, X. N. Tang, K.-C. Lau, C.Y. Ng, C. Nicolas, D. S. Peterka, M. Ahmed, Melita L. Morton, Branko Ruscic, R. Yang, L. X. Wei, C. Q. Huang, B. Yang, J. Wang, L. S. Sheng, Y. W. Zhang, and F. Qi, J. Chem. Phys., 124, 074302 (2006). "Direct Identification of Propargyl Radical in Combustion Flames by VUV Photoionization Mass Spectrometry".

Xi Xing, M.-K. Bahng, P. Wang, K. C. Lau, S.-J. Baek, and C. Y. Ng, J. Chem. Phys., 125, 133304 (2006). "Rovibrationally selected and resolved state-to-state photoionization of ethylene using the infrared-vacuum ultraviolet pulsed field ionization-photoelectron method".

R. A. Dressler and Y. Chiu, D. J. Levandier, X. N. Tang, Y. Hou, C. Chang, C. Houchins, H. Xu, and C. Y. Ng, J. Chem. Phys., 125, 132306 (2006). "The Study of State-Selected Ion-Molecule Reactions using the Pulsed-Field Ionization-Photoion Technique".

**PI Esmond Ng**

Volkan Akelik, George Biros, Omar Ghattas, David Keyes, Kwok Ko, Lie-Quan Lee, and Esmond G. Ng. "Adjoint Methods for Electromagnetic Shape Optimization of the Low-Loss Cavity for the International Linear Collider", Proceedings of SciDAC 2005, Scientific Discovery Through Advanced Computing, 26-30 June 2005, San Francisco, CA. J. Physics: Conference Series 16 (2005), pp. 435-445, Institute of Physics Publishing.

Patrick Amestoy, Sherry Li, and Esmond G. Ng. "Diagonal Markowitz Scheme With Local Symmetrization". To appear in SIAM J. Matrix Anal. Appl.

P. Amestoy, X.S. Li, and S. Pralet, "Unsymmetric Ordering Using a Constraint Markowitz Scheme". To appear in SIAM J. Matrix Analysis and Applications.

W. Gao, X.S. Li, C. Yang, and Z. Bai, "An Implementation and Evaluation of the AMLS Method for Sparse Eigenvalue Problems". Submitted to ACM Trans. on Math. Software.

Laura Grigori, Michel Cosnard, and Esmond G. Ng. "On the Row Merge Tree for Sparse LU Factorization with Partial Pivoting". To appear in BIT.

L. Grigori and X.S. Li, "Towards an Accurate Performance Modeling of Parallel Sparse Factorization". Submitted to Applicable Algebra in Engineering, Communication and Computing, May 26, 2006.

Ingyu Lee, Padma Raghavan, and Esmond G. Ng. "Effective Preconditioning Through Ordering Interleaved With Incomplete Factorization". SIAM J. Matrix Anal. Appls. 27, no. 4 (2006), pp.1069-1088.

X.S. Li, "An Overview of SuperLU: Algorithms, Implementation, and User Interface". ACM Trans. on Math. Software, Vol. 31, No. 3, September 2005, pp. 302-325.

X. S. Li, W. Gao, P. J. R. Husbands, C. Yang, and E.G. Ng, "The Roles of Sparse Direct Methods in Large-scale Simulations". Proceedings of SciDAC 2005, Scientific Discovery Through Advanced Computing, 26-30 June 2005, San Francisco, CA. J. Physics: Conference Series 16 (2005), pp. 476-480, Institute of Physics Publishing.

K. Nakajima, "Parallel programming models for finite-element method using preconditioned iterative solvers with multicolor ordering on various types of SMP cluster". IEEE Proceedings of HPC Asia 2005, 83-90.

K. Nakajima, "Parallel iterative solvers for finite-element methods using an OpenMP/MPI hybrid programming model on the Earth Simulator". Parallel Computing, 31, 1048-1065.

K. Nakajima, "Performance of large-scale finite-element applications in earth science on BlueGene/L prototype system using parallel iterative solvers of GeoFEM". IPSJ Proceedings of HPCS2005, 17-24.

K. Nakajima, "Sparse approximate inverse preconditioner for contact problems on the Earth Simulator using OpenMP". International Journal of Computational Methods (in press).

K. Nakajima, "The Impact of Parallel Programming Models on the Linear Algebra Performance for Finite Element Simulations". Proceedings of VECPAR 2006 Conference (to appear as a paper for publication in post-conference volume of Lecture Notes in Computer Science).

Chao Yang, Weiguo Gao, Zhaojun Bai, Xiaoye S. Li, Lie-Quan Lee, Parry Husbands, and Esmond G. Ng. "An Algebraic Sub-structuring Algorithm for Large-scale Eigenvalue Calculation". SIAM J. Sci. Comput. 27, no. 3 (2005), pp. 873-892.

Chao Yang, Weiguo Gao, Zhaojun Bai, Xiaoye Li, Lie-Quan Lee, Parry Husbands, and Esmond G. Ng, "Algebraic Sub-structuring for Electromagnetic Applications". Proceedings of the PARA'04 Workshop on State-of-the-art in Scientific Computing, Lecture Notes in Computer Science, pp. 365-374, Springer. To appear in 2005.

Chao Yang, Pawel A. Penczek, and Esmond G. Ng, "Unified 3-D Structural and Projection Orientation Refinement Using Quasi-Newton Algorithm". J. Structural Biology 149 (2005), pp. 53-64.

**PI Dimitrios Nikolopoulos**

Experiences with Multithreaded Memory Allocators in Parallel Mesh Generation Applications. Andrey Chernikov, Scott Schneider, Christos Antonopoulos, Nikos Chrisochoides and Dimitrios S. Nikolopoulos. Submitted for conference publication to IEEE/ACM IPDPS'2007, October 2007.

A Multigrain Delaunay Mesh Generation Method for Multicore SMT-based Architectures. Christos Antonopoulos, Filip Blagojevic, Andrey Chernikov, Nikos Chrisochoides and Dimitrios S. Nikolopoulos. Submitted for publication to the Journal of Parallel and Distributed Computing, August 2006.

Algorithm Software and Hardware Optimizations for Delaunary Mesh Generation on Simultaneous Multithreaded Architectures. Christos Antonopoulos, Filip Blagojevic, Andrey Chernikov, Nikos Chrisochoides and Dimitrios S. Nikolopoulos. Submitted for publication to the Journal of Parallel and Distributed Computing, August 2006.

Scott Schneider, Christos D. Antonopoulos and Dimitrios S. Nikolopoulos. Scalable Locality-Conscious Multithreaded Memory Allocation. Proceedings of the 2006 ACM SIGPLAN International Symposium on Memory Management, pp. 84-94, Ottawa, Canada, June 2006. ACM Press. ISBN 1-59593-221-6

**PI Jerry Nolen**

"Application of a New Procedure for Design of 325 MHz RFQ" P. N. Ostroumov, V. N. Aseev, and A. A. Kolomiets Journal of Instrumentation, JINST 1 P04002, April 2006,

Physics Design of the 8-GeV H-Minus Linac P. N. Ostroumov New Journal of Physics, http://www.iop.org/EJ/njp Status: ACCEPTED FOR PUBLICATION

Parallelization of a Beam Dynamics Code TRACK and First Large Scale RFQ Simulations, J. Xu, B. Mustapha, V. N. Aseev, and P. N. Ostroumov, Phys. Rev. ST, Status: TIS

Computational Needs for the RIA Accelerator Systems P. N. Ostroumov, J. A. Nolen, and B. Mustapha Proceedings of the 8th International Computational Accelerator Physics Conference (ICAP-04), St. Petersburg, Russia, June 29-July 2, 2004; Nucl. Instrum. Methods A558, 25-31 (2006), Status: PUBLISHED

**PI Arthur Nozik**

Yong-Hyun Kim and S. B. Zhang, "First-principles pH theory", Phys. Rev. Lett., submitted.

C. Engtrakul, Yong-Hyun Kim, J. M. Nedeljkovic, S. P. Ahrenkiel, K. E. H. Gilbert, J. L. Alleman, S. B. Zhang, O. I. Micic, A. J. Nozik, and M. J. Heben, "Self-Assembly of Linear Arrays of Semiconductor Nanoparticles on Carbon Single-Walled Nanotubes", J. Phys. Chem. B, in press (2006).

Yong-Hyun Kim, S. B. Zhang, Y. Yu, L. F. Xu, and C. Z. Gu, "Dihydrogen bonding, p-type conductivity, and the true origin of workfunction change on hydrogenated diamond (001) surfaces", Phys. Rev. B 74, 075329 (2006).

## O

**PI Volker Oberacker**

"Three-dimensional unrestricted time-dependent Hartree-Fock fusion calculations using the full Skyrme interaction", A.S. Umar and V.E. Oberacker, Phys. Rev. C73, 054607 (2006)

"Time-dependent Hartree-Fock fusion calculations for spherical, deformed systems", A.S. Umar and V.E. Oberacker, Phys. Rev. C74, 024606 (2006)

"Heavy-ion interaction potential deduced from density-constrained time-dependent Hartree-Fock calculation", A.S. Umar and V.E. Oberacker, Phys. Rev. C74, 021601(R) (2006)

**PI Joseph Oefelein**

Oefelein, J. C., Drozda T. G. and Sankaran, V. (2006). Large Eddy Simulation of Turbulence-Chemistry Interactions in Reacting Flows: The Role of High-Performance Computing and Advanced Experimental Diagnostics (invited). Journal of Physics, to appear.

Oefelein, J. C., Sankaran, V. and Drozda T. G. (2006). Large eddy simulation of swirling particle-laden flow in a model axisymmetric combustor, Proceedings of the Combustion Institute, 31, in print.

Oefelein, J. C. (2006). Large eddy simulation of turbulent combustion processes in propulsion and power systems (invited topical review). Progress in Aerospace Sciences, 42: 2-37.

Oefelein, J. C., Schefer, R. W. and Barlow, R. S. (2006). Toward validation of large eddy simulation for turbulent combustion (invited), AIAA Journal, 44(3) 418-433.

Oefelein, J. C. (2006). Mixing and combustion of cryogenic oxygen-hydrogen shear-coaxial jet flames at supercritical pressure (invited). Combustion Science and Technology, 178(1-3): 229-252.

Oefelein, J. C. (2005). Thermophysical characteristics of LOX-H2 flames at supercritical pressure. Proceedings of the Combustion Institute, 30: 2929-2937.

**PI Serdar Ogut**

Juan C. Idrobo, Serdar Ogut, and Julius Jellinek, "Size dependence of static polarizabilities of optical absorption spectra of Ag_n (n = 2-8) clusters", Phys. Rev. B 72, 085445 (2005).

Juan C. Idrobo, Hakim Iddir, Serdar Ogut, Alexander Ziegler, Nigel Browning, and R. O. Ritchie, "Ab initio structural energetics of beta-Si3N4 surfaces", Phys. Rev. B 72, 241301(R) (2005).

Hakim Iddir, Vladimir Skavysh, Serdar Ogut, Nigel Browning, and Mark M. Disko, "Preferential Growth of Pt on Rutile TiO2", Phys. Rev. B 73, 041403(R) (2006).

Juan C. Idrobo, Mingli Yang, Koblar Jackson, and Serdar Ogut,"First Principles Absorption Spectra of Si_n (n=20-28) Clusters: Time-Dependent Local-Density Approximation versus Predictions from Mie Theory", Phys. Rev. B 74, 153410 (2006).

Serdar Ogut, Juan C. Idrobo, Julius Jellinek, and Jinlan Wang, "Structural, Electronic, and Optical Properties of Noble Metal Clusters from First Principles", to appear (December 2006) in Journal of Cluster Science Vol. 17 (available online).

Juan C. Idrobo, Serdar Ogut, Karoly Nemeth, Julius Jellinek, and Riccardo Ferrando, "First Principles Absorption Spectra of Ag_11 Isomers", submitted to Phys. Rev. B (2006).

Hakim Iddir, Serdar Ogut, Peter Zapol, and Nigel Browning, "Diffusion Mechanisms of Native Point Defects in Rutile TiO2", submitted to Physical Review Letters (2006).

**PI Leonid Oliker**

Leonid Oliker, Andrew Canning, Jonathan Carter, John Shalf, Stephane Ethier, "Scientific Application Performance on Leading Scalar and Vector Supercomputing Platforms", International Journal of High Performance Computing Applications, LBNL 60800.

Michael Wehner, Leonid Oliker, John Shalf, Art Mirin, Patrick Worley, "Towards Ultra-High Resolution Models of Climate and Weather", International Journal of High Performance Computing Applications. LBNL 60799

Jonathan Carter, Min Soe, Leonid Oliker, Yoshinori Tsuda, George Vahala, Linda Vahala, and Angus Macnab, "Magnetohydrodynamic Turbulence Simulations on the Earth Simulator Using the lattice Boltzmann Method" High performance computing, networking, and storage conference (SC), 2005, LBNL-58002 *Gorden Bell Finalist*

Leonid Oliker, Jonathan Carter, Michael Wehner, Andrew Canning, Stephane Ethier, Bala Govindasamy, Art Mirin , David Parks, Patrick Worley, Shigemune Kitawaki, Yoshinori Tsuda, "Leading Computational Methods on Scalar and Vector HEC Platforms", High performance computing, networking, and storage conference (SC), 2005. LBNL-58053

Leonid Oliker, Rupak Biswas, Rob Van der Wijngaart, David Bailey, Allan Snavely, "Performance Evaluation and Modeling of Ultra-Scale Systems" Frontiers of Parallel Processing for Scientific Computing, SIAM Publications, to appear (LBNL-58054)

John Shalf, Shoaib Kamil, Leonid Oliker, David Skinner, "Analyzing UltraScale Application Communication Requirements for a Reconfigurable Hybrid Interconnect", High performance computing, networking, and storage conference (SC), 2005. LBNL-58052

Michael Welcome, Charles Rendleman, Leonid Oliker, Rupak Biswas, "Performance Characteristics of an Adaptive Mesh Refinement Calculation on Scalar and Vector Platforms", ACM International Conference on Computing Frontiers, Ischia, Italy, 2006. (LBNL-59238)

Jonathan Carter and Leonid Oliker, "Performance Evaluation of Lattice-Boltzmann Magnetohyrodynamics Simulations on Modern Parallel Vector Systems", Proceedings of the 2nd Teraflop Workshop, Stuttgard, Germany. Lecture Notes in Computer Science (LNCS), Springer, 2006, in press (LBNL-58004)

Jonathan Carter, Leonid Oliker, John Shalf, "Performance Evaluation of Scientific Applications on Modern Parallel Vector Systems", International Meeting on High Performance Computing for Computational Science (VECPAR) 2006

**PI Doug Olson**

"Longitudinal double-spin asymmetry and cross section for inclusive jet production in polarized proton collisions at sqrt{s} = 200 GeV", B.I. Abelev et al., ep-ex/0608030, submitted to Phys.Rev.Lett.

"Anti-Lambda polarization in high energy p p collisions with polarized beams.", Qing-hua Xu, Zuo-tang Liang, Ernst Sichtermann, Phys. Rev. D73, 077503 (2006)

"Prospects of medium tomography using back-to-back hadron correlations", T. Renk, K. Eskola, HIP-2006-46-TH, Oct 2006, hep-ph/0610059, Submitted.

"Forward Neutral Pion Production in p+p and d+Au Collisions at sqrt(sNN)=200 GeV" Phys. Rev. Lett. 97 (2006) 152302

"Identified baryon and meson distributions at large transverse momenta from Au+Au collisions at sqrt(sNN) = 200 GeV" Phys. Rev. Lett. 97 (2006) 152301

"Strange baryon resonance production in sqrt(sNN) = 200 GeV p+p and Au+Au collisions" Phys. Rev. Lett. 97 (2006) 132301

"The multiplicity dependence of inclusive p_t spectra from p-p collisions at sqrt s = 200 GeV" Phys. Rev. D 74 (2006) 032006

"Identified hadron spectra at large transverse momentum in p+p and d+Au collisions at sqrt(sNN) = 200 GeV" Phys. Lett. B 637 (2006) 161

"Multiplicity and Pseudorapidity Distributions of Charged Particles and Photons at Forward Pseudorapidity in Au + Au Collisions at sqrt(sNN) = 62.4 GeV" Phys. Rev. C 73 (2006) 034906

"Directed flow in Au+Au collisions at sqrt(sNN) = 62 GeV" Phys. Rev. C 73 (2006) 034903

"Transverse-momentum pT correlations on (eta,phi) from mean-pT fluctuations in Au-Au collisions at sqrt(sNN)=200 GeV" J. Phys. G 32 (2006) L37

"Incident Energy Dependence of pt Correlations at RHIC" Submitted April 29, 2005, published October 19, 2005 Phys. Rev. C 72 (2005) 044902

"Multi-strange baryon elliptic flow in Au+Au collisions at sqrt(sNN)= 200 GeV" Phys. Rev. Lett. 95 (2005) 122301

## P

**PI Bahram Parvin**

Systems Biology, Elsvier publisher (edited), Oct. 2005.

Geometric Approach to Segmentation and Protein Localization in Cell Culture Assays, Int. Symposium on Visual Computing, Dec. 2005

**PI Edward Patton**

Mao, S., E. G. Patton, Z.-G. Feng, E. E. Michaelides, 2006: Impact of an imposed wall-jet on canopy turbulence and the net ecosystem-atmosphere exchange of carbon dioxide, Boundary Layer Meteorology, in revision.

**PI Joyce Penner**

Guo, H. J. E. Penner, M. Herzog and S. Xie, 2006: Investigation of the first and second aerosol indirect effects on clouds during the May 2003 ARM Intensive Operational Period at the Southern Great Plains, J. Geophys. Res., submitted.

