Publications Resulting from Computations at NERSC

As Reported on the Allocation Year 2008 Request Forms

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

PI Mowfak Al-Jassim

Y. Yan, J. L. F. Da Silva, S.-H. Wei, and M. Al-Jassim, "Atomic structure of In2O3ZnO system" Appl. Phys. Lett. 90, 261904 (2007).

Y. Yan, J. Li, S.-H. Wei, and M. Al-Jassim, A possible approach to overcome doping asymmetry in wide bandgap semiconductor" Phys. Rev. Lett. 98, 135506 (2007).

Y. Yan, M.M. Al-Jassim, and S.-H. Wei, "Doping of ZnO with group-IB elements" Appl. Phys. Lett. 89, 181912 (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)

PI Greg Aldering

SN2005ap: A Most Brilliant Explosion, Quimby, R. M., Aldering, G., Wheeler, C., Akerloff, C. W., and Rykoff, E. S. (2007), Astrophysical Journal, 668, 99.

How to Find More Supernovae with Less Work: Object Classification Techniques for Difference Imaging Bailey, S., Aragon, C., Romano, R., Thomas, R. C., Weaver, B. A., and Wong, D. (2007), Astrophysical Journal, 665, 1246.

Snapping Supernovae at z>1.7, Aldering, G., Kim, A. G., Kowalski, M., Linder, E. V., Perlmutter, S. (2007), Astroparticle Physics, 27, 213-225.

Nearby Supernova Factory Observations of SN 2006D: On Sporadic Carbon Signatures in Early Type Ia Supernova Spectra, Thomas, R. C., Aldering, G., Antilogus, P., Aragon, C., Bailey, S., Baltay, C., Baron, E., Bauer, A., Buton, C., Bongard, S., Copin, Y., Gangler, E., Gilles, S., Kessler, R., Loken, S., Nugent, P., Pain, R., Parrent, J., Pecontal, E., Pereira, R., Perlmutter, S., Rabinowitz, D., Rigaudier, G., Runge, K., Scalzo, R., Smadja, G., Wang, L., Weaver, B. A. (2007), Astrophysical Journal, 654, L53-L56.

On the Progenitor of SN 2005gl, the Nature of Type IIn Supernovae, Gal-Yam, A., Leonard, D. C., Fox, D. B., Cenko, S. B., Soderberg, A. M., Moon, D.-S., Sand, D. J., Li, W., Filippenko, A. V., Aldering, G., Copin, Y., (2007), Astrophysical Journal, 656, 372-381.

Visible, near-infrared spectrophotometry of the Deep Impact ejecta of Comet 9P/Tempel 1, Hodapp, K. W., Aldering, G., Meech, K. J., Cochran, A. L., Antilogus, P., Pecontal, E., Chickering, W., Blanc, N., Copin, Y., Lynch, D. K., Rudy, R. J., Mazuk, S., Venturini, C. C., Puetter, R. C., Perry, R. B., (2007), Icarus, 187, 185-198.

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.

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.

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.

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

PI Yoram Alhassid

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

"Scrambling of Hartree-Fock Levels as a universal Brownian-Motion Process," Y. Alhassid, H. A. Weidenmueller, and A. Wobst, arXiv: cond-mat/0604630, Phys. Rev. B, in press (2007).

"Thermodynamics of Ultra-Small Metallic Grains in the Auxiliary-Field Monte Carlo Approach," Y. Alhassid, L. Fang, and S. Schmidt, arXiv: cond-mat/0702304 (2007).

"The Shell Model Monte Carlo Approach to Heavy Deformed Nuclei," Y. Alhassid, L. Fang and H. Nakada, arXive:0710.1656 (2007).

PI Paul Alivisatos

S. Y. Quek, L. Venkataraman, H. J. Choi, S. G. Louie, M. S. Hybertsen, and J. B. Neaton "Amine-Gold Linked Single-Molecule Circuits: Experiment and Theory", Nano Letters, in press (2007)

K. H. Khoo, J. B. Neaton, H. J. Choi, and S. G. Louie, "Contact dependence of the conductance of H2 molecular junctions from first principles", Phys. Rev. B, in press (2007)

S. Y. Quek, J. B. Neaton, M. S. Hybertsen, E. Kaxiras, and S. G. Louie, "Negative Differential Resistance in Transport through Organic Molecules on Silicon", Phys. Rev. Lett. 98, 066807 (2007)

L. Kong, J. R. Chelikowsky, J. B. Neaton, and S. G. Louie, "Real-space ab initio calculations of spin-dependent transport properties of magnetic molecular junctions", Phys. Rev. B, in press (2007)

K. H. Khoo, J. B. Neaton, Y. W. Son, M. L. Cohen, and S. G. Louie, "Negative differential resistance in carbon wires covalently bridging carbon nanotubes", Phys. Rev. B, submitted (2007)

PI Jonathan Arons

A. Spitkovsky, 2007b, "Acceleration of Particles in Unmagnetized Electron-Positron Collisionless Shocks," ApJ Lett, submitted

A. Spitkovsky, 2007a, "On the structure of relativistic collisionless shocks in electron-ion plasmas," ApJ Lett, accepted, arXiv:0706.3126

P. Chang, A. Spitkovsky, J. Arons, 2007, "Long Term Evolution of Magnetic Turbulence in Relativistic Collisionless Shocks: Electron-Positron Plasmas," ApJ, accepted, arXiv:0704.3832

E. Amato & J. Arons, 2006, "Heating and Non-thermal Particle Acceleration in Relativistic, Transverse Magnetosonic Shock Waves in Proton-Electron-Positron Plasmas", ApJ, 653, 325

Bucciantini, N., Quataert, E., Arons, J., Metzger, B. D., Thompson, T. A., 2007, "Magnetar-driven bubbles and the origin of collimated outflows in gamma-ray bursts," MNRAS, 380, 1541

PI Cynthia Atherton

K. Ellingsen, M. Gauss, R. Van Dingenen, F. J. Dentener, L. Emberson3, A. M. Fiore, M. G. Schultz, D. S. Stevenson, C. S. Atherton, D. J. Bergmann, I. Bey, T. Butler, J. Drevet, H. Eskes, D. Hauglustaine, I. S. A. Isaksen, L. W. Horowitz, M. Krol, J. F. Lamarque, M. Lawrence, T. van Noije, J. Pyle, S. Rast, J. Rodriguez, N. Savage, S. Strahan, K. Sudo, S. Szopa, O. Wild, 2007: Global ozone air quality: a multi-model assessment of risks to human health and crops, submitted to Atmospheric Chemistry and Physics Discussions.

PI Ahmet Aydemir

A. Y. Aydemir, Shear flows at the tokamak edge and their role in core rotation and the L-H transition, Phys. Rev. Lett, 98, 225002 (2007)

A. Y. Aydemir, Shear flows at the tokamak edge and their interaction with edge-localized modes, Phys. Plasmas, 14, 056118 (2007).

PI Dmitri Babikov

M. Zhao and D. Babikov, "On optimal control of adiabatic motion of ions in a trap", submitted to Phys. Rev. Let., 2007.

E. Vetoshkin and D. Babikov, "Semiclassical wavepacket study of anomalous isotope effect in ozone formation", accepted by J. Chem. Phys., 2007.

E. Vetoshkin and D. Babikov, "Semi-classical wavepacket treatment of scattering resonances: Application to the delta zero-point energy effect in recombination reactions", Phys. Rev. Lett. 99, 138301, 2007.

M. Zhao and D. Babikov, "Anharmonic properties of the vibrational quantum computer", J. Chem. Phys. 126, 204102 (12 pages), 2007. Baer, Ferdinand mp188

PI Ferdinand Baer

Baer, F., H. Wang, J. J. Tribbia, A. Fournier, 2006: Climate Modeling With Spectral Elements. Mon. Wea. Rev., V.134, 3610-3624.

Wang, H., J. J. Tribbia, F. Baer, A. Fournier, M. Taylor, 2007: A Spectral Element Version of CAM2. Mon. Wea. Rev., V.135, No. 11, in press.

Christopher D. Blakely, 2007:"A Hybrid Meshless/Spectral-Element Method for Elliptic Partial Differential Equations". International Journal of Comp. Math., accepted, 2006.

Christopher D. Blakely, 2007: "A Hybrid Meshless/Spectral-Element Method for the Shallow Water Equations on the Sphere", Computational Methods in Applied Sciences, ed. Eugenio Onate, Springer-Verlag, in press.

Christopher D. Blakely, A. Gelb, A. Navarra, 2007: "An Automated Method for Recovering Piecewise Smooth Functions on Spheres Free of Gibbs Oscillations". Sampling Theory in Signal and Image Processing, Vol. 6, No.3.

PI David Bailey

J. H. Chen, A. Choudhary, B. de Supinski, M. DeVries, E. R. Hawkes, S. Klasky, W. K. Liao, K. L. Ma, J. Mellor-Crummy, N. Podhorski, R.Sankaran, S. Shende, C. S. Yoo, "Terascale Direct Numerical Simulations of Turbulent Combustion using S3D," (to appear) IOP Journal, 2008.

M. Tikir, L. Carrington, E. Strohmaier, A. Snavely, "A Genetic Algorithms Approach to Modeling the Performance of Memory-bound Computations", Proceedings of SC07, the International Conference for High Performance Computing, Networking, and Storage), November 2007, Reno, NV, to appear.

A. Tiwari, J. K. Hollingsworth, "Tuning Parallel Programs in Parallel" (submitted to IPDPS'08).

Y. Zhang, F. Fowler, K. Huck, A. Malony, A. Porterfield, D. Reed, S. Shende, V. Taylor and X. Wu, "USQCD Computational Performance Studies with PERI", SciDAC 2007, Journal of Physics: Conference Series, vol. 78, 2007.

Xingfu Wu and Valerie Taylor, "Processor Partitioning: An Experimental Performane Analysis of Parallel Applications on SMP Cluster Systems", 19th IASTED International Conference on parallel and Distributed Computing and Systems (PDCS 2007), Nov. 2007, MIT, Cambridge, MA.

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.

David H. Bailey and Jonathan M. Borwein, "Finding General Explicit Formulas for Ising Integral Recursions," manuscript, Oct 2006.

David H. Bailey, Richard E. Crandall and Jonathan M. Borwein, "Resolution of the Quinn-Rand-Strogatz Constant of Nonlinear Physics," manuscript, Jun 2007.

David H. Bailey, Jonathan M. Borwein, Richard E. Crandall and Deirdre K. Manna, "New Representations for Spin Integrals," manuscript, Aug 2007.

Natalie J. Durgin, Sofia M. Garcia, Tamara Flournoy and David H. Bailey, "`Syncing' Up with the Quinn-Rand-Strogatz Constant: Hurwitz-Zeta Functions in Non-Linear Physics," manuscript, Sep 2007.

PI Krishnan Balasubramanian

Theoretical Studies on Structures of Neptunyl Carbonates: NpO2(CO3)m(H2O)nq (m=1-3, n=0-3) in Aqueous Solution K. Balasubramaniana, and Zhiji Cao, Inorganic Chemistry,(2007) in press

PI Perla Balbuena

A. Martinez-Limia, J. Zhao, and P. B. Balbuena, Molecular dynamics study of the initial stages of catalyzed single-wall carbon

F. Tarazona-Vasquez and P. B. Balbuena, "Pt(II) uptake by dendrimer outer pockets: Modeling binding of Pt(II) in large dendrimers," J. Phys. Chem.B, submitted, August 1, 2007.

F. Tarazona-Vasquez and P. B. Balbuena, "Pt(II) uptake by dendrimer outer pockets: 2. Solvent-mediated complexation," J. Phys. Chem. B., submitted, August 1, 2007.

F. Tarazona-Vasquez and P. B. Balbuena, "Pt(II) uptake by dendrimer outer pockets: 1. Solventless ligand exchange reaction," J. Phys. Chem. B., submitted, August 1, 2007.

Y. Ma and P. B. Balbuena, "Pt-surface segregation in bimetallic Pt3M alloys: A density functional theory study," Surf. Sci.., in press.

Y. Ma and P. B. Balbuena, "OOH dissociation on Pt clusters," Chem. Phys. Lett., in press.

Z. Gu and P. B. Balbuena, "Chemical environment effects on the atomic oxygen absorption into Pt(111) surfaces," J. Phys. Chem C., in press.

P. Hirunsit and P. B. Balbuena, "Effects of confinement on small water clusters structure and proton transfer," J. Phys. Chem A., in press.

Sergio R Calvo and Perla B. Balbuena, Theoretical analysis of reactivity on Pt(111) and Pt-Pd(111) alloys," Surf. Sci., in press.

Diego A. Gsmez Gualdrsn and Perla B. Balbuena, "Classical Molecular Dynamics of Clathrate-Methane-Water-Kinetic Inhibitor Composite Systems," J. Phys. Chem., in press.

Zhihui Gu and Perla B. Balbuena, "Absorption of atomic oxygen into subsurfaces of Pt(100) and Pt(111): Density functional theory study," J. Phys. Chem. C., 111, 9877-9883, (2007).

Yuguang Ma and Perla B. Balbuena, "Designing Oxygen Reduction Catalysts: Insights from Metalloenzymes," Chem. Phys. Lett., 440, 130-133, (2007).

Santiago Aparicio-Martinez and Perla B. Balbuena, "On the properties of Aqueous Amide Solutions through Classical Molecular Dynamics Simulations ," Mol. Sim., in press.

Yuguang Ma and Perla B. Balbuena, "Catalytic Activity Tuning of a Biomimetic HO-FeV=O Oxidant for Methane Hydroxylation by Substituents on Aromatic Rings: A Theoretical Study," J. Phys. Chem. B., 111, 2711-2718, (2007).

