# 2007 Publications Resulting from the Use of NERSC Resources

On their Allocation Year 2008 ERCAP Request Forms Principal Investigators reported 1,464 refereed publications (published or submitted) for the preceding 12 months, based on using, at least in part, NERSC resources.

## A

**PI Mowfak Al-Jassim**

Y. Yan, 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).

## B

**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).

## C

**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.

## D

**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.

## E

**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).

## F

**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

## G

**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([email protected]) + 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 tropical precipitation. Climate Dynamics, submitted.

Abiodun BJ, Prusa JM, and Gutowski WJ, 2007: Implementation of a non-hydrostatic, adaptive grid dynamics core in CAM3. Climate Dynamics, submitted.

Prusa JM, Smolarkiewicz PK and Wyszogrodzki AA, 2007: EULAG, a computational model for multiscale flows. Computers and Fluids, submitted.

## H

**PI Stephan Haas**

Phys. Rev. Lett. 98, 257201 (2007)

arXiv:0707.205 (submitted to Phys. Rev. Lett.)

**PI Bruce Harmon**

Add-drop filters using three-dimensional photonic crystals, P. Kohli, R. Biswas, G. Tuttle and K.-M. Ho, SPIE online newsroom DOI: 10.1117/2.1200707.0594 (2007).

Photonic Band gap crystals, R. Biswas, M. Sigalas, C. M. Soukoulis, K.-M. Ho, G. Tuttle, Wiley Encyclopedia of Electrical and Electronics Engineering (John Wiley & Sons) (2007).

Add-drop filters in 3-dimensional layer-by-layer photonic crystals using waveguides and resonant cavities, P Kohli, C. Christensen, J. Muehlmeier, R. Biswas, G. Tuttle, and K.-M. Ho, Appl. Phys. Lett. 89, 231103 (2006).

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

Simulations of Sub-wavelength Metallo-dielectric Photonic Crystals for Gas Sensing, R. Biswas, I. Puscasu, M. Pralle, M. McNeal, J. Daly, A. Greenwald, E. Johnson, S. Neginhal, C.G. Ding, MRS Symp. Proceedings Symposium 952E, F 2.2 (2006)

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

Interplay between indirect interaction and charge density wave in Pb adsorbed In(4x1)-Si(111)", M. Hupalo, T. L. Chan, C. Z. Wang, K. M. Ho, and M. C. Tringides, Phys. Rev. B 76, 045415 (2007).

"The structure of ultra-thin H-passivated [112] silicon nanowires", N. Lu, C. V. Ciobanu, T. L. Chan, F.-C. Chuang, C. Z. Wang, and K. M. Ho, J. Phys. Chem. C 111, 7933 (2007).

"Formation of local haeckelite structures induced by vacancy defects in a graphene layer", Gun-Do Lee, C. Z. Wang, Euijoon Yoon, Nong-Moon Hwang, and K. M. Ho, Phys. Rev. B 74, 245411(2006).

"Structures of Si7H2m (m=1-7) clusters by global optimization", Mingsheng Tang, C.Z. Wang, W. C. Lu, and K.M. Ho, Phys. Rev. B 74, 195413, (2006).

"Strongly-Driven Coarsening of Height-Selected Pb Islands on Si(111)", Maozhi Li, J. Evans, C. Z. Wang, M. Hupalo, M. C. Tringides, T. L. Chan, K. M. Ho, Surf. Sci. Lett. In press, Available online 20 September 2007.

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

"Cluster-in-jellium model and icosahedral ordering tendencies in liquid Al alloys", Y. X. Yao, C. Z. Wang and K. M. Ho, Phys. Rev. B, submitted

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

**PI Charles Harris**

"Photo-induced beta-Hydrogen Elimination and Radical Formation with CpW(CO)3(CH2CH3): Ultrafast IR and DFT Studies" E.A. Glascoe, M.F. Kling, J.E. Shanoski, C.K. Payne, B.V. Mork, T.D. Tilley and C.B. Harris, Organometallics, 26, 1424-1432 (2007).

"The influence of the metal spin state in iron assisted alkene isomerization studied with ultrafast infrared spectroscopy" E.A. Glascoe, K.R. Sawyer, J.E. Shanoski and C.B. Harris, J. Phys. Chem. C, 111, 8789-8795 (2007).

Glascoe, E.A. "Internal Rearrangement Dynamics of Organometallic Complexes Investigated with Ultrafast Infrared Spectroscopy" Ph.D. Thesis, University of California, Berkeley, CA, December 2006.

"The mechanism for iron-catalyzed alkene isomerization. Part I. Density functional theory modeling of spin-crossover processes" K.R. Sawyer, E.A. Glascoe, J.F. Cahoon, J.P. Schlegel and C.B. Harris, J. Am. Chem. Soc., submitted.

"The mechanism for iron-catalyzed alkene isomerization. Part II. Time-resolved infrared studies of Fe(CO)4(eta2-1-hexene) in neat alkene solution" K.R. Sawyer, E.A. Glascoe, J.F. Cahoon, J.P. Schlegel, H. Frei and C.B. Harris, J. Am. Chem. Soc., submitted.

**PI Martin Head-Gordon**

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

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

Miller, T.F. and C. Predescu, "Sampling diffusive transition paths," J. Chem. Phys. 126, 144102 (2007)

Chandler D, Garrahan JP, Jack RL, et al., "Lengthscale dependence of dynamic four-point susceptibilities in glass formers," PHYSICAL REVIEW E 74 (5): Art. No. 051501 Part 1 NOV 2006

Jung, Y. and M. Head-Gordon, A fast correlated electronic structure method for computing interaction energies of large van der Waals complexes applied to the fullerene-porphyrin dimer, Phys. Chem. Chem. Phys. 8, 2831-2840 (2006).

Jung, Y., Y. Shao, and M. Head-Gordon, Fast evaluation of scaled opposite spin second order Mxller- Plesset correlation energies using auxiliary basis expansions and exploiting sparsity, J. Comput. Chem. 28, 1953-1964 (2007).

Rhee, Y.M. and M. Head-Gordon, Scaled second order perturbation corrections to configuration interaction singles: efficient and reliable excitation energy methods, J. Phys. Chem. A 111, 5314-5326 (2007).

**PI Teresa Head-Gordon**

M. S. Lin, N. L. Fawzi, and T. Head-Gordon (2007). Hydrophobic potential of mean force as a solvent function for protein structure prediction. Structure 15, 727-740.

M. S. Lin and T. Head-Gordon (2007). Improved energy selection of native loops from loop decoys. Submitted to JCTC.

E.-H. Yap, N. Lux Fawzi & T. Head-Gordon (2007). A coarse-grained alpha-carbon protein model with anisotropic hydrogen-bonding. Proteins, Struct. Func.. Bioinformatics in press

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

T. Head-Gordon and S. Rick (2007). Consequences of chain networks on thermodynamic, dielectric and structural properties for liquid water. Phys. Chem. Chem. Phys. 8, 83-91.

R. M. Lynden-Bell and T. Head-Gordon (2007). Solvation in modified water models: toward understanding hydrophobic solvation. Mol. Phys. 104, 3593-3605.

R. M. Lynden-Bell and T. Head-Gordon (2007). Hydrophobic hydration of Gay Berne particles in modified water models. Submitted.

R. K. Murakra and T. Head-Gordon (2007). Dielectric relaxation of aqueous solutions of hydrophobic and hydrophilic peptides. JPC-B, in press.

R. K. Murakra and T. Head-Gordon (2007). Single particle and collective hydration dynamics of hydrophobic and hydrophilic peptides. J. Chem. Phys. 126, 215101-215109.

M. E. Johnson, T. Head-Gordon, A. A. Louis (2007). Representability problems for coarse-grained water models. J. Chem. Phys. 126, 144509-144519.

N. Lux Fawzi, Y. Okabe, E.-H. Yap & T. Head-Gordon (2007). Fibril stability and elongation studies of the Alzheimer Aβ1-40 peptide. J. Mol. Biol. 365, 535-550

N. Lux Fawzi, K. Kohlstedt, Y. Okabe & T. Head-Gordon (2007). Protofibril Assemblies of the Arctic, Dutch and Flemish Mutants of the Alzheimer Aβ1-40 peptide. Biophys. J. in press

N. Lux Fawzi, A. Phillips, J. Z. Ruscio, M. Doucleff, D. E. Wemmer & T. Head-Gordon (2007). Structure and dynamics of the Alzheimer Aβ21-30 peptide from the interplay of NMR experiments and simulation. Submitted to JACS

**PI Brian Hingerty**

Watt DL, Utzat CD, Hilario P, Basu AK. Mutagenicity of the 1-Nitropyrene-DNA Adduct N-(Deoxyguanosin-8-yl)-1-aminopyrene in Mammalian Cells. Chem Res Toxicol. 2007 (in press)

Xu P, Oum L, Beese LS, Geacintov NE, Broyde S. Following an environmental carcinogen N2-dG adduct through replication: elucidating blockage and bypass in a high-fidelity DNA polymerase. Nucleic Acids Res. 2007;35(13):4275-88.