Guo, H. J. E. Penner, M. Herzog, Examining the aerosol indirect effect under contrasting environments during the ACE-2 experiment, 2006: Atmos. Chem. Phys., submitted.

Feng, Y. and J.E. Penner, 2006: Global Modeling of Nitrate and Ammonium: Interaction of Aerosols and Tropospheric Chemistry, J. Geophys. Res., in press.

Liu, X., J.E. Penner, and M. Herzog, 2005: Global modeling of aerosol dynamics: Model description, evaluation and interactions between sulfate and non-sulfate aerosols, J. Geophys. Res.,110, D18206, doi:10.1029/2004JD005674.

Jablonowski, C., M. Herzog, J.E. Penner, R.C. Oemke, Q.F. Stout, B. van Leer, and K.G. Powell, 2005: Block-Structured Adaptive Grids on the Sphere: Advection Experiments, Mon. Weath. Rev., in press.

**PI Stephen Pennycook**

Klie, R. F., J. P. Buban, M. Varela, A. Franceschetti, C. Jooss, Y. Zhu, N. D. Browning, S. T. Pantelides, and S. J. Pennycook, "Enhanced Current Transport at Grain Boundaries in High-Tc Superconductors," Nature 435, 475-478 (2005).

Gapud, A. A., D. Kumar, S. K. Viswanathan, C. Cantoni, M. Varela, J. Abiade, S. J. Pennycook, and D. K. Christen, "Enhancement of Flux Pinning in YBa2Cu3O7-delta Thin Films Embedded with Epitaxially Grown Y2O3 Nanostructures Using a Multi-Layering Process," Supercond. Sci. Technol. 18, 1502-1505 (2005).

Goyal, A., S. Kang, K. J. Leonard, P. M. Martin, A. A. Gapud, M. Varela, M. Paranthaman, A. O. Ijaduola, E. D. Specht, J. R. Thompson, D. K. Christen, S. J. Pennycook, and F. A. List, "Irradiation-Free, Columnar Defects Comprised of Self-Assembled Nanodots and Nanorods Resulting in Strongly Enhanced Flux- Pinning in YBa2Cu3O7-delta Films," Supercond. Sci. Technol. 18, 1533-1538 2005).

Prabhumirashi, P., V. P. Dravid, A. R. Lupini, M. F. Chisholm, and S. J. Pennycook, "Atomic-Scale Manipulation of Potential Barriers at SrTiO3 Grain Boundaries," Appl. Phys. Lett. 87 121917 (2005).

Rashkeev, S. N., K. van Benthem, S. T. Pantelides, and S. J. Pennycook, "Single Hf Atoms Inside the Ultrathin SiO2 Interlayer Between a HfO2 Dielectric Film and the Si Substrate: How Do They Modify the Interface?" Microelectron. Eng. 80, 416419 (2005).

Pennycook, S. J., "Studies of Catalysis with Single-Atom Sensitivity by Aberration-Corrected STEM and First-Principles Theory," Abstracts of Papers of The American Chemical Society 229, U865e (2005).

van Benthem, K., A. R. Lupini, M. Kim, H. S. Baik, S. Doh, J. H. Lee, M. P. Oxley, S. D. Findlay, L. J. Allen, J. T. Luck, and S. J. Pennycook, "Three-Dimensional Imaging of Individual Hafnium Atoms Inside a Semiconductor Device," Appl. Phys. Lett. 87, 034104 (2005).

S. A. Chambers, J. R. Williams, M. A. Henderson, A. G. Joly, M. Varela, and S. J. Pennycook, "Structure, Band Offsets and Photochemistry at Epitaxial &alpha-Cr2O3/ &alpha-Fe2O3 Heterojunctions", Surface Science Letters 587, L197-L207, (2005).

Miao, G. X., P. LeClair, A.Gupta, G. Xiao, M. Varela, and S. J. Pennycook, "Magnetic Tunnel Junctions Based on CrO2/SnO2 Epitaxial Bilayers," App. Phys. Lett. 89, 022511 (2006).

Pena, V., Z. Sefrioui, D. Arias, C. Leon, J. Santamaria, M. Varela, S. J. Pennycook, M. Garcia-Hernandez, and J. L. Martinez, "Strain Induced Phase Separation in La0.67Ca0.33MnO3 Ultrathin Films," J. Phys. Chem. Solids 67, 472475 (2006).

Frey, N.A., S. Srinath, H. Srikanth, M. Varela, S. J. Pennycook, G. X. Miao, and A. Gupta, "Magnetic Anisotropy in Epitaxial CrO2 and CrO2/Cr2O3 Bilayer Thin Films," Phys. Rev. B: Condens. Matter : Condens. Matter 74, 024420 (2006).

Sefrioui, Z., V. Cros, A. Barthelemy, V. Pena, C. Leon, J. Santamaria, M. Varela, and S. J. Pennycook, "Tunnel Magnetoresistance in La0.7Ca0.3MnO3/PrBa2Cu3O7/La0.7Ca0.3MnO3," Appl. Phys. Lett. 88, 022512 (2006).

S. N. Rashkeev, A. R. Lupini, S. H. Overbury, S. J. Pennycook, and S. T. Pantelides, "The role of the nanoscale in catalytic CO oxidation by supported Au and Pt nanostructures", Submitted to Journal of Catalysis, September (2006).

W. Luo, A. Franceschetti, M. Varela, J. Tao, S. J. Pennycook, and S. T. Pantelides, "Orbital-occupancy versus charge ordering and the strength of electron correlations in electron-doped CaMnO3", Submitted to Phys. Rev. Lett., October (2006).

**PI Saul Perlmutter**

A Probabilistic Approach to Classifying Supernovae Using Photometric Information, Natalia V. Kuznetsova and Brian M. Connolly, submitted for publication in ApJ.

Measurement of Omega_M, Omega_Lambda from a blind analysis of Type Ia supernovae with CMAGIC: Using color information to verify the acceleration of the universe, A. Conley, et al., ApJ, 644, 1 (2006).

Spectra of High-Redshift Type Ia Supernovae and a Comparison with their Low-Redshift Counterparts, I. M. Hook, et al., AJ, 130, 2788 (2005)

Spectroscopic Observations and Analysis of the Unusual Type Ia SN 1999ac, G. Garavini, et al., AJ, 130, 2278 (2005).

E.Linder, M.White Going non-linear with dark energy cosmologies Phys. Rev. D72(2005)061304, astro-ph/0508401.

A.Wetzel, J.Cohn, M.White, D.Holz, M.Warren The clustering of massive halos ApJ in press, astro-ph/0606699.

E.Huff, A.Schulz, M.White, D.Schlegel, M.Warren Simulations of baryon oscillations to appear in Astroparticle Physics, astro-ph/0607061.

S.Dodelson, C.Shapiro, M.White Reduced shear power spectrum Phys. Rev. D73(2006)023009, astro-ph/0508296.

L.vanWaerbeke, M.White, H.Hoekstra, C.Heymans Redshift and shear calibration: impact on cosmic shear studies and survey design Astroparticle Physics 26(2006)91, astro-ph/0603696.

C.Heymans, M.White, A.Heavens, C.Vale, L.vanWaerbeke Potential sources of contamination to weak lensing measurements: constraints from N-body simulations MNRAS 371(2006)750, astro-ph/0604001.

E.Semboloni, L.vanWaerbeke, C.Heymans, T.Hamana, S.Colombi, M.White, Y.Mellier Cosmic variance of weak lensing surveys in the non-linear regime MNRAS in press, astro-ph/0606648.

"The type Ia supernova SNLS-03D3bb from a super-Chandrasekhar-mass white dwarf star", Howell, D. et al. Nature, Volume 443, Issue 7109, pp. 308-311 (2006).

"Towards a Cosmological Hubble Diagram for Type II-P Supernovae," Nugent, P.; Sullivan, M.; Ellis, R.; Gal-Yam, A.; Leonard, D.; Howell, D.; Astier, P.; Carlberg, R.; Conley, A.; Fabbro, S.; Fouchez. D.; Neill, J.; Pain, R.; Perrett, K.; Pritchet, C. The Astrophysical Journal, July, 2006.

"Long gamma-ray bursts and core-collapse supernovae have different environments," Fruchter, A. S.; et al. Nature, Volume 441, Issue 7092, pp. 463-468 (2006).

"On the Afterglow and Host Galaxy of GRB 021004: A Comprehensive Study with the Hubble Space Telescope," Fynbo, J. P. U.et al. The Astrophysical Journal, Volume 633, Issue 1, pp. 317-327.

"Photometric Selection of High-Redshift Type Ia Supernova Candidates," Sullivan, M.; et al. The Astronomical Journal, Volume 131, Issue 2, pp. 960-972.

"Measurement of Omega_m and Omega_lambda, from a Blind Analysis of Type Ia Supernovae with CMAGIC: Using Color Information to Verify the Acceleration of the Universe," Conley, A.et al. The Astrophysical Journal, Volume 644, Issue 1, pp. 1-20.

**PI Franz-Josef Pfreundt**

"Integrated Performance Analysis of Computer Systems (IPACS)", G. Falcone et al, Praxis der Informationsverarbeitung und Kommunikation, PIK3-05 154-163 IPACS-Benchmark - Integrated Performance Analysis of Computer Systems (IPACS) Michael Krietemeyer, Matthias Merz [Eds.] ISBN 3-8325-1253-5, Logos Verlag Berlin.

**PI Ali Pinar**

Vaibhav Donde, Vanessa Lopez, Bernard Lesieutre, Ali Pinar, Chao Yang, and Juan Meza, Identification of severe multiple contingencies in electric power networks, submitted to IEEE Transaction on Power Systems, (LBNL-60511).

Bernard Lesieutre, Sandip Roy, Vaibhav Donde, and Ali Pinar, Power system extreme event analysis using graph partitioning, In Proceedings of the North American Power Symposium.

Ali Pinar, Adam Reichert, Bernard Lesieutre, "Computing the Criticality of Lines in Power Systems," submitted to the IEEE International Symposium on Circuits and Systems (ISCAS).

Shoaib Kamil, Ali Pinar, Daniel Gunter, Michael Lijewski, Leonid Oliker, John Shalf, and David Skinner, Reconfigurable hybrid interconnection for static and dynamic scientific applications, submitted to SC06, (LBNL-60060).

**PI Michael Pindzola**

Double autoionization of hollow atom states, M S Pindzola, F J Robicheaux, and J P Colgan, Phys. Rev. A 72, 022709 (August 2005).

Alignment effects in charge transfer and excitation for H+ and He+2 collisions with H2+, D J Phalen, M S Pindzola, and F J Robicheaux, Phys. Rev. A 72, 022720 (August 2005).

Double and triple photoionization of Li and He, J P Colgan, M S Pindzola, and F J Robicheaux, Phys. Rev. A 72, 022727 (August 2005).

Electron-impact ionization of H2+ using a time-dependent close-coupling method, M S Pindzola, F J Robicheaux, and J P Colgan, J. Phys. B 38, L285 (September 2005).

Electron-impact ionization of Mo+ using a time-dependent close-coupling method, J A Ludlow and M S Pindzola, Phys. Rev. A 72, 032729 (September 2005).

Excitation and charge transfer in p + H(2s) collisions, M S Pindzola, T G Lee, T Minami, and D R Schultz, Phys. Rev. A 72, 062703 (December 2005).

The effects of radiative cascade on the X-ray diagnostic lines of Fe+16, S D Loch, M S Pindzola, C P Ballance, and D C Griffin, J. Phys. B 39, 85 (January 2006).

The search for oscillations in the near threshold photo double ionization cross sections of helium, U Kleiman, T Topcu, M S Pindzola, and F J Robicheaux, J. Phys. B 39, L61 (February 2006).

Bose-Einstein condensate flow in a corrugated magnetic waveguide, M C Witthoeft and M S Pindzola, Phys. Scr. 73, 274 (February 2006).

Electron-impact double ionization of H-, M S Pindzola, F J Robicheaux, and J P Colgan, J. Phys. B 39, L127 (March 2006).

Low energy electron-impact single ionization of helium, J P Colgan, M S Pindzola, G Childers, and M A Khakoo, Phys. Rev. A 73, 042710 (April 2006).

Energy differential cross sections for the triple photoionization of Lithium, J P Colgan and M S Pindzola, J. Phys. B 39, 1879 (April 2006).

Electron-impact ionization of H2 using a time-dependent close-coupling method, M S Pindzola, F J Robicheaux, and J P Colgan, Phys. Rev. A 73, 052706 (May 2006).

Lattice, time-dependent Schrodinger equation approach for charge transfer in collisions of Be+4 with atomic hydrogen, T Minami, M S Pindzola, T G Lee, and D R Schultz, J. Phys. B 39, 2877 (June 2006).

Double Autoionization of He- (2s2 2p 2P), M S Pindzola, F J Robicheaux, and J P Colgan, Phys. Rev. A 73, 062720 (June 2006).

Double and triple differential cross sections for the low energy electron-impact ionization of hydrogen, J P Colgan and M S Pindzola, Phys. Rev. A 74, 012713 (July 2006).

Doubly excited resonances in the photoionization spectrum of Li+: experiment and theory, S W J Scully, I Alvarez, C Cisneros, E D Emmons, M F Gharaibeh, D leitner, M S Lubell, A Muller, R A Phaneuf, R Puttner, A S Schlachter, S Schippers, W Shi, C P Ballance, and B M McLaughlin, J. Phys. B 39, 3957 (Sept. 2006).

**PI Tomasz Plewa**

On the evolution of thermonuclear flames on large scales Zhang, J., Messer, O. E., Khokhlov, A. M., Plewa, T. 2006, ApJ, in press (astro-ph/0610168)

Detonating Failed Deflagration Model of Thermonuclear Supernovae I. Explosion Dynamics Plewa, T., 2006, ApJ, submitted

Detonating Failed Deflagration Model of Thermonuclear Supernovae II. Gross Observational Properties Kasen, D., Plewa, T., 2006, ApJ, submitted

**PI Gerald Potter**

Klein, Stephen A., X. Jiang, J. Boyle, S. Malyshev, and S. Xie, 2006: Diagnosis of the summertime warm and dry bias over the U. S. Southern Great Plains in the GFDL climate model using a weather forecasting approach. Geophys. Res. Lett., 33, L18805, doi:10.1029/2006GL027567.

Evaluating parameterizations in general circulation models: Climate simulation meets weather prediction by Phillips et al., 2004: Bulletin of the American Meteorological Society, 85, 1903-1915.

Impact of a revised convective triggering mechanism on Community Atmosphere Model, Version 2, simulations: Results from short-range weather forecasts by Xie et al. : Journal of Geophysical Research, 109, D14102, doi:10.1029/2004JD004692, 2004.

Simulations of midlatitude frontal clouds by single-column and cloud-resolving models during the Atmospheric Radiation Measurement March 2000 cloud intensive operational period by Xie et al. : Journal of Geophysical Research, 110, D15503, doi: 10.1029/2004JD005119, 2005.

Diagnosis of Community Atmospheric Model 2 (CAM2) in numerical weather forecast configuration at Atmospheric Radiation Measurement sites by Boyle et al.: Journal of Geophysical Research, 110, D15516, doi: 10.1029/2004JD005109, 2005.

Moisture and temperature balances at the Atmospheric Radiation Measurement Southern Great Plains Site in forecasts with the Community Atmosphere Model (CAM2) by Williamson et al. : Journal of Geophysical Research, 110, D15516, doi: 10.1029/2004JD005109, 2005.

**PI Larry Pratt**

Pratt, L. M.; Merry, S.; Son, N. C.; Quan, P.; Thanh, B. T. Tetrahedron, In press A Computational Study of Halomethyllithium Carbenoid Mixed Aggregates with Lithium Halides and Lithium Methoxide

Pratt, L. M.; Tran Phan, D. H.; Tran, P. T.; Nguyen, N. V. Submitted for publication in J. Phys. Chem. A. Basis set and Electron Correlation Effects on Lithium Carbenoid Dimerization Energies

**PI Joel Primack**

"The shape of dark matter halos: dependence on mass, redshift, radius, and formation" Brandon Allgood, Ricardo Flores, Joel R. Primack, Andrey V. Kravtsov, Risa H. Wechsler, Andreas Faltenbacher, James S. Bullock 2006, MNRAS, 367, 1781-1796

"Constraining the Projected Radial Distribution of Galactic Satellites with the Sloan Digital Sky Survey" J. Chen et al. 2006, ApJ, 647, 86

"Bars and Cold Dark Matter Halos", P. Colin, O. Valenzuela, & A. Klypin 2006, ApJ, 644, 687

"Modeling Luminosity-Dependent Galaxy Clustering Through Cosmic Time" Conroy, C., Wechsler, R.H, Kravtsov, A.V., 2006, ApJ, 647, 201

"The Effects of Feedback in Simulations of Disk-Galaxy Major Mergers", T.J. Cox, Patrik Jonsson, Joel R. Primack & Rachel S. Somerville 2006, MNRAS in press [astro-ph/0503201]

"Imprints of mass accretion on properties of galaxy clusters", Andreas Faltenbacher, Brandon Allgood, Stefan Gottloeber, Gustavo Yepes, Yehuda Hoffman 2005, MNRAS 362, 1099-1108

"The Shape of Galaxy Cluster Dark Matter Haloes: Systematics of Its Imprint on Cluster Gas, and Comparison to Observations", Ricardo A. Flores, Brandon Allgood, Andrey V. Kravtsov, Joel R. Primack, David A. Buote & James S. Bullock 2005, MNRAS, submitted [astro-ph/0508226], revised version submitted

"Impact of Dark Matter Substructure on the Matter and Weak Lensing Power Spectra" Bradley Hagan, Chung-Pei Ma, Andrey V. Kravtsov 2005, ApJ, 633, 537-541

"SUNRISE: polychromatic dust radiative transfer in arbitrary geometries", Patrik Jonsson, 2006, MNRAS, 372, 2

"The Dark Side of the Halo Occupation Distribution", Andrey V. Kravtsov, Andreas A. Berlind, Risa H. Wechsler, Anatoly A. Klypin, Stefan Gottloeber, Brandon Allgood, and Joel R. Primack 2004, Astrophys.J., 609, 35-45

"Galaxy-galaxy lensing: dissipationless simulations versus the halo model", Rachel Mandelbaum, Argyro Tasitsiomi, Uros Seljak, Andrey V. Kravtsov, Risa H. Wechsler 2005, MNRAS, 362, 1451-1462

"Shapes of Stellar Systems and Dark Halos from Simulations of Galaxy Major Mergers", G.S. Novak, T.J. Cox, J.R. Primack, P. Jonsson, A. Dekel, 2006, ApJ, 646, L9

"The Dependence of Halo Clustering on Halo Formation History, Concentration, and Occupation", Risa H. Wechsler, Andrew R. Zentner, James S. Bullock, Andrey V. Kravtsov, Brandon Allgood 2006, ApJ, in press [astro-ph/0512416]

"Modeling Galaxy-Mass Correlations in Dissipationless Simulations", Tasitsiomi, A., Kravtsov, A., Wechsler, R. H. & Primack, J., 2004, Astrophys.J., 614, 533-546

"The Physics of Galaxy Clustering I: A Model for Subhalo Populations", Andrew R. Zentner, Andreas A. Berlind, James S. Bullock, Andrey V. Kravtsov & Risa H. Wechsler 2005, ApJ, 624, 505-525

## Q

## R

**PI Abhay Ram**

"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.