Diego A. Gomez Gualdrsn, S. Aparicio-Martinez, and Perla B. Balbuena, "Computational studies of structure and dynamics of clathrate inhibitor monomers in solution," Ind. and Eng. Chem. Res., 46, 131-142, (2007).

F. Tarazona-Vasquez and P. B. Balbuena, "Dendrimer-Tetrachloroplatinate Precursor Interactions. 2. Non Covalent Binding in PAMAM Outer Pockets," J. Phys. Chem. A, 111, 945-953, (2007).

F. Tarazona-Vasquez and P. B. Balbuena, "Dendrimer-Tetrachloroplatinate Precursor Interactions. 1. Hydration of Pt(II) Species in PAMAM Outer Pockets," J. Phys. Chem. A, 111, 932-944, (2007).

L. R. Saenz, P. B. Balbuena, and J. M. Seminario, "Platinum testbeds: Interaction with oxygen," J. Phys. Chem., 110, 11968-11974, (2006).

S. R. Calvo and P. B. Balbuena, "Density functional theory analysis of reactivity of PtxPdy alloy clusters," Surf. Sci., 601, 165-171, (2007).

PI Arun Bansil

S. Sahrakorpi, R.S. Markiewicz, M. Lindroos, X. J. Zhou, T. Yoshida5, W. L. Yang3,4, T. Kakeshita, H. Eisaki, S. Uchida, Seiki Komiya, Yoichi Ando, F. Zhou, Z. X. Zhao, T. Sasagawa, A. Fujimori, Z. Hussain, Z.-X. Shen, and A. Bansil, "Appearance of Universal Metallic Dispersion in a Doped Mott Insulator", submitted to Nature Physics.

Tanmoy Das, R.S. Markiewicz, and A. Bansil, "Nodeless d-wave superconducting pairing due to residual antiferromagnetism in underdoped Pr2-xCexCuO4-d", Phys. Rev. Lett. 98, 197004 (2007).

R.S. Markiewicz and A. Bansil, "Collapse of the Magnetic Gap of Cuprate Superconductors within a Three-Band Model of Resonant Inelastic X-Ray Scattering", Phys. Rev. Lett. 96, 107005 (2006).

H. Lin, S. Sahrakorpi, R.S. Markiewicz, and A. Bansil,"Raising Bi-O Bands above the Fermi Energy Level of Hole-Doped Bi2Sr2CaCu2O8+d and Other Cuprate Superconductors", Phys. Rev. Lett. 96, 097001 (2006).

P. E. Mijnarends, S. Kaprzyk, B. Barbiellini, Yinwan Li, J. F. Mitchell, P. A. Montano, and A. Bansil, " Magnetic momentum density, Fermi surface, and directional magnetic Compton profiles in LaSr2Mn2O7 and La1.2Sr1.8Mn2O7", Phys. Rev. B 75, 014428 (2007).

Yinwan Li, P. A. Montano, B. Barbiellini, P. E. Mijnarends, S. Kaprzyk and A. Bansil, "Spin moment over 10-300 K and delocalization of magnetic electrons above the Verwey transition in magnetite", J. Phys. Chem. Solids 68, 1556 (2007).

W. Meevasana, X.J. Zhou, S. Sahrakpori, W.S. Lee, W.L. Yang, K. Tanaka, N. Mannella, T. Yoshida, D. H. Lu, Y.L. Chen, R.H. He, Hsin Lin, S. Komiya, Y. Ando, F. Zhou, W.X. Ti, J.W. Xiong, Z. X. Zhao, T. Sasagawa, T. Kakeshita, K. Fujita, S. Uchida, H. Eisaki, A. Fujimori, Z. Hussain, R. S. Markiewicz, A. Bansil, N. Nagaosa, J. Zaanen, T.P. Devereaux, and Z.-X. Shen, "The hierarchy of multiple many-body interaction scales in high-temperature superconductors", Phys. Rev. B 75, 174506 (2007).

R.S. Markiewicz, and A. Bansil, "Dispersion anomalies induced by the low-energy plasmon in the cuprates", Phys. Rev. B 75, 020508 (2007).

R.S. Markiewicz, S. Sahrakorpi, and A. Bansil, "Paramagnon-induced dispersion anomalies in the cuprates", cond-mat/0701524, to be published, Phys. Rev. B.

T. Yoshida, X. J. Zhou, K. Tanaka, W. L. Yang, Z. Hussain, Z.-X. Shen, A. Fujimori, S. Sahrakorpi, M. Lindroos, R. S. Markiewicz, A. Bansil, Seiki Komiya, Yoichi Ando, H. Eisaki, T. Kakeshita, and S. Uchida, "Systematic doping evolution of the underlying Fermi surface of La2-xSrxCuO4", Phys. Rev. B 74, 224510 (2006).

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

D. Nissenbaum, B. Barbiellini, and A. Bansil, "Decorrelation of samples in quantum Monte Carlo calculations and scaling of autocorrelation time in Li and H2O clusters", Phys. Rev. B 76, 033412 (2007).

S.W.H. Eijt, B. Barbiellini , A.J. Houtepen, D. Vanmaekelbergh, P.E. Mijnarends and A. Bansil, Positron studies of surfaces, structure and electronic properties of nanocrystals, Phys. Stat. Sol. (c) 4, 3883 (2007).

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

PI Michael Barad

Barad, M., P. Colella, and S.G Schladow, An adaptive cut-cell method for environmental fluid mechanics, submitted to the International Journal for Numerical Methods in Fluids.

Barad, M.F. and O.B. Fringer, 2007. Numerical simulations of shear instabilities in open-ocean internal gravity waves, Proceedings of the Fifth International Symposium on Environmental Hydraulics, Tempe, Arizona, USA.

Barad, M.F., O.B. Fringer, and P. Colella, Dec. 2006. Multiscale simulations of internal gravity waves, Proceedings of the Sixth International Symposium on Stratified Flows, Perth, Australia. Baron, Edward mp90

PI Edward Baron

R. C. Thomas, G. Aldering, P. Antilogos, ..., E. Baron, et al. (The Nearby Supernova Factory), Nearby Supernova Factory Observations of SN 2006D: On Sporadic Carbon Signatures in Early Type Ia Supernova Spectra, ApJ (Letters), (2007), 654, L53--56.

S. Knop, P. Hauschildt, & E. Baron, General Relativistic Radiative Transfer, A&A, (2007), 463, 315--320.

J. Parrent, D. Branch, M. A. Troxel, D. Casebeer, D. Jeffery, W. Ketchum, E. Baron, F. J. D. Serduke, & A. V. Filippenko, Direct Analysis of Spectra of the Unusual Type Ib Supernova 2005bf, PASP, (2007), 119, 135--142.

E. Baron, D. Branch, & P. Hauschildt, Reddening, Abundances, and Line Formation in SNe II, ApJ, (2007), 662, 1148--.

E. Baron & P. Hauschildt, A 3D Radiative Transfer Framework: II. Line Transfer Problems, A&A, (2007), 468, 255--261.

B. Chen, R. Kantowski, E. Baron, S. Knop, & P. Hauschildt, Solving the Transfer Equation for Arbitrary Flows in Stationary Spacetimes, MNRAS, (2007), 380, 104--112.

S. Knop, P. Hauschildt, E. Baron, & S. Dreizler, Analysing SN 2003Z with PHOENIX, A&A, (2007), 469, 1077--1081.

W. Ketchum, E. Baron, & D. Branch, Detailed Spectral Analysis of the Type Ib Supernova 1999dn. Paper I: Hydrogen-free Models ApJ, (2007), in press.

J. L. Prieto, ..., E. Baron, & J. Parrent, A Study of the Type IIn/Ia Supernova 2005gj from X-rays to the Infrared: Paper I, AJ, (2007), submitted

E. Baron, D. J. Jeffery, D. Branch, E. Bravo, D. Garcia-Senz, & P. H. Hauschildt, Detailed Spectral Modeling of a 3-D Pulsating Reverse Detonation Model: Too Much Nickel, ApJ (Letters), (2007), submitted.

S. Bongard, E. Baron, G. Smadja, D. Branch, & P. H. Hauschildt, Multi-layered Spectral Formation in SNe Ia Around Maximum Light, ApJ, (2007), submitted.

PI Don Batchelor

Experimental and numerical characterization of ion-cyclotron heated protons on the Alcator C- Mod tokamak, V. Tang, R. R. Parker, P. T. Bonoli, et. al., Plasma Phys. Control. Fusion 49, 873 (2007).

Evolution of nonthermal particle distributions in radio frequency heating of fusion plasmas, P. T. Bonoli, D. B. Batchelor, L. A. Berry, et. al., Journal of Physics: Conference Series 78 012006 (2007).

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., Journal of Physics: Conference Series 46, 82 (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).

PI Victor 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 Phototransduction 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., 53, 2519-2532, 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, 124313, 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, Volume 6325 Physical Chemistry of Interfaces and Nanomaterials V, Mark Spitler, Frank Willig, Editors, 63250R (Aug. 30, 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.

Proceeding of the 14th International conference on Photosynthesis, Glasgow, U.K., submitted, 2007 Ligation of the C-terminus of the D1-polypeptide of photosystem II to the Oxygen Evolving Complex of Photosystem II, by Jose A. Gascon, Eduardo M. Sproviero, James P. McEvoy, Gary W. Brudvig and Victor S. Batista.

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

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

Photochem. Photobiol., 190, 274-282, 2007 The MP/SOFT Methodology for Simulations of Quantum Dynamics: Model Simulations of the Photoisomerization of the Retinyl Chromophore in Rhodopsin, by Xin Chen and Victor S. Batista. Batista, Victor m410

PI Pat Behling

Wu, L., F. He, Z. Liu, and C. Li, 2007: Atmospheric Teleconnections of Tropical Atlantic Variability: Interhemispheric, Tropical Extratropical, and Cross-Basin Interactions. J. Climate, *20*, 856-870.

He, F., Z. Liu: The Nature of Decadal Variability of Atlantic Meridional Overturning Circulation: coupled air-sea interaction organized by damped ocean mode. In Prep

Wu L., Z. Liu, C. Li and Y. Sun, (2007). Extratropical control of recent tropical Pacific decadal climate variability: a relay teleconnection. Clim. Dyn, 28 (1), 99-112, doi: 10.1007/s00382-006-0198-5. CCR #890.

Liu, Z., Y. Liu, L. Wu, and R. Jacob (2007). Seasonal and Long Term Atmospheric Responses to Reemerging North Pacific Ocean Variability: A Combined Dynamical and Statistical Assessment. Journal of Climate 20(6), pgs: 955-980, doi: 10.1175/JCLI4041.1. CCR #897

PI John Bell

A. S. Almgren, J. B. Bell and M. Zingale, "Low Mach Number Modeling of Type Ia Supernovae. III. Reactions", submitted for publication.

A.S. Almgren, J.B. Bell, and M. Zingale, "MAESTRO: A Low Mach Number Stellar Hydrodynamics Code ", SciDAC 2007, J. of Physics: Conference Series, Boston, Massachusetts, July 2007.

J. Bell, A. Aspden, M. Day, M. Lijewski, "Numerical simulation of low Mach number reacting flows", SciDAC 2007, J. of Physics: Conference Series, Boston, Massachusetts, July 2007. LBNL Report No. LBNL-63088.

S.E. Woosley, A.S. Almgren, J.B. Bell, G. Glatzmaier, D. Kasen, A.R. Kerstein, H. Ma, P. Nugent, F. Ropke, V. Sankaran and M. Zingale, "Type Ia Supernovae ", SciDAC 2007, J. of Physics: Conference Series, Boston, Massachusetts, July 2007.

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, Proc. Combust. Inst. 31 1299-1307 (2007).

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, Proc. Combust. Inst. 31 1309-1317 (2007).

M. Day, I. Shepherd, J. Bell, J. Grcar, M. Lijewski, "Displacement Speeds in Turbulent Premixed Flame Simulations", Proc. ECCOMAS-CFD 2007.

P. Colella, J. Bell, N. Keen, T. Ligocki, M. Lijewski, B. Van Straalen "Performance and Scaling of Locally-Structured Grid Methods for Partial Differential Equations" presented at SciDAC 2007 Annual Meeting.

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.

Martin, D.F., Colella, P.. and Graves, D.T. "A Cell-Centered Adaptive Projection Method for the Incompressible Navier-Stokes Equations in Three Dimensions", LBNL-62025, submitted to Journal of Computational Physics.

McCorquodale, P., Colella, P., Balls, G.T., and Baden, S.B. "A Local Corrections Algorithm for Solving Poisson's Equation in Three Dimensions", LBNL-62377, submitted to Communications in Applied Mathematics and Computational Science.

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.

D. Trebotich, "Simulation of Biological Flow and Transport in Complex Geometries using Embedded Boundary / Volume-of-Fluid Methods", Journal of Physics: Conference Series, 78 (2007) 012076.

D. Trebotich, G. H. Miller and M. D. Bybee, "A Penalty Method to Model Particle Interactions in DNA-laden Flows", accepted to appear J. Nanosci. Nanotech. (2007).

G. H. Miller and D. Trebotich, "Toward a Mesoscale Model for the Dynamics of Polymer Solutions", J. Comput. Theoret. Nanosci. 4(4):704-708 (2007).

D. Trebotich, G. H. Miller and M. D. Bybee, "A Hard Constraint Algorithm to Model Particle Interactions in DNA-laden Flows", Nanoscale and Microscale Thermophysical Engineering 11 (1):121-128 (2007).

D. Trebotich, "Modeling complex biological flows in multi-scale systems using the APDEC framework", Journal of Physics: Conference Series, 46 (2006) 316-321.