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

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

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

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

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

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

Zhang L, Rechkoblit O, Wang L, Patel DJ, Shapiro R, Broyde S. Mutagenic nucleotide incorporation and hindered translocation by a food carcinogen C8-dG adduct in Sulfolobus solfataricus P2 DNA polymerase IV (Dpo4): modeling and dynamics studies. Nucleic Acids Res. 2006 Jul 4;34(11):3326-37.

Jia L, Shafirovich V, Shapiro R, Geacintov NE, Broyde S. Related Articles, Links Flexible 5-guanidino-4-nitroimidazole DNA lesions: structures and thermodynamics. Biochemistry. 2006 May 30;45(21):6644-55.

Rechkoblit O, Malinina L, Cheng Y, Kuryavyi V, Broyde S, Geacintov NE, Patel DJ. Stepwise translocation of Dpo4 polymerase during error-free bypass of an oxoG lesion. PLoS Biol. 2006 Jan;4(1):e11.

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

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

**PI Kai-Ming Ho**

"Initial Bilayer Growth of Ag Films on NiAl(110)" B. Unal, F. Qin, Y. Han. D.-J. Liu, D. Jing, A.R. Layson, C.J. Jenks, J.W. Evans, P.A. Thiel, Phys. Rev. B in press (2007).

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

"Strongly-Driven Coarsening of Height-Selected Pb Islands on Si(111)", Maozhi Li, J. Evans, C. Z. Wang, M. Hupalo, M. C. Tringides, T. L. Chan, K. M. Ho, Surf. Sci. Lett. In press, Available online 20 September 2007.

"Interplay between indirect interaction and charge density wave in Pb adsorbed In(4x1)-Si(111)", M. Hupalo, T. L. Chan, C. Z. Wang, K. M. Ho, and M. C. Tringides, Phys. Rev. B 76, 045415 (2007).

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

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

"Evolution of a symmetry gap and synergetic quantum well states in ultrathin Ag films on Au(111) substrates", L. Huang, G. Gong, E. Gergert, F. Forster , A. Bendounan, F. Reinert, Z. Y. Zhang, Europhys. Lett. 78 (5): Art. No. 57003 (2007)

"Tuning the quantum stability and superconductivity of ultrathin metal alloys", M. M Ozer, Y. Jia, Z. Y. Zhang , J. R. mpson, H. H. Weitering, SCIENCE 316 (5831): 1594-1597 JUN 15 2007

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

"Interplay between elastic interactions and kinetic processes in stepped Si (001) homoepitaxy" W. Hong, Z. Y. Zhang, Z. G. Suo, Phys. Rev. B 74 (23): 235318 (2006)

"Initial interactions between water molecules and Ti-adsorbed carbon nanotubes" Yang Lei, Zheng Xiao Guo, Wenguang Zhu, Zhenyu Zhang, and Sheng Meng Appl. Phys. Lett. (in press)

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

## I

**PI Hong Im**

Wang, Y. and Rutland, C. J. (2007) Direct numerical simulation of ignition in turbulent n-heptane liquid fuel spray ets, Combust. Flame, accepted.

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

Cook, D. J., Pitsch, H., Chen, J. H. and Hawkes, E. R. (2007), Flamelet-based modeling of H2/Air Auto-ignition with hermal inhomogeneities, Proc. Combust. Inst. 31:2903-2911.

Hawkes, E. R., Sankaran, R., Sutherland, J. and Chen, J. H. (2007) Scalar mixing in direct numerical simulations of emporally-evolving plane jet flames with detailed CO/H2 kinetics, Proc. Combust. Inst. 31:1633-1640.

Sankaran, R., Hawkes, E. R., Chen, J. H., Lu, T. and Law, C. K. (2007) Structure of a spatially-developing lean ne-air turbulent bunsen flame, Proc. Combust. Inst. 31:1291-1298.

Yoo, C. S. and Im, H. G. (2007) Transient soot dynamics in turbulent nonpremixed ethylene-air counterflow flames, c. Combust. Inst. 31:701-708.

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

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

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

**PI Valerie Izzo**

D.G. Whyte, R. Granetz, M. Bahktiari, V. Izzo, T. Jernigan, J. Terry, M. Reinke, B. Lipschultz, J. Nucl. Mater. 363-365, (2007).

R.S. Granetz, D.G. Whyte, V.A. Izzo, et al., Nucl. Fusion 46 (2006) 1001.

## J

**PI Peter Jacobs**

S-L Blyth, et al., A cone jet-finding algorithm for heavy-ion collisions at LHC energies, J. Phys. G 34:271, 2007

**PI Stephen Jardin**

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

Breslau, J, Jardin, SC, Park, W.,"3D modeling of the sawtooth instability in a small tokamak", Phys Plasmas 14 Art. NO. 056105 MAY 2007

Ferraro N and Jardin S, "Finite element implementation of Braginskii's gyroviscous stress with application to the gravitational instability", Physics of Plasmas, 13: 092101 (2006)

N. M. Ferraro, "Finite Larmor Radius Effects on the Magnetorotational Instability", to appear in The Astrophysical Journal, 662, p 512-516 (2007)

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

Jardin, S.C., Breslau, J. A., Ferraro, N, "A High-Order Implicit Finite Element Method for Integrating the Extended-Magneto-Hydrodynamic Equations in Two Dimensions", J. Comp. Phys 226, pages 2146-2174 Oct (2007)

L-P. Ku, P. R. Garabedian, J. Lyon, A. Grossman, T. K. Mau, A. Turnbull, M. Zarnstorff, and the ARIES-CS Team, "Physics Design for ARIES-CS," to appear in Fusion Science and Technology.

J. F. Lyon, L-P. Ku, L. El-Guebaly, L. Bromberg, and the ARIES-CS Team, "Systems Studies and Optimization of the ARIES-CS Power Plant," to appear in Fusion Science and Technology.

T.K. Mau, T. Kaiser, A. A. Grossman, A. R. Raffray, X. R. Wang, J. F. Lyon, R. Maingi, L. P. Ku, M. C. Zarnstorff and the ARIES-CS Team, "Divertor Configuration and Heat Load Studies for the ARIES-CS Reactor," to appear in Fusion Science and Technology.

J. F. Lyon, L-P. Ku, L. El-Guebaly, et. al., "Parametric Studies of the ARIES-CS Power Plant," 22nd IEEE/NPSS Symposium on Fusion Engineering, Albuquerque, NM, June 17-21 (2007).

T. K. Mau, T. B. Kasier, J. F. Lyon, R. Mangi, A. R. Raffray,X. Wang, L-P. Ku, M. Zarnstorff, "Divertor Heat Loads from Thermal and Alpha Particles in a Compact Stellerator Reactor," 22nd IEEE/NPSS Symposium on Fusion Engineering, Albuquerque, NM, June 17-21 (2007).

J. F. Lyon, L-P. Ku, L. El-Guebaly, et. al., "Analysis of the ARIES-CS Compact Stellarator Power Plant," 16th International Workshop on Stellarators, Toki, Japan, Oct 14-19 (2007).

R. Samtaney, B. van Straalen, P. Colella and S. C. Jardin, Adaptive mesh simulations of multi-physics processes during pellet injection in tokamaks J. Phys.: Conf. Ser. 78 012062, 2007

Daniel R. Reynolds, Ravi Samtaney and Carol S. Woodward, A Fully Implicit Numerical Method for Single-Fluid Resistive Magnetohydrodynamics,Journal of Computational Physics 219 (2006) 144:162

**PI Julius Jellinek**

STRUCTURAL, ELECTRONIC, AND OPTICAL PROPERTIES OF NOBLE METAL CLUSTERS FROM FIRST PRINCIPLES S. Ogut, J. C. Idrobo, J. Jellinek, and J. Wang J. Clust. Sci. 17, 609-626 (2006).