"Role of trapped electron mode turbulence in internal transport barrier control in the Alcator C-Mod Tokamakak", D. R. Ernst, P. T. Bonoli, P. J. Catto, W. Dorland, C. L. Fiore, R. S. Granetz, M. Greenwald, A. E. Hubbard, M. Porkolab, M. H. Redi, J. E. Rice, K. Zhurovich, and the Alcator C-Mod Group, Phys. Plasmas, 11(5) 2637 (2004).

D. R. Ernst, N. Basse, P. T. Bonoli, P. J. Catto, W. Dorland, C. L. Fiore, M. Greenwald, A. E. Hubbard, E. S. Marmar, M. Porkolab, J. E. Rice, K. Zeller and K. Zhurovich, "Mechanisms for ITB Formation and Control in Alcator C-Mod Identified Through Gyrokinetic Simulations of TEM Turbulence," Proc. 20th Int'l. Atomic Energy Agency Fusion Energy Conference, Vilamoura, Portugal, 1-6 November 2004, oral paper IAEA-CN-116/TH/4-1. http://www-naweb.iaea.org/napc/physics/fec/fec2004/datasets/TH_4-1.html

C L Fiore, P T Bonoli, D R Ernst, M J Greenwald, E S Marmar, M H Redi, J E Rice, S J Wukitch and K Zhurovich, "Internal transport barrier production and control in Alcator C-Mod," Plasma Phys. Control. Fusion 46 B281-B291. EPS Invited Oral 2004.

C. L. Fiore, D. R. Ernst, J. E. Rice, N. Basse, P. T. Bonoli, M. J. Greenwald, E. S. Marmar, S. J. Wukitch, K. Zhurovich, "Internal Transport Barriers in Alcator C-Mod," submitted to C-Mod Special Issue, Fusion Science and Technology, Augst, 2005.

N. P. Basse et al., "Characterization of core and edge turbulence in L- and enhanced D-alpha H-mode Alcator C-mod plasmas," Physics of Plasmas, 12(5) May 2005, p 52512-1-14.

C. L. Fiore et al., "Control of internal transport barriers on Alcator C-mod," Physics of Plasmas 11(5), May 2004, p 2480-7.

J. C. Wright, L. A. Berry, D. B. Batchelor P. T. Bonoli, E. F. Jaeger, E. D Azevedo M. D. Carter, C. K. Phillips, R. W. Harvey H. Okuda, D. N. Smithe, D. A. D Ippolito J. R. Myra, M. Brambilla, and R. J. Dumont, ``Nonthermal particle and full-wave diffraction effects on heating and current drive in the ICRF and LHRF regimes,'' Nucl. Fusion, 45(9), September 2005.

Y. Lin, S. J.Wukitch, A. Parisot, J. C. Wright, N. Basse, P. Bonoli, E. Edlund, L. Lin, M. Porkolab, S.Wolfe, G. Schilling, and P. Phillips, ``Ion cyclotron range of frequencies wave phenomena in the mode conversion region in Alcator C-Mod,'' Plasma Phys. Controlled Fusion, 47(-1):0, 2005.

J. C. Wright, P. T. Bonoli, M. Brambilla, E. Azevedo, L. A. Berry, D. B. Batchelor, E. F. Jaeger, M. D. Carter, C. K. Phillips, H. Okuda, R. .W. Harvey, J. R.Myra, D. A. D Ippolito, and D. N. Smithe, ``Full-wave electromagnetic field simulations of lower hybrid waves in tokamaks,'' In P. Bonoli and S. Wukitch, editors, 16th Topical Conference on Radio Frequency Power in Plasmas and, number to be published, page 1, New York, 2005. American Institute of Physics.

**PI David Randall**

Ahlgrimm, M., and D. A. Randall, 2006: Diagnosing monthly mean boundary-layer properties from re- analysis data using a bulk boundary-layer model. J. Atmos. Sci., 63, 998-1012.

Benedict, J., and D. A. Randall, 2006: An analysis of the MJO based on TRMM rainfall data. Revised for J. Atmos. Sci.

Blossey, P. N., C. S. Bretherton, J. Cetrone, and M. Khairoutdinov, 2006: Cloud-resolving model simulations of KWAJEX: Model sensitivities and comparisons with satellite and radar observations. J. Atmos. Sci., in press.

Bretherton, C. S., P. N. Blossey, and M. Khairoutdinov, 2005: An Energy-Balance Analysis of Deep Convective Self-Aggregation above Uniform SST. J. Atmos. Sci., 62, 4273-4292, DOI: 10.1175/ JAS3614.1

Bony, S., R. Colman, V. M. Kattsov, R. P. Allen, C. S. Bretherton, J.-L. Dufresne, A. Hall, S. Hallegatte, M. M. Holland, W. Ingram ,D. A. Randall, B. J. Soden, G. Tselioudis, and M. J. Webb, 2006: How well do we understand and evaluate climate change feedback processes? J. Climate ,19, 3445-3482.

DeMott, C., and D. A. Randall, 2006: Summertime high frequency precipitation variability in GCMs. J. Atmos. Sci. (in press).

Khairoutdinov, M., and D. A. Randall, 2006: High-resolution simulations of shallow-to-deep convection transition over land. J. Atmos. Sci. (in press)

Khairoutdinov, M., and D. A. Randall, 2006: Evaluation of the simulated interannual and subseasonal variability in an AMIP-style simulation using the CSU Multiscale Modeling Framework. Undergoing revisions for J. Climate.

Ovtchinnikov, M., T. Ackerman, R. Marchand, and M. Khairoutdinov, 2006: Evaluation of the Multiscale Modeling Framework Using Data from the Atmospheric Radiation Measurement Program. J. Climate, 19, 1716-1729, DOI: 10.1175/JCLI3699.1

Randall, D. A., M. E. Schlesinger, V. Galin, V. Meleshko, J.-J. Morcrette, and R. Wetherald, 2006: Cloud Feedbacks. In Frontiers in the Science of Climate Modeling, J. T. Kiehl and V. Ramanathan, Eds., Cambridge University Press, pp. 217-250.

Tulich, S. N., D. A. Randall, and B. E. Mapes, 2006: Vertical-mode and cloud decomposition of large- scale convectively coupled gravity waves in a two-dimensional cloud-resolving model. J. Atmos. Sci. (in press).

Wyant, M. C., M. Khairoutdinov, and C. S. Bretherton, 2006: Climate sensitivity and cloud response of a GCM with a superparameterization. Geoph. Res. Lett., 33, DOI:10.1029/2005GL025464.

**PI Sergey Rashkeev**

A.Y.Borisevich, S.Wang, S.N.Rashkeev, M.V.Glazoff, S.J.Pennycook, and S.T.Pantelides. Substrate-dependent nanoparticle agglomeration controls catalyst longevity. Advanced Materials (submitted).

S.N.Rashkeev, A.R.Lupini, S.H.Overbury, S.J.Pennycook, and S.T.Pantelides. The role of the nanoscale in catalytic CO oxidation by supported Au and Pt nanostructures. Journal of Catalysis (submitted).

S.N.Rashkeev, K. van Benthem, S.T.Pantelides, and S.J.Pennycook. Single Hf atoms inside the ultrathin SiO2 interlayer between a HfO2 dielectric film and the Si substrate: How do they modify the interface? Microelectronic Engineering 80, 416-419 (2005).

**PI Lawrence Rauchwerger**

N. Thomas, G. Tanase, O. Tkachyshyn, J. Perdue, N.M. Amato, L. Rauchwerger, ``A Framework for Adaptive Algorithm Selection in STAPL'', in Proc. of ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming (PPOPP), Chicago, IL, June, 2005.

Shawna Thomas, Gabriel Tanase, Lucia K. Dale, Jose E. Moreira, Lawrence Rauchwerger, O. B. Bayazit, Jyh-Ming Lien, and N. M. Amato. Swarming behavior using probabilistic roadmap techniques. Lecture Notes in Computer Science, 2005(3342):112--125, January 2005.

O. B. Bayazit, Dawen Xie, and N. M. Amato. Iterative relaxation of constraints: A framework for improving automated motion planning. In Proc. IEEE Int. Conf. Intel. Rob. Syst. (IROS), pages 586--593, 2005.

J. H. Chang and M. L. Adams. Effectiveness of various transport synthetic accelerationmethods with and without GMRES. In Proc. Conf. Mathematics and Computation, Supercomputing, Reactor Physics and Nuclear and Biological Applications, 2005.

J.-M. Lien and N. M. Amato. Approximate convex decomposition of polygons. Comp. Geom.: Theory Appl., 2006.

Jyh-Ming Lien, Samuel Rodriguez, Jean-Philippe Malric, and Nancy M. Amato. Shepherding behaviors with multiple shepherds. In Proc. IEEE Int. Conf. Robot. Autom. (ICRA), pages 3413--3418, April 2005.

A. E. Maslowski and M. L. Adams. Behavior of continuous finite element discretizations of the slab-geometry transport equation. In Proc. Conf. Mathematics and Computation, Supercomputing, Reactor Physics and Nuclear and Biological Applications, 2005.

W. McLendon III, B. Hendrickson, S. Plimpton, and L. Rauchwerger. Finding strongly connected components in distributed graphs. J. Par. Dist. Comp., 65(8):901--910, March 2005.

S. J. Plimpton, B. Hendrickson, S. Burns, W. McLendon III, and L. Rauchwerger. Parallel algorithms for transport on unstructured grids. J. Nucl. Sci. Eng., 150(7):1--17, 2005.

S. Rodriguez, J.-M. Lien, and N. M. Amato. Planning motion in completely deformable environments. In Proc. IEEE Int. Conf. Robot. Autom. (ICRA), 2006.

S. Rus, G. He, and L. Rauchwerger. Scalable array SSA and array data flow analysis. In Proceedings Annual Workshop on Programming Languages and Compilers for Parallel Computing, 2005. Silvius Rus, Dongmin Zhang, and Lawrence Rauchwerger. The value evolution graph and its use in memory reference analysis. In Proceedings of the 13-th International Conference on Parallel Architectures and Compilation Techniques, Antibes Juan-les-Pins, France, October 2004.

S. Thomas, G. Song, and N. Amato. Protein folding by motion planning. Physical Biology, pages S124--S155, 2005. S. Thomas, X. Tang, L. Tapia, and N. M. Amato. Simulating protein motions with rigidity analysis. In Proc. Int. Conf. Comput. Molecular Biology (RECOMB), 2006.

H. Yu and L. Rauchwerger. An adaptive algorithm selection framework. IEEE Transactions on Parallel and Distributed Systems, 2006.

Hao Yu, Dongmin Zhang, and Lawrence Rauchwerger. An adaptive algorithm selection framework. In Proceedings of the 13-th International Conference on Parallel Architectures and Compilation Techniques, Antibes Juan-les-Pins, France, October 2004.

S.Rus, G.He, C.Alias and L. Rauchwerger, ``Region Array SSA'', in Proc. of the 13th International Conference on Parallel Architecture and Compilation Techniques (PACT), Seattle, WA, 2006.

Nancy M. Amato, ``Parallel Protein Folding with STAPL,'' special issue of extended papers from the Third IEEE International Workshop On High Performance Computational Biology (HiCOMB 2004), Concurrency and Computation: Practice and Experience, accepted December 2004.

**PI John Rehr**

Ab initio calculations of mean free paths and stopping powers, A. P. Sorini, J. J. Kas, J. J. Rehr, M. P. Prange and Z. H. Levine, Phys. Rev. B 74, 165111 (2006).

Ab initio calculations of inelastic losses and optical constants, J. J. Rehr, J. J. Kas, M. P. Prange, F. D. Vila, A. L. Ankudinov, L.W. Campbell, and A. P. Sorini, arXiv:cond-mat/0601241, 2006 (submitted)

Inelastic Losses and Multi-electron Excitations in X-ray Spectra, J. J. Rehr, J. J. Kas, M. P. Prange, A. P. Sorini, and L. W. Campbell, (UW preprint 2006, submitted).

Experimental determination of the core-excited electron density of states, J.~A. Soininen, A. Mattila, J. J. Rehr, S. Galambosi, and K. Hamalainen, J. Phys.: Condens. Matter 18, 7327-7336 (2006).

Practical aspects of electron energy-loss spectroscopy (EELS) calculations using FEFF8, M.S. Moreno, K. Jorissen, and J.J.Rehr, Micron, (in press, 2006)

Experimental determination of the core-excited electron density of states, J.~A. Soininen, A. Mattila, J. J. Rehr, S. Galambosi, and K. Hamalainen, J. Phys.: Condens. Matter 18, 7327-7336 (2006).

**PI Edward Rezayi**

Vortex Lattices in Rotating Atomic Bose Gases with Dipolar Interactions, N.R. Cooper, E.H. Rezayi, and S.H. Simon, Phys. Rev. Lett. 95, 200402 (1985).

Vortex lattices in atomic Bose gases with non-local interactions, N.R. Cooper, E.H. Rezayi, and S.H. Simon, Solid State Comm. 140, 61 (2006).

Competreing Compressible and Incompressible Phases in Rotating Atomic Bose Gases at Filling Factor \nu=2, N.R. Cooper, and E.H. Rezayi submitted to Physical Review A.

Non-Abelian quantum Hall states of electrons at filling factor 12/5 and 13/5 in the first excirted Landau level, E.H. Rezayi, and N. Read, submitted to Physical Review B, Rapid Communications.

A \nu=2/5 Paired Wavefunction, S.H. Simon, E.H. Rezayi, N.R. Cooper, and I. Berdnikov, submitted to Physical Review B.

Angular Momentum Projection Hamiltonians for Quantum Hall States, S.H. Simon, E.H. Rezayi and N.R. Cooper, submitted to Physical Review B.

**PI Tony Rollett**

J. J. Hoyt, M. Asta and D. Y. sun, "Molecular dynamics simulations of the crystal-melt interfacial free energy and mobility in Mo and V," Phil. Mag. 86, 3651-3664 (2006)

D. Y. Sun, M. I. Mendelev, C. A. Becker, K. Kudin, T. Haxhimali, M. Asta, J. J. Hoyt, A. Karma and D. J. Srolovitz, "Crystal-Melt Interfacial Free Energies in HCP Metals: A Molecular Dynamics Study of Mg," Phys. Rev. B 73, 024116 (2006).

E. A. Marquis, D. N. Seidman, M. Asta and C. Woodward, "Composition Evolution of Nanoscale Al3Sc Precipitates in an Al-Mg-Sc Alloy: Experiments and Computations," Acta Mater. 54, 119-130 (2006).

Z. G. Xia, D. Y. Sun, M. Asta and J. J. Hoyt, "Molecular Dynamics Calculations of the Crystal-Melt Interfacial Mobility for Hexagonal-Close-Packed Mg," Phys. Rev. B (submitted).

R. S. Aga, J. R. Morris, J. J. Hoyt and M. I. Mendelev, "A quantitative parameter-free prediction of simulated crystal nucleation time," Phys. Rev. Letters 96, 245701 (2006).

R. L. Davidchack, J. R. Morris and B. B. Laird, "The anisotropic hard sphere crystal-melt interfacial free energy from fluctuations," J. Chem. Phys. 125, 094710 (2006).

M. I. Mendelev, J. Schmalian, C. Z. Wang, J. R. Morris and K. M. Ho, "Interface mobility and the liquid-glass transition in a one-component system described by an EAM potential," Phys. Rev. B 74, 104206 (2006).

R. S. Aga, J. R. Morris, V. Levashov and T. Egami, "Local structural fluctuations in a supercooled liquid," to appear in Mat. Sci. Eng. A.

J. R. Morris, U. Dahlborg and M. Calvo-Dahlborg, "Recent developments and outstanding challenges in theory and modeling of liquid metals," to appear in J. Non-cryst. Sol.