PI Roy Benedek

Li2MnO3-stabilized LiMO2 (M=Mn, Ni, Co) electrodes for lithium-ion batteries M. M. Thackeray, S. H. Kang, C. S. Johnson, J. T. Vaughey, R. Benedek, and S. A. Hackney Journal of Materials Chemistry 17 (30): 3112-3125 (2007)

Free energies for acid attack reactions of lithium cobaltate R. Benedek and A. van de Walle Journal of the Electrochemical Society (submitted)

Phase stability of cation-doped LiMnO$_{2}$ within the GGA+U approximation N. N. Shukla, S. Shukla, R. Prasad, and R. Benedek Modelling and Simulation in Materials Science and Engineering (submitted)

Reaction free energy for proton-lithium ion exchange in lithium battery cathode materials R. Benedek, M. M. Thackeray, and A. van de Walle Chemistry of Materials (submitted)

PI George Bertsch

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

"Global study of the spectroscopic properties of the first 2+ state in even-even nuclei," B. Sabbey, M. Bender, G.F. Bertsch, and P.-H. Heenen, Phys. Rev. C 75, 044305 (2007. Bethel, Edward (Wes) m636

PI Wes Bethel

J. Gosink, J.C. Anderson, and K.I. Joy, "Variable Interactions in Query Driven Visualization," IEEE Transactions on Visualization and Computer Graphics (Proceedings of IEEE Visualization 2007), 13(6), October 2007

E.W. Bethel, C.R. Johnson, K. Joy, S. Ahern, V. Pascucci, H. Childs, J. Cohen, M. Duchaineau, B. Hamann, C. Hansen, D. Laney, P. Lindstrom, J. Meredith, G. Ostrouchov, S.G. Parker, C.T. Silva, A. Sanderson, X. Tricoche. SciDAC Visualization and Analytics Center for Enabling Technology, In Journal of Physics, Conference Series, 78, 2007, Boston MA, USA

Hank Childs. "Architectural Challenges and Solutions for Petascale Postprocessing." Journal of Physics, Conference Series SciDAC 2007, 78, 2007, Boston, MA, USA

C. Jones, K.-L. Ma, A. Sanderson, L. Myers. "Visual Interrogation of Gyrokinetic Particle Simulations," In Journal of Physics, Conference Series SciDAC 2007, 78, 2007, Boston MA, USA

G. Weber, V. Beckner, H. Childs, T. Ligocki, M. Miller, B. van Straalen, E. W. Bethel, "Visualization Tools for Adaptive Mesh Refinement Data." Proceedings of the 4th High End Visualization Workshop, June 2007, Tyrol, Austria.

PI Amitava Bhattacharjee

N. Bessho and A. Bhattacharjee, Fast collisionless reconnection in electron-positron plasmas, Phys. Plasmas 14, 056503 (2007)

P. Zhu, C. C. Hegna, C. R. Sovinec, A. Bhattacharjee, and K. Germaschewski, Intermediate nonlinear regime of a line-tied g-mode, Phys. Plasmas, 14, 055903 (2007).

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, J. Geophys. Res., 112, A06222 (2007).

C. S. Ng and A. Bhattacharjee, A Constrained Tectonics Model for Coronal Heating, Astrophys. J., submitted (2007).

C. S. Ng and A. Bhattacharjee, Anisotropic MHD Turbulence, AIP Conf. Proc., 932, 137 (2007).

K. Germaschewski, A. Bhattacharjee, and C.-S. Ng The Magnetic Reconnection Code: an AMR-based fully implicit simulation suite in: Numerical Modeling of Space Plasma Flows, ASP Conference Series, Vol. 359 (2006) N. B. Pogorelov and G. P. Zank (Eds.)

PI Julian Borrill

S. Masi et al., "The millimeter sky as seen with BOOMERanG", New Astronomy Reviews, 51:236-243, 2007.

G. De Troia et al., "Searching for non-Gaussian signals in the BOOMERanG 2003 CMB map: preliminary results",New Astronomy Reviews, 51:250-255, 2007.

F. Piacentini et al., "CMB polarization with BOOMERanG 2003", New Astronomy Reviews, 51:244-249, 2007

P. Ade et al., "First season QUaD CMB temperature and polarization power spectra" accepted to ApJ

Yoon et al., "The Robinson Gravitational Wave Background Telescope (BICEP): a bolometric large angular scale CMB polarimeter", Millimeter and Submillimeter Detectors and Instrumentation for Astronomy III, Proceedings of SPIE, 6275, 2006 astro-ph/0606278

"Making Maps from Planck LFI 30GHz Data" M.A.J. Ashdown, C. Baccigalupi, A. Balbi, J.G. Bartlett, J. Borrill, C. Cantalupo, G. de Gasperis, K.M. Gorski, V. Heikkila, E. Hivon, E. Keihanen, H. Kurki-Suonio, C.R. Lawrence, P. Natoli, T. Poutanen, S. Prunet, M. Reinecke, R. Stompor, B. Wandelt - submitted to Astronomy & Astrophysics (astro-ph/0702483)

PI Joel Bowman

Potential Energy Surface and Reaction Dynamics of the OH+NO2 Reaction, C. Chen, B. Schepler, B. Braams, J. M. Bowman, J. Chem. Phys. 127, 09xxx (2007).

Quasiclassical Trajectory Calculations of Acetaldehyde Dissociation on a Global Potential Energy Surface Indicate Significant Non-transition State Dynamics Shepler, B. C.; Braams, B. J.; Bowman, J. M. J. Phys. Chem. A.; (Letter); 2007; ASAP Article; DOI: 10.1021/jp074646q

PI Bastiaan Braams

A. R. Sharma, J. Wu, B. J. Braams, S. Carter, R. Schneider, B. Shepler and J. M. Bowman. Potential energy surface and MULTIMODE vibrational analysis of C2H3+. Journal of Chemical Physics 125, #224306, 2006.

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", revised version submitted to Journal of Hydrology, 2007.

Kuhn, Gabriel, Shiraj Khan, Auroop R. Ganguly, Marcia L. Branstetter, "Geospatial-temporal dependence among weekly precipitation extremes with applications to observations and climate model simulations in South America," Advances in Water Resources, vol. 30 (2007), pp. 2401-2423.

PI Eduardo Bringa

R.A. Lebensohn, E.M. Bringa, and A. Caro, "Continuum mesoscale modelling of nanocrystalline fcc metals under shock-loading using an spectral formulation fed by molecular dynamics results", Journal de Physique IV 134, 17 (2006).

A. Caro, P. Klaver, et al., "The computational modeling of alloys at the atomic scale: from ab initio and thermodynamics to radiation-induced heterogeneous precipitation", JOM 59, 52 (2007).

R. Devanathan, P. Durham, J. Du, L. R. Corrales, E. M. Bringa, "Molecular dynamics simulation of amorphization of forsterite by cosmic rays", Nucl. Instr. and Meth. in Phys. Res. B 255, 172 (2007).

D. Schwen and E.M. Bringa, "Simulation of ion tracks in diamond and graphite", Nucl. Instr. and Meth. in Phys. Res. B 256, 187 (2007).

J. Marian, L.A. Zepeda-Ruiz, N. Couto, E.M. Bringa, G.H. Gilmer, P.C. Stangeby and T. D. Ronglien, "Characterization of sputtering products during graphite exposure to deuterium ions by molecular dynamics", Journal of Applied Physics 101, 044506 (2007).

E.M. Bringa et al., "Cosmic-ray induced amorphization of silicates in the inter-stellar medium", Astrophysics Journal 662, 372 (2007).

R. Lebensohn, E.M. Bringa, and A. Caro, "A viscoplastic micromechanical model for the yield strength of nanocrystalline materials", Acta Materialia 55, 261 (2007).

D. Farkas, E.M. Bringa, and A. Caro, "Annealing twins in nanocrystalline fcc metals: A molecular dynamics simulation", Phys. Rev. B 75, 184111 (2007).

B. Cao, E.M. Bringa, and M.A. Meyers, "Shock Compression of Monocrystalline Copper: Atomistic Simulations", Metallurgical and Materials Transactions A, in press.

A. Gyulassy, M.A. Duchaineau, V. Natarajan, V. Pascucci, E.M. Bringa, A. Higginbotham, y B. Hamann, "Topologically clean distance fields", in press, IEEE Transactions on Visualization and Computer Graphics, IEEE Computer Society,

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

A. Caro, E. Bringa, D. Farkas, G. Gilmer and L. Zepeda-Ruiz, "Mobility and mechanical response of dirty interfaces in nanocrystalline Cu", submitted to Acta Materialia.

P. Erhart, A. Caro, M. Caro, and B. Sadigh, "Short-range order and precipitation in Fe-rich Fe--Cr alloys", submitted to Phys. Rev. B.

P. Erhart, B. Sadigh, and A. Caro, "Are there stable long-range ordered Fe_{1-x}Cr_x compounds?", submitted to Appl. Phys. Lett.

PI Eric Brown

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. J. Am. Chem. Soc. 2007, 129, 3267-3286.

Brown, E. C.; Marks, T. J.; Ratner, M. A. J. Phys. Chem. 2007 In Press. (Preprint available)

PI David Bruhwiler

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

PI Andrew Canning

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

B. Lee, A. Canning, L.W. Wang, "Effects of d-electrons in pseudopotential screened-exchange density functional calculations", Phys. Rev. B (submitted).

C. Voemel, S. Tomov, O. Marques, A. Canning, L-W Wang and J. Dongarra, "State-of-the-art eigensolvers for electronic structure calculations of large scale nano-systems", Submitted to Journal of Computational Physics

L. Oliker, A. Canning, J. Carter, et. al., "Scientific Application Performance on Candidate PetaScale Platforms", International Parallel & Distributed Processing Symposium (IPDPS) 2007. LBNL-62952. WINNER: Best paper application track

L. Oliker, J. Shalf, J. Carter, A. Canning et. al., "Performance Characteristics of Potential Petascale Scientific Applications", Petascale Computing: Algorithms and Applications, Chapman & Hall / CRC Press, in press

L. Oliker, A. Canning, J. Carter, J. Shalf, S. Ethier, "Scientific Application Performance on Leading Scalar and Vector Supercomputing Platforms", International Journal of High Performance Computing Applications , in press

L.W. Wang, Z. Zhao, J. Meza, "A linear scaling three dimensional fragment method for large scale electronic structure calculations", (submitted).

PI Fausto Cattaneo

Fausto Cattaneo, Paul Fischer, Aleksandr Obabko "Numerical simulations of magneto-rotational turbulence in cylindrical geometry", Mini-conference on Angular Momentum Transport in Laboratory and Nature, 49th Annual Meeting of the Division of Plasma Physics November 12-16, Orlando, Florida, 2007

PI Paola Cessi

Wolfe, C. L. and Paola Cessi, 2008: "Overturning Circulation in an Eddy-Resolving Model: The Effect of the Pole-to-Pole Temperature Gradient", submitted to Journal of Physical Oceanography.

PI Yuen-Dat Chen

Measurement of the ne and Total 8B Solar Neutrino Fluxes with the Sudbury Neutrino Observatory Phase I Data SetAharmim et al, Phys. Rev. C 75, 045502 (2007) A Search for Neutrinos from the Solar hep Reactions and the Diffuse Supernovae Neutrino Background with the Sudbury Neutrino Observatory, ApJ 653 (2006) 1545

"Validation of spallation neutron production and propagation within Geant4", M. G. Marino et al., NIM A 582, pp. 611-620 (2007).

PI Choong-Seock Chang

G. Park, J. Cummings, C.S. Chang, Podhorszki, S. Klasky, etc, "Coupled simulation of kinetic pedestal growth and MHD ELM crash," Journal of Physics: Conference Series 78, 012087 (2007)

D.A. Batchelor, M. Beck, A. Becoulet, R.V. Budny, C.S. Chang, et al, "Simulation of Fusion Plasmas: Current Status and Future Direction," Plasma Science and Technology 9, 312 (2007)

Gunyoung Park and C.S. Chang, "A 5-1/2-dimensional theory for fast and accurate evaluation of the cyclotron resonance heating using representation," Phys. Plasmas 14, 052503 (2007)

Y. Chen and S. Parker, Phys. Plasmas 14, 082301 (2007)

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: Conference Series 46 (2006) 87

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 220, 839 (2007)

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.

J. Lang, Y. Chen, S. Parker, Phys. Plasmas 14 082315 (2007)

Y. Nishimura, Z. Lin, and W. X. Wang, Electromagnetic global gyrokinetic simulation of shear Alfven wave dynamics in tokamak plasmas, Phys. Plasmas 14, 042503 (April 2007).

Y. Nishimura1, Y. Xiao, and Z. Lin, Guiding center orbit studies in a tokamak edge geometry employing Boozer and Cartesian coordinates, Contributions Plasma Phys., in press, 2007.

Z Lin, Y Nishimura, Y Xiao, I Holod, W L Zhang and L Chen, Global gyrokinetic particle simulations with kinetic Electrons, Plasma Phys. Contr. Fusion., in press, 2007.

H. Strauss, et al., Nuclear Fusion (2006) (IAEA paper)

T. S. Hahm, P. H. Diamond, O. D. Gurcan, and G. Rewoldt,Theory of intrinsic rotation and momentum transport, Phys. Plasmas 14, 072302 (2007)

PI James Chelikowsky

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. 97, 147201 (2006).

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 6, 2887 (2006).

J.R. Chelikowsky: The Role of Self-Purification and the Electronic Structure of Magnetically Doped Semiconductor Nanocrystals, Phase Transitions 79, 739 (2006).

Y. Zhou, Y. Saad, M.L. Tiago, and J.R. Chelikowsky: Parallel Self-Consistent-Field Calculations via Chebyshev-Filtered Subspace Acceleration, Phys. Rev. E 74, 066704 (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, Nano Lett. 7, 1878 (2007).

J.R. Chelikowsky, M.L. Tiago, Y. Saad, and Y. Zhou: Algorithms for the Evolution of Electronic Properties in Nanocrystals, Comp. Phys. Comm. 177, 1 (2007).