SITE-SPECIFIC POLARIZABILITIES: PROBING THE ATOMIC RESPONSE OF SILICON CLUSTERS TO AN EXTERNAL ELECTRIC FIELD K. Jackson, M. Yang, and J. Jellinek In Lecture Series in Computer and Computational Sciences, Vol. 6, G. Maroulis and T. Simos, Eds., Brill, Leiden, 2006, pp. 165-176

GOLD-COATED TRANSITION METAL ANION [[email protected]_20]- WITH ULTRAHIGH MAGNETIC MOMENT J. Wang, J. Bai, J. Jellinek, and X. C. Zeng J. Am. Chem. Soc. 129, 4110-4111 (2007) (Communication)

FIRST-PRINCIPLES ISOMER-SPECIFIC ABSORPTION SPECTRA OF Ag_11 J. C. Idrobo, S. Ogut, K. Nemeth, J. Jellinek, and R. Ferrando Phys. Rev. B 75, 233411(1-4) (2007)

COMPUTATIONAL ELECTRON SPECTROSCOPY OF GAS PHASE METAL CLUSTERS J. Jellinek and P. H. Acioli In The Chemical Physics of Solid Surfaces, Vol. 12, Atomic Clusters: From Gas Phase to Deposited, D. P. Woodruff, Ed., Elsevier, Amsterdam, 2007, pp.299-326

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

SITE-SPECIFIC ANALYSIS OF RESPONSE PROPERTIES OF SODIUM CLUSTERS K. A. Jackson, M. Yang, and J. Jellinek in Latest Advances in Atomic Cluster Collisions: Structure and Dynamics from Nuclear to the Biological Scale, A. V. Solovov, Ed., Imperial College Press, London (in press)

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

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

**PI Chueng-Ryong Ji**

Perturbative QCD analysis of exclusive $J/\psi+\eta_c$ production in $e^+e^-$ annihilation, H.M.Choi and C.R.Ji, Phys. Rev. D, in press; arXiv:0707.1173 [hep-ph].

Zero-Mode Contribution in Nucleon-Delta Transition, J.Yu, T.Wang, C.R.Ji and B.Q.Ma, Phys.Rev.D76, 074009 (2007).

Distribution amplitudes and decay constants for (pi, K, rho, K*) mesons in light-front quark model, H.M.Choi and C.R.Ji, Phys. Rev. D75, 034019 (2007).

The box diagram in Yukawa theory, B.Bakker, J.Boomsma and C.R.Ji, Phys. Rev. D75, 065010 (2007).

Conformal Symmetry and Pion Form Factor: Soft and Hard Contributions, H.M.Choi and C.R.Ji, Phys. Rev. D74, 093010 (2006)

**PI De-en Jiang**

Jiang, D. E.; Dai, S. "Electronic ground state of higher acenes." Journal of Physical Chemistry, submitted.

Chen, Z. F;. Jiang, D. Ea;. Lu, X.; Bettinger, H. F.; Dai, S.; Schleyer, P. v. R.; Houk, K. N. "Open-Shell Singlet Character of Cyclacenes and Short Zigzag Nanotubes." Organic Letters, submitted.

## K

**PI Andrey Kalinichev**

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

**PI Martin Karplus**

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

Probing Polar Solvation Dynamics in Proteins: A Molecular Dynamics Simulation Analysis, J. Phys. Chem. B. 111, 1482-1490 (2006), by A. A. Golosov and M. Karplus.

A Kinetic Model of Coordinated Myosin V, Biochemistry 46, 6318-6330 (2007), by Y. Wu, Y. Q. Gao and M. Karplus.

Minimum Free Energy Pathways and Free Energy Profiles for Conformational Transitions Based on Atomic Molecular Dynamics Simulations, J. Chem. Phys. 126, 164106/1-17, by A. van der Vaart and M. Karplus.

The Signaling Pathway of Rhodopsin, Structure 15, 611-623 (2007), by Y. Kong and M. Karplus.

How Subunit Coupling Produces the gamma-Subunit Rotary Motion in F1-ATPase, Proc. Natl. Acad. Sci. USA, submitted, by J. Pu and M. Karplus.

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

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

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

The Signaling Pathway of PDZ Domains, Proteins: Struct. Funct. Bioinformatics, to be submitted, by Y. Kong and M. Karplus.

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

**PI Thomas Katsouleas**

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

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

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

C. Huang et al., "QUICKPIC: A highly efficient particle-in-cell code for modeling wakefield acceleration in plasmas", Journal Comp. Phys. Volume 217, Issue 2, 20 September 2006. Pages 658-679.

E. Oz et al., "Ionization-induced electron trapping in ultrarelativistic plasma wakes", Phys. Rev. Lett. 98, 084801 (2007).

I. Blumenfeld et al., "Energy doubling of 42 GeV electrons in a metre-scale plasma wakefield accelerator", Nature 445, 741-744 (15 February 2007).

**PI Paul Kent**

Payne, C. M., Xiongce Zhao, Cummings, P. T. Molecular simulation of DNA transport in solution, Molecular Simulation, 33, 399, 2007

Zhao Xiongce, Payne, C. M., Peter Cummings, J. W. Lee, Single stranded DNA molecules translocation through nanoelectrode gaps, Nanotechnology, 18, 424018, 2007

Zhao Xiongce, Rignall, T. R., McCabe, C., Adney, W. S., Himmel, M. E., Energy Storage Mechanism of the Trichoderma reesei Cel7A I Linker Peptide from Molecular Dynamics Simulation, submitted to J. Am. Chem. Soc.

Zhao Xiongce, Payne, C. M., Peter Cummings, Controlled translocation of DNA segments through nanoelectrode gaps from molecular dynamics, submitted to J. Phys. Chem. C

Miguel Fuentes-Cabrera, Xiongce Zhao, P. R. C. Kent, and Bobby G. Sumpter. Electronic structure of xDNA. Journal of Physical Chemistry B 111 9057 (2007)

Y. He, S. Graser, P. J. Hirschfeld and H. -P. Cheng, Structure of BSCCO supermodulation from ab initio calculations. Submitted to Phys. Rev. Let (2007). arXiv:0709.0662

Agapito LA, Cheng HP. Ab initio calculation of a graphene-ribbon-based molecular switch. J. Phys. Chem 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. Phys. Rev. B 75 (23) 235429 JUN 2007

Cao C, He Y, Torras J, et al. Fracture, water dissociation, and proton conduction in SiO2 nanochains. J. Chem. Phys. 126 (21) 211101 JUN 7 2007

Wang LL, Cheng HP. Embedding atom-jellium model for metal surface. Eur. Phys. J. D (1-3): 247-250 JUL 2007

Schmidt M, Masson A, Brechignac C, et al. Hydrogen peroxide and ammonia on protonated ice clusters J. Chem. Phys. 126 (15) 154315 APR 21 2007

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

Zhang JW, Cheng HP. Anomalous Hall effect in disordered Fe ferromagnetic films. Phys. Rev. B 74 (21) 212409 DEC 2006

Simulations of azobenzene containing alkanethiol SAMs on Au(111) surface. J. Phys. Chem. (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 Pd cluster as nano-sensor (submitted).

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

**PI David Keyes**

V. Akcelik, G. Biros, O. Ghattas, J. Hill, D. Keyes, and B. van Bloeman Waanders, "Parallel PDE constrained optimization," in Frontiers of Parallel Computing, M. Heroux, P. Raghaven, and H. Simon, eds, SIAM, 2006.

J. Brannick, M. Brezina, S. MacLachlan, T. Manteuffel, S. McCormick, and J. Ruge, "An energy-based AMG coarsening strategy," Journal on Numerical Analysis,. Lin. Alg. Appl., 13, 133, 2006.

M. Brezina, R. Falgout, S. MacLachlan, T. Manteuffel, S. McCormick and J. Ruge, "Adaptive Algebraic Multigrid," SIAM Journal of Scientific Computing, 27, 1534, 2006.

M. Brezina, C. Tong, R. Becker, "Parallel Algebraic Multigrids for Structural Mechanics," SIAM Journal of Scientific Computing, to appear.

E. Chow, "An Aggregation Multilevel Method Using Smooth Error Vectors," SIAM Journal of Scientific Computing, 27, 1727, 2006.

R. D. Falgout, J. E. Jones, and U. M. Yang, "The Design and Implementation of hypre, a Library of Parallel High Performance Preconditioners," chapter in Numerical Solution of Partial Differential Equations on Parallel Computers, A. M. Bruaset, P. Bjorstad, and A. Tveito, eds., Springer- Verlag, 2006.

I. Lee, P. Raghavan, and E. G. Ng, "Effective Preconditioning Through Ordering Interleaved with Incomplete Factorization," SIAM J. Matrix Anal. Appls., 27, 106, 2006.

T. Manteuffel, S. McCormick, O. Rohrle and J. Ruge, "Projection multilevel methods for quasilinear elliptic partial differential equations: numerical results," SIAM Journal on Numerical Analysis, 44, 120, 2006.

T. Manteuffel, S. McCormick and O. Rohrle, "Projection multilevel methods for quasilinear elliptic partial differential equations: theoretical results," SIAM Journal on Numerical Analysis, 44, 139, 2006.