**PI William Rowan**

R. V. Bravenec and W. M. Nevins, A System for Direct Comparisons of Nonlinear Simulations of Turbulence with Measurements, Rev. Sci. Instrum. 77, 015101 (2006).

T.L. Rhodes, W.A. Peebles, M.A. Van Zeeland, J.S. deGrassie, R.V. Bravenec, K.H. Burrell, G.R. McKee, J. Lohr, C.C. Petty, X.V. Nguyen, E.J. Doyle, C.M. Greenfield, L. Zeng, and G. Wang, ETG Scale Turbulence and Transport in the DIII-D Tokamak, presented at the 21st IAEA Fusion Energy Conference, to be published in Fusion Energy 2006, paper EX/PR-37 (International Atomic Energy Agency, Vienna, 2007).

**PI Edward Rubin**

The Joint Genome Institute was able to produce over 70 publications last year including a number of high profile outcomes listed here. These were all based on data from the pipeline which was enabled by NERSC resources. See http://www.jgi.doe.gov/News/pubs.html.

Key Papers Published in Nature/Science are listed here:

"Phytophthora Genome Sequences Uncover Evolutionary Origins and Mechanisms of Pathogenesis," Science, 313:1261-1266 (2006), Boore, et al

"The Genome of Black Cottonwood, Populus trichocarpa," Science, in press, Rohksar, Tuskan et al

"Symbiosis Insights through Metagenomic Analysis of a Microbial Consortium," Nature, in press, Woyke et al

"Sequencing and Analysis of Neanderthal Genomic DNA," Noonan, et al, in press, Science.

"Accelerated Evolution of Conserved Noncoding Sequences in the Human Genome," Science, in press, Prabhakar et al

"Metagenomic analysis of phosphorus removing sludge communities," Nature Biotechnology, in press, Hugenholtz et al

**PI Robert Ryne**

W. P. Leemans, B. Nagler, A. J. Gonsalves, Cs. Toth, K. Nakamura, C. G. R. Geddes, E. Esarey, C. B. Schroeder, S. M. Hooker, "GeV electron beams from a centimetre-scale accelerator," Nature Physics, V 2, p. 696.

H. Shan, J. Qiang, K. Yelick and E. Strohmaier, "Performance analysis of a high energy colliding beam simulation code on four high-performance computing architectures," to appear in the 35th International Conference on Parallel Processings. (peer reviewed).

C. G. R. Geddes, Cs. Toth, J. van Tilborg, E. Esarey, C. B. Schroeder, J. Cary, and W. P. Leemans, "Guiding of relativistic laser pulses by preformed plasma channels," Phys. Rev. Lett. 95, 145002 (2005).

M. J. Hogan, C. D. Barnes, C. E. Clayton, F. J. Decker, S. Deng, P. Emma, C. Huang, R. H. Iverson, D. K. Johnson, C. Joshi, T. Katsouleas, P. Krejcik, W. Lu, K. A. Marsh, W. B. Mori, P. Muggli, C. L. O. Connell, E. Oz, R. H. Siemann, and D. Walz, "Multi-GeV Energy Gain in a Plasma-Wakefield Accelerator", Phys. Rev. Lett., 95, 054802 (2005).

J. Amundson, P. Spentzouris, J. Qiang, R. Ryne, "Synergia: An accelerator modeling tool with 3-D space charge," J. Comp. Phys. 211, issue 1, pp. 229- 248 (2006).

K. Ko, et al, "Advances in Electromagnetic Modeling Through High Performance Computing," Physica C 441, 258-262 (2006).

J. Qiang, M. A. Furman, R. D. Ryne, W. Fischer, K. Ohmi, "Recent advaces of strong-strong beam-beam simulation," Nuclear Instruments & Methods in Physics Research A558, 351, (2006).

C. Ng, et al, "Simulation dark current in NLC structures," Nuclear Instruments and Methods in Physics Research A 558, 192-195 (2006).

J. Amundson, W. Pellico, L. Spentzouris, P. Spentzouris, T. Sullivan, "An experimentally robust technique for halo measurement using the IPM at the Fermilab Booster", to be published at Nuclear Inst. and Methods in Physics Research, A.

D.A. Dimitrov, R.E. Giacone, D.L. Bruhwiler, R. Busby, J.R. Cary, C.G.R. Geddes, E. Esarey and W.P. Leemans, "Coupling of Laser Energy into Plasma Channels," Phys. Plasmas (2006), submitted.

J. Qiang, S. Lidia, R. D. Ryne, and C. Limborg-Deprey, "A Three-Dimensional Quasi-Static Model for High Brightnees Beam Dynamics simulation," Phys. Rev. ST Accel. Beams 9, 044204 (2006).

G. Fubiani, J. Qiang, E. Esarey, W.P. Leemans, G. Dugan, "Space charge modeling of dense electron beams with large energy spreads," Phys. Rev. ST Accel. Beams 9, 064402 (2006).

## S

**PI Roman Samulyak**

R. Samulyak, T. Lu, P. Parks, A magnetohydrodynamic simulation of pellet ablation in the electrostatic approximation, Nucl. Fusion, 2006. Accepted

Z. Xu, M.N. Kim, W. Oh, J. Glimm, R. Samulyak, X.L. Li, and C. Tzanos, Atomization of a high speed jet, Int. J. Multiscale Comp. Eng., 2006. Accepted

R. Samulyak, J. Du, J. Glimm, Z. Xu, A numerical algorithm for MHD of free surface flows at low magnetic Reynolds numbers, J. Comp. Phys., 2006. Submitted

R. Samulyak, T. Lu, Y. Prykarpatskyy, J. Glimm, Z. Xu, M.N. Kim, Comparison of heterogeneous and homogenized numerical models of cavitation, Int. J. Multiscale Comp. Eng., 4 (2006), No 3, 377 - 389.

**PI Henry Schaefer**

"Unimolcular Thermal Fragmentation of ortho-benzyne", X. Zhang, A. T. Maccarone, M. R. Nimlos, S. Kato, V. M. Bierbaum, G. B. Ellison, B. Ruscic, A. C. Simmonett, W. D. Allen and H. F. Schaefer III.

"The IR Fingerprint of the Elusive NCCO Radical", A. C. Simmonett, F. A. Evangelista, W. D. Allen and H. F. Schaefer III.

"Ionization Potentials of Small Lithium Clusters (Lin) and Hydrogenated Lithium Clusters (LinH)", S. E. Wheeler and H. F. Schaefer, J. Chem. Phys. 122, 204328, (2005).

"Popular Theoretical Methods Predict Benzene and Arenes to be Nonplanar", D. Moran, A. C. Simmonett F. E. Leach, W. D. Allen, P. v. R. Schleyer and H. F. Schaefer III, J. Am. Chem. Soc., 128, 9342, (2006).

M. Schuurman, W. D. Allen, and H. F. Schaefer, "The ab Initio Limit Quartic Force Field of BH3", J. Comput. Chem. 26, 1106, (2005).

"On the nature of the Moller-Plesset critical point", A. V. Sergeev, D. Z. Goodson, S. E. Wheeler and W. D. Allen, J. Chem. Phys. 123, 064105, (2005).

**PI Rocco Schiavilla**

"Two-body electrodisintegration of 3He at high momentum transfer", R. Schiavilla, O. Benhar, A. Kievsky, L.E. Marcucci, and M. Viviani, Phys. Rev. C72, 064003 (2005)

"Induced polarization in the 2H(gamma,n)p reaction at low energy", R. Schiavilla, Phys. Rev. C72, 034001(2005)

**PI Dalton Schnack**

D. D. Schnack, D. C. Barnes, D. P. Brennan, C. C. Hegna, E. Held, C. C. Kim, S. E. Kruger, A. Y. Pankin, and C. R. Sovinec, Computational modeling of fully ionized magnetized plasmas using the fluid approximation, Phys. Plasmas 13, 058103 (2006).

**PI David Schultz**

Electron-impact ionization of Pb+q for q=1-10, S D Loch, J A Ludlow, M S Pindzola, N R Badnell, F Scheuermann, K Kramer, K Huber, and E Salzborn, Phys. Rev. A 72, 032713 (September 2005).

Electron-impact ionization of atomic ions in the W isonuclear sequence, S D Loch, J A Ludlow, M S Pindzola, A Whiteford, and D C Griffin, Phys. Rev. A 72, 052716 (November 2005).

Electron-ion recombination of Be-like C, N, and O, M Fogel, N R Badnell, P Glans, S D Loch, S Madzunkov, M S Pindzola, and R Schuch, Astronomy and Astrophysics 442, 757 (November 2005).

Electron-impact excitation cross sections for Fe+16 in the configuration-average distorted-wave approximation, M S Pindzola, S D Loch, C P Ballance, and D C Griffin, Phys. Rev. A 73, 012718 (January 2006).

Ionization state, excited populations, and emission of impurities in dynamic finite density plasmas: I: The generalized collisional-radiative model for light elements, H P Summers, W J Dickson, M G O'Mullane, N R Badnell, A D Whiteford, D H Brocks, J Lang, S D Loch, and D C Griffin, Plasma Physics and Controlled Fusion 48, 263 (January 2006).

Atomic data from the Iron project: LX: Electron-impact excitation of the n=3,4 levels of Fe+17, M C Witthoeft, N R Badnell, G del Zanna, K A Berrington, and J C Pelan, Astronomy and Astrophysics 446, 361 (January 2006).

Dielectronic recombination data for dynamic finite-density plasmas: IX: The Fluorine isonuclear sequence, O Zatsarinny, T W Gorcyzca, J. Fu, T K Korista, N R Badnell, and D W Savin, Astronomy and Astrophysics 447, 379 (February 2006).

Dielectronic recombination data for dynamic finite-density plasmas: X: The Hydrogen isonuclear sequence, N R Badnell, Astronomy and Astrophysics 447, 389 (February 2006).

Dielectronic recombination data for dynamic finite-density plasmas: XI: The Sodium isoelectronic sequence, Z Altun, A Yumak, N R Badnell, S D Loch, and M S Pindzola, Astronomy and Astrophysics 447, 1165 (March 2006).

Dielectronic recombination of Fe XXIII forming Fe XXII: Laboratory measurements and theoretical calculations, D W Savin, G Gwinner, M Griesar, R Repnow, M Schnell, D Schwalm, A Wolf, S G Zhou, S Kieslich, A Muller, S Schippers, J P Colgan, S D Loch, N R Badnell, M H Chen, and M F Gu, Astrophysical Journal 642, 1275 (May 2006).

Collisional radiative calculations of the He line emission in low temperature plasmas, C P Ballance, D C Griffin, S D Loch, R F Boivin, and M S Pindzola, Phys. Rev. A 74, 012719 (July 2006).

Relativistic radiatively damped R-matrix calculations of the electrom-impact excitation of W+46, C P Ballance and D C Griffin, J. Phys. B 39, 3617 (August 2006).

**PI Edward Seidel**

Diener P., Herrmann F., Pollney D., Schnetter E., Seidel E., Takahashi R., Thornburg J. & Ventrella J., 2006, Phys. Rev. Lett. 96, 121101, "Accurate evolution of orbiting binary black holes."

Diener P., Dorband E. N., Schnetter E. & Tiglio M., 2005, gr-qc-0512001, "Optimized high order derivative and dissipation operators satisfying summation by parts, and applications in three-dimensional multi-block evolutions.", submitted to Journal of Scientific Computing.

Schnetter E., Diener P., Dorband E. N. & Tiglio M., 2006, Classical and Quantum Gravity, 23, S553-S578, "A Multi-block infrastructure for three-dimensional time-dependent numerical relativity."

**PI Marjorie Shapiro**

Measurement of b Hadron Masses in Exclusive J/psi Decays at CDF D. Acosta et al., The CDF Collaboration, submitted to PRL, hep-ex/0508022.

Search for H -> bb-bar Produced in Association with W Bosons in ppbar Collisions at sqrt s = 1.96 TeV A. Abulencia et al., The CDF Collaboration, Accepted by PRL, but not yet published, hep-ex/0512051.

Measurement of the Ratios of Branching Fractions BR(B0s ? D-s p+)/BR(B0 ? D- p+) and BR(B+ ? D-bar0 p+)/BR(B0 ? D- p+) A. Abulencia et al., The CDF Collaboration, Accepted by PRL, but not yet published, hep-ex/0508014.

**PI Junko Shigemitsu**

``Accurate Determination of $\alpha_s$ from Realistic Lattice QCD'', Q.Mason,..., A. Gray,......, J. Shigemitsu et al.; hep-lat/0503005, Phys. Rev. Lett. \underbar{95}:052002, (2005).

``The $\Upsilon$ Spectrum and $m_b$ from Full Lattice QCD'', A.Gray, ...., E.Gulez, ....,J.Shigemitsu, M.Wingate et al. ; hep-lat\0507013, Phys. Rev. D\underbar{72}:094507 (2005).

``The $B$ Meson Decay Constant from Unquenched Lattice QCD'', A.Gray, M.Wingate, ...., E.Gulez, ....., J.Shigemitsu et al.; hep-lat/0507015, Phys. Rev. Lett. \underbar{95}:212001 (2005).

``$B$ Meson Semileptonic Form Factors from Unquenched Lattice QCD'', E.Gulez, A.Gray, M.Wingate, C.Davies, P.Lepage, J.Shigemitsu; Phys. Rev. D\underbar{73}:074502 (2006).

``Unquenched Determination of the Kaon Parameter $B_K$ from Improved Staggered Fermions'', E.Gamiz, S.Collins, C.Davies, P.Lepage, J.Shigemitsu, M.Wingate; Phys. Rev. D\underbar{73}:114502 (2006).

**PI Donald Sinclair**

J.B.Kogut and D.K.Sinclair, ``The RHMC algorithm for theories with unknown spectral bounds,'' arXiv:hep-lat/0608017.

J.B.Kogut and D.K.Sinclair, ``Evidence for O(2) universality at the finite temperature transition for lattice QCD with 2 flavours of massless staggered quarks,'' Phys. Rev. D 73, 074512 (2006)

J.B.Kogut and D.K.Sinclair, ``Quantization and simulation of Born-Infeld non-linear electrodynamics on a lattice,'' Phys. Rev. D 73, 114508 (2006) [arXiv:hep-lat/0603017].

G.T.Bodwin, J.Lee and D.K.Sinclair, ``Spin correlations and velocity-scaling in color-octet NRQCD matrix elements,'' Phys. Rev. D 72, 014009 (2005) [arXiv:hep-lat/0503032].

**PI George Smoot**

astro-ph/0604512 submitted to Astronomy & Astrophysics Title: Power Spectrum Analysis of Far-IR Background Fluctuations in 160 Micron Maps From the Multiband Imaging Photometer for Spitzer Authors: B. Grossan, G. F. Smoot

astro-ph/0601307 submitted for the 2006 edition of "The Review of Particle Physics" Title: Cosmic Microwave Background Mini-Review Authors: Douglas Scott, George Smoot

astro-ph/0504088 Astroparticle Physics 25 (2006) 375-379 Title: GZK cutoff distortion due to the energy error distribution shape Authors: Ivone F. M. Albuquerque, George F. Smoot

**PI Philip Snyder**

Brennan, D.P., and L.E. Sugiyama Tearing Mode Stability in a Low Beta Plasma with Sawteeth, Phys. Plasmas 13, 052515 (2006).

Brennan, D.P., et al. Computing Nonlinear Magnetohydrodynamic Edge Localized Instabilities in Fusion Plasmas, J. Phys.: Conf. Ser. 46, 63 (2006).

Candy, J., and R.E. Waltz Velocity Space Resolution, Entropy Production, and Upwind Dissipation in Eulerian Gyro-Kinetic Simulations, Phys. Plasmas 13, 03231 (2006).

Candy, J., R.E. Waltz, S.E. Parker, and Y. Chen Relevance of the parallel Nonlinearity in Gyrokinetic Simulations of Tokamak Plasmas, Phys. Plasmas 13, 074501 (2006).

Choi, M., V.S. Chan, R.I. Pinsker, et al. Simulation of Fast Alfven Wave Interaction with Beam ions over a Range of Cyclotron Harmonics in DIII-D Tokamak , Nucl. Fusion 46, S409 (2006).

Chu, M.S, V.S. Chan, P.A. Politzer, et al. Kinetic Alfven Wave and Associated Current Drive at Center of Tokamaks, to appear in Phys. Plasmas.

Estrada-Mila, C., J. Candy, and R.E. Waltz Density peaking and Turbulent Pinch in DIII-D Discharges, Phys. Plasmas 13, 074505 (2006).

Estrada-Mila, C., J. Candy, and R.E. Waltz Turbulent Transport of Alpha Particles and Helium Ash in Reactor Plasmas, to appear in Phys. Plasmas.

Hinton, F.L. and R.E. Waltz, Gyrokinetic Turbulent Heating, Phys. Plasmas 13, 102301 (2006).

Kinsey, J.E., R.E. Waltz, J. Candy The Effects of Safety Factor and Magnetic Shear on Turbulent Transport in Nonlinear Gyro-Kinetic Simulations, Phys. Plasmas 13, 022305 (2006).

Snyder, P.B., H.R. Wilson, and X.Q. Xu, Nonlinear Dynamics of ELMs: Numerical Studies of Flow Shear Effects and 3D Nonlinear ELM Dynamics, Phys. Plasmas 12, 056115 (2005).

Staebler, G.M., J.E. Kinsey, R.E. Waltz, Gyro-Landau Fluid Equations for Trapped and Passing Particles, Phys. Plasmas 12, 102508 (2005).

Staebler, G.M., and H.E. St. John, Predicted Toroidal Rotation Enhancement of Fusion Power Production in ITER, Nucl. Fusion 46, L6 (2006).