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

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

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

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

H. Kwak, M. L. Tiago and J. R. Chelikowsky: Quantum Confinement and Strong Coulombic Correlation in ZnO Nanocrystals, Phys. Rev. B (submitted).

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

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

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

T.-L. Chan, M. L. Tiago, E. Kaxiras and J.R. Chelikowsky, The role of quantum confinement on doping silicon nanocrystals, Phys. Rev. Lett. (submitted).

T.-L. Chan, M.L. Tiago, and J.R. Chelikowsky: Algorithms for Defects in Nanostructures, Physica B (in press.)

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

S. Beckman and J.R. Chelikowsky: The structure and properties of vacancies in Si nano-crystals calculated by real space pseudopotential methods, Physica B (in press).

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

PI Jacqueline Chen

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," Proc. of the Combustion Institute, 31:1633-1640, (2007).

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. (2006).

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

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).

PI Liu Chen

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).

Resonant and Non-Resonant Particle Dynamics in Alfven Mode Excitations, F. Zonca and L. Chen, Plasma Phys. Control. Fusion 48, 537-556 (2006). Eigenmode Stability Analysis of Drift-Mirror Modes in Nonuniform Plasmas, D. Klimushkin and L. Chen, Ann. Geophys. 24, 2435-2439 (2006).

Physics of Burning Plasmas in Toroidal Magnetic Confinement Devices, F. Zonca, S. Briguglio, L. Chen, G. Fogaccia, T. Hahm, A. Milovanov, and G. Vlad, Plasma Phys. Control. Fusion 48, B15-B28 (2006).

Statistical analysis of fluctuations and noise-driven transport in particle-in-cell simulations of plasma turbulence, I. Holod and Z. Lin, Phys. Plasmas 14, 032306 (2007).

Electromagnetic global gyrokinetic simulation of shear Alfven wave dynamics in tokamak plasmas, Y. Nishimura, Z. Lin, and W. X. Wang, Phys. Plasmas 14, 042503 (2007).

Gyrokinetic theory and simulation of mirror instability, H. Qu, Z. Lin, and L. Chen, Phys. Plasmas 14, 042108 (2007).

Simulation of Fusion Plasmas: Current Status and Future Direction, D. A. Batchelor, M. Beck, A. Becoulet, R. V. Budny, C. S. Chang, P. H. Diamond, J. Q. Dong, G. Y. Fu, A. Fukuyama, T. S. Hahm, D. E. Keyes, Y. Kishimoto, S. Klasky, L. L. Lao, K. Li, Z. Lin, B. Ludaescher, J. Manickam, N. Nakajima, T. Ozeki, N. Podhorszki, W. M. Tang, M. A. Vouk, R. E. Waltz, S. J. Wang, H. R. Wilson, X. Q. Xu, M. Yagi, and F. Zonca, Plasma Sci. Technol. 9, 312-387 (2007).

Linear comparison of gyrokinetic codes with trapped electrons, G. Rewoldt, Z. Lin, and Y. Idomura, Comp. Phys. Commun. 177, 775-780 (2007).

Theory of Alfvin Waves and Energetic Particle Physics in Burning Plasmas, L. Chen and F. Zonca, Nuclear Fusion 47, S727-S734 (2007).

Electron Fishbones: Theory and Experimental Evidence, F. Zonca et al, Nuclear Fusion 47, 1588-1597(2007).

Nonlinear Equilibria, Stability and Generation of Zonal Structures in Toroidal Plasmas, L. Chen and F. Zonca, Nuclear Fusion 47, 886-891(2007).

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

Global gyrokinetic particle simulations with kinetic electrons Z. Lin, Y. Nishimura, Y. Xiao, I. Holod, W. L. Zhang and L. Chen, Plasma Phys. Control. Fusion 49, December, 2007.

Dynamic Coronal Loops in Three Dimensions, Y. Mok, R. Lionello, Z. Mikic, and J.A. Linker, submitted to The Astrophysical Journal Letter (2007).

PI Yang Chen

B. Nevins, S. E. Parker, Y. Chen, et. al.,''Verification of gyrokinetic delta-f simulations of electron temperature gradient turbulence'', Physics of Plasmas 14,084501 (2007)

J. Lang, Y. Chen and S. E. Parker, ``Trapped electron mode turbulence'', Physics of Plasmas 14, 082315 (2007)

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

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, 220, 839 (2007)

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," AIP Conference Proceedings, Vol. 871 p.193-203, (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)

PI Yixin Chen

Y. Chen and M. Chen, Extended Duality for Nonlinear Programming, Computational Optimization and Its Applications, submitted, 2007.

V. Clark, Y. Chen, J. Wilkens, J. Alaly, K. Zakaryan, and J. Deasy, IMRT Treatment Planning for Prostate Cancer using Prioritized Prescription Optimization and Mean-Tail-Dose Functions, Linear Algebra and Its Applications, accepted, 2007.

C. Hsu, Y. Chen, and B. Wah, Subgoal Ordering and Granularity Control for Incremental Planning, International Journal on Artificial Intelligence Tools, 16(4): 707-723, 2007.

V. Clark, I. E. Naqa, Y. Chen, and J. Deasy, Automated IMRT treatment planning using prioritized prescription optimization, the XVth International Conference on the Use of Computers in Radiation Therapy (ICCR-07), Toronto, Canada, June 2007.

B. Wah, Y. Chen, and T. Wang, Simulated Annealing with Asymptotic Convergence for Nonlinear Constrained Optimization, Journal of Global Optimization, 39(1): 1-37, 2007.

C. Hsu, B. Wah, R. Huang, and Y. Chen, Constraint Partitioning for Solving Planning Problems with Trajectory Constraints and Goal Preferences, Proc. International Joint Conference on Artificial Intelligence (IJCAI-07), pp. 1924-1929, 2007.

PI Hai-Ping Cheng

Agapito LA, Cheng HP Ab initio calculation of a graphene-ribbon-based molecular switchJOURNAL OF PHYSICAL CHEMISTRY C 111 (38): 14266-14273 SEP 27 2007

He Y, Zhang C, Cao C, et al. Effects of strain and defects on the electron conductance of metallic carbon nanotubes PHYSICAL REVIEW B 75 (23): Art. No. 235429 JUN 2007

Cao C, He Y, Torras J, et al. Fracture, water dissociation, and proton conduction in SiO2 nanochains JOURNAL OF CHEMICAL PHYSICS 126 (21): Art. No. 211101 JUN 7 2007

Wang LL, Cheng HP Embedding atom-jellium model for metal surface EUROPEAN PHYSICAL JOURNAL D 43 (1-3): 247-250 JUL 2007

Schmidt M, Masson A, Brechignac C, et al. Hydrogen peroxide and ammonia on protonated ice clusters JOURNAL OF CHEMICAL PHYSICS 126 (15): Art. No. 154315 APR 21 2007

Muralidharan K, Cao C, Wan YX, et al. Environment dependent dynamic charge potential for silica: Application to nanoscale silica structures CHEMICAL PHYSICS LETTERS 437 (1-3): 92-98 MAR 22 2007

Zhang JW, Cheng HP Anomalous Hall effect in disordered Fe ferromagnetic films PHYSICAL REVIEW B 74 (21): Art. No. 212409 DEC 2006

Simulations of azobenzene containing alkanethiol SAMs on Au(111) surface, Journal of Physical Chemistry (in press)

Cao C., He. Y., Cheng HP Hydrogen dissociation and band modification of CNT-supported Pd4 cluster (submitted).

Cao C., Kemper L. He, Y. Cheng HP CNT-supported Pdn cluster as nano-sensor (submitted).

He Y., Cao, C., Cheng HP Predictive simulation of nano-tube fracture under stress (submitted).

He Y., Graser S., Hirschfeld, P.J., Cheng HP Supermodulation in the atomic structure of high-Tc superconductor Bi2Sr2CaCu2O8 from ab initio calculations (submitted)

PI Wai-Yim Ching

J. Buban, K. Matsunaga, J. Chen, N. Shibata, W.Y. Ching, T. Yamamoto, Y. Ikuhara, "Grain Boundary Strengthening in Alumina in 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, 2933-2948 (2006).

W. Y. Ching, Jun Chen, Paul Rulis, Lizhi Ouyang, and Anil Misra, "Ab initio Modeling of Clean and Y-doped Grain Boundaries in Alumina and Intergranular Glassy Films (IGF) in b-Si3N4", J. Materials Science, 41 (16) 5061-5067, (2006).

A. Hunt, W.Y. Ching, Y.-M. Chiang, and A. Moewes "Electronic structure of LiFePO4 and FePO4 studied using resonant inelastic x-ray scattering", Phys. Rev. B73, 205120-1-10 (2006).

Jun Chen, Paul Rulis, Lizhi Ouyang, S. Satpathy, and W.Y. Ching,, "Vacancy enhanced ferromagnetism in Fe-doped rutile TiO2", Phys. Rev. B74, 235207-1-5 (2006).

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

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

Sitaram Aryal, Paul Rulis and W. Y. Ching, "Density functional calculation of the electronic structure and optical properties of Aluminosilicate polymorphs (Al2SiO5)", American Mineralogy (inpress, 2007).

P. Rulis, Hongzhi Yao, L. Ouyang, and W.Y. Ching "Electronic structure, bonding, charge distribution and X-ray absorption spectra of the (001) surfaces of fluorapatite and hydroxyapatite", (submitted to Phys. Rev. B).

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

PI Mei-Yin Chou

"Enhanced Electron-Hole Interaction and Optical Absorption in a Silicon Nanowire," L. Yang, C. D. Spataru, S. G. Louie, and M. Y. Chou, Phys. Rev. B (Rapid Communications) 75, 201304 (2007).

"Band-Structure Contribution to the Quantum Size Effect in Pb(100) Films," C. M. Wei and M. Y. Chou, Phys. Rev. B 75, 195417(2007).

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

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

"Quantum Confinement Effect in Si/Ge Core-Shell Nanowires," L. Yang, R. N. Musin, X.-Q. Wang, and M. Y. Chou, submitted to Phys. Rev. Lett.

"LaMg2PdH7, a New Complex Metal Hydride Containing Tetrahedral [PdH4]4- Anions," K. Yvon, J.-Ph. Rapin, N. Penin, Z. Ma, and M. Y. Chou, J. Alloys Compd. 446-447, 34 (2007).

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

"Electronic and Vibrational Properties of gamma-AlH3," Y. Wang and M. Y. Chou, submitted to Phys. Rev. B; arXiv:0707.4604v1[cond-mat.mtrl-sci].

"Phase Stability of Mixed Alkali Alanates," Zhu Ma and M. Y. Chou, in preparation.

PI Daryl Chrzan

E. Ertekin, M. S. Daw and D. C. Chrzan. Elasticity theory of topological defects in carbon nanotubes and graphene. Accepted for publication in Philosophical Magazine Letters.

S. P. Beckman and D. C. Chrzan. The reconstruction energies of partial dislocation cores in GaAs. Accepted for publication in Physical Review B. (Listed as submitted in last year's ERCAP request.)

PI Catherine Chuang

Kelly, J.T., C.C. Chuang, and A.S. Wexler, Influence of dust composition on cloud droplet formation, ATMOSPHERIC ENVIRONMENT 41 (14): 2904-2916 MAY 2007.

PI Aurora Clark

A. E. Clark, "Density Functional and Basis Set Dependence of Predicted Ln(H2O)83+ Properties", Journal of Chemical Theory and Computation, submitted.

A. Dinescu, A. E. Clark, " Thermodynamic and Structural Features of Aqueous Ce(III)", Inorg. Chem., submitted.

PI Bruce Cohen

Characterizing electron temperature gradient turbulence via numerical simulation, W. M. Nevins et al., Phys. Plasmas 13, 122306 (2006).

B. Nevins, S. E. Parker, Y. Chen, et. al.,''Verification of gyrokinetic delta-f simulations of electron temperature gradient turbulence'', Physics of Plasmas 14,084501 (2007)

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

[Candy 2006a] J. Candy and R.E. Waltz, Velocity-Space Resolution, Entropy Production, and Upwind Dissipation in Eulerian Gyrokinetic Simulations, Phys. Plasmas 13, 032310 (2006).

[Candy 2006b] 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).

"Micro-tearing modes in the mega ampere spherical tokamak", D J Applegate, C M Roach, J W Connor, S C Cowley, W Dorland, R J Hastie and N Joiner, Plasma Phys. Control. Fusion 49 No 8 (August 2007) 1113-1128

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

"Studies of improved electron confinement in low density L-mode NSTX discharges," D. Stutman, et al., PoP 13, 092511 (2006).

"Small-scale turbulence in a closed field-line geometry," P. Ricci, B. N. Rogers and W. Dorland, Phys. Rev. Letters, 97, 245001 Dec (2006).

"Observation of Trapped Electron Mode Turbulence in Tokamak Plasmas Through Direct Comparison of Nonlinear Gyrokinetic Simulations with Density Fluctuation Measurements",

D. R. Ernst, N. P. Bassi, W. Dorland, C. L. Fiore, L. Lin, A. Long, E. S. Marmar, M. Porkolab, and K. Zhurovich, submitted, PRL.

"Fluctuation Spectra in Kinetic, Alfvenic Turbulence," Gregory G. Howes,, William Dorland, Steven C. Cowley, Gregory W. Hammett, Eliot Quataert, Alexander A. Schekochihin, and Tomoya Tatsuno, submitted, PRL

"A Model of Critically Balanced Turbulence in Magnetized Weakly Collisional Plasmas: Implications for the Dissipation Range of the Solar Wind," G. G. Howes, S. C. Cowley, W. Dorland, G. W. Hammett, E. Quataert, and A. A. Schekochihin. submitted, Journal and Geophysical Research.