S. McCormick, "Projection multilevel methods for quasilinear elliptic partial differential equations: V-cycle theory," SIAM J. Mult. Modeling Sim., 4, 133, 2006.

E. Prudencio, R. Byrd, and X.-C. Cai, "Parallel full space SQP Lagrange-Newton- Krylov-Schwarz algorithms for PDEconstrained optimization problems," SIAM Journal of Scientific Computing, 27, 130, 2006.

U. M. Yang, "Parallel Algebraic Multigrid Methods - High Performance Preconditioners," chapter in Numerical Solution of Partial Differential Equations on Parallel Computers, A. M. Bruaset, P. Bjorstad, and A. Tveito, eds., Springer-Verlag, 2006.

**PI Kwiseon Kim**

Q. Zhao, P. A. Graf, W. B. Jones, A. Franceschetti, J. Li, L.-W. Wang, and K. Kim, Shape dependence of band-edge exciton fine structure in CdSe nanocrystals, Nano Lett., 2007, 10.1021/nl0713070

P. A. Graf, K. Kim, W. B. Jones, L. W. Wang, Surface passivation optimization using DIRECT, J. Comput. Phys., 224, 2, (2007), 824-835

P. A. Graf and W. B. Jones, A Projection Based Multiscale Optimization Method for Eigenvalue Problems, J. Glob. Optim , 39, (2007) 235-245.

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

P. Piquini, P. A. Graf, and Alex Zunger, Band gap design of quaternary (In,Ga)(As,Sb) semiconductors via the inverse band structure approach, (submitted).

J. Schrier, D.O. Demchenko, L.W. Wang, A.P. Alivisatos, Optical properties of ZnO/ZnS and ZnO/ZnTe heterostructures for solar cell applications, Nanolett. 7. 2377 (2007).

**PI Spencer Klein**

"Multiyear Search for a Diffuse Flux of Muon Neutrinos with AMANDA-II," A. Achterberg et al., Phys. Rev. D76, 042008 (2007).

"Detection of atmospheric neutrinos with the IceCube 9-string detector," A. Achterberg et al., Phys. Rev. D76, 027101 (2007).

" Five years of searches for point sources of astrophysical neutrinos with the AMANDA-II neutrino telescope," A. Achterberg et al., Phys. Rev. D75, 102001 (2007).

"Search for Neutrino Induced Cascades from Gamma-Ray Bursts with AMANDA," A. Achterberg et al., Astrophysical J. 664. 397 (2007).

"Limits on the muon flux from neutralino annihilations at the center of the Earth with AMANDA," A. Achterberg et al., Astropart. Phys. 26, 129 (2006).

**PI Kwok Ko**

Volkan Akcelik, Kwok Ko, Lie-Quan Lee, Zenghai Li, Cho-Kuen Ng, and Liling Xiao, Shape Determination for Deformed Electromagnetic Cavities, Journal of Computational Physics, to be published

Lie-Quan Lee, et al, Enabling technologies for petascale electromagnetic accelerator simulation, 2007 J. Phys.: Conf. Ser. 78 012040.

F. Zhou, A. Kabel, J. Rosenzweig, R. Agustsson, G. Andonian, D. Cline, A. Murokh, and V. Yakimenko, Experimental characterization of the transverse phase space of a 60-MeV electron beam through a compressor chicane; Phys. Rev. ST Accel. Beams 9, 114201 (2006).

**PI Boris Kogan**

Huffaker RB, Weiss JN, Kogan B. Effects of early afterdepolarizations on reentry in cardiac tissue: a simulation study. Am J Physiol Heart Circ Physiol. 2007 Jun; 292(6):H3089-102.

**PI Joel Koplik**

"Hydrodynamic interaction of two particles in confined linear shear flows at finite Reynolds number," by Y. Yan, J. F. Morris and J. Koplik, Phys. Fluids in press (2007).

**PI V. Rao Kotamarthi**

Zubrow, A., Chen, L., Kotamarthi, V. R., EAKF-CMAQ: Introduction and evaluation of a data assimilation for CMAQ based on the Ensemble Adjustment Kalman filter. Submitted to the Journal of Geophysical Research, 2007.

**PI Henry Krakauer**

"Finite-size correction in many-body electronic structure calculations," by Hendra Kwee, Shiwei Zhang and Henry Krakauer, submitted to Physical Review Letters. It will be available in preprint form at the eprint archive (arXiv.org).

**PI Petr Kral**

B. Wang and P. Kral, Dragging of Polarizable Nanodroplets by Ions Solvated at Nanometer Separations, Submitted to Nature Nanotechnology.

**PI Arnold Kritz**

G. Park, J. Cummings, C.S. Chang, N. Podhorszki, S. Klasky, S. Ku, A. Pankin, R. Samtaney, A. Shoshani, P. Snyder, H. Strauss, L. Sugiyama and the CPES Team (2007) Coupled simulation of kinetic pedestal growth and MHD ELM crash, J. Phys.: Conf. Ser. 78, 012087.

C.R. Sovinec, D.C. Barnes, R.A. Bayliss, D.P. Brennan, E.D. Held, S.E. Kruger, A.Y. Pankin, D.D. Schnack and the NIMROD Team (2007) Two-fluid studies of edge relaxation events in tokamaks, J. Phys.: Conf. Ser. 78, 012070.

A.Y. Pankin, G. Bateman, D.P. Brennan, A.H. Kritz, S. Kruger, P. B. Snyder, and C. Sovinec (2007) Modeling of ELM dynamics for DIII-D and ITER, Plasma. Phys. Control. Fusion 49, S63-75.

**PI Scott Kruger**

D.G. Whyte, R. Granetz, M. Bahktiari, V. Izzo, T. Jernigan, J. Terry, M. Reinke, B. Lipschultz, J. Nucl. Mater. 363-365, 1160 (2007).

R.S. Granetz, D.G. Whyte, V.A. Izzo, et al., Nucl. Fusion 46 (2006) 1001.

**PI Young-Kyun Kwon**

Y.-K. Kwon and P. Kim, "Unusually High Thermal Conductivity in Carbon Nanotubes", in Subhash L. Shinde and Jitendra S. Goela (eds.), High Thermal Conductivity Materials, pp. 227--265 (Chapter 8), Springer, New York (2006).

M. Lee, J. Im, B.Y. Lee, S. Myung, J. Kang, L. Huang, Y.-K. Kwon, and S. Hong, "Linker-free directed assembly for high-performance integrated devices based on nanotubes and nanowires", Nature Nanotech. 1, 66 (2006).

H. J. Song, Y. Lee, T. Jiang, A.-G. Kussow, M. Lee, S. Hong, Y.-K. Kwon, and H. C. Choi, "Self-clusterized Glycines on Single Walled Carbon Nanotubes for Alcohol Sensing", J. Phys. Chem. C, in press.

T. W. Kim, Y. J. Hong, G.-C. Yi, J.-H. Kwon, M. Kim, H. N. Han, D. H. Kim, K. H. Oh, K.-J. Kong, and Y.-K. Kwon, "Morphology of Patterned, Uniform, and Faceted GaN Microcrystals", submitted for publication.

S. Woo and Y.-K. Kwon, "New Hydrogen Storage Nanomaterial with Potential Pockets: Ethylene Oxides", submitted for publication.

## L

**PI Andrew Lacis**

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

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

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

V. B. Podobedov, D. F. Plusquellic, K. E. Siegrist, G. T. Fraser, Q. Ma, and R. H. Tipping, Collision-Induced Absorption by the Water Vapor Continuum in the Region from 0.3 to 2.7 THz, J. Quant. Spec. Rad. Transfer, in press (2007).

A. Goldman, R. H. Tipping, Q. Ma, C.D. Boone, P.F. Bernath, P. Demoulin, F. Hase, M. Schneider, J. W. Hannigan, M. T. Coffey, and C. P. Rinsland, On the line parameters for the X1Sg+ (1-0) infrared quadrupolar transitions of 14N2. J. Qaunt. Spec. Rad. Transfer. 103, 168-174 (2007).

Yu. I. Baranov, W. J. Lafferty, and G. T. Graser, Q. Ma. R. H. Tipping, Water-vapor Continuum Absorption in the 800 cm-1 to 1250 cm-1 (to be submitted).

**PI Jean-Francois Lamarque**

Lamarque, J.-F., D. E. Kinnison, P.G. Hess and F. Vitt, Simulated lower stratospheric trends between 1970 and 2005: identifying the role of climate and composition changes. Submitted for publication in J. Geophys. Res., 2007.

**PI Don Lamb**

Calder,A.C. , Townsley, D. M., Seitenzahl, I. R., Peng, F., Messer, O. E. B., Vladimirova, N., Brown, E. F., Truran, J. W., and Lamb, D. Q., Capturing the Fire: Flame Energetics and Neutronizaton for Type Ia Supernova Simulations, Astrophysical Journal, 2007, vol. 656, pp. 313+.