Waltz, R.E., M.E. Austin, K.H. Burrell, and J. Candy, Gyro-Kinetic Simulations of Off-Axis Minimum-q Profile Corrugations, Phys. Plasmas 13, 052301 (2006).

Waltz, R.E., J. Candy, and C.C. Petty Projected Profile Similarity in Bohm and Gyro-Bohm Scaled DIII-D L- and H-Modes, Phys. Plasmas 13, 072304 (2006).

**PI Masha Sosonkina**

J. Jones, L. Liu, and M. Sosonkina, Granularity of Component Interfaces for Iterative Linear Algebra, in Proc. 2006 HPC-GECO/Compframe Workshop, Paris, France, 2006, 4 pages.

J. Jones, M. Sosonkina, and Y. Saad, Component-based iterative methods for sparse linear systems, Concurrency and Computation: Practice and Experience, accepted October 2005.

N. Ustemirov, M. Sosonkina, M.S. Gordon and M.W. Schmidt, Dynamic Algorithm Selection in Parallel GAMESS Calculations, in Proc. 2006 Int'l Conference on Parallel Processing Workshops, Columbus, OH, 2006, 8 pages.

**PI Ivo Souza**

"Ab initio calculation of the anomalous Hall conductivity by Wannier interpolation" Xinjie Wang, Jonathan R. Yates, Ivo Souza, and David Vanderbilt, Physical Review B 74, 195118 (2006)

"Ab initio study of the nonlinear optics of III-V semiconductors in the terahertz regime" Eric Roman, Jonathan R. Yates, Marek Veithen, David Vanderbilt, and Ivo Souza (to appear in Physical Review B)

**PI Carl Sovinec**

E. B. Hooper, T. A. Kopriva, B. I. Cohen, D. N. Hill, H. S. McLean, R. D. Wood, S. Woodruff, and C. R. Sovinec, Magnetic Reconnection during Flux Conversion in a Driven Spheromak, Physics of Plasmas 12, 92503, (2005).

D. D. Schnack, D. C. Barnes, D. P. Brennan, C. C. Hegna, E. Held, C. C. Kim, S. E. Kruger, A. Y. Pankin, and C. R. Sovinec, Computational modeling of fully ionized magnetized plasmas using the fluid approximation, Phys. Plasmas 13, 058103 (2006).

P. Zhu, A. Bhattacharjee, and K. Germaschewski, Intermediate nonlinear evolution of the Parker instability: Formation of convection-induced discontinuities and absence of finite-time singularities, Phys. Rev. Lett. 96, 065001 (2006).

P. Zhu, C. C. Hegna, and C. R. Sovinec, Nonlinear growth of a line-tied g-mode near marginal stability, accepted for publication in Phys. Plasmas (2006).

P. Zhu, C. R. Sovinec, C. C. Hegna, K. Germaschewski, and A. Bhattacharjee, Nonlinear ballooning instability in the near-Earth magnetotail: Growth, structure, and possible role in substorms, submitted to J. Geophys. Res. (2006).

**PI Frank Spera**

Spera, F. J., Yuen, D. A. ,Giles, G. (2006) Tradeoffs in Chemical and Thermal Variations in the Post- perovskite Phase Transition: Mixed phase regions in the Deep Lower Mantle?, Physics Earth Planet Int., in Press.

White, S. M., Crisp, J. A., and Spera, F. J. (2006), Long-term volumetric eruption rates and magma budgets, Geochem. Geophys. Geosyst. 7, doi:10. 1029/2005GC001002.

Nevins, D. Spera, F. J., (2006) Accurate Computation Of Shear Viscosity From Equilibrium Molecular Dynamics Simulations, Molecular simulation, Sub 9/2006

**PI Don Spong**

"Compression of magnetohydrodynamic simulation data using singular value decomposition," D. del- Castillo-Negrete, S. P. Hirshman, D. A. Spong, E. F. D'Azevedo, Journal of Computational Physics, doi: 10.1016/j.jcp.2006.07.022 (2006).

"Bootstrap current in quasi-symmetric stellarators," A. S. Ware, D. A. Spong, L. A. Berry, S. P. Hirshman, J. F. Lyon, Fusion Science and Technology, Volume 50, Number 2, August 2006, Pages 236-244.

"Sheared plasma flow generation: a new measure for stellarator optimization," Fusion Science and Technology, Vol. 50, Oct., 2006.

"Magnetic island induced bootstrap current on island dynamics in tokamaks," Shaing, K.C.; Spong, D.A., Physics of Plasmas, v 13, n 2, Feb. 2006, p 22501-1-9.

"Recent advances in quasi-poloidal stellarator physics issues," Spong, D.A.; Hirshman, S.P.; Lyon, J.F.; Berry, L.A.; Strickler, D.J., Nuclear Fusion, v 45, n 8, Aug. 2005, p 918-25.

"Generation and damping of neoclassical plasma flows in stellarators," Spong, D.A., Physics of Plasmas, v 12, n 5, May 2005, p 56114-1-9.

"Mesoscale transport properties induced by near critical resistive pressure-gradient-driven turbulence in toroidal geometry ," L. Garcma and B.A. Carreras, Physics of Plasmas 13, 022310 (2006).

"Renormalization of tracer turbulence leading to fractional differential equations," R. Sanchez, B.A. Carreras, D.E. Newman, V.E. Lynch and B.Ph. van Milligen, Physical Review E 74, 016305 (2006).

"On the use of critical gradient models in fusion plasma transport studies ," B.A. Carreras, V.E. Lynch, B.Ph. van Milligen and R. Sanchez, Physics of Plasmas 13, 062301 (2006).

"Study of the interaction between diffusive and avalanche-like transport in near-critical dissipative-trapped-electron-mode turbulence," J.A. Mier, L.Garcia and R. Sanchez, Physics of Plasmas (in press, 2006).

**PI Garrison Sposito**

Bourg I.C., Sposito G. (2006). Molecular dynamics simulations of kinetic isotope fractionation during the diffusion of ionic species in liquid water, Geochimica et Cosmochimica Acta (submitted).

**PI Phillip Sprangle**

R.F. Hubbard, "Plasma Channels and Accelerator Applications - A Tutorial," to appear in Proceedings of the 12th Advanced Accelerator Concepts Workshop, Lake Geneva, WI 2006

M. Levin, A. Pukhov, A. Zigler, K. Sugiyama, K. Nakajima, R.F. Hubbard, A. Ting, D.F. Gordon, P. Sprangle, and D. Kaganovich, "Long plasma channels in segmented capillary discharges," Phys. Plasmas 13, 83108-1 (2006)

T. Palchan, S. Eisenmann, A. Zigler, D. Kaganovich, R.F. Hubbard, M. Fraenkel, D Fisher, and Z. Henis, "All optical electron injector using an intense ultrashort pulse laser and a solid wire target," Appl. Phys. B: Lasers and Optics 83, 219 (2006)

**PI Ashok Srinivasan**

Y. Yu, A. Srinivasan, and N. Chandra. Scalable Time-Parallelization of Molecular Dynamics Simulations in Nano Mechanics. Proceedings of the 35 th International Conference on Parallel Processing (ICPP), (2006) 119-126.

**PI Malcolm Stocks**

"Intrinsic Volume Scaling of Thermoinduced Magnetization in Antiferromagnetic Nanoparticles", G. Brown, A. Janotti, M. Eisenbach, G. M. Stocks, Phys. Rev. B 72, 140405 (2005)

"Epitaxial Stabilization of Ferromagnetism in the Nanophase of FeGe", C. Zeng, P. R. C. Kent, M. Varela, M. Eisenbach, G. M. Stocks, M. Torija, J. Shen, H. H. Weitering, Phys. Rev. Lett. 96, 127201 (2006)

"On Calculating the Magnetic State of Nanostructures", G. M. Stocks, M. Eisenbach, B. Zjfalussy, B. Lazarovits, L. Szunyogh, P. Weinberger, (to be published in Prog. Mat. Sci.)

"Localization/quasi-delocalization transitions and quasi-mobility-edges in shell-doped nanowires", Zhong J. X., G. M. Stocks, Nano Letters 6, 128 (2006).

"Mean-field approximations for the electronic states in disordered alloys", J. S. Faulkner, S. Pella, A. Rusanu, Y. Puzyrev, Th. Leventouri, G. M. Stocks, and B. Ujfalussy, Phil. Mag. 86, 2661 (2006).

"Electronic Structure and Exchange Coupling of Mn Impurities in III-V Semionductors", Schulthess, T.C., W. M. Temmerman, Z. Szotek, W. H. Butler, and G. M. Stocks, Nature Materials 4, 838-844 (2005).

"Size and structure dependent chemisorption of carbon monoxide on cobalt clusters", F. A. Reboredo and G. Galli, Journal Physical Chemistry 110(15), 7979-7984 (2006)

"First-principles study of rare-earth oxides", L. Petit, A. Svane, Z. Szotek, W. M. Temmerman, Prys. Rev. B 72, 205118 (2005)

"Electronic structure of transition-metal impurities in p-type ZnO", L. Petit, T. C. Schulthess, A. Svane, Z. Szotek, W. M. Temmeman, A. Janotti, Phys. Rev. B 73, 045107 (2006).

"Calculation of helium defect clustering properties in iron using a multi-scale approach", T. Seletskaia, Yu.N. Osetsky, R.E. Stoller, G.M. Stocks, J. Nuclear Mat. 351, 109 (2006)

**PI Alberto Striolo**

A. Striolo, The Mechanism of Water Diffusion in Narrow Carbon Nanotubes, Nano Letters, 6 (2006) 633-639.

N.R. Tummala and A. Striolo, Equilibrium Structure and Hydrogen-Bond Dynamics for Water in Organic Media, Jurnal of the American Chemical Society, (2006) submitted.

**PI Erich Strohmaier**

E. Strohmaier and H. Shan, "Apex-Map: A Global Data Access Benchmark to Analyze HPC Systems and Parallel Programming Paradigms", to appear in Proceedings of SC|05, Nov. 2005.

J. Weinberg, A. Snavely, M.O. McCracken, and E. Strohmaier, "Measurement of Spatial and Temporal Locality in Memory Access Patterns", Proceedings of SC|05, Nov. 2005.

H. Shan and E. Strohmaier, "Performance Comparison of Cray X1E, XT3, NEC SX8 and AMD/IB", Proceedings of Cray Users Group Meeting (CUG 2006), May 2006. Lugano, Switzerland.

E. Strohmaier and H. Shan, "Apex-Map: A Synthetic Scalable Benchmark Probe to Explore Data Access Performance on Highly Parallel Systems", to appear in Concurrency and Computation: Practice and Experience.

E. Strohmaier, "PC: A Quantitative Measure for Performance Complexity", LBNL-61133, to appear CTWatch, 2006

**PI Maxim Sukharev**

"Light trapping and guidance in plasmonic nanocrystals", M. Sukharev and T. Seideman (2006) (submitted to NanoLetters).

"Analysis of Surface Waves Generated on Subwavelength-Structured Silver Films", G. Gay, O. Al-loschery, J. Weiner, H. J. Lezec, C. O'Dwyer, M. Sukharev, T. Seideman, arXiv:physics/0608116 (2006) (submitted to Physical Review Letters).

"Coherent Control Approaches to light guidance in the nanoscale", M. Sukharev, T. Seideman, Journal of Chemical Physics, 124, 144707 (2006).

"Phase and Polarization Control as a Route to Plasmonics Nanodevices", M. Sukharev, T. Seideman, Nanoletters, 6, 715 (2006). Also in Proceedings of SPIE, 6115, 611517 (2006).

"Optical control of nonradiative decay in polyatomic molecules", M. Sukharev, T. Seideman, Physical Review A, 71, 012509 (2005).

## T

**PI Xianzhu Tang**

"Force-free magnetic relaxation in driven plasmas," X.Z. Tang and A.H.Boozer, Physical Review Letters 94, 225004 (2005).

"Constrained resonance in magnetic self-organization," X.Z. Tang and A.H. Boozer, Physical Review Letters 95, 155002 (2005).

"Flux amplification in helicity injected spherical tori," X.Z.Tang and A.H.Boozer, Phys. Plasmas 12, 042113 (2005).

"Chandrasekhar-Kendall modes and Taylor relaxation in an axisymmetric torus," X.Z. Tang and A.H. Boozer, Phys. Plasmas 12, 102102 (2005).

"Spherical Tokamak with a plasma center column," X.Z.Tang and A.H.Boozer, Physics of Plasmas 13, 042514 (2006).

**PI Owen Toon**

Smith, J. A., A. S. Ackerman, E. J. Jensen, and O. B. Toon, The role of deep convection in establishing the isotopic composition of water vapor in the tropical transition layer, Geophys. Res. Lett. 33, doi10.1029/2005GL024078, 2006.

Kirkpatrick, M. P., A. S. Ackerman, D. E. Stevens, and N. N. Mansour, On the application of the dynamic Smagorinsky model to large-eddy simulations of the cloud-topped atmospheric boundary layer, J. Atmos. Sci. 63, 526-546, 2006.

Jensen, E. J., and A. S. Ackerman, Homogeneous aerosol freezing in the topos of high-altitude tropical cumulonimbus clouds, Geophys. Res. Lett. 33 (L08802), doi:10.1029/2005GL024928, 2006.

N. Mansour, Study of near-surface models in large-eddy simulations of a neutrally stratified atmospheric boundary layer, submitted to Boundary Layer Meteor.

**PI Doug Toussaint**

Charmed meson decay constants in three-flavor lattice QCD, C. Aubin, C. Bernard, C. DeTar, M. Di Pierro, E. D. Freeland, Steven Gottlieb, U. M. Heller, J. E. Hetrick, A. X. El-Khadra, A. S. Kronfeld, L. Levkova, P. B. Mackenzie, D. Menscher, F. Maresca, M. Nobes, M. Okamoto, D. Renner, J. Simone, R. Sugar, D. Toussaint, H. D. Trottier, Phys.Rev.Lett. 95 (2005) 122002 (hep-lat/0506030).

Semileptonic decays of $D$ mesons in three-flavor lattice QCD, C. Aubin, C. Bernard, C. DeTar, M. Di Pierro, A. El-Khadra, Steven Gottlieb, E. B. Gregory, U. M. Heller, J. Hetrick, A. S. Kronfeld, P. B. Mackenzie, D. Menscher, M. Nobes, M. Okamoto, M. B. Oktay, J. Osborn, J. Simone, R. Sugar, D. Toussaint, H. D. Trottier, Phys.Rev.Lett. 94 (2005) 011601 (hep-ph/0408306).

QCD Thermodynamics with Three Flavors of Improved Staggered Quarks, The MILC Collaboration: C. Bernard, T. Burch, C. DeTar, Steven Gottlieb, E.B. Gregory, U.M. Heller, J. Osborn, R. Sugar, D. Toussaint, Phys.Rev. D71 (2005) 034504 (hep-lat/0405029)

## U

## V

**PI George Vahala**

A. Macnab, G. Vahala and L. Vahala, "Non-uniform grid Lattice Boltzmann Simulations of 1D Dissipative MHD", Prog. Comput. Fluid Dynamics, 5, 37-49 (2005)

G. Vahala, J. Carter, M. Soe, J. Yepez, L. Vahala and A. Macnab, "Performance of Lattice Boltzmann Codes for Navier-Stokes and MHD Turbuelnce on the Earth Simulator, CRAY X-1 and Power 3/4 Architecture", Parallel CFD 2005, submitted for publication in 'Parallel CFD 2005",

J. Carter, M. Soe, L. Oliker, Y. Tsuda, G. Vahala, L. Vahala and A. Macnab, "MHD Turbulence SImulations on the Earth Simulator Using the Lattice Boltzmann Method" , finalist for Gordon Bell Prize 2005; published in Proc. of SC|05 (Nov. 2005)

A. Macnab, G. Vahala, L. Vahala, J. Carter, M. Soe and W. Dorland, "The Lattice Boltzmann Representation for Plasma Physics", Physica A362, 48 - 56 (2006)

G. Vahala, L. Vahala and J. Yepez, "Quantum Lattice Representation for Vector Solitons in an External Potential", Physica A362, 215 - 221 (2006)

J. Yepez, G. Vahala, L. Vahala and M. Soe, "Entropic Lattice Botlzmann Simulation of Navier-Stokes Turbulence", submitted to Phys. Rev. E

B. Keating, G. Vahala, J. Yepez, M. Soe and L. Vahala, "Entropic Lattice Boltzmann Representations Required to Recover Navier-Stokes Flows", submitted to Phys. Rev. E

**PI James Vary**

Ionel Stetcu, Bruce R. Barrett, Petr Navratil, and James P. Vary, Effective operators within the ab initio no-core shell model, Phys. Rev. C 71,044325 (2005); nucl-th/ 0412004, Report-no: UCRL-JRNL-208306.

D. Chakrabarti, A. Harindranath, L. Martinovic, G. Pivovarov and J.P. Vary, Ab initio results for the broken phase of scalar light front field theory, Phys. Letts. B 617, 92 (2005) hep-th/0310290.

D. Chakrabarti, A. Harindranath and J.P. Vary, A Transition in the Spectrum of the Topological Sector of Phi4(2) Theory at Strong Coupling, Phys. Rev. D 71, 125012(2005); hep-th/05104094.

I. Stetcu, B. R. Barrett, P. Navratil and J. P. Vary, Long- and short-range correlations in the ab initio no- core shell model, Phys. Rev. C 73, 037307 (2006).

B. R. Barrett, I. Stetcu, P. Navratil and J. P. Vary, From non-Hermitian effective operators to large-scale No-Core Shell Model calculations for light nuclei, in Non-Hermitian Operators, H. Geyer, Ed., J. Phys. A. Math. Gen. 39 (2006) 9983; UCRL-PROC-219600; nucl-th/0603034.