J. Lang, Y. Chen and S. E. Parker, ``Trapped electron mode turbulence'', Physics of Plasmas 14, 082315 (2007)

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

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, 220, 839 (2007)

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

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",Phys. Plasmas (2007)

"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.

[Hooper, 2007a] E. B. Hooper, B. I. Cohen, D. N. Hill, L. L. LoDestro, H. S. McLean, C. A. Romero Talamas, R. D.

E. B. Hooper, B. I. Cohen, D. N. Hill, L. L. Lodestro, H. S. McLean, C. A. Romero Talamas, R. D. Wood, and C. R. Sovinec, Magnetic reconnection in the spheromak: physics and consequences, J. Fusion Energy 26, 71 (2007).

[Romero-Talamas, 2007] C.A. Romero-Talamas, E. B. Hooper, D.N. Hill, B. I. Cohen, H. S. McLean, R. D. Wood, and J. M. Moller, J. Fusion Energy 26, 169 (2007).

PI Marvin Cohen

J. Noffsinger, F. Giustino, S.G. Louie, M.L. Cohen, "Superconductivity and Fermi Surface Nesting in Super-Hard Carbides," submitted to Phys. Rev. Lett.

L. Yang, M.L. Cohen, and S.G. Louie, "Exciton effects in the optical spectra of graphene nanoribbons," Nano Lett. 7, 3112 (2007).

L. Yang, C.-H. Park, Y.-W. Son, M.L. Cohen, and S.G. Louie, "Quasiparticle Energies and Band Gaps of Graphene Nanoribbons," accepted to Phys. Rev. Lett.

M. Ishigami, J.D. Sau, S. Aloni, M.L. Cohen, and A. Zettl, "Symmetry breaking in boron nitride nanotubes," Phys. Rev. Lett. 97, 176804 (2006).

F. J. Ribeiro, P. Tangney, S. G. Louie and M. L. Cohen, "Hypothetical Hard Structures of Carbon with Cubic Symmetry," Phys. Rev. B 74, 172101 (2006).

Y.-W. Son, M. L. Cohen, and S. G. Louie, "Half-Metallic Graphene Nanoribbons," Nature 444, 347 (2006).

Y.-W. Son, M.L. Cohen, and S.G. Louie, "Energy Gaps in Graphene Nanoribbons," Phys. Rev. Lett. 97, 216803 (2006).

P. Zhang, S.G. Louie, and M.L. Cohen, "Electron-Phonon Renormalization in Cuprate Superconductors," Phys. Rev. Lett. 98, 067005 (2007).

J.D. Sau and M.L. Cohen, "Possibility of increased mobility in Ge-Sn alloy system," Phys. Rev. B 75, 045208 (2007).

K.T. Chan, J.D. Sau, P.H. Zhang, and M.L. Cohen, "Ab initio calculations of phonon splitting in antiferromagnetic ZnCr2O4," Phys. Rev. B 75, 054304 (2007).

W.D. Luo, P.H. Zhang, and M.L. Cohen, "Splitting of the zone-center phonon in MnO and NiO," Solid State Comm. 142, 504 (2007).

F. Giustino, J.R. Yates, I. Souza, M.L. Cohen, and S.G. Louie, "Electron-Phonon Interaction via Electron and Lattice Wannier Functions: Superconductivity in Boron-Doped Diamond Reexamined," Phys. Rev. Lett. 98, 047005 (2007).

PI Michael Colvin

V.V. Krishnan, Edmond Y. Lau, Justin Yamada, Daniel P. Denning, Samir S. Patel, Michael E. Colvin and Michael F. Rexach, Intra-molecular cohesion of coils mediated by phenylalanine-glycine motifs in the natively unfolded domain of a nucleoporin Submitted to PLOS Computational Biology (2007)

PI Peter Cummings

Massless Fermion in multilayer graphene, Latil, Henrard, Meunier, Physical Review B (RC), in press (2007)

Tuning the conductance of carbon nanotube with encapsulated molecules, Vincent Meunier and Bobby G Sumpter, Nanotechnology, 18 in press (2007).

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

Polarization in Nanotubes and Nanotubular Structures, M. Buongiono Nardelli, S.M. Nalhmanson, and V. Meunier, in Solution Manual For Nanoengineeringo f Structural, Functional, and Smart Materials, edited by M.J. Schulz, A.D. Kelkar, and M.J. Sundaresan, CRC Press, page 94-95 (2007).

Investigation of the Nanoscale Self-Assembly of Donor-s-Acceptor Molecules Bobby G. Sumpter, Vincent Meunier, Alvaro Vazquez-Mayagoitia, and Ronald K. Castellano, Int. J. Quant. Chem., 107, 2233 (2007).

Re-oxidation of TiO2(110) via Ti interstitials and Line Defects, K. T. Park, M. Pan, V. Meunier, and E. W. Plummer, Phys. Rev. B, 75, 245415 (2007).

Structure and Stability of Small Boron and Boron Oxide Clusters Michael L. Drummond, Vincent Meunier, Bobby G. Sumpter, J. Phys. Chem. A, 111, 6539 (2007).

Tuning the electronic properties of coaxial nanoscale cables through chemical doping, A. G. Souza Filho, Vincent Meunier, M. Terrones, Bobby G. Sumpter, E. B. Barros, F. Villalpando, Y.A. Kim, H. Muramatsu, T. Hayashi, M. Endo, and M. S. Dresselhaus, Nano Letters, 7(8) 2383-2388 (2007).

Conductivity properties of benzo-homologated DNA bases, Miguel Fuentes-Cabrera, Vincent Meunier, and Bobby G. Sumpter, Nanotechnology, 18 in press (2007).

Density Functional Theory Studies of Quantum Transport in Molecular Systems, V. Meunier, W. Lu, B.G. Sumpter, and J Bernholc, Int. J. Quantum Chem., 106(15), 3334-3342 (2006).

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, 74 125318 (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).

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).

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

Imaging defects in graphene and carbon nanotubes with a scanning tunneling microscope, Ph. Lambin , H. Amara, J.C. Charlier, and V. Meunier book chapter to appear in Chemistry of Nanotube, ASP press (2006).

Koparde, V. N. and Cummings, P. T., "Molecular dynamics study of water adsorption on TiO2 nanoparticles," Journal of Physical Chemistry C, 111, 6920-6926 (2007).

Leng, Y. S., Dyer, P. J., Krstic, P. S., Harrison, R. J. and Cummings, P. T., "Calibration of chemical bonding between benzenedithiolate and gold: the effects of geometry and size of gold clusters," Molecular Physics, 105, 293-300 (2007)

Mamontov, E., Vlcek, L., Wesolowski, D. J., Cummings, P. T., Wang, W., Anovitz, L. M., Rosenqvist, J., Brown, C. M. and Sakai, V. G., "Dynamics and structure of hydration water on rutile and cassiterite nanopowders studied by quasielastic neutron scattering and molecular dynamics simulations," Journal of Physical Chemistry C, 111, 4328-4341 (2007).

Payne, C. M., Zhao, X. and Cummings, P. T., "Molecular simulations of DNA transport in solution," Molecular Simulation, 33, 399-403 (2007).

Predota, M., Cummings, P. T. and Wesolowski, D. J., "Electric double layer at the rutile (110) surface. 3. Inhomogeneous viscosity and diffusivity measurement by computer simulations," Journal of Physical Chemistry C, 111, 3071-3079 (2007).

Pu, Q., Leng, Y. S., Tsetseris, L., Park, H. S., Pantelides, S. T. and Cummings, P. T., "Molecular dynamics simulations of stretched gold nanowires: The relative utility of different semiempirical potentials," Journal of Chemical Physics, 126, Art. No. 144707 (2007).

Striolo, A., McCabe, C., Chan, E. R., Glotzer, S. C., and Cummings, P. T., "Aggregation of POSS Monomers in Liquid Hexane: A Molecular-Simulation Study," J. Phys. Chem. B, accepted for publication (2007).

Payne, C. M., Zhao, X. C., Vlcek, L., Cummings, P. T., "Molecular Dynamics Simulation of ss-DNA Translocation Through a Copper Nanoelectrode Gap,"J. Phys. Chem. C, submitted for publication (2007)

Chan, E. R., Striolo, A., McCabe, C., Cummings, P. T., and Glotzer, S. C., "Coarse-grained force field for simulating polymer-tethered silsesquioxane self-assembly in solution," J. Chem. Phys. 127 (2007) Art. No. 114102. Selected for publication in the October 1, 2007 issue of Virtual Journal of Nanoscale Science & Technology. Selected for publication in the October 1, 2007 issue of Virtual Journal of Biological Physics Research.

PI Larry Curtiss

S. P. Adiga, P. Zapol P, and L. A. Curtiss, Structure and morphology of hydroxylated amorphous alumina surfaces, J. Phys. Chem. C 111 7422 (2007).

Selective and Efficient Oxidative Dehydrogenation of Propane on Sub-nanometer Platinum Clusters, Stefan Vajda, Michael J. Pellin, Jeffrey P. Greeley, Christopher L. Marshall, Larry A. Curtiss, Gregory A. Ballentine, Jeffrey W. Elam, Stephanie Catillon-Mucherie, Paul C. Redfern, and Peter Zapol, submitted.

PI Valerie Daggett

Beck, et al. Dynameomics: Mass Annotation of Protein Dynamics and Unfolding in Water by High-Throughput All-Atom Molecular Dynamics Simulations. Genome Biology, In press.

Simms, et al. The Dynameomics data warehouse: Design of a computational lab workflow and scientific data repository. BMC Bioinformatics, Submitted.

Kehl, et al. The Dynameomics OLAP Database: A Multi-Dimensional Analysis Optimized Database for Dynamic Protein Data. BMC Bioinformatics, Submitted.

Benson & Daggett. Native Protein Flexibility as a Determinant of Dynamical Changes and Unfolding Events. PNAS, Submitted.

PI Ronald Davidson

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

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

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 A577, 86 (2007).

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 A577, 79 (2007).

Recent U.S. Advances in Ion-Beam-Driven High Energy Density Physics and Heavy Ion Fusion, B. G. Logan, J. J. Barnard, F. Bieniosek, C. M Celata, R. C. Davidson, A. Friedman, E. Gilson, I. Kaganovich, J. W. Kwan, M. Leitner, A. Molvik, H. Qin, P. Roy, A. Sefkow, P.A. Seidl, E.A. Startsev, S.S. Yu, W.W. Waldron, R.J. Briggs, R. A. Kishek, D. R. Welch and C. Olson, Nuclear Instruments and Methods in Physics Research A577, 1 (2007)

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 A577, 70 (2007).

S. P. Gerhardt, E. V. Belova, M. Yamada, et al., Inductive sustainment of oblate FRCs with the assistance of magnetic diffusion, shaping, and finiteLarmor radius stabilization, submitted to Physics of Plasmas (2007).

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

S. P. Gerhardt, M. Yamada, E.V. Belova, H. Ji, M. Inomoto, Y. Ren, and B. McGeeham, Method for inductively forming an oblate field reversed configuration utilizing a spheromak and an Ohmic solenoid, submitted to Phys. Plasmas, 2007.

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

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

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

Yamada, M., H. Ji, E. Belova, S. P. Gerhardt, R. C. Davidson, and D. Mikkelsen, Oblate field-reversed configurations through a Self-organized Plasma with Induction, Reconnection, and Injection Techniques: the SPIRIT concept, Plasma and Fusion Research in Japanese Society of Plasma Fusion, in press (2007).

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

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

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

S. P. Gerhardt, E. Belova, M. Inomoto, M. Yamada, H. Ji, Y. Ren, and A. Kuritsyn, Equilibrium and stability studies of oblate field reversed configurations in the Magnetic Reconnection Experiment, Phys. Plasmas 13, 112508 (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).

M. Inomoto, S. P. Gerhardt, M. Yamada, H. Ji, E. Belova, Y. Ren, and A. Kuritsyn, Coupling between global geometry and the local Hall effect leading to reconnection-layer symmetry breaking, Phys. Rev. Let. 97, 135002 (2006).

M. R. Brown, C. D. Cothran, J. Fung, M. Chang, J. Horwitz, M. Schaffer, J. Leuer and E. Belova, Dipole trapped shperomak in a prolate flux conserver, Phys. Plasmas 13, 102503 (2006).

PI Eric DeWeaver

Lorenz, D. J., and E. DeWeaver, 2007: The response of the extratropical hydrological cycle to global warming. J. Climate, 20, 3470-3484.

Lorenz, D. J., and E. DeWeaver, 2007: Tropopause height and the zonal wind response to global warming in the IPCC scenario integrations. J. Geophys. Research, 112, D10119, doi:10.1029/2006JD008087.

PI David Dean

Complex coupled-cluster approach to an ab initio description of open quantum systems, G. Hagen, D.J. Dean, M. Hjorth-Jensen, and T. Papenbrock, in press, Phys. Lett. B (2007).