Hearn, N. C., Plewa, T., Drake, R. P., and Kuranz, C., Flash Code Simulations of Rayleigh-Taylor and Richtmyer-Meshkov Instabilities in Laser-Driven Experiments, Astrophysics and Space Science, 2007, vol. 307, pp. 227-231.

Jordan IV, G.C., Fisher, R.T., Townsley, D.M., Calder, A.C., Graziani, C., Asida, S., Lamb, D.Q. and Truran, J.W., Three-Dimensional Simulations of the Deflagration Phase of the Gravitationally Confined Detonation Model of Type Ia Supernovae, Submitted to ApJ Letters, 2007.

Townsley, D.M., Calder, A.C., Asida, S., Seitenzahl, I.R., Peng, F., Vladimirova, N., Lamb, D.Q. and Truran, J.W., Flame Evolution During the Deflagration Phase of Type Ia Supernovae, Submitted to the Astrophysical Journal, 2007.

Zhang, J., Bronson Messer, O. E., Khokhlov, A. M. and Plewa, T., On the Evolution of Thermonuclear Flames on Large Scales, Astrophysical Journal, 2007, vol. 656, 347+.

Zhiglo, A.V., Flame Capturing Technique, 1: Adaptation to gas expansion, Astrophysical Journal Supplement Series, 2007, vol. 169, pp. 386-400.

**PI Uzi Landman**

"Structural Evolution of Au Nanoclusters: From Planar to cage to nanotube Motifs", X. Xing, B. Yoon, J. H. Parks, U. Landman, Phys. Rev. B 74, 165423 (2006).

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

"Size-Dependent Evolution of Structures and Chemical Reactivity of Gold Nanosclusters: AuN-, N=15-24", B. Yoon, P. Koshkinen, B. Huber, O. Kostki, B. von Issendorff, H. Hakkinen, M. Moseler, U. Landman, Chem. Phys. Chem. 8 , 157 (2007).

"Size-Dependent Evolution of Structures and Chemical Reactivity of Gold Nanosclusters: AuN-, N=15-24", B. Yoon, P. Koshkinen, B. Huber, O. Kostki, B. von Issendorff, H. Hakkinen, M. Moseler, U. Landman, Chem. Phys. Chem. 8 , 157 (2007).

"Structural and Transport Properties of Nb Nanowires", Z. Dai, C. Zhang, R. N. Barnett, A. Marchenkov and U. Landman, Physica Status Solidi (a) 204, 1712 (2007).

"Predicted Oxidation of CO Catalyzed by Au Nanoclusters on a Thin Defect-Free MgO Film Supported on a Mo(100) Surface", C. Zhang, B. Yoon, and U. Landman, J. Am. Chem. Soc (Communication) 129, 2229 (2007).

"Structured and Viscous Water in Sub-nanometer Gaps", T.-D. Li, J. Gao, R. Szoszkiewicz, U. Landman, E. Riedo, Phys. Rev. B. 75, 115415 (2007).

"Factors in gold nanocatalysis: oxidation of CO in the non-scalable size regime", M. Arenz, U. Landman, U. Heiz, Topics in Catalysis, 44, 145 (2007).

**PI Jean-Noel Leboeuf**

P.L. Pritchett, "Onset of Magnetic Reconnection", in Reconnection of Magnetic Fields, edited by J. Birn and E. Priest, pp. 121-132, Cambridge Univ. Press, Cambridge, 2007.

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

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

P.L. Pritchett, "Kinetic Properties of Magnetic Merging in the Coalescence Process", Phys. Plasmas, 14, 052102, 2007.

Study of the interaction between diffusive and avalanche-like transport in near-critical dissipative- trapped-electron-mode turbulence, J. A. Mier, L. Garcma, and R. Sanchez, Phys. Plasmas 13, 102308 (2006).

Renormalization of tracer turbulence leading to fractional differential equations, R. Sanchez, B. A. Carreras, D. E. Newman, V. E. Lynch, and B. Ph. van Milligen, Phys. Rev. E 74, 016305 (2006).

Viktor K. Decyk, Henry J. Gardner: A Factory Pattern in Fortran 95. International Conference on Computational Science (1) 2007: 583-590.

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.

Stability of Highly Shifted Equilibria in a Large-Aspect-Ratio Tokamak, P.-A. Gourdain, S. C. Cowley, J.- N. Leboeuf, and R. Y. Neches, Phys. Rev. Lett. 97, 055003 (2006).

**PI Frank Lee**

Magnetic moment of vector mesons in the background field method F.X. Lee, S. Moerschbacher, W. Wilcox, PoS(LATTICE 2007)151. hep-lat/0710.2329

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

Mass and width of strange baryon resonances in QCD sum rules. J.P. Singh and F.X. Lee, submitted to Nucl. Phys. A. nucl-th/0612059

On the locality and scaling of overlap fermions at coarse lattice spacings. T. Draper, N. Mathur, J.B. Zhang, A. Alexandru, Y. Chen, S.J. Dong, I. Horvath, F.X. Lee, K.F. Liu, S.Tamhankar, submitted to Phys. Rev. D. hep-lat/0609034

Excited decuplet baryons from QCD sum rules. F.X. Lee, Nucl. Phys. A 791, 352 (2007). nucl-th/0605065

Spectroscopy of light hadrons in anisotropic lattice QCD. F.X. Lee, Int. J. Mod. Phys. A21, 5253 (2006).

**PI Patrick Lee**

Sung-sik Lee and Patrick A. Lee , "Observation of emergent photon in Monte Carlo simulation of exciton condensate" Physical Review B74, 035107 (2006).

**PI T. S. Harry Lee**

Dynamical Coupled-Channel Model of Meson Production Reactions in the Nucleon Resonance Region A. Matsuyama, T. Sato, T.-S. H. Lee, Physics Reports {\bf 439}, 193-253 (2007)

Extraction and Interpretation of $\gamma N \rightarrow \Delta$ Form Factors within a Dynamical Model B. Julia-Diaz, T.-S.H. Lee, T. Sato, L.C. Smith Phys.Rev. {\bf C75}, 015205 (2007)

Study of Nucleon Resonances with Electromagnetic Interactions T.-S. H. Lee and L.C. Smith J. Phys. G.: Nucl. Part. Phys. {\bf 34}, S83-S106 (2007)

Dynamical Coupled-channel Model of $\pi N$ scattering in the W $\leq$ 2 GeV nucleon resonance region B. Julia-Diaz, T.-S.H. Lee, A. Matsuyama, T. Sato Accepted by Phys. Rev. C

Regge Approach to Charged-Pion Photoproduction at Invariant Energies above 2-GeV A. Sibirtsev, J. Haidenbauer, S. Krewald, T.-S.H. Lee, U.-G. Meissner, and A.W. Thomas Accepted by Euro. J. Phy.

**PI Wei-li Lee**

Ethier, S., W.M. Tang, R. Walkup, and L. Oliker, "Large Scale Gyrokinetic Particle Simulation of Microturbulence in Magnetically Confined Plasmas", to appear in IBM Journal of Research and Development (2007).

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

Jenkins, Thomas G., and W. W. Lee, "Fluctuations and Discrete Particle Noise in Gyrokinetic Simulation of Drift Waves", Phys. Plasmas 14, 032307 (2007).

Wang, W.X., T.S. Hahm, W. Lee, G. Rewoldt, J. Manickam, and W.M. Tang, "Nonlocal Properties of Gyrokinetic Turbulence and Role of ExB Flow Shear", Phys. Plasmas 14, 072306 (2007).

M.F. Adams, S. Ethier and N. Wichmann, Performance of particle in cell methods on highly concurrent computational architectures, J. Phys.: Conference Series, Vol. 78, 012001 (2007).

Adams, M.F., and Y. Nishimura, "Parallel Algebraic Multigrid Methods in Gyrokinetic Turbulence Simulations", Commun. Comput. Phys. 2, 827 (2007).

R. A. Kolesnikov, W. W. Lee, H. Qin, and E. Startsev, "High frequency gyrokinetic particle simulation", Phys. Plasmas 14, 072506 (2007).

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

Rewoldt, G., Z. Lin, and Y. Idomura, "Linear Comparison of Gyrokinetic Codes with Trapped Electrons", Report PPPL-4195, submitted to Comp. Phys. Commun. (2007)

Oliker, L., A. Canning, J. Carter, C. Iancu, M. Lijewski, S. Kamil, J. Shalf, H. Shan, E. Strohmaier, S. Ethier, and T. Goodale, "Scientific Application Performance on Candidate Petascale Platforms", Proceedings of IEEE International Parallel and Distributed Processing Symposium, 2007, Long Beach, CA (2007) (Best Paper Award).