K. D. Sviratcheva, J. Draayer, and J. P. Vary, Underlying symmetries of realistic interactions and the nuclear many-body problem, Phys. Rev. C 73, 034324 (2006).

A. Nogga, P. Navratil, B.R. Barrett and J.P. Vary, Spectra and binding energy predictions of chiral interactions for 7Li, nucl-th/0511082, Phys. Rev. C 73, 064002 (2006).

B.R. Barrett, S. Quaglioni, I. Stetcu, P. Navratil, W.E. Ormand, J.P. Vary and A. Nogga, No Core Shell Model for Nuclear Structure and Reactions, Proceedings of the Third ANL/MSU/INT/JINA RIA Theory Workshop, Argonne National Lab, April 4-7, 2006, World Scientific, to appear.

J. P. Draayer, K. D. Sviratcheva, T. Dytrych, C. Bahri, K. Drumev, J. P. Vary, Fermion Systems with Fuzzy Symmetries (Leveraging the Known to Understand the Unknown), Proceedings of the Third ANL/MSU/ INT/JINA RIA Theory Workshop, Argonne National Lab, April 4-7, 2006, World Scientific, to appear.

A. Negret, T. Adachi, B.R. Barrett, C. Baumer, A.M. van den Berg, G.P.A. Berg, P. von Brentano, D. Frekers, D. De Frenne, H. Fujita, K. Fujita, Y. Fujita, E.-W. Grewe, P. Haefner, M.N. Harakeh, K. Hatanaka, K. Heyde, M. Hunyadi, E. Jacobs, Y. Kalmykov, A. Korff, K. Nakanishi, P. Navratil, P. von Neumann-Cosel, L. Popescu, S. Rakers, A. Richter, N. Ryezayeva, Y. Sakemi, A. Shevchenko, Y. Shimbara, Y. Shimizu, Y. Tameshige, A. Tamii, M. Uchida, J. Vary, H.J. Woertche, M. Yosoi, L. Zamick, Gamow-Teller Strengths in the A = 14 Multiplet: A Challenge to the Shell Model, Phys. Rev. Lett. 97, 062502 (2006).

S.J. Brodsky, D. Chakrabarti, A. Harindranath, A. Mukherjee and J.P. Vary, Hadron Optics: Diffraction Patterns in Deeply Virtual Compton Scattering, SLAC-PUB-11615, UFIFT-HEP-06-02, UCRL- JRNL-220485, hep-ph/0604262, Physics Letters B (accepted for publication August 2006).

A.M. Shirokov, J.P. Vary, A.I. Mazur and T.A. Weber, Realistic Nuclear Hamiltonian: Ab exitu approach, Submitted to PLB, ArXiv nucl-th/0512105, LLNL preprint number UCRL-JRNL-217903, SLAC preprint number SLAC-PUB-11614.

J.P. Vary, S. Popescu, S. Stoica, and P. Navratil, No-Core Shell Model for 48-Ca, 48-Sc and 48-Ti, Submitted to Physical Review C, ArXiv nucl-th/0607041.

## W

**PI Haobin Wang**

M. Thoss and H. Wang, "Quantum Dynamical Simulation of Ultrafast Molecular Processes in the Condensed Phase", Chem. Phys., 322, 210 (2006).

I. Kondov, H. Wang, and M. Thoss, "Computational study of titanium (IV) complexes with organic chromophores", Int. J. Quan. Chem., 106, 1291 (2006).

I. Kondov, M. Thoss, and H. Wang, "Theoretical study of ultrafast heterogeneous electron transfer reactions at dye-semiconductor interfaces: Coumarin 343 at titanium oxide", J. Phys. Chem. A., 110, 1364 (2006).

H. Wang and M. Thoss, "Quantum mechanical evaluation of the Boltzmann operator in correlation functions for large molecular systems: a multilayer multi-configuration time-dependent Hartree approach'', J. Chem. Phys., 124, 034114 (2006).

H. Wang, D.E. Skinner, and M. Thoss, "Calculation of reactive flux correlation functions for systems in a model condensed phase environment: a multilayer multi-configuration time-dependent Hartree approach'', J.Chem.Phys., accepted.

**PI Lin-Wang Wang**

J. Li, L.W. Wang, "Ab initio study of semiconductor quantum dots and wires", Phys. Rev. B 72, 125325(2005) [LBNL-57945]

B. Lee, L.W. Wang, "Electronic structure of Calcium hexaborides" Appl. Phys. Lett. 87, 262509 (2005) [LBNL-57944].

L.W. Wang, "Charging effects in a CdSe nano-tetrapod", J. Phys. Chem. 109, 23330 (2005) [LBNL-60843]

A. Franceschetti, L.W. Wang, G. Bester, A. Zunger, "Confinement-induced vs. correlation-induced electron localization in model semiconductor nano circuits", Nanolett. 6, 1069 (2006)[LBNL-60847].

E. Rotenberg, Y.Z. Wu, J.M. Ann, M.A. Van Hove, A. Canning, L.W. Wang, Z.Q. Qiu, "Non-free-electron momentum and thickness-dependent evolution of quantum well states in the Cu/Co/Cu (001) system", Phys. Rev. B 73, 75426 (2006) [LBNL-57817]

W. B. Jones, G. Bester, A. Canning, A. Franceschetti, P. A. Graf, K. Kim, J. Langou, L.W. Wang, J. Dongarra, and A. Zunger, "NanoPSE:A Nanoscience Problem Solving Environment for Atomistic Electronic Structure of Semiconductor Nanostructures", in "the Proceedings of Science Discovery through Advanced Computing (SciDAC 2005)", Journal of Physics: Conference Series 16, 277 (2005) [LBNL-61599]

C. Yang, J. Meza, L.W. Wang, "A constrained optimization algorithm for total energy minimization in electronic structure calculation", J. Comp. Phys. (in press).

Y. Zhang, G.M. Dalpian, B. Fluegel, Su-Huai Wei, A. Mascarenhas, X.-Y. Huang, J. Li, L.W. Wang, "A novel approach of tuning the physical properties of organic-inorganic hybrid semiconductors", Phys. Rev. Lett. 96, 26405 (2006) [LBNL-60842].

A.Y, Nazzal, H.X. Fu, L.W. Wang, "Electronic properties and tunability in Si quantum rings", J. Appl. Phys. 98, 83703 (2005) [LBNL-60844].

X. Cartoixa, L.-W. Wang, D.Z.-Y. Ting, Y.-C. Chang, "Higher-order contributions to Rashba and Dresselhaus effects", Phys. Rev. B 73, 205341 (2006) [LBNL-60845].

Z. Zhao, L.W. Wang, J. Meza, "Motif based Hessian matrix for ab initio geometry optimization of nanostructures", Phys. Rev. B 73, 193309 (2006) [LBNL-59974]

J. Schrier, L.W. Wang, "Electronic structure of nanocrystal quanutm dot quantum wells", Phys. Rev. B 73, 245332 (2006) [LBNL-60838]

J. Schrier, L.W. Wang, "On the size-dependent behavior of nanocrystal-ligand bonds", J. Phys. Chem. B 110, 11982 (2006) [LBNL-59148]

D.O. Demchenko, L.W. Wang, "Optical transition and nature of Stokes shift in spherical CdS quantum dots", Phys. Rev. B 73, 155326 (2006) [LBNL-59231]

B. Lee, L.W. Wang, "Electronic structure of zinc-blende AlxGa1-xN: screened-exchange study", Phys. Rev. B 73, 153309 (2006) [LBNL-59272]

Y. Zhang, A. Mascarenhas, L.W. Wang, "An impurity state of a perturbed host state?", Phys. Rec. B (in press)

B. Lee, L.W. Wang, "Band gap bowing and electron localization of GaInN", J. Appl. Phys. (in press).

Z. Zhao, L.W. Wang, F. Wu, "Wavefunction localizations in bulged CdSe nanowires", J. Theor. Comp. Nanosci. (in press).

C. Yang, L.W. Wang, J. Meza, "The use of trust region in Kohn-Sham total energy minimization", J. Comp. Phys. (in press).

C. Voemel, J. Dongarra, O. Marques, S. Tomov, L.W. Wang, "The use of bulk states to accelerate the band edge state calculation of a semiconductor quantum dot", J. Comp. Phys. (in press). [LBNL-60147].

A. Garcia-Lekue and L.W. Wang, "Elastic quantum transport calculations for molecular nanodevices using plane waves", Phys. Rev. B (in press).

L.W. Wang, Xavier Cartoixa, "A motif based polarization model", Phys. Rev. Lett. (submitted).

L.W. Wang, Z. Zhao, J. Meza, "Linear scaling 3D Fragment method for large scale electronic structrure calculations", LBNL technical report (num-61691), 2006.

**PI Andrew Ware**

"Bootstrap Current in Quasi-Symmetric Stellarators", A. S. Ware, D. A. Spong, L. A. Berry, S. P. Hirshman, and J. F. Lyon, Fusion Sci. Tech. 50, 236 (2006).

**PI Warren Washington**

Climate change in the 20th and 21st centuries and climate change commitment in the CCSM2 2005 Journal of Climate 19 2597-2616 published G. A. Meehl CGD W. M. Washington CGD B. D. Santer other W. D. Collins CGD J. M. Arblaster CGD A. Hu CGD D. M. Lawrence CGD H. Teng CGD L. E. Buja CGD W. G. Strand CGD

Monsoon regimes in CCSM3 2006 Journal of Climate 19 2842-2495 published G. A. Meehl CGD J. M. Arblaster CGD D. M. Lawrence CGD A. Seth other E. K. Schneider other B. P. Kirtman other D. Min other

Understanding future patterns of increased precipitation intensity in climate model simulations 2005 Geophysical Research Letters 32 L18719 10.1029/2005GL023680 published G. A. Meehl CGD J. M. Arblaster CGD C. Tebaldi ISSE

Future changes of El Nino in two global coupled climate models 2006 Climate Dynamics 26 549-566 10.1007/s00382-0098-0 published G. A. Meehl CGD H. Teng CGD G. W. Branstator CGD

Megadroughts in the Indian monsoon and southwest North America and a mechanism for associated multi-decadal Pacific sea surface temperature anomalies 2006 Journal of Climate 19 1605-1623 published G. A. Meehl CGD A. Hu CGD

Twenty-first century Arctic climate change in the CCSM3 IPCC scenario simulations 2006 Climate Dynamics 26 601-616 published H. Teng CGD W. M. Washington CGD G. A. Meehl CGD L. E. Buja CGD G. W. Strand CGD

Twenty-first-century cliamte change commitment from a multi-model ensemble 2006 Geophysical Research Letters 33 10.1029/2005GL024766 published H. Teng CGD L. E. Buja CGD G. A. Meehl CGD

**PI William Weber**

R. Devanathan, L. R. Corrales, W. J. Weber, A. Chartier and C. Meis, "Atomistic simulation of collision cascades in zircon", Nuclear Instruments and Methods B 250(1-2) (2006) 46-49.

R. Devanathan and W. J. Weber, "Insights into the radiation response of pyrochlores from calculations of threshold displacement events", Journal of Applied Physics 98(8) (2005) 086110.

R. Devanathan, L. R. Corrales, W. J. Weber, A. Chartier and C. Meis, "Molecular dynamics simulation of energetic uranium recoil damage in zircon", Molecular Simulation (in press).

R. Devanathan, P. Durham, J. Du, L. R. Corrales and E. M. Bringa, "Molecular dynamics simulation of amorphization of forsterite by cosmic rays", Nuclear Instruments and Methods B (accepted).

P. Durham, R. Devanathan, E. M. Bringa, L. R. Corrales, A. G. Tielens and W van Breugel, "Atomistic simulation of cosmic ray-induced amorphization of silicate grains", Astrophysical Journal Letters (accepted).

F. Gao, R. Devanathan, Y. Zhang, M. Posselt and W. J. Weber, "Atomic-level simulation of epitaxial recrystallization and phase transformation in SiC", Journal of Materials Research 21(6) (2006) 1420-1426.

M. Posselt, F. Gao, and W. J. Weber, Atomistic Simulations on the Thermal Stability of the Antisite Pair in 3C- and 4H-SiC, Physical Review B 73 [12] (2006) 125206, 1-8.

F. Gao, Y. Zhang, M. Posselt, and W. J. Weber, Atomic-Level Simulations of Epitaxial Recrystallization and Amorphous-to-Crystalline Transition in 4H-SiC, Physical Review B 74 [10] (2006) 104108, 1-9.

**PI Michael Weinert**

Atomic and electronic structure of the Fe3O4(111)/MgO(111) model polar oxide interface. V.K. Lazarov, M. Weinert, S.A. Chambers, and Gajdardziska-Josifovska, Phys. Rev. B 72, 195401 (2005).

Role of Ga polarization and defect sites in the magentization of Mn-doped GaN. D.J. Keavnery, S.H.Cheung, S.T. King, M. Weinert, and L. Li, Phys. Rev. Lett. 95, 257201 (2005).

Magnetic instability and meta-magentism on the surface of the bulk paramagnetic intermetallic compound YCo$_{2}$. S. Khmelevskyi, P. Mohn, J. Redinger, and M. Weinert, Physica B 378-380, 109 (2006).

Unusual adsorption site of hydrogen on the unreconstructed Ir(100) surface. D. Lerch, A. Klein, A. Schmidt, S. M\"uller, L. Hammer, K. Heinz, and M. Weinert, Phys. Rev. B 73, 075430 (2006).

Selective doping of an antiferromagnetic semiconductor: magnetism and spin-polarized carriers in MnGeN2. S. T. King, V. K. Lazarov, S. H. Cheung, M. L. Harland, D. J. Keavney, Z. Gai, M. Gajdardziska-Josifovska, M. Weinert, and L. Li, Phys. Rev. Lett. (submitted).

Atomic Structure of Metastable GaN ``Ghost'' Islands and a Mechanism for Their Conversion. S. T. King, M. Weinert, and L. Li, Phys. Rev. B (submitted).

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. Rev. B (submitted).

**PI Harold Weitzner**

G. Y. Fu, W. Park, H. Strauss, J. Breslau, J. Chen, S. Jardin, and L. E. Sugiyama, "Global hybrid simulations of energetic particle effects on n = 1 mode in tokamaks: internal kink and fishbone instability", Phys. Plasmas 2006.

G.M. Zaslavsky and M. Edelman, "Fractional Kinetics of Pseudochaotic Dynamics", in Fractional differentiation and its applications, Eds: A. Le Mechaute, J.A. Tenreiro Machado, J.C. Trigeassou, J. Sabatier, 183-193, Books on demand, Germany (2005).

G. M. Zaslavsky, A. A. Stanislavsky, and M. Edelman, "Chaotic and pseudochaotic attractors of perturbed fractional oscillator", Chaos 16, 013102 (2006).

G.M. Zaslavsky, M. Edelman, "Stickiness of trajectories in a perturbed Anosov system", Regular & Chaotic Dynamics 11 (2): 329-336 (2006).

I.P. Smirnov, A.L. Virovlyansky, M. Edelman, G.M. Zaslavsky, "Chaos- induced intensification of wave scattering", Phys. Rev. E,(2005).

G.M. Zaslavsky and M. Edelman, "Polynomial Dispersion of Trajectories in Sticky Dynamics", Phys. Rev. E, (2005).

R. Maingi, C. S. Chang et al., "Effect of gas fueling location on H mode access in NSTX", Plas. Phys. Cont. Fusion (2005)

P. Garabedian and L.-P. Ku, Reactors with stellarator stability and tokamak transport, Fusion Sci. Technol. {\bf 47} (2005) 400-405.

J. Lyon, L.-P. Ku, L. El-Guebaly, P. Garabedian and L. Bromberg, Optimization of stellarator reactor parameters, Fusion Sci. Technol. {\bf 47} (2005) 414-421.

P. Garabedian, Bifurcated equilibria and magnetic islands in tokamaks and stellarators, Comm. Appl. Math. Comp. Sci. {\bf 1} (2006) 79-90.

P. Garabedian, Computational theory of magnetic fusion, with applications to the ITER project, International Journal of Computational and Applied Mathematics {\bf 1} (2006), to be published.

L.-P. Ku and P. Garabedian, New classes of quasi-axisymmetric stellarator configurations, Fusion Sci. Technol. {\bf 48} (2006), to be published.

**PI Zhaofang Wen**

"An Envolutionary Path towards Virtual Shared Memory with Random Access," J L. Brown, S. Goudy, M, Heroux, S. S. Huang, Z. Wen, Annual ACM Symposium on Parallel Architectures and Algorithms, Aug, 2006, Boston, MA.