Coupled-cluster theory for three-body Hamiltonians, G. Hagen, T. Papenbrock, D.J. Dean, A. Schwenk, A. Nogga, M. Wloch, P. PiecuchPhys. Rev. C 76, 034302 (2007)

Benchmark calculations for 3H, 4He, 16O and 40Ca with ab-initio coupled-cluster theory, G. Hagen, D. J. Dean, M. Hjorth-Jensen, T. Papenbrock, A. Schwenk, Phys. Rev. C 76, 044305 (2007)

Comment on "Ab Initio study of 40-Ca with an importance-truncated no-core shell model", D. J. Dean, G. Hagen, M. Hjorth-Jensen, T. Papenbrock, A. Schwenk, Phys. Rev. Lett. (2007)

Parity-projected shell model Monte Carlo level densities for fp-shell nuclei, C. Ozen, K. Langanke, G. Martinez-Pinedo, and D.J. Dean, Phys. Rev. C75, 064307 (2007)

Particle-Number Projection and the Density Functional Theory Authors: J. Dobaczewski, M.V. Stoitsov, W. Nazarewicz, P.-G. Reinhard arXiv:0707.4324 (submitted to Phys. Rev. C)

Additivity of effective quadrupole moments and angular momentum alignments in the A~130 nuclei, M. Matev, A.V. Afanasjev, J.Dobaczewski, G.A.Lalazissis, W.Nazarewicz, arXiv:0707.0767 (submitted to Phys. Rev. C, 2007)

PI James Demmel

J. Demmel, Y. Hida, X. Li, and J. Riedy, "Extra-precise iterative refinement for overdetermined least squares problems," LAPACK Working Note 188, May 2007. (submitted to TOMS)

PI Stephen Derenzo

S. Derenzo et. al. "LBNL facility for new scintillator material discovery" , IEEE transactions on Nuclear Science (to appear)

PI Thomas Devereaux

W.S. Lee, S. Johnston, T.P. Devereaux, and Z.-X. Shen, Aspects of Electron-Phonon Self-Energy Revealed from Angle-Resolved Photoemission Spectroscopy, Phys. Rev. B 75, 195116 (2007).

W. Meevasana, X.J. Zhou, S. Sahrakorpi, W.S. Lee, W.L. Yang, N. Mannella, T. Yoshida, Y.L. Chen, K. Tanaka, R.H. He, Hsin Lin, S. Komiya, Y. Ando, F. Zhou, W.X. Ti, J.W. Xiong, Z. X. Zhao, T. Sasagawa, T. Kakeshita, K. Fujita, S. Uchida, H. Eisaki, A. Fujimori, Z. Hussain, R. S. Markiewicz, A. Bansil, N. Nagaosa, J. Zaanen, T.P. Devereaux, and Z.-X. Shen, Hierarchy of Multiple Many-Body Interaction Scales in High-Temperature Superconductors, Phys. Rev. B 75, 174506 (2007).

K. Tanaka, W.S. Lee, D.H. Lu, A. Fujimori, T. Fujii, Risdiana, I. Terasaki, D.J. Scalapino, T.P. Devereaux, Z. Hussain, and Z.-X. Shen, Distinct Fermi-Momentum Dependent Energy Gaps in Deeply Underdoped Bi-2212, Science 314, 1910 (2006).

W. Meevasana, T.P. Devereaux, N. Nagaosa, Z.-X. Shen, and J. Zaanen, Overdamped c-axis Charge Dynamics and the Coupling to Polar Phonons in Cuprate Superconductors, Phys. Rev. B. 74, 174524 (2006).

Y. Chen, A. Iyo, W. Yang, X. Zhou, D. Lu, H. Eisaki, T. P. Devereaux, Z. Hussain, and Z.-X. Shen, Anomalous Fermi-Surface Dependent Pairing in a Self-Doped High-Tc Superconductor, Phys. Rev. Lett. 97, 236401 (2006).

Jian-Xin Zhu, K. McElroy, J. Lee, T. P. Devereaux, Qimiao Si, J. C. Davis, A. V. Balatsky, Effects of t1 Scattering on Fourier-Transformed Inelastic Tunneling Spectra in High-Tc Cuprates with Bosonic Modes, Phys. Rev. Lett. 97, 177001 (2006).

W. Meevasana, N.J.C. Ingle, D.H. Lu, J.R. Shi, F. Baumberger, K.M. Shen, W.S. Lee, T. Cuk, H. Eisaki, T.P. Devereaux, N. Nagaosa, J. Zaanen, and Z.-X. Shen, Doping Dependence of the Coupling of Electrons to Bosonic Modes in the Single-Layer High-Temperature Bi2Sr2CuO6 Superconductor, Phys. Rev. Lett. 96, 157003 (2006).

A. V. Chubukov, T. P. Devereaux and M. V. Klein, Resonance Mode in B1g Raman Scattering a Way to Distinguish Between Spin-Fluctuation and Phonon-Mediated d?~H~Rwave Superconductivity, Phys. Rev. B 73, 094512 (2006).

Jian-Xin Zhu, A. V. Balatsky, T. P. Devereaux, Q. Si, J. Lee, K. McElroy, and J. C. Davis, Fourier-Transformed Inelastic STM Tunneling into High-Temperature Cuprates with Bosonic Modes, Phys. Rev. B 73, 014511 (2006).

W.S. Lee, D.H. Lu, W.L. Yang, T. Cuk, K.M. Shen, X.J. Zhou, W. Meevasana, C. T. Lin, J.-i. Shimoyama, T. P. Devereaux, and Z. X. Shen, Band Renormalization Effect in Bi2Sr2Ca2Cu3O10+d, invited paper to appear in High Tc Superconductors and Related Transition Metal Oxides, eds. A. Bussmann-Holder and H. Keller (Springer, Berlin, 2007).

T. P. Devereaux and R. Hackl, Inelastic Light Scattering in Strongly Correlated Materials, Reviews of Modern Physics 79, 175 (2007).

X. J. Zhou, T. Cuk, T. Devereaux, N. Nagaosa, and Z.-X. Shen, cond-mat/0604284, Polaronic Behavior and Electron-Phonon Coupling in High Temperature Cuprate Superconductors as Revealed from Angle-Resolved Photoemission Spectroscopy, to appear in a book by J. R. Schrieffer on Superconductivity.

PI Pat Diamond

Statistical analysis of fluctuations and noise-driven transport in particle-in-cell simulations of plasma turbulence, I. Holod and Z. Lin, Phys. Plasmas 14, 032306 (2007).

Electromagnetic global gyrokinetic simulation of shear Alfven wave dynamics in tokamak plasmas, Y. Nishimura, Z. Lin, and W. X. Wang, Phys. Plasmas 14, 042503 (2007).

Gyrokinetic theory and simulation of mirror instability, H. Qu, Z. Lin, and L. Chen, Phys. Plasmas 14, 042108 (2007).

Simulation of Fusion Plasmas: Current Status and Future Direction, D. A. Batchelor, M. Beck, A. Becoulet, R. V. Budny, C. S. Chang, P. H. Diamond, J. Q. Dong, G. Y. Fu, A. Fukuyama, T. S. Hahm, D. E. Keyes, Y. Kishimoto, S. Klasky, L. L. Lao, K. Li, Z. Lin, B. Ludaescher, J. Manickam, N. Nakajima, T. Ozeki, N. Podhorszki, W. M. Tang, M. A. Vouk, R. E. Waltz, S. J. Wang, H. R. Wilson, X. Q. Xu, M. Yagi, and F. Zonca, Plasma Sci. Technol. 9, 312-387 (2007).

Linear comparison of gyrokinetic codes with trapped electrons, G. Rewoldt, Z. Lin, and Y. Idomura, Comp. Phys. Commun. 177, 775-780 (2007).

Theory of Alfvin Waves and Energetic Particle Physics in Burning Plasmas, L. Chen and F. Zonca, Nuclear Fusion 47, S727-s734 (2007).

Electron Fishbones: Theory and Experimental Evidence, F. Zonca et al, Nuclear Fusion 47, 1588-1597(2007).

Nonlinear Equilibria, Stability and Generation of Zonal Structures in Toroidal Plasmas, L. Chen and F. Zonca, Nuclear Fusion 47, 886-891(2007).

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

Global gyrokinetic particle simulations with kinetic electrons, Z. Lin, Y. Nishimura, Y. Xiao, I. Holod, W. L. Zhang and L. Chen, Plasma Phys. Control. Fusion 49, December, 2007.

Nonlinear gyrokinetic theory of toroidal momentum pinch, T. S. Hahm, P. H. Diamond, O. D. Gurcan, G. Rewoldt, PHYSICS OF PLASMAS 14, 072302 (2007).

Spatial and spectral evolution of turbulence, O. D. Gurcan, P. H. Diamond, T. S. Hahm, PHYSICS OF PLASMAS 14, 055902 (2007).

Intrinsic rotation and electric field shear, O. D. Gurcan, P. H. Diamond, T. S. Hahm, R. Singh, PHYSICS OF PLASMAS 14, 042306 (2007).

Global electromagnetic simulation with kinetic electrons, Y. Nishimura, Z. Lin, and L. Chen, to appear in Comm. Comput. Phys. 2007.

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).

Resonant and Non-Resonant Particle Dynamics in Alfven Mode Excitations, F. Zonca and L. Chen, Plasma Phys. Control. Fusion 48, 537-556 (2006).

Physics of Burning Plasmas in Toroidal Magnetic Confinement Devices, F. Zonca, S. Briguglio, L. Chen, G. Fogaccia, T. Hahm, A. Milovanov, and G. Vlad, Plasma Phys. Control. Fusion 48, B15-B28 (2006).

PI Dimitre Dimitrov

D. A. Dimitrov, D. L. Bruhwiler, D. Smithe, P. Messmer, and J. R. Cary, D. Kayran and I. Ben-Zvi, "INITIAL 3D VORPAL SIMULATIONS FOR RF ELECTRON GUN MODELING", in Proceeding of 41st Advanced ICFA Beam Dynamics Workshop onEnergy Recovery Linacs, Daresbery Laboratory, UK (2007), to be published.

PI Chris Ding

Tseng, Y. H. and Ding, C.H.Q. (2007), 'Efficient parallel I/O in Community Atmosphere Model (CAM)', International Journal of High Performance Computing Applications (in press).

PI Viatcheslav Dobrovitski

"Dynamical control of electron spin coherence in a quantum dot: A theoretical study", W. Zhang, V. V. Dobrovitski, L. F. Santos, L. Viola, and B. N. Harmon, Phys. Rev. B 75, 201302 (Rapid Communication) (2007)

"Suppression of electron spin decoherence in a quantum dot" W. Zhang, V. V. Dobrovitski, B. N. Harmon, L. F. Santos, and L. Viola, J. Mod. Opt. B (in print)

"Extending quantum coherence time of an electron spin in a quantum dot via dynamical decoupling method" N. P. Konstantinidis, W. Zhang, V. V. Dobrovitski, L. F. Santos, L. Viola, and B. N. Harmon Phys. Rev. B (submitted)

PI Sebastian Doniach

Chu, V.B., Y. Bai, J. Lipfert, D. Herschlag, and S. Doniach. Evaluation of Ion Binding to DNA Duplexes Using a Modified Poisson Boltzmann Theory. Biophysical Journal 93, 2007.

Bai, Y., K. Travers, V. Chu, J. Lipfert, S. Doniach, D. Herschlag. Quantitative and comprehensive decomposition of the ion atmosphere around nucleic acids. 2007. Accepted to Journal of the American Chemical Society.

Bai, Y., Chu, V.B., Lipfert, J., Pande, V.S., Herschlag, D., Doniach, S. Experimental and computational reconstruction of the unfolded state ensemble in nucleic acid folding. 2007. Submitted to the Proceedings of the National Academy of Sciences USA.

PI William Dorland

Dissipation-Scale Turbulence in the Solar Wind, Howes, Gregory G.; Cowley, Steven C.; Dorland, William; Hammett, Gregory W.; Quataert, Eliot; Schekochihin, Alexander A., accepted for publication in AIP Conference Proceedings on "Turbulence and Nonlinear Processes in Astrophysical Plasmas" (2007).

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

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

Characterizing electron temperature gradient turbulence via numerical simulation, W. M. Nevins et al., Phys. Plasmas 13, 122306 (2006).

Turbulent transport of alpha particles in reactor plasmas , C. Estrada-Mila, J. Candy, and R. E. Waltz Phys. Plasmas 13, 112303 (2006).

Astrophysical Gyrokinetics: Basic Equations and Linear Theory, Howes, Gregory G.; Cowley, Steven C.; Dorland, William; Hammett, Gregory W.; Quataert, Eliot; Schekochihin, Alexander A., The Astrophysical Journal, Volume 651, Issue 1, pp. 590-614 (2006).

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

P. Cassak, J. F. Drake and M. A. Shay, On the Onset of fast magnetic reconnection, Astrophys. J. Lett. 644, L145, 2006.

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

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

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

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

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

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

R.G. Kleva and P.N. Guzdar, Zonal flow sawteeth and the time period between edge-localized transport bursts in tokamaks, Phys. Plasmas 14, 012303, 2007.

PI John Drake

Identification of human-induced changes in atmospheric moisture content B. D. Santera,b, C. Mearsc, F. J. Wentzc, K. E. Taylora, P. J. Glecklera, T. M. L. Wigleyd, T. P. Barnette, J. S. Boylea, W. Bru( ggemannf, N., Proceeding of the National Academies of Science, 15248~X53 82537

PI Barry Dunietz

Conductance of a cobalt(II) terpyridine complex based molecular transistor: A computational analysis Trilisa M. Perrine and Barry D. Dunietz, Journal of Physical Chemistry A: Lester Special Issue, (accepted).

Gating of single molecule transistors: Combinging field-effect and chemical control" Trilisa M. Perrine, Ron G. Smith, Christopher Marsh, and Barry D. Dunietz (submitted).

PI Michel Dupuis

A. Venkatnathan, R. Devanathan and M. Dupuis, "Atomistic Simulations of Hydrated Nafion and Temperature Effects on Hydronium Ion Mobility", J. Phys. Chem. B 111 (2007) 7234.

R. Devanathan, A. Venkatnathan and M. Dupuis, "Atomistic Simulation of Nafion Membrane: 1. Effect of Hydration on Membrane Nanostructure", J. Phys. Chem. B 111 (2007) 8069.

R. Devanathan, A. Venkatnathan and M. Dupuis, "Atomistic Simulation of Nafion Membrane. 2. Dynamics of Water Molecules and Hydronium Ions", J. Phys. Chem. B (2007) DOI: 10.1021/jp0761057.

V-A. Glezakou, M. Dupuis and C. J. Mundy, "Acid/base equilibria in clusters and their role in proton exchange membranes: computational insight", Phys. Chem. Chem. Phys. (2007) DOI: 10.1039/b709752b.