Hahm, T.S., P.H. Diamond, Z. Lin, G. Rewoldt, O. Gurcan, and S. Ethier, "On the Dynamics of Edge-Core Coupling", Phys. Plasmas 12, 090903 (2007).

Wang, W.X., G. Rewoldt, W.M. Tang, F.L. Hinton, J. Manickam, L.E. Zakharov, R.B. White, and S. Kaye, "Nonlocal neoclassical transport in tokamak and spherical torus experiments", Phys. Plasmas 13, 082501 (2006).

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

Lewandowski, J.L.V., G. Rewoldt, S. Ethier, W. W. Lee and Z. Lin, "Global Particle-In-Cell Simulations of Microturbulence with Kinetic Electrons", Phys. Plasmas 13, 072306 (2006).

W. W. Lee, Integrated Multiscale Gyrokinetic Particle Simulation of Fusion Plasmas, 20th International Conference on Numerical Simulation of Plasmas, (Austin, TX, October, 2007).

R. Kolesnikov, Electromagnetic high frequency gyrokinetic particle-in-cell simulation, 20th International Conference on Numerical Simulation of Plasmas, (Austin, TX, October, 2007)

W. X. Wang, T.S. Hahm, G. Rewoldt, J. Manickam and W.M. Tang, "Gyrokinetic studies of Nonlocal Properties of Turbulence-driven and Neoclassical Transport", 21th IAEA Conference on Plasma Physics and Controlled Nuclear Fusion Research, (Chengdu, China, October 2006)

W. W. Lee, S. Ethier, T. G. Jenkins, W. X. Wang, J. L. V. Lewandowski, G. Rewoldt, W. M. Tang, S. E. Parker, Y. Chen, and Z.Lin, 21th IAEA Conference on Plasma Physics and Controlled Nuclear Fusion Research, (Chengdu, China, 2006)

W. W. Lee, Kinetic Simulation of Fusion Plasmas, Masterworks Session, Supercomputing 06, (Tampa, FL, November 2006).

**PI Xuhui Lee**

Huang, J., X. Lee, E. G. Patton: 2007, A modeling study of flux imbalance and the influence of entrainment in the convective boundary layer, submitted to Boundary-Layer Meteorology.

**PI William Lester**

P. T. A. Galek, N. C. Handy, and W. A. Lester, Jr. Quantum Monte Carlo Studies on Small Molecules, Mol. Phys. 104, 3069 (2006).

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

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

R. Whitesides, D. Domin, R. Salomon-Ferrer, W.A. Lester, Jr., and M. Frenklach, Graphene Layer Growth Chemistry: Five-Six-Ring Flip Reaction, J. Phys. Chem., accepted for publication.

M. T, Nguyen, M. H. Matus, W. A. Lester, Jr., and D. A. Dixon, Heats of Formation of Triplet Ethylene and Ethylidene, J. Chem. Phys., accepted for publication.

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

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

**PI Mary Ann Leung**

Leung, M.A., Reinhardt, W.P., "Efficient parallel implementation of the Bose-Hubbard model: Exact numerical groundstates and dynamics of gaseous Bose-Einstein Condensates", Comp. Phys. Comm., 177 (4), (2007), 348-356

**PI Rui Li**

"Curvature-Induced Bunch Self-Interaction for an Energy-Chirped Bunch in Magnetic Bends", Rui Li, to be appear in recent PRST-AB journal (2007).

**PI Shi Ying Lin**

C. Xu, B. Jiang, D. Xie, S. C. Farantos, S. Y. Lin and H. Guo, "Analysis of the HO2 vibrational spectrum on an accurate ab initio potential energy surface", J. Phys. Chem. A, in press.

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

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

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

D. Xie, C. Xu, T.-S. Ho, H. Rabitz, G. Lendvay, S. Y. Lin and H. Guo, "Global analytical potential energy surfaces for HO2(X2A") based on high level ab initio calculations!1, J. Chem. Phys. 126, 074315 (2007).

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

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

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

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

S. Y. Lin and H. Guo, "Quantum statistical study of O + O2 isotopic exchange reactions: Cross sections and rate constants", J. Phys. Chem. A 110, 5305 (2006).

S. Y. Lin and H. Guo, "Exact quantum dynamics of N(D_2) + H2 reaction: Cross-sections, rate constants, and dependence on reactant rotation", J. Chem. Phys., 124, 031101 (2006).

**PI Yu Lin**

Lin, Y., X. Y. Wang, M. Brown, M. Schaffer, and C. D. Cothran, Modeling Swarthmore Spheromak Reconnection Experiment Using hybrid code, Plasma Physics and Controlled Fusion, in press, 2008.

Yoon, P., Y. Lin, X. Y. Wang, and A. T. Y. Lui, Drift instabilities for current sheet equilibrium with guide field, J. Geophys. Res., submitted, 2008.

**PI Feng Liu**

D. Yu and F. Liu, Synthesis of Carbon Nanotubes by Rolling up Patterned Graphene Nanoribbons Using Selective Atomic Adsorption, Nano Lett. 7, 3046 (2007)

L. Bai, D. Yu, G-H Lu, F Liu, Q. Wang, H Yilmaz, Confining P diffusion in Si by an As-doped barrier layer, App. Phys. Lett. 91, 016926 (2007)

Q. Yan, B. Huang, J. Yu, FW Zheng, J. Zang, J. Wu, BL Gu, F. Liu, WH Duan Intrinsic current-voltage characteristics of graphene nanoribbon transistors and effect of edge doping, NANO LETTERS 7,1469(2007)

J. Zang, O. Aldas-Palacios, Liu F MD simulation of structural and mechanical transformation of single-walled carbon nanotubes under pressure COMMUNICATIONS IN COMPUTATIONAL PHYSICS 2 (3): 451-465 JUN 2007

DJ Shu DJ, M Wang, F. Liu, et al. Nucleation-mediated lateral growth on foreign substrate JOURNAL OF PHYSICAL CHEMISTRY C 111 (3): 1071-1075 JAN 25 2007

J. Zang, MH Huang, F. Liu, Mechanism for nanotube formation from self-bending nanofilms driven by atomic-scale surface-stress imbalance PHYSICAL REVIEW LETTERS 98 (14): Art. No. 146102 (2007)

GH Lu, Q. Wang, F. Liu, First-principles calculation of interaction between interstitial O and As dopant in heavily As-doped Si JOURNAL OF APPLIED PHYSICS 101 (2): Art. No. 026104 JAN 15 2007

C. Zhang, JC Cao, XG Guo, et al. Impurity mediated absorption continuum in single-walled carbon nanotubes APPLIED PHYSICS LETTERS 90 (2): Art. No. 023106 JAN 8 2007

SC Li, Y. Han, JT Jia, et al. Determination of the Ehrlich-Schwoebel barrier in epitaxial growth of thin films PHYSICAL REVIEW B 74 (19): Art. No. 195428 NOV 2006

**PI Keh-Fei Liu**

N. Mathur, A. Alexandru, Y. Chen, S.J. Dong, T. Draper, I. Horvath, F.X. Lee, K.F. Liu, S. Tamhankar, and J.B. Zhang, `a_0(1450) and \sigma(600) Mesons from Lattice QCD', Phys. Rev. D (to appear), [hep-ph/0607110].

H.Y. Cheng, C.K. Chua, and K.F. Liu, `Scalar Glueball, Scalar Quarkonia, and their Mixing, Phys. Rev. D74, 094005 (2006), [hep-ph/0607206].

Terrence Draper, Nilmani Mathur, Andrei Alexandru, Ying Chen, Shao-Jing Dong, Ivan Horvath, Frank X. Lee, Keh-Fei Liu, Sonali Tamhankar, Jianbo Zhang, `On the Locality and Scaling of Overlap Fermions at Coarse Lattice Spacings', submitted for publication, [hep-lat/0609034].

K.F. Liu, A. Alexandru, I. Horvath, `Gauge Field Strength Tensor from the Overlap Dirac Operator', submitted for publication, [hep-lat/0703010].

K.F. Liu, `Pattern of Light Scalar Mesons', Prog. Theo. Phys. Suppl. 168, 1 (2007), [arXiv:0706.1262].

E.-M. Ilgenfritz, K. Koller, Y. Koma, G. Schierholz, T. Streuer (U. Kentucky), V. Weinberg, `Exploring the structure of the quenched QCD vacuum with overlap fermions', Phys. Rev. D76, 034506 (20070, [arXiv:0705.0018].