**PI Martin White**

Heymans, Catherine, White, Martin, Heavens, Alan, Vale, Chris, and van Waerbeke, Ludovic, Potential sources of contamination to weak lensing measurements: constraints from N-body simulations, Monthly Notices of the Royal Astronomical Society, 371, 760 (2006)

Schulz, A. E. and White, Martin, Scale-dependent bias and the halo model, Astroparticle Physics, 25, 177 (2006)

Dodelson, Scott, Shapiro, Charles, and White, Martin, Reduced shear power spectrum, Physical Review D, 73, (2006)

Vale, Chris and White, Martin, Finding clusters in SZ surveys, New Astronomy, 11, 217 (2006)

Conroy, Charlie, Coil, Alison L., White, Martin, Newman, Jeffrey A., Yan, Renbin, Cooper, Michael C., Gerke, Brian F., Davis, Marc, and Koo, David C., The DEEP2 Galaxy Redshift Survey: The Evolution of Void Statistics from z ~ 1 to z ~ 0, Astrophysical Journal, 635, 1005 (2005)

Schulz, A. E., Hennawi, Joseph, and White, Martin, Characterizing the shapes of galaxy clusters using moments of the gravitational lensing shear, Astroparticle Physics, 24, 419 (2005)

White, Martin, Baryon oscillations, Astroparticle Physics, 24, 344 (2005)

Cohn, J. D. and White, Martin, The formation histories of galaxy clusters, Astroparticle Physics, 24, 333 (2005)

Ho, Shirley and White, Martin, Cluster arc statistics, Astroparticle Physics, 24, 272 (2005)

Linder, Eric V. and White, Martin, Going nonlinear with dark energy cosmologies, Physical Review D, 72, (2005)

Huterer, Dragan and White, Martin, Nulling tomography with weak gravitational lensing, Physical Review D, 72, (2005)

**PI James Wiley**

ZHENG, L. J., KOTSCHENREUTHER, M.T.,J. Comput. Phys. {\bf 221} (2006) 748.

E. Spencer, W. Horton and I. Doxas, The Dynamics of Storms and Substorms with the WINDMI Model, Advances in Space Research, in press (2005).

E.G. Evstatiev, W. Horton and P.J. Morrison, Relativistic multi-wave model for plasma-wave interaction, to appear in Physics of Plasmas, July, 2005.

E.G. Evstatiev, P.J. Morrison, and W. Horton, A relativistic beam-plasma system with electromagnetic waves, Phys. Plasmas 12, 072108 (2005).

W. Horton, M.J. Mithaiwala, E.A. Spencer, and I. Doxas, WINDMI, a family of Physics network models for storms and substorms, a chapter in the book Multiscale Coupling of Sun-Earth Processes, ed. by A.T.Y. Lui, Y. Kamide, and G. Consolini, Elsevier Publ. Co., Amsterdam, The Netherlands, 2005) pp. 431-446.

R. Presura, V.V. Ivanov, Y. Sentoku, V.I. Sotnikov, P.J. Laca, N. Le Galloudec, A. Kemp, R. Mancini, H. Ruhl, A.L. Astanovitskiy, T.E. Cowan, T. Ditmire, C. Chiu, W. Horton, P. Valanju and S. Keely, Laboratory Simulation of Magnetospheric Plasma Shocks, Astrophysics and Space Science 298: 299-303 (2005).

W. Horton, C. Chiu, and T. Ditmire, Laboratory Simulations of Bow Shocks and Magnetospheres, Astrophysics and Space Science 298: 395-401 (2005).

W. Horton, J. C. Perez, T. Carter and R. Bengtson, Vorticity probes and the characterization of vortices in the Kelvin-Helmholtz instability in the large plasma device experiment, Physics of Plasmas 12, No. 2, 022303 (2005).

W. Horton, H.V. Wong, P.J. Morrison, A. Wurm, J.H. Kim, J.C. Perez, J. Pratt, G.T. Hoang, B.P. LeBlanc and R. Ball, Temperature gradient driven electron transport in NSTX and Tore Supra, Nuclear Fusion 45, 1-10 (2005).

H. Vernon Wong, B.-Y. Xu, W. Horton, J. Pratt, and J.W. Van Dam, Nonlinear evolution of the firehouse instability in a magnetic dipole geotail geometry, Phys. Plasmas 12, 056502 (2005).

ZHENG, L.-J., KOTSCHENREUTHER, M. T., CHU, M.S., Phys. Rev. Lett {\bf 95} (2005) 255003.

**PI John Wilkins**

Comparison of screened hybrid density functional theory to diffusion Monte Carlo in calculations of total energies of silicon phases and defects. E. R. Batista, J. Heyd, R. G. Hennig, B. P. Uberuaga, R. L. Martin, G. E. Scuseria, C. J. Umrigar, and J. W. Wilkins. Phys. Rev. B 74, 121102(R) (2006).

Questioning the existence of a unique ground state structure for Si clusters. W. Hellmann, R. G. Hennig, S. Goedecker, C. J. Umrigar, B. Delley, T. Lenosky. submitted to Phys. Rev. Lett. (2006).

Impurities block the alpha to omega martensitic transformation in titanium. R.G. Hennig, D.R. Trinkle, J. Bouchet, S.G. Srinivasan, R.C. Albers, and J.W. Wilkins. Nature Materials 4, 129 (2005).

Systematic pathway generation and sorting in martensitic transformations: Titanium alpha to omega. D.R. Trinkle, D.M. Hatch, H.T. Stokes, R.G. Hennig and R.C. Albers. Physical Review B 72, 014105 (2005).

A new mechanism for the alpha to omega martensitic transformation in pure titanium. D.R. Trinkle, R.G. Hennig, S.G. Srinivasan, D.M. Hatch, M.D. Jones, H.T. Stokes, R.C. Albers, and J.W. Wilkins. Physical Review Letters 91, 025701 (2003).

Complexity of Small Silicon Self-Interstitial Defects. D.A. Richie, J. Kim, S.A. Barr, K.R. A. Hazzard, R.G. Hennig, and J.W. Wilkins. Physical Review Letters 92, 45501 (2004).

**PI Andrew Williamson**

L. Dal Negro, S. Hamel, N. Zaitseva , J.H. Yi, A.J. Williamson, M. Stolfi, J. Michael, G. Galli, and L.C. Kimerling, Synthesis, Characterization and Modeling of Colloidal and Thin Film Silicon Nanocrystals, IEEE Nano Photonics, in press

L. Dal Negro, J.H. Yi, J. Michael, L.C. Kimerling, S. Hamel, A.J. Williamson, and G. Galli, Light-Emitting Silicon Nanocrystals and Photonic Structures in Silicon Nitride, IEEE Proceedings on Silicon Photonics, in press

L. Dal Negro, J.H. Yi, M. Jurgen, L.C. Kimerling, S. Hamel, A.J. Williamson, G. Galli, and T. Sargeant, Light-Emitting Silicon-Rich Nitride Systems And Photonic Structures, Journal of Experimental Nanoscience, in press

T. Vo, A.J. Williamson, and G. Galli, First Principles Simulations of the Structural and Electronic Properties of Silicon Nanowires, Physical Review B, 74 045116 (2006).

L. Dal Negro, J.H. Yi, L.C. Kimerling, S. Hamel, A.J. Williamson, and G. Galli, Light emission from silicon-rich nitride nanostructures, Applied Physics Letters 88, 183103 (2006).

Y.-H. Kim, Y. Zhao, A.J. Williamson, M. Heben, and S. Zhang, Non-dissociative adsorption of H2 molecules in light-element-doped fullerenes, Physical Review Letters 96, 016102 (2005).

N. Drummond, A.J. Williamson, R.J. Needs and Giulia Galli, Electron emission from diamondoids: A diffusion quantum Monte Carlo study, Physical Review Letters 95, 096801 (2005).

**PI Stan Woosley**

Schmidt, W., Niemeyer, J. C., Hillebrandt, W., Roepke, F. K., "A localised subgrid scale model for fluid dynamical simulations in astrophysics. II. Application to type Ia supernovae" Astronomy and Astrophysics 450, 283-294 (2006)

Blinnikov, S. I., Roepke, F. K., Sorokina, E. I., Gieseler, M., Reinecke, M., Travaglio, C., Hillebrandt, W., Stritzinger, M., "Theoretical light curves for deflagration models of type Ia supernova" Astronomy and Astrophysics 453, 229-240 (2006)

Roepke, F. K., Gieseler, M., Reinecke, M., Travaglio, C., and Hillebrandt, W., "Type Ia supernova diversity in three-dimensional models" Astronomy and Astrophysics 453, 203-217 (2006)

Roepke, F. K., Hillebrandt, W., Niemeyer, J.C., and Woosley, S.E., "Multi-spot ignition in type Ia supernova models" Astronomy and Astrophysics 448, 1-14 (2006)

Roepke, F.K., Woosley, S.E., and Hillebrandt, W., "Off-center ignition in type Ia supernova: I. Initial evolution and implications for delayed detonation" submitted to the Astrophysical Journal, 2006

"Anisotropies in the Neutrino Fluxes and Heating Profiles in Two-dimensional, Time-dependent, Multi-group Radiation Hydrodynamics Simulations of Rotating Core-Collapse Supernovae," (R. Walder, A. Burrows, C.D. Ott, E. Livne, I. Lichtenstadt, & M. Jarrah), Astrophys. J., 626, 317 (2005) (astro-ph/0412187).

"One-Armed Spiral Instability in a Slowly Rotating, Post-Bounce SupernovaCore," (Christian Ott, Shangli Ou, A. Burrows, and Joel E. Tohline), Astrophys. J., 625, L119, 2005 (astro-ph/0503187).

"The Spin Periods and Rotational Profiles of Neutron Stars at Birth," (Christian Ott, Adam Burrows, Todd Thompson, Eli Livne, & Rolf Walder),Astrophys. J. Suppl., 164, 130, 2006 (astro-ph/0508462).

Multi-Dimensional Radiation/Hydrodynamic Simulations of Protoneutron Star Convection," (Luc Dessart, Adam Burrows, Christian D. Ott, & Eli Livne), Astrophys. J., 645, 534, 2006.

"A New Mechanism for Core-Collapse Supernova Explosions," (A. Burrows, E. Livne, L. Dessart, C.D. Ott, & J. Murphy), Astrophys. J., 640, 878, 2006.

"Multi-Dimensional Simulations of the Accretion-Induced Collapse of White Dwarfs to Neutron Stars," (L. Dessart, A. Burrows, C.D. Ott, E. Livne, S.-Y. Yoon, & N. Langer), Astrophys. J., 644, 1063, 2006.

"Features of the Acoustic Mechanism of Core-Collapse Supernova Explosions," (A. Burrows, E. Livne, L. Dessart, C.D. Ott, & J. Murphy), accepted to Astrophys. J., 655, January 20, 2006.

"Low Mach Number Modeling of Type Ia Supernovae. II. Energy Evolution"(Almgren, A. S., Bell, J. B., Rendleman, C. A., & Zingale, M.) ApJ, 649, 927, 2006

Kuhlen, M., Woosley, S.E. and Glatzmaier, G.A. (2006) "Carbon ignition in Type Ia Supernovae. II. A three-dimensional numerical model", ApJ 640, 407-419

"RAM: A Relativistic Adaptive Mesh Refinement Hydrodynamics Code," Zhang, W., MacFadyen, A.I., 2006, ApJS, 164, 255

"X-ray flares following short gamma-ray bursts from shock heating of binary stellar companions," MacFadyen, A.I., Ramirez-Ruiz, E. & Zhang, W., 2006, submitted to ApJL

**PI Jianzhong Wu**

Density functional theory for planar electric double layers: Closing the gap between simple and polyelectrolytes (Li. ZD and J. Wu), JOURNAL OF PHYSICAL CHEMISTRY B 110 (14), 7473-7484 (2006)

Density functional theory for polyelectrolytes near oppositely charged surfaces (Li. ZD and J. Wu), PHYSICAL REVIEW LETTERS 96 (4), 048302 (2006)

Microstructure of block copolymers near selective surfaces: Theoretical predictions and configurational-bias Monte Carlo simulation (Cao DP, Wu JZ) MACROMOLECULES 38 (3): 971-978 (2005)

**PI Ruqian Wu**

J.S. Hong, and R.Q. Wu, "Prediction of ferromagnetic ordering and magnetic anisotropy of Mn monolayer on Nb(001) surface, Phys. Rev. B 73, 094450 (2006).

C. Sorg, N. Ponpandian, M. Bernien, K. Baberschke, and H. Wende, R.Q. Wu, Induced Magnetism of Oxygen in Surfactant Grown Fe, Co, and Ni Monolayers, Phys. Rev. B, 73, 064409 (2006).

L. F. Yin, D. H. Wei, N. Lei, L. H. Zhou, C. S. Tian, G. S. Dong, X. F. Jin, L. P. Guo and Q. J. Jia, and R. Q. Wu, Magnetocrystalline Anisotropy in Permalloy Revisited, Phys. Rev. Lett. 97, 067203 (2006).

S.C. Hong, J.I. Lee and R.Q. Wu, Oscillatory magnetism of palladium nano-film depending on its film thickness: density functional study, J. Magn. Magn. Mater. (2006).

C.S. Jo and R.Q. Wu, "The correlation between atomic structure and magnetic circular dichroism at the Fe/GaAs(001) interface)", in final preparation.

S.C. Hong and R.Q. Wu, "The magnetic anisotropy energy of (Ga,Mn)As", in final preparation.

**PI Donald Wuebbles**

Guillas, S., G. Tiao, D. J. Wuebbles and A. Zubrow, 2006: Statistical diagnostic and correction of a chemistry-transport model for the prediction of total column ozone. Atmos. Chem. Phys. 6, 525-537.

Hayhoe, K., C. Wake, B. Anderson, J. Bradbury, A. DeGaetano, X.-Z. Liang, J. Zhu, E. Maurer, and D. Wuebbles, 2006: Translating global changes into regional trends: evaluating past and future climate in the U.S. Northeast. Bulletin Amer. Met. Soc., in press.

Li, Y., K. O. Patten, D. Youn, and D. Wuebbles, 2006: Potential impacts of CF3I on ozone as a replacement for CF3Br in aircraft applications. Atmos. Chem. Phys., in press.

Lin, J.-T., K. O. Patten, X.-Z. Liang, and D. J. Wuebbles, 2006: Climate Change Effects on Ozone Air Quality in the United States and China with Constant Precursor Emissions, Geophys. Res. Lett., submitted for publication.

Lin, J., K. O. Patten, X.-Z. Liang, and D. J. Wuebbles, 2006: Summertime Ozone Background Levels over the United States: A Global Model Perspective, J. Geophys. Res., submitted for publication.

Miller, A. J., A. Cai, G. Tiao, D. J. Wuebbles, L. E. Flynn, S.-K.Yang, E. C. Weatherhead, V. Fioletov, I. Petropavlovskikh, X.-L. Meng, S. Guillas, R. M. Nagatani, and G. C. Reinsel, 2006: Examination of Ozonesonde data for trends and trend changes incorporating solar and Arctic Oscillation signals. J. Geophys. Res., in press.

Pan, L. L., J. C. Wei, D. E. Kinnison, R. Garcia, D. J. Wuebbles, and G. P. Brasseur, 2006: A set of diagnostics for evaluating chemistry-climate models in the extrratropical tropopause region. J. Geophys. Res., submitted.

Tao, Z., S. M. Larson, A. Williams, M. Caughey and D. J. Wuebbles, 2005: Area, mobile, and point source contributions to ground level ozone: a summer simulation across the continental USA. Atmos. Environ., 39, 1869-1877.

Wallington, T. J., M. D. Hurley, J. Xia, D. J. Wuebbles, S. Sillman, A. Ito, J. E. Penner, D. A. Ellis, J. Martin, S. A. Mabury, O. J. Nielsen, M. P. Sulbaek Andersen, 2006: Formation of C7F15COOH (PFOA) during the Atmospheric Oxidation of 8:2 Fluorotelomer Alcohol (n-C8F17CH2CH2OH). Env. Sc. and Technol., 40, 924-930.

Youn, D., W. Choi, H. Lee, and D. J. Wuebbles, 2006: Interhemispheric differences in the trends of the stratospheric long-lived tracers during the last decade, Geophys. Res. Lett. 33, L03807, doi:10.1029/2005GL024274.

## X

## Y

**PI Chao Yang**

C. Yang, P. A. Penczek, A. Leith, F. J. Asturias, R. M. Glaeser and J. Frank. The Parallelization of SPIDER on distributed-memory computers using MPI, to appear in Journal of Structural Biology, 2006.

P. A. Penczek, C. Yang, J. Frank and C. M. T. Spahn, Estimation of variance in single-particle reconstruction using the bootstrap technique, Journal of Structural Biology, vol 154, pages 168-183, 2006.

C. Yang, P. A. Penczek and E. G. Ng, Unified 3-D structure and projection orientation refinement using Quasi-Newton Algorithm, Journal of Structural Biology, vol 149, pages 53-64, 2006.

**PI Katherine Yelick**

Katherine Yelick, Paul Hilfinger, Susan Graham, Dan Bonachea, Jimmy Su, Amir Kamil, Kaushik Datta, Phillip Colella, and Tong Wen, "Parallel Languages and Compilers: Perspective from the Titanium Experience." Journal of High Performance Computing Applications. To appear.

Edward Givelberg, Katherine Yelick, "Distributed Immersed Boundary Simulations in Titanium." SIAM Journal on Scientific Computing, Volume 28 Issue 4, Pages 1361-1378, 2006.

Christian Bell, Dan Bonachea, Rajesh Nishtala, and Katherine Yelick, "Optimizing Bandwidth Limited Problems Using One-Sided Communication and Overlap," 20th International Parallel & Distributed Processing Symposium (IPDPS), Rhodes Island, Greece, April 25-29, 2006. Also available as Lawrence Berkeley National Lab Tech Report LBNL-59207.

Amir Kamil, Jimmy Su, and Katherine Yelick, "Making Sequential Consistency Practical in Titanium." Supercomputing 2005 (SC|05), Seattle, Washington, November 2005.

Amir Kamil and Katherine Yelick, "Concurrency Analysis for Parallel Programs with Textually Aligned Barriers." 18th International Workshop on Languages and Compilers for Parallel Computing (LCPC), Hawthorne, New York, October 2005.

Kaushik Datta, Dan Bonachea and Katherine Yelick. "Titanium Performance and Potential: an NPB Experimental Study." 18th International Workshop on Languages and Compilers for Parallel Computing (LCPC), Hawthorne, New York, October 2005.

