Publications Resulting from Computations at NERSC

As Reported on the Allocation Year 2007 Request Forms

A / B / C / D / E / F / G / H / I / J / K / L / M / N / O / P / R / S / T / V / W / Y / Z /

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.

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), 787ÿ

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);

PI Cai Wei

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, 496ÿ (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).

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 Chen07Yang Chen05n 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 =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 =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).

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 propeties 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.

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).

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.

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. Fransisco, 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.

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. Glasc