**PI Stewart Loken**

A Standard format for Les Houches event files. J.Alwall et al. FERMILAB-PUB-06-337-T, CERN-LCGAPP-2006-03, Sep 2006. 8pp. Written within the framework of the MC4LHC-06 workshop: Monte Carlos for the LHC: A Workshop on the Tools for LHC Event Simulation (MC4LHC), Geneva, Switzerland, 17-16 Jul 2006. Published in Comput.Phys.Commun.176:300-304,2007. e-Print: hep-ph/0609017

**PI Steven Louie**

J. Deslippe, C.D. Spataru, D. Prendergast, and S.G. Louie, "Bound Excitons in Metallic Single-walled Carbon Nanotubes," Nano Lett. 7, 1626 (2007).

F. Wang, D. Cho, B. Kessler, J. Deslippe, P.J. Schuck, S.G. Louie, A. Zettl, T.F. Heinz, Y.R. Shen, "Observations of Excitons in One-Dimensional Metals," accepted to Phys. Rev. Lett.

C.-H. Park, F. Giustino, M.L. Cohen, and S.G. Louie, "Velocity renormalization and carrier lifetime in graphene from the electron-phonon interaction," Phys. Rev. Lett. 99, 086804 (2007).

M.J. Comstock, N. Levy, A. Kirakosian, J. Cho, F. Lauterwasser, J.H. Harvey, D.A. Strubbe, J.M.J. Frechet, D. Trauner, S.G. Louie, and M.F. Crommie, "Reversible Photomechanical Switching of Individual Engineered Molecules at a Metallic Surface," Phys. Rev. Lett. 99, 038301 (2007).

Y. Wang, X.H. Lu, E. Kioupakis, R. Yamachika, D. Wegner, S.G. Louie, M.F. Crommie, J.E. Dahl, S.G. Liu, and R.M.K. Carlson, "Spatially resolved electronic and vibronic characteristics of tetramantane diamondoid," submitted to Nature Materials.

P. Tangney, M. L. Cohen, and S. G. Louie, "Giant Wave-Drag Enhancement of Friction in Sliding Carbon Nanotubes," Phys. Rev. Lett. 97, 195901 (2006).

T. Miyake, P.H. Zhang, M.L. Cohen, and S.G. Louie, "Quasiparticle Energy of Semicore d-electrons in ZnS: Combined LDA+U and GW approach," Phys. Rev. 74, 245213 (2006).

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

I.H. Choi, P.Y. Yu, P. Tangney, and S.G. Louie, "Vibrational Properties of Single-Walled Carbon Nanotubes Under Pressure from Raman Scattering Experiments and Molecular Dynamics," Phys. Status Sol. (b) 244, 121 (2007).

J.B. Neaton, M.S. Hybertsen, and S.G. Louie, "Renormalization of Molecular Electronic Levels at Metal-Molecule Interfaces," Phys. Rev. Lett. 97, 216405 (2006).

**PI Walter Loveland**

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

G.L. Malli, (Communication) "Dissociation energy of Ekaplutonium fluoride E126F", J. Chem. Phys. 124,071102(2006).

G.L. Malli, (Communication) "Electronic structure and prediction of atomization energy of naked homoleptic uranium hexacarbonyl U(CO)6", J. Chem. Phys. 124,021102(2006).

R. Arratia-Perez and G.L. Malli, "Relativistic molecular orbital study of the optical and magnetic properties of hexachloro protoactinate (IV): PaCl6-2, J. Chem.Phys. 124,074321(2006).

G.L. Malli and M.Siegert, " Dramatic effects of relativity for the correlation energy of molecules of heavy atom: all-electron all-virtual spinor space (AVSS) relativistic coupled-cluster calculations for PbH4", Intern J of Quantum Chem. (Submitted on Sept 24, 2007).

W.Loveland, "Synthesis of transactinide nuclei using radioactive beams", Phys.Rev. C76, 014612(2007)

W.Loveland, "Comment on the possibility of synthesizing a doubly magic superheavy nucleus", Phys.Rev.C75, 069801(2007).

J.F.Liang,D.Shapira, J.R.Breene, C.J.Gross,.....W.Loveland and D.Peterson, "Fusion of radioactive 132Sn with 64Ni, Phys.Rev. C75,054607(2007).

W. Loveland, D.J.Morrissey and G.T.Seaborg, "Modern Nuclear Chemistry", Wiley, New York, 671 pages (2006).

R.W. Stoenner, R.L. Klobucher, P.E. Haustein, G.J. Virtes, J.B. Cumming and W. Loveland, "Angular distribution in multifragmentation", Phys. Rev. C 73,047602(2006).

W. Loveland, D. Peterson, A.M. Vinodkumar,...et al Fusion enhancement in the 38S + 208Pb reaction, Phys. Rev. C 74, 044607 (2006).

W. Loveland, A.M. Vinodkumar, R.S.Naik, P.H. Sprunger...et al The fusion of 9Li with 70Zn , Phys. Rev C 74, 064609 (2006)

A.M. Vinodkumar, W. Loveland, P. Sprunger, D. Peterson Capture cross sections for the near symmetric 124Sn + 96Zr reaction, Phys. Rev C 74, 064612(2006).

## M

**PI Chung-Pei Ma**

M. Boylan-Kolchin, C.-P. Ma, and E. Quataert (2007), Monthly Notices of the Royal Astronomical Society, in press. "Dynamical Friction and Galaxy Merging Timescales"

M. Boylan-Kolchin and C.-P. Ma (2006), MNRAS, 374, 1227. Satellite Accretion onto Massive Galaxies with Central Black Holes

L. Desroches, E. Quataert, C.-P. Ma, and A. West (2007), MNRAS, 377, 402. "Luminosity Dependence in the Fundamental Plane Projections of Elliptical Galaxies"

**PI Steven Manson**

"Dynamical and Relativistic Effects in Experimental and Theoretical Studies of Inner-Shell Photoionization of Sodium," D. Cubaynes, H. L. Zhou, N. Berrah, J.-M. Bizau, J. D. Bozek, S. Canton, S. Diehl, X.-Y. Han, A. Hibbert, E. T. Kennedy, S. T. Manson, L. VoKy and F. J. Wuilleumier, J. Phys. B 40, F121-F129 (2007).

**PI Shaolin Mao**

S. Mao, E.G. Patton, Z.G. Feng, and E.E. Michaelides, Impact of imposed wall-jet on canopy turbulence and the net ecosystem-atmosphere exchange of carbon dioxide, Accepted for publication on Boundary-Layer Meteorology, 2007.

S. Mao, Z.G. Feng, and E.E. Michaelides, Large-eddy simulation of low-level jet-like flow in canopy, Environmental Fluid Mechanics, 7(1) 73-93, 2007.

M. Leclerc, S.Mao and E.E. Michaelides, Flux footprint analysis over horizontal inhomogeneous canopies, resubmitted, 2007.

S. Mao, E.E. Michaeldies, CO2 flux footprint analysis over horizontally inhomogeneous plant canopy using large-eddy simulation, submmitted to Atmospheric Environment, 2007.

**PI Angelo Mascarenhas**

Y. Zhang, L.-W. Wang, and A. Mascarenhas, Quantum coaxial cables for solar energy harvesting, Nano. Lett. 7, 1264 (2007).

L. C. Lew Yan Voon, Y. Zhang, B. Lassen, M. Willatzen, Qihua Xiong, and P. C. Eklund, Electronic Properties of Semiconductor Nanowires (invited review paper), J. Nanotechnology (in press).

**PI Artem Masunov**

Ivan A. Mikhailov, Sergio Tafur, Artëm E. Masunov; Double Excitations and State to State Transition Dipoles in Excited Singlet States of Linear Polyenes: Time Dependent Density Functional Theory vs. Multiconfigurational Methods. Submitted to Phys. Rev. A

**PI Manos Mavrikakis**

A. U. Nilekar, J. Greeley, M. Mavrikakis, "A simple rule of thumb for diffusion on transition metal surfaces", Angewandte Chemie International Edition 45, 7046 (2006).

L. C. Grabow, Y. Xu, M. Mavrikakis, "Lattice strain effects on CO oxidation on Pt(111)", Physical Chemistry Chemical Physics 8, 3369 (2006) - including cover-page image.

S. Kandoi, J. Greeley, M. Sanchez-Castillo, St. T. Evans, A. A. Gokhale, J. A. Dumesic, M. Mavrikakis, "Prediction of Experimental Methanol Decomposition Rates on Platinum from First-Principles", Topics in Catalysis 37, 17 (2006).

J. Greeley, M. Mavrikakis, "Near Surface Alloys for Hydrogen Fuel Cell Applications", Catalysis Today 111, 52 (2006).

T. Mitsui, E. Fomin, F. Ogletree and M. Salmeron, A. U. Nilekar, M. Mavrikakis, "Manipulation and patterning of the surface concentration of hydrogen on Pd(111) by electric fields", Angewandte Chemie International Edition 46, 5757 (2007).