A. Auer, G. Baumgartner, D. E. Bernholdt, A. Bibireata, V. Choppella, D. Cociorva, X. Gao, R. Harrison, S. Krishanmoorthy, S. Krishnan, C.-C. Lam, M. Nooijen, R. Pitzer, J. Ramanujam, P. Sadayappan, and A. Sibiryakov, "Automatic Code Generation for Many-Body Electronic Structure Methods: The Tensor Contraction Engine," Molecular Physics, Vol. 104 Issue 2, p211-228, 2006.

Q. Lu, S. Krishnamoorthy and P. Sadayappan, "Combining analytical and empirical approaches in tuning matrix transposition," Proc. Intl. Conf. on Parallel Architectures and Compilation Techniques (PACT 2006), Sept. 2006.

Katherine Yelick, Paul Hilfinger, Susan Graham, Dan Bonachea, Jimmy Su, Amir Kamil, Kaushik Datta, Phillip Colella, and Tong Wen, "Parallel Languages and Compilers: Perspective from the Titanium Experience." Journal of High Performance Computing Applications. To appear.

Christian Bell, Dan Bonachea, Rajesh Nishtala, and Katherine Yelick, "Optimizing Bandwidth Limited Problems Using One-Sided Communication and Overlap," 20th International Parallel & Distributed Processing Symposium (IPDPS), Rhodes Island, Greece, April 25-29, 2006. Also available as Lawrence Berkeley National Lab Tech Report LBNL-59207.

Cristian Coarfa, Yuri Dotsenko, John Mellor-Crummey. "Experiences with Sweep3D implementations in Co-array Fortran." The Journal of Supercomputing, 36(2):101-121, May 2006. (Special Issue on Computer Science Research Supporting High-Performance Applications, Rod Oldehoeft, guest editor.) Springer, Netherlands.

Apan Qasem, Ken Kennedy and John Mellor-Crummey. "Automatic tuning of whole applications using direct search and a performance-based transformation system." The Journal of Supercomputing, 36(2):183-196, May 2006. (Special Issue on Computer Science Research Supporting High-Performance Applications, Rod Oldehoeft, guest editor.) Springer, Netherlands. [DOI]

C. Falzone, A. Chan, E. Lusk, and W. Gropp, "Collective Error Detection for MPI Collective Operations." Beniamino Di Martino, Dieter Kranzlmuller, and Jack Dongarra, Eds., Recent Advances in Parallel Virtual Machine and Message Passing Interface, Springer Lecture Notes in Computer Science #3666, September 2005, pp 138-147.

N. Desai, A. Lusk, R. Bradshaw, and E. Lusk, "MPISH: A Parallel Shell for MPI Programs," in Proc. of the 12th European PVM/MPI Users' Group meeting, Recent Advances n Parallel Virtual Machine and Message Passing Interface, Lecture Notes in Computer Science 3666, Springer, 2005, pp. 333-342

Darius Buntinas and William Gropp, "Designing a Common Communication Subsystem," Recent Advances in Parallel Virtual Machine and Message Passing Interface, Beniamino Di Martino, Dieter Kranzlu|ller, and Jack Dongarra, 156-166, 12th European PVM/MPI User's Group Meeting, Sorrento, Italy, 2005.

William Gropp and Rajeev Thakur, "An Evaluation of Implementation Options for MPI One-Sided Communication," Recent Advances in Parallel Virtual Machine and Message Passing Interface, Beniamino Di Martino, Dieter Kranzlu|ller, and Jack Dongarra, 415-424, 12th European PVM/MPI User's Group Meeting, Sorrento, Italy, 2005.

Lei Huang, Barbara Chapman and Chunhua Liao, "An Implementation and Evaluation of Thread Subteam for OpenMP Extensions." Workshop on Programming Models for Ubiquitous Parallelism (PMUP 06), Seattle, WA, September 2006.

Laksono Adhianto, Barbara Chapman, "Autoscoping Support for OpenMP Compiler", Workshop on Tools and Compilers for Hardware Acceleration (TCHA 06), Seattle WA, September 2006.

**PI Pui-kuen Yeung**

Donzis, D.A., Sreenivasan, K.R. and Yeung, P.K. (2005) Scalar dissipation rate and Dissipative anomaly in isotropic turbulence. Journal of Fluid Mechanics Vol. 532, 199-216.

Yeung, P.K., Donzis, D.A. and Sreenivasan, K.R. (2005) High-Reynolds-number simulation of inertial-convective range in turbulent mixing. Physics of Fluids Vol. 17, 081703 (4 pages).

Yeung, P.K., Pope, S.B., Lamorgese, A.G. and Donzis, D.A. (2006) Acceleration and dissipation statistics of numerically simulated isotropic turbulence. Physics of Fluids Vol. 18, 065103 (14 pages).

## Z

**PI Peter Zapol**

Carbon Ad-Dimer Defects in Carbon Nanotubes M. Sternberg, L. A. Curtiss, D. M. Gruen, G. Kedziora, D. A. Horner, P. C. Redfern, P. Zapol Phys. Rev. Lett. 96, 075506 (2006)

SIPs: Shift-and-Invert Parallel Spectral Transformations, H. Zhang, B. Smith, M. Sternberg, and P. Zapol, ACM Transactions on Mathematical Software (accepted, 2007)

Modeling the structure and electronic properties of TiO2 Nanoparticles A. S. Barnard, S. Erdin, Y. Lin, P. Zapol, J. W. Halley Phys. Rev. B 73, 205405 (2006)

**PI Shengbai Zhang**

D. C. Look, G. C. Farlow, P. Reunchan, S. Limpijumnong, S. B. Zhang, and K. Nordlund, "Evidence for native-defect donors in n-type ZnO", Phys. Rev. Lett. 95, 225502(2005).

J. Li, S.-H. Wei, S.-S. Li, J.-B. Xia, "Design of shallow acceptors in ZnO: First-principles band-structure calculations", Phys. Rev. B 74, R081201 (2006).

X. N. Li, S. E. Asher, S. Limpijumnong, B. M. Keyes, C. L. Perkins, T. M. Barnes, H. R. Moutinho, J. M. Luther, S. B. Zhang, S.-H. Wei, T. J. Coutts, "Impurity effects in ZnO and nitrogen-doped ZnO thin films fabricated by MOCVD", J. Crys. Growth 287, 94 (2006).

S. Limpijumnong, X. N. Li, S. H. Wei, and S. B. Zhang, "Probing deactivations in nitrogen doped ZnO by vibrational signatures: A first principles study", PHYSICA B 376: 686 (2006).

X. N. Li, S. E. Asher, S. Limpijumnong, S. B. Zhang, S.-H. Wei, T. M. Barnes, T. J. Coutts, R. Noufi, "Unintentional doping and compensation effects of carbon in metal-organic chemical-vapor deposition fabricated ZnO thin films", J. Vac. Sci. Technol A 24, 1213 (2006).

T. J. Coutts, X. Li, T. M. Barnes, B. M. Keyes, C. L. Perkins, S. E. Asher, S. B. Zhang, S.-H. Wei, and S. Limpijumnong, "Synthesis and characterization of nitrogen-doped ZnO films grown by MOCVD", Chapter 3 in Zinc Oxide Bulk, Thin Films and Nanostructures, C. Jagadish and S. J. Pearton, eds. (Elsevier, Amsterdam, 2006), pp. 43-84.

W. Z. Xu, Z. Z. Ye, Y. J. Zeng, L. P. Zhu, B. H. Zhao, L. Jiang, J. G. Lu, H. P. He, and S. B. Zhang, "ZnO light-emitting diode grown by plasma-assisted metal organic chemical vapor deposition", Appl. Phys. Lett. 88, 173506 (2006).

Y. J. Zeng, Z. Z. Ye, W. Z. Xu, J. G. Lu, H. P. He, L. P. Zhu, B. H. Zhao, C. Che, and S. B. Zhang, "p-type behavior in nominally undoped ZnO thin films by oxygen plasma growth", APPLIED PHYSICS LETTERS 88, 262103 (2006).

J. G. Lu, Z. Z. Ye, G. D. Yuan, Y. J. Zeng, F. Zhuge, L. P. Zhu, B. H. Zhao, and S. B. Zhang, "Electrical characterization of ZnO-based homojunctions", Appl. Phys. Lett. 89, 053501 (2006).

M.-H. Du and S. B. Zhang, "Topological defects and the Staebler-Wronski effect in hydrogenated amorphous silicon", Appl. Phys. Lett. 87, 191903 (2005).

S. Na-Phattalung, M. F. Smith, K. Kim, M. H. Du, S. H. Wei, S. B. Zhang, S. Limpijumnong, "First-principles study of native defects in anatase TiO2", Phys. Rev. B 73, 125205 (2006).

W. E. McMahon, I. G. Batyrev, T. Hannappel, J. M. Olson, and S. B. Zhang, "5-7-5 line defects on As/Si(100): A general stress-relief mechanism for V/IV surfaces", Phys. Rev. B 74, 033304 (2006).

M.-H. Du, S. Limpijumnong, and S. B. Zhang, "Hydrogen-mediated nitrogen clustering in dilute III-V nitrides", Phys. Rev. Lett. 97, 075503 (2006).

M. H. Du, S. Limpijumnong, and S. B. Zhang, "Ion relaxation and hydrogen LVM in H-irradiated GaAsN", PHYSICA B 376: 583 (2006).

J. Li, P. Carrier, S.-H. Wei, S.-S. Li, J.-B. Xia, "Mutual Passivation of Donors and Isovalent Nitrogen in GaAs", Phys. Rev. Lett. 96, 035505 (2006).

**PI Xiao-Feng Zhang**

"Crystal structures and displacive transition in IrN2, OsN2, RuN2, and RhN2" R. Yu, Q. Zhan, L.C. De Jonghe Angew. Chem. Int. Ed., in press (2006).

**PI Yeliang Zhang**

S. Chandra, M. Parashar, J. Yang, Y. Zhang, S. Hariri. Investigating Autonomic Runtime Management Strategies for SAMR Applications. International Journal of Parallel Programming, Springer Science+Business Media B.V., 33(2-3):247-259, June 2005

S. Hariri, B. Khargharia, H. Chen, Y. Zhang, B. Kim, H. Liu and M. Parashar, "The Autonomic Computing Paradigm", Cluster Computing: The Journal of Networks, Software Tools and Applications, Special Issue on Autonomic Computing, Vol. 9, No. 2, 2006, Springer-Verlag.

Y. Zhang, X. S. Li, O. Marques. Towards an Automatic and Application-Based Eigensolver Selection. LACSI Symposium, October 11 !V 13, 2005, Santa Fe, New Mexico 2005.

J. Nieplocha, M. Krishnan, B. Palmer, V. Tipparaju, Y. Zhang. Exploiting Processor Groups to Extend Scalability of the GA Shared Memory Programming Model. Accepted by Computing Frontiers 2005 Conference May 4-6, 2005, Ischia, Italy.

Yeliang Zhang, Vinod Tipparaju, Jarek Nieplocha, Salim Hariri. Parallelization of the NAS Conjugate Gradient Benchmark Using the Global Arrays Shared Memory Programming Model. Accepted by Joint Workshop on High-Performance Grid Computing and High-Level Parallel Programming Models held in conjunction with IPDPS 2005.

Yeliang Zhang, Salim Hariri, Jianwei Xiang and Jim Yeh. PARM: Physics Aware Runtime Manager for Large-scale Scientific and Engineering Applications. Accepted as a poster at The 15th IEEE International Symposium on High Performance Distributed Computing, June 19-23 2006, Paris, France.

**PI Zhenyu Zhang**

Desorption of H from Si(111) by resonant excitation of the Si-H vibrational stretch mode, ZH Liu, LC Feldman, NH Tolk, ZY Zhang, PI Cohen, Science 312, 1024 (2006).

Generalized electron counting in determination of metal-induced reconstruction of compound semiconductor surfaces, LX Zhang, EG Wang, QK, Xue, SB Zhang, ZY Zhang, Phys. Rev. Lett. 97, 126103 (2006).

Tuning solid surfaces from hydrophobic to superhydrophilic by submonolayer surface modification, S Meng, ZY Zhang, E Kaxiras, Phys. Rev. Lett. 97, 036107 (2006).

Polygonization and anomalous graphene interlayer spacing of multi-walled carbon nanofibers, M Yoon, J Howe, G Tibbetts, G Eres, Z Zhang (submitted to Phys. Rev. Lett.)

Chemical contribution to surface-enhanced Raman scattering, BNJ Persson, K Zhao, ZY Zhang, Phys. Rev. Lett. 96, 207401 (2006).

One-dimensional arrays of nanoshell dimers for single molecule spectroscopy via surface-enhanced raman scattering, K Zhao, HX Xu, BH Gu, BH, ZY Zhang, J. Chem. Phys. 125, 081102 (2006).

Quantum size effects in Pb films from first principles: The role of the substrate, Y Jia, B Wu, HH Weitering, ZY Zhang, Phys. Rev. B 74, 035433 (2006).

Evolution of a Symmetry Gap and Synergetic Quantum Well States in Ultrathin Ag Films on Au(111) Substrates, L Huang, XG Gong, E Gergert, F Forster, A Bendounan, F Reinert, Z Zhang (submitted to Phys. Rev. Lett.)

**PI Ping Zhu**

P. Zhu, A. Bhattacharjee, and K. Germaschewski, Intermediate nonlinear evolution of the Parker instability: Formation of convection-induced discontinuities and absence of finite-time singularities, Phys. Rev. Lett., 96, 065001, doi:10.1103/PhysRevLett.96.065001 (2006).

P. Zhu, C. C. Hegna, and C. R. Sovinec, Nonlinear growth of a line-tied g-mode near marginal stability, Phys. Plasmas 13, 102307 (2006).

P. Zhu, C. R. Sovinec, C. C. Hegna, K. Germaschewski, and A. Bhattacharjee, Nonlinear ballooning instability in the near-Earth magnetotail: Growth, structure, and possible role in substorms, submitted to J. Geophys. Res. (2006).

P. Zhu, C. C. Hegna, C. R. Sovinec, A. Bhattacharjee, and K. Germaschewski, Intermediate nonlinear regime of a line-tied g-mode, to appear in Phys. Plasmas (2007).

**PI Alex Zunger**

L. He and A. Zunger, "Multiple Charging of InAs/GaAs Quantum Dots by Electrons or Holes: Addition Energies and Ground State Configurations," Physical Review B 73, 115324 (2006).

G.A. Narvaez, G. Bester and A. Zunger, "Pressure Effects on Neutral and Charged Excitons in Self- Assembled (InGa)As/GaAs Quantum Dots," Physical Review B. Rapid Communications 72, 041307 (2005).

L. He, G. Bester and A. Zunger, "Electronic Phase Diagrams of Carriers in Self-Assembled InAs/GaAs Quantum Dots: Violation of Hund's Rule and the Aufbau Principle for Holes," Physical Review Letters 95, 246,804 (2005).

G.A. Narvaez, G. Bester and A. Zunger, "Excitons, Biexcitons and Trions in Self-Assembled InGaAs/ GaAs Quantum Dots: Recombination Energies, Polarization and Radiative Lifetimes vs. Dot Height," Physical Review B 72, 245,318 (2005).

G. Narvaez, L. He, G. Bester and A. Zunger, "Theoretical Predictions of the Electronic and Optical Properties of Single and Coupled (In, Ga)As/GaAs Quantum Dot," Physica E 32 93 (2006).

A. Franceschetti, J.M. An, and A. Zunger, "Impact ionization can explain carrier multiplication in PbSe quantum dots" (submitted to Phys. Rev. Lett.).

J.M. An, A. Franceschetti and A. Zunger, "The peculiar electronic structure of PbSe quantum dots" (submitted to Nano Letters).

A. Franceschetti, L.W. Wang, G. Bester and A. Zunger, "Confinement-Induced vs. Correlation- Induced Electron Localization in Model Semiconductor Nano Circuits," Nano Letters 6, 1069 (2006).

G. Bester, X.F. Wu, D. Vanderbilt and A. Zunger, "Importance of second-order piezoelectric effects in zinc-blende semiconductors", Physical Review Letters 96, 187602 (2006).

G. Trimarchi, P. Graf and A. Zunger, "Exploring the configurational space of binary alloys: Different sampling for different cell shapes", Physical Review B, 74, 014204 (2006)

G.A. Narvaez, G. Bester and A. Zunger, "Dependence of the Electronic Structure of Self-Assembled InGaAs/GaAs Quantum Dots on Height and Composition" Journal of Applied Physics 98, 043,708 (2005).

G.A. Narvaez and A. Zunger, "Nominally forbidden transitions in the interband optical spectrum of quantum". Physical Review B 74, 045316 (2006).

S. V. Barabash, V. Blum,S. Muller and Alex Zunger, Prediction of unusual stable ordered structures of Au-Pd alloys via a first-principles cluster expansion, Physical Review B 74, 035108 (2006)

G.A. Narvaez, G. Bester and A. Zunger, "Carrier relaxation mechanisms in self-assembled (In,Ga)As/ GaAs quantum dots: Efficient P -> S Auger relaxation of electrons". Physical Review B 74, 075403 (2006).

S.V. Dudiy and A. Zunger, Searching for alloy configurations with target physical properties: Impurity design via a genetic algorithm inverse band structure approach, Physical Review Letters 97 : 046401 (2006).

**PI Piotr Zyla**

"Review of Particle Physics", W.-M. Yao et al., Journal of Physics G 33, 1 (2006)

"Measurement of the Asymmetry in the Decay of Omega+ --> Lambda-bar K+ --> p-bar pi+ K-", L.C. Lu et al., Phys. Rev. Lett. 96, 242001 (2006)