PI Charlotte Elster

Three-Body Elastic and Inelastic Scattering at Intermediate Energies, H. Liu, Ch. Elster, W. Glockle, nNucl. Phys. A790, 262c (2007), and nucl-th/0610006.

Three-Body Scattering at Intermediate Energies, H. Liu, Ch. Elster, W. Glockle, Phys. Rev. C 72, 054003 (2005).

PI Roland Faller

Qi Sun and Roland Faller: Phase Separation in Polyisoprene/Polystyrene Blends by a Systematically Coarse-Grained Model, J Chem Phys 126(14), 144908 (2007)

Jayeeta Ghosh and Roland Faller: State Point Dependence of Systematically Coarse-Grained Potentials, Molecular Simulation 33(9 & 10), 759-767 (2007)

Qi Sun, Florence R. Pon and Roland Faller: Multiscale modeling of Polystyrene in various environments, Fluid Phase Equilibria 261(1-2), 35-40 (2007)

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

PI William Fawley

C. Schroeder et al., "Design of a free-electron laser driven by the LBNL laser-plasma-accelerator", Proc. 2007 Frontiers in FEL Physics Workshop, Elba Island; submitted for publication in Nucl. Inst. Methods A.

W.M. Fawley, "Production of Ultrashort FEL XUV Pulses via a Reverse Undulator Taper", Proc. 2007 Frontiers in FEL Physics Workshop, Elba Island; submitted for publication in Nucl. Inst. Methods A.

PI Andrew Felmy

James R. Rustad and E.J Bylaska. Ab initio calculation of isotopic fractionation in aqueous boron, Journal Of The American Chemical Society 129 (8): 2222 (2007).

Eric J. Bylaska, Marat Valiev, James R. Rustad, and John H. Weare, Structures of the Hydration Shells of the Al3+ Ion. The Journal of Chemical Physics, 126, 104505(2007).

Eric J. Bylaska, Michel Dupuis, and Paul G. Tratnyek, Electron Transfer Reactions of Polychlorinated Ethylenes: Concerted Versus Stepwise Cleavages, Journal of Physical Chemistry A, submitted 2007.

Marat Valiev, Eric J. Bylaska, Michel Dupuis, and Paul G. Tratnyek, Combined ab-initio quantum mechanical and molecular mechanics Studies of the Electron Transfer Reactions of Carbon Tetrachloride, Journal of Physical Chemistry A, submitted October 2007.

Stuart Bogatko, Eric J. Bylaska, and John H. Weare, Structures and Dynamics in Fe3+ Hydration shells: relation to Al3+ ion hydration structure. Journal of Physical Chemistry, B, submitted October 2007.

Patrick Nichols, Eric J. Bylaska, and Wibe de Jong, Equatorial and Apical Solvent Shells of the UO22+ Ion, Journal of Chemical Physics, submitted October 2007.

PI Wu-chun Feng

"Semantics-based Distributed I/O for mpiBLAST.", Pavan Balaji, Wu-chun Feng, Jeremy Archuleta, Heshan Lin, Rajkumar Kettimuthu, Rajeev Thakur, Xiaosong Ma. In Proceedings of the ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming, Salt Lake City, Utah, USA, February 2008.

"ParaMEDIC: Parallel Metadata Environment for Distributed I/O and Computing.". Pavan Balaji, Wu-chun Feng, Jeremy Archuleta, and Heshan Lin. International Storage Challenge Award. In Proceedings of the ACM/IEEE Supercomputing Conference, Reno, Nevada, November 2007.

PI Graham Fleming

Evidence for wavelike energy transfer through quantum coherence in photosynthetic systems. G. S. Engel, T. R. Calhoun, E. L. Read, T. K. Ahn, T. Mancal, Y.-C. Cheng, R. E. Blankenship, G. R. Fleming, Nature, 446, 782 (2007).

Coherence dynamics in photosynthesis: protein protection of excitonic coherence. H. Lee, Y.-C. Cheng, G. R. Fleming. Science 316, 1462 (2007).

Efficient Simulation of Three-Pulse Photon-Echo Signals with Application to the Determination of Electronic Coupling in a Bacterial Photosynthetic Reaction Center, Y.-C. Cheng, H. Lee, and G. R. Fleming, J. Phys. Chem. A, 111, 9499, (2007).

Elucidation of population and coherence dynamics using cross-peaks in two-dimensional electronic spectroscopy, Y.-C. Cheng, G. S. Engel, and G. R. Fleming, Chem. Phys. (2007); doi:10.1016/j.chemphys.2007.07.049 (article in press).

Cross-peak-specific two-dimensional electronic spectroscopy, E. L. Read, G. S. Engel, T. R. Calhoun, T. Mancal, T. K. Ahn, R. E. Blankenship, G. R. Fleming, PNAS 104, 14203 (2007).

PI Michael Fox-Rabinovitz

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.

Fox-Rabinovitz, M.S., J. Cote, M. Deque, B. Dugas, J. McGregor, A. Belochitski, 2007: Stretched-Grid Model Intercomparison Project: Decadal Regional Climate Simulations with Enhanced Variable and Uniform Resolution GCMs, Meteorology and Atmospheric Physics, submitted.

Krasnopolsky, V.M., and M.S. Fox-Rabinovitz, and Belochitski, 2007: Decadal Climate Simulations Using Accurate and Fast Neural Network Emulation of Full, Long- and Short Wave, Radiation, submitted to Monthly Weathr Review.

PI Alberto Franceschetti

J.M. An, A. Franceschetti, and A. Zunger, "The Peculiar Electronic Structure of PbSe Quantum Dots", Nano Letters 6, 2728 (2006).

M. Califano, A. Franceschetti, and A. Zunger, "Lifetime and Polarization of the Radiative Decay of Excitons in CdSe Nanocrystal Quantum Dots", Phys. Rev. B 75, 115401 (2007).

A. Franceschetti and M.C. Troparevsky, "Radiative Recombination of Triexcitons in CdSe Colloidal Quantum Dots", J. Phys. Chem. C (Letters) 111, 6154 (2007).

J.M. An, A. Franceschetti, and A. Zunger, "The Excitonic Exchange Splitting and Radiative Lifetime in PbSe Quantum Dots", Nano Letters 7, 2129 (2007).

J.M. An, A. Franceschetti, and A. Zunger, "Electron and Hole Addition Energies in PbSe Quantum Dots", Phys. Rev. B 76, 045401 (2007).

Q.Z. Zhao, P.A. Graf, W.B. Jones, A. Franceschetti, J. Li, L.W. Wang, and K. Kim, "Shape Dependence of Band-Edge Exciton Fine Structure in CdSe Nanocrystals", Nano Letters, nl0713070 (2007).

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

J.M. An, A. Franceschetti, and A. Zunger, "Pauli Blocking versus Electrostatic Attenuation of Optical Transition Intensities in Charged PbSe Quantum Dots, Phys. Rev. B (Rapid Communications), in press.

PI Stuart Freedman

T. Araki et al.[KamLAND Collaboration], "Search for the Invisible Decay of Neutrons with KamLAND", Phys. Rev. Lett. 96, 101802 (2006).

S. Enomoto et al., "Neutrino geophysics with KamLAND and future prospects", Earth and Planetary Sci. Lett. 258, 147, (2007).

S. Abe et al. [KamLAND Collaboration], "Precision Measurement of Neutrino Oscillation Parameters with KamLAND", Submitted to Physical Review Letters, arXiv:0801.4589

PI Arthur Freeman

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

S. H. Rhim, R. Saniz, J. Yu, L.-H. Ye, A. J. Freeman, Interface electronic structure, two-dimensional metallicity, and possible superconductivity in CuCl/Si superlattices, Phys. Rev. B, in press.

PI Alex Friedman

R. H. Cohen, A. Friedman, D.P. Grote and J.-L. Vay, "Large-Timestep Mover for Particle Simulations of Arbitrarily Magnetized Species," Nuclear Instruments and Methods in Physics Research A 577, 52 (2007).

J. E. Coleman, A. Friedman, W. L. Waldron, F. M. Bieniosek, R. J. Briggs, D. P. Grote, E. Henestroza, P. K. Roy, P. A. Seidl, and S. S. Yu, "Beam Experiments on the Pulse Line Accelerator," Nuclear Instruments and Methods in Physics Research A, 577, 197 (2007).

A. Friedman, "Overview of Theory and Simulation in the Heavy Ion Fusion Science Virtual National Laboratory," Nuclear Instruments and Methods in Physics Research A, 577, 37 (2007).

D. P. Grote, J. W. Kwan, and G. A. Westenskow, "Design and Modeling of the Multi-Beamlet Injector," Nuclear Instruments and Methods in Physics Research A, 577, 58 (2007).

I. Haber, D. Feldman, R. Fiorito, A. Friedman, D. P. Grote, R. A. Kishek, B. Quinn, M. Reiser, J. Rodgers, P. G. Ohea, D. Stratakis, K. Tiana, J.-L. Vay, and M. Walter, "Measurement and Simulation of the Time- Dependent Behavior of the UMER Source," Nuclear Instruments and Methods in Physics Research A, 561, 157 (2006).

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, and S. H. Chilton, "Space-Charge Transport Limits of Ion Beams in Periodic Quadrupole Focusing Channels," Nuclear Instruments and Methods in Physics Research A 577, 203 (2007).

W. M. Sharp, D. P. Grote, R. H. Cohen, A. Friedman, J.-L. Vay, P. A. Seidl, P. K. Roy, J. E. Coleman, J. Armijo and I. Haber, "Simulating electron clouds in high-current ion accelerators with solenoid focusing," Nuclear Instruments and Methods in Physics Research A 577, 146 (2007).

J. L. Vay, M. A. Furman, P. A. Seidl, R. H. Cohen, A. Friedman, D. P. Grote, M. Kireef Covo, A. W. Molvik, P. H. Stoltz, S. Veitzer, and J. P. Verboncoeur, "Self-consistent simulations of heavy-ion beams interacting with electron-clouds," Nuclear Instruments and Methods in Physics Research A 577, 69 (2007).

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

PI Inez Fung

Lee JE, Fung I, DePaolo DJ, Henning, CC. Analysis of the global distribution of water isotopes using the NCAR atmospheric general circulation model. JOURNAL OF GEOPHYSICAL RESEARCH-ATMOSPHERES. Vol 112, issue D16, article D16306, 2007.

Fung, I. Challenges of climate modeling. DISCRETE AND CONTINUOUS DYNAMICAL SYSTEMS-SERIES B. Vol 7, issue 3, pp 543-551. 2007.

PI Miguel Furman

M. A. Furman, "A preliminary assessment of the electron cloud effect for the FNAL main injector upgrade," published by invitation in the New Journal of Physics Focus Issue: Accelerator and Beam Physics, New J. Phys. 8 (2006) 279

PI Giulia Galli-Gygi

Electronic properties of MoS2 nanoparticles, T.Li and G.Galli, J.Phys.Chem.C 2007 (in press)

Single functional group interactions with individual carbon nanotubes, Raymond W. Friddle1,Melburne C. LeMieux1,Giancarlo Cicero, Alexander B. Artyukhin, Vladimir V. Tsukruk, Jeffrey C. Grossman, Giulia Galli, and Aleksandr Noy, Nature Nanotechnology 2007 (in press).

Structural characterization of aldehyde-terminated self-assembled monolayers", A.Riposan, Y. Li, Y.Tan, G. Galli and G. Liu J.Phys.Chem. A 2007 (accepted). A First-Principles Study of Aromatic Isocyanide Self-Assembled Monolayers on Au(111) Surface, Yan Li and Deyu Lu, Giulia Galli, Sally A. Swanson and J. Campbell Scott (submitted for publication).

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. Y. Du, J. S. Francisco, G. K. Schenter, and B. C. Garrett, "Ab initio and Analytical Intermolecular Potential for ClO-H2O", Journal of Chemical Physics 126, 114304 (2007)

S. Kathmann, G. Schenter and B. Garrett, "The critical role of anharmonicity in aqueous ionic clusters relevant to nucleation," J. Phys. Chem. C 111, 4977 (2007)

M. Valiev, BC Garrett, MK Tsai, K Kowalski, SM Kathmann, GK Schenter, and M Dupuis. "Hybrid Approach for Free Energy Calculations with High-Level Methods: Application to the S(N)2 Reaction of CHCl3 and OH- in Water." Journal of Chemical Physics 127, 51102 (2007)

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 117, 73 (2007)

T. Pankewitz, A. Lagutschenkov, G. Niedner-Schatteburg, S. S. Xantheas, Y.-T. Lee, "The Infrared Spectrum of NH4+(H2O): Evidence for mode specific fragmentation" Journal of Chemical Physics 126, 074307 (2007)

M. N. Slipchenko, B. G. Sartakov and A. F. Vilesov, S. S. Xantheas, "A study of NH stretching vibrations in small ammonia clusters by infrared spectroscopy in He droplets and ab-initio calculations" Roger E. Miller memorial issue (invited), Journal of Physical Chemistry A 111, 7460 (2007)

L. Rubio-Lago, D. Zaouris, Y. Sakellariou, D. Sofikits and T. N. Kitsopoulos, F. Wang and X. Yang, B. Cronin and M. N. R. Ashfold, S. S. Xantheas, "Photofragment slice imaging studies of pyrrole and the Xepyrrole cluster" Journal of Chemical Physics 127, 064306 (2007)

T. A. Blake, E. D. Glendening, R. L. Sams, S. W. Sharpe and S. S. Xantheas, "High Resolution Infrared Spectroscopy in the 1200 to 1300 cm-1 Region and Accurate Theoretical Estimates for the Structure and Ring Puckering Barrier of Perfluorocyclobutane" Thom H. Dunning Jr. Festschrift (invited), Journal Physical Chemistry A (in press, web release date: 06-Jul-2007, DOI:10.1021/jp072521f)

M. V. Kirov, G. S. Fanourgakis and S. S. Xantheas, "A Strong-Weak-Effective-Bond?(SWEB) discrete model for the combinatorial optimization of polyhedral water clusters: Validation from electronic structure calculations and discovery of a new lowest energy isomer of the pentagonal dodecahedron (H2O)20 cluster" Journal of Chemical Physics (submitted)

S. S. Xantheas, "The elusive structure of H3O+(H2O)20" Journal of Chemical Physics (submitted)

G. S. Fanourgakis and S. S. Xantheas, "Development of Transferable Interaction Potentials for Water: IV. Quantitative description of vibrational spectra of clusters and liquid water" Journal of Chemical Physics (submitted)

PI Jose Gascon

Computational studies of the O2-evolving complex of photosystem II and biomimetic oxomanganese complexes Coordination Chemistry Reviews, In Press, Corrected Proof, Available online 16 September 2007

PI Silvina Gatica

S. M. Gatica, H. I. Li, R. A. Trasca, M. W. Cole and R. D. Diehl, Xe Adsorption on a C60 Monolayer on Ag(111), submitted to Phys. Rev. B. (2007)

PI Cameron Geddes

D.A. Dimitrov, R.E. Giancone, D.L. Bruhwiler, R. Busby, J.R. Cary, C.G.R. Geddes, E. Esarey, W.P. Leemans, "Coupling of laser energy into plasma channels", Phys. Plasmas 14, 043105 (2007).

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

E. Esarey, C.B. Schroeder, E. Cormier-Michel, B.A. Shadwick, C.G.R. Geddes, and W.P. Leemans, "Thermal effects in plasma-based accelerators", Physics of Plasmas 14, 056707 (2007).

K. Nakamura, B. Nagler, Cs. Toth, C. G. R. Geddes, C. B. Schroeder, E. Esarey, W. P. Leemans, A.J. Gonsalves, S.M. Hooker, "GeV electron beams from a centimeter-scale channel guided laser wakefield accelerator", Phys. Plasmas 14, 056708.

C.G.R. Geddes, D. Bruhwiler, J.R. Cary, E. Cormier-Michel, E.Esarey, C.B. Schroeder, W.A. Isaacs, N. Stinus, P. Messmer, A. Hakim, K. Nakamura, A.J. Gonsalves, D. Panasenko, G.R. Plateau, Cs. Toth, B.Nagler, J. van Tilborg, T. Cowan, S. M. Hooker and W.P. Leemans, Laser wakefield simulations towards development of compact particle accelerators, Journal of Physics: Conference Series, 78, 012021 (2007).

J R Cary, P Spentzouris, J Amundson, L McInnes, M Borland, B Mustapha, B Norris, P Ostroumov, Y Wang, W Fischer, A Fedotov, I Ben-Zvi, R Ryne, E Esarey, C Geddes, J Qiang, E Ng, S Li, C Ng, R Lee, L Merminga, H Wang, D L Bruhwiler, D Dechow, P Mullowney, P Messmer, C Nieter, S Ovtchinnikov, K Paul, P Stoltz, D Wade-Stein, W B Mori, V Decyk, C K Huang, W Lu, M Tzoufras, F Tsung, M Zhou, G R Werner, T Antonsen, T Katsouleas, "COMPASS, the COMmunity Petascale project for Accelerator Science and Simulation," Journal of Physics: Conference Series, 78, 012009 (2007).

F.S. Tsung, T. Antonsen, D.L. Bruhwiler, J.R. Cary, V.K. Decyk, E. Esarey, C.G.R. Geddes, C. Huang, A. Hakim, T. Katsouleas, W. Lu, P. Messmer, W.B. Mori, M. Tzoufras and J. Vieira, "Three-Dimensional Particle-in-Cell Simulations of Laser Wakefield Experiments," J. Physics: Conf. Series. 78, 012077 (2007).

D.L. Bruhwiler, T. Antonsen, J.R. Cary, J. Cooley, V.K. Decyk, E. Esarey, C.G.R. Geddes, C. Huang, A. Hakim, T. Katsouleas, P. Messmer, W.B. Mori, F.S. Tsung, J. Vieira and M. Zhou, "Towards the petascale in electromagnetic modeling of plasma-based accelerators for high-energy physics," Journal of Physics: Conference Series 46, 215 (2006).

C.G.R. Geddes, K. Nakamura, G.R. Plateau, Cs. Toth, E. Cormier-Michel, E. Esarey, C.B. Schroeder, J.R. Cary, and W.P. Leemans, "Stable ultrafast electron bunches with low absolute momentum spread from plasma down ramp injection," submitted to PRL.

PI Ahmed Ghoniem

Wee, Dh., and Ghoniem, A.F., "Modified interpolation kernels and treating diffusion and remeshing in vortex methods," J. Comput. Phys., 213, 2006, pp. 239-263.

Marzouk, Y.M. and Ghoniem, A.F., "Vorticity structure and evolution in a transverse jet," J. Fluid Mech., 575:267-305, 2007.

Schlegel, F., Wee, Dh., and Ghoniem, A.F., "A fast 3d particle method for simulations of buoyant flows", J. Comput Phys, under review.

PI James Glimm

E. George, J. Glimm, X. L. Li, Y. H. Li and X. F. Liu,The Influence of Scale-Breaking Phenomena on Turbulent Mixing Rates, Phys. Rev. E, 73, 016304-1-016304-5, 2006.

J. Glimm and X. L. Li, Recent Progress in Turbulent Mixing, Proceedings of the 10th International Workshop on the Physics of Compressible Turbulent Mixing, 17-21 July, Paris, France, Edited by M. Legrand and M. Vandenboomgarde, 2006.

X. F. Liu, E. George, W. Bo and J. Glimm, Turbulent Mixing with Physical Mass Diffusion, Phys. Rev. E, 73, 056301-1-056301-8, 2006.

J.-J. Liu, J. Glimm and X.-L. Li, A Conservative Front Tracking Method, Hyperbolic Problems: Theory, Numerics, and Applications, Edited by F. Asakura, H. Aiso, S. Kawashima, Matsumura A, S. Nishibata and K. Nishihara, Yokohama Publishers, Osaka, Japan, 57-62, 2006.

Jinjie Liu, Hyun-Kyun Lim, James Glimm and Xiaolin Li, A Conservative Front Tracking Method in N-Dimensions, J. of Sci. Comp, in press, 2006.

Z. L. Xu, M. Kim, W. Oh, J. Glimm, R. Samulyak, X. L. Li and C. Tzanos, Discrete Bubble Modeling of Unsteady Cavitating Flow, International Journal for Multiscale Computational Engineering, 4, 377-389, 2006.

J. Glimm, B. Fix, X.-L. Li, J.-J. Liu, X.-F. Liu, T.-S. Liu, R. Samulyak and Z.-L. Xu, Front Tracking under TSTT, Proceedings of the IGPP-CalSpace Conference, Astronomical Society of the Pacific, 15,359, 2007.

H. Lee, H. Jin, Y. Yu and J. Glimm, On the Validation of Turbulent Mixing Simulations of Rayleigh-Taylor Mixing, submitted to Phys of Fluids, 2007.

H. Lim, Y. Yu, H. Jin, D. Kim, H. Lee, J. Glimm, X.-L. Li and D. H. Sharp,Multi Scale Models for Fluid Mixing, submitted to Special Issue of CMAME, 2007.

X. F. Liu, Y. H. Li, J. Glimm and X. L. Li, A Front Tracking Algorithm For Limited Mass Diffusion, accepted by J. of Comp. Phys., 2007.

T. Lu, R. Samulyak and J. Glimm, Direct Numerical Simulation of Bubbly Flows and its Applications, Phys. Fluid Eng., 129, 595-604, 2007.

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, Yan Yu, Recent Progress in the Stochastic Analysis of Turbulent Mixing, Contemporary Mathematics, 429, 33-44, 2007.

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 Yadin Goldschmidt

1. "Dynamic and Thermodynamic Properties of Porous Vortex Matter in Bi2Sr2CaCu2O8 in an Oblique Magnetic Field", by N. Avraham, Y.Y. Goldschmidt, J. T. Liu, Y. Myasoedov, M. Rappaport, E. Zeldov, C. J. van der Beek,M. Konczykowski and T. Tamegai, Phys. Rev. Lett. 99, 087001 (2007).

2. "Langevin Dynamics of the vortex matter two-stage melting transition in Bi2Sr2CaCu2O8 in the presence of straight and of tilted columnar defects" byYadin Y. Goldschmidt and Jin-Tao Liu, Phys. Rev. B, November 1, 2007, accepted, in print.

PI Giorgio Gratta

Naoko Kurahashi and Giorgio Gratta, "High-Requency Ambient Noise as Background to Deep Ocean Transient Signal Detection", submitted to The Journal of Acoustical Society of America, arXiv:0712.1833v1 [physics.ao-ph

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. 125, 164312 (2006) (8 pages).

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) 103, 17143-17148 (2006).

Nanostructured plasmonic sensors M. E. Stewart, C. R. Anderton, L. B. Thompson, J. Maria, S. K. Gray, J. Rogers, and R. G. Nuzzo, Chem. Rev., in press (2007).

Tailoring the sensing capabilities of nanohole arrays in gold films with Wood's anomaly-surface plasmon polaritons J. M. McMahon, J. Henzie, T. Odom, G. C. Schatz, and S. K. Gray, Optics Express, submitted (2007).

PI Chris Greene

"Collisional stability of fermionic Feshbach molecules." J. J. Zirbel, K.-K. Ni, S. Ospelkaus, J. P. D'Incao, C. E. Wieman, J. Ye, D. S. Jin (submitted to PRL)

"Recombination of H3+ Ions in the Afterglow of a He-Ar-H2 Plasma." J. Glosik, I. Korolov, R. Plasil, O. Novotny, T. Kotrik, P. Hlavenka, J. Varju, C.H. Greene, V. Kokoouline, and I.A. Mikhailov. Submitted to Phys. Rev. Lett. (2007).

"Dissociative recombination of H3+ in the ground and excited states." S.Fonseca dos Santos, V.Kokoouline, and C.H.Greene. J. Chem. Phys. 127, 124309 (2007).

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

"Method for finding of three-body resonances using hyperspherical coordinates and slow variable representation." J. Blandon, V. Kokoouline, and F. Masnou-Seeuws. Phys. Rev. A 75, 042508 (2007)

"FERM3D: A finite element R-matrix general electron-molecule scattering code." S. Tonzani, Computer Physics Communications 176, 146 (2007)

"Diffraction in low-energy electron scattering from DNA: bridging gas phase and solid state theory" L. Caron, S. Tonzani, C. H. Greene and L. Sanche. J. Chem. Phys. (submitted)

PI Jeffrey Grossman

Yosuke Kanai and Jefferey C. Grossman "Insights on Interfacial Charge Transfer Across P3HT/Fullerene Photovoltaic Heterojunction from Ab Initio Calculations" Nano Letters, 7, 1967 (2007).

Joo-Hyoung Lee, John Reed, Giulia Galli, and Jeffrey C. Grossman "Lattice thermal conductivity of porous Si:molecular dynamics study" to appear in Applied Physics Letters.

Zhigang Wu, J. B. Neaton, and Jeffrey C. Grossman "Quantum confinement and electronic properties of tapered silicon nanowires" under review at Physical Review Letters.

Yosuke Kanai and Jeffrey C. Grossman "Interfacial Properties of the P3HT/Carbon-Nanotube Photovoltaic Heterojunction: A Density Functional Theory Study" submitted to Applied Physics Letters.

PI Hua Guo

S. Y. Lin and H. Guo, Phys. Rev. A, 74, 022703 (2006). Quantum state-to-state cross sections for atom-diatom reactions, A Chebyshev real wave packet approach.

S. Y. Lin, D. Xie, and H. Guo, J. Chem. Phys., 125, 091103 (2006). Revelation of non-statistical behavior in HO2 vibration by a new ab initio potential energy surface.

S. Y. Lin, H. Guo, P. Honvault, D. Xie, J. Phys. Chem. B, 110, 23641 (2006), Quantum dynamics of the H + O2 !w O + OH reaction on an accurate ab initio potential energy surface.

D. Xie, C. Xu, T.-S. Ho, H. Rabitz, G. Lendvay, S. Y. Lin, and H. Guo, J. Chem. Phys., 126, 074315 (2007), Global analytical potential energy surfaces for HO2( ) based on high level ab initio calculations.

A. Van Wyngarden, K. Mar, K. Boering, J. J. Lin, Y. T. Lee, S. Y. Lin, H. Guo, G. Lendvay, J. Am. Chem. Soc., 129, 2866 (2007). Non-statistical behavior of reactive scattering in the 18O + 32O2 isotope exchange reaction.

S. Y. Lin, L. Banares, and H. Guo, J. Phys. Chem. A, 111, 2376 (2007), Differential and integral cross sections of the N(2D) + H2 !w NH + H reaction from exact quantum and quasi-classical trajectory studies.

P. Honvault, S. Y. Lin, D. Xie, and H. Guo, J. Phys. Chem. A, 111, 5349 (2007), Differential and integral cross sections for the H + O2 !w HO + O combustion reaction.

C. Xu, D. Xie, P. Honvault, S. Y. Lin, and H. Guo, J. Chem. Phys., 127, 024304 (2007), Rate constant for OH(2@) + O(3P) + O2( ) reaction on an improved ab initio potential energy surface and implications for the interstellar oxygen problem.

PI William Gutowski

Abiodun BJ, Gutowski WJ, and Prusa JM, 2007: Implementation of a non-hydrostatic, adaptive grid dynamics core in CAM3. Part II: dynamical influences on ITCZ behavior and tropic