J. Greeley, M. Mavrikakis, "On the role of subsurface oxygen and ethylenedioxy in ethylene epoxidation on silver", Journal of Physical Chemistry C, 111, 7992 (2007).

Y. Xu, H. Marbach, R. Imbihl, I. G. Kevrekidis, M. Mavrikakis, "The effect of co-adsorbed oxygen on the adsorption and diffusion of potassium on Rh(110): A first-principles study", Journal of Physical Chemistry C, 111, 7446 (2007).

J. Knudsen, A. U. Nilekar, R. T. Vang, J. Schnadt, E. Kunkes, J. A. Dumesic, M. Mavrikakis, F. Besenbacher, "A Cu/Pt Near-Surface Alloy for water-gas shift catalysis", Journal of the American Chemical Society, 129, 6485 (2007).

J. Zhang, M.B. Vukmirovic, K. Sasaki, A.U. Nilekar, F. Uribe, M. Mavrikakis, R.R. Adzic, "Platinum Monolayer Electrocatalysts for Oxygen Reduction", Electrochimica Acta 52, 2257 (2007).

R. R. Adzic, J. Zhang, K. Sasaki, M. B. Vukmirovic, M. Shao, J. X. Wang, A. U. Nilekar, M. Mavrikakis, J. A. Valerio, F. Uribe, "Platinum Monolayer Fuel Cell Electrocatalysts", Topics in Catalysis (in press).

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

L. C. Grabow, A. A. Gokhale, St. Evans, J. A. Dumesic, M. Mavrikakis, "Mechanism of the water gas shift reaction on Pt: first-principles, experiments, and microkinetic modeling", (submitted).

N. Schumacher, K. Andersson, L. C. Grabow, M. Mavrikakis, J. Nerlov, and I. Chorkendorff, "Interaction of CO2 with Cu overlayers on Pt(111)", (submitted).

A. A. Gokhale, J. A. Dumesic, M. Mavrikakis, "On the mechanism of low temperature water-gas-shift reaction on copper", (submitted).

**PI William McCurdy**

Wim Vanroose, D. A. Horner, F. Martmn T. N. Rescigno and C. W. McCurdy, "Double Photoionization of Aligned Molecular Hydrogen", Phys. Rev. A 74, 052702 (2006).

T. N. Rescigno, Wim Vanroose, D. A. Horner, F. Martmn and C. W. McCurdy, "First Principles Study of Double Photoionization of H2 Using Exterior Complex Scaling", J. Elec. Spectros., Rel. Phenom. 161, 85 (2007).

C.S. Trevisan, A.E. Orel and T. N. Rescigno, "Low-energy Electron Scattering by Formic Acid", Phys. Rev. A 74, 042716 (2006).

D. A. Horner, W. Vanroose, T. N. Rescigno, F. Martin and C. W. McCurdy, "Role of Nuclear Motion in Double Ionization of Molecular Hydrogen by a Single Photon", Phys. Rev. Lett. 98, 073001 (2007).

D. J. Haxton, C. W. McCurdy and T. N. Rescigno, "Dissociative Electron Attachment to the H2O molecule I: Complex-valued Potential Energy Surfaces for the 2B1, 2A1 and 2B2 Metastable States of the Water Anion", Phys. Rev. A. 75, 012710 (2007).

D. J. Haxton, T. N. Rescigno and C. W. McCurdy, "Dissociative Electron Attachment to the H2O molecule II: Nuclear Dynamics on Coupled Electronic Surfaces Within the Local Complex Potential Model", Phys. Rev. A. 75, 012711 (2007).

F. L. Yip. D. A. Horner, C. W. McCurdy and T. N. Rescigno, "Single and Triple Differential Cross Sections for Double Photoionization of H-(\", Phys. Rev. A. 75, 042715 (2007).

. D. J. Haxton, T. N. Rescigno and C. W. McCurdy, Comment on A Wave Packet Method for Treating Nuclear Dynamics on Complex Potentials, J. Phys. B 40, 1461 (2007).

A. Palacios, T. N. Rescigno and C. W. McCurdy, "Extracting Amplitudes for Single and Double Ionization from a Time-Dependent Wavepacket", Phys. Rev. A 76, 043420 (2007).

D. A. Horner, F. Morales, T. N. Rescigno, F. Martin and C. W. McCurdy, "Two-Photon Double Ionization of Helium Above and Below the Threshold for Sequential Ionization", Phys. Rev. A 76, 030701(R) (2007).

T. N. Rescigno, C. W. McCurdy, D. J. Haxton, C. S. Trevisan and A. E. Orel, "Nuclear Dynamics in Resonant Electron Collisions with Small Polyatomic Molecules", J. Phys. Conference Series (accepted).

K. Houfek, T. N. Rescigno and C. W. McCurdy, "Probing the Nonlocal Approximation to Resonant Collisions of Electrons with Diatomic Molecules", Phys. Rev. A (accepted).

**PI Donghai Mei**

Donghai Mei, N. Aaron Deskins and Michel Dupuis "A Density Functional Theory Study of Formaldehyde Adsorption on Ceria", Surf. Sci.,2007 (in press)

**PI David Mikkelsen**

S.M. Kaye, et al., Nucl. Fusion 47 (2007) 499

M. Greenwald, et al., Fusion Sci Technol. 51 (2007) 266

F. M. Levinton, et al., Phys. Plasmas 14 (2007) 056119

J.E. Menard, et al., Nucl. Fusion 47 (2007) S645

K.-L. Wong, et al., Phys. Rev. Lett. 99 (2007) 135003

D. Stutman, et al., Phys. Plasmas 13 (2006) 092511

**PI Thomas Miller**

T. F. Miller, III and C. Predescu, J. Chem. Phys., 126, 144102 (2007).

T. F. Miller, III, E. Vanden-Eijnden, and D. Chandler, PNAS, 104, 14559 (2007).

**PI William Miller**

J. Liu and W. H. Miller, Using the Thermal Gaussian Approximation for the Boltzmann Operator in Semiclassical Initial Value Time Correlation Functions, J. Chem. Phys. 125, 224104.1-13 (2006).

T. F. Miller and C. Predescu, Sampling Diffusive Transition Paths, 126 144102.1-12 (2007).

C. Venkataraman and W. H. Miller, Chemical Reaction Rates Using the Semiclassical Van-Vleck Initial Value Representation, J. Chem. Phys. 126, 094104.1-8 (2007).

J. Liu and W. H. Miller, Real Time Correlation Function in a Single Phase Space Beyond the Linearized Semiclassical Initial Value Representation, J. Chem. Phys. 126, 234110.1-11 (2007).

N. Ananth, C. Venkataraman and W. H. Miller, Semiclassical (SC) Description of Electronically Non-Adiabatic Dynamics via the Initial Value Representation (IVR), J. Chem. Phys. 127, 084114.1-9 (2007).

J. Liu and W. H. Miller, Linearized Semiclassical Initial Value Time Correlation Functions Using the Thermal Gaussian Approximation: Applications to condensed phase systems, J. Chem. Phys. (accepted)

**PI Warren Mori**

M. Tzoufras et al., "Stability of arbitrary electron velocity distribution functions to electromagnetic modes," Phys. Plasmas 14-062108 (2007)

C. Ren, E. G. Blackman, and W.-F. Fong, "Understanding the saturation of proton-driven Weibel instabilities and implications for astrophysics," Phys. Plasmas 14-012901 (2007)

G. Li et al., "Laser channeling in mm-scale underdense plasmas of fast ignition targets," submitted to Phys. Rev. Lett.

C. Huang, V. K. Decyk, M. Zhou, W. Lu, W. B. Mori, J. H. Cooley, T. M. Antonsen Jr, B. Feng, T. Katsouleas, J. Vieira and L. O. Silva, J. Phys.: Conf. Ser. 46, pp 190-199 (2006).

C. Huang, V.K. Decyk, C. Ren, M. Zhou, W. Lu, W.B. Mori, J.H. Cooley, T.M. Antonsen, Jr. and T. Katsouleas, Journal of Computational Physics, 217, pp 658-679 (2006).

Oz E., Deng S., Katsouleas T, Muggli P., Barnes C.D., Blumenfeld I., Decker F.J., Emma P., Hogan M.J., Ishchebeck R., Iverson R.H., Kirby N., Krejcik P., O'Connell C., Siemann R.h., Walz D., Auerbach D., Clayton D.E., Huang C., Johnson D.K., Joshi C., Lu W., Marsh K.A., Mori W.B., Zhou M., "Ionization- induced electron trapping in ultra-relativistic plasma wakes", Physical Review Letters, vol 98, no. 8 pp. 084801/1-4 23 February 2007.

Thomas AGR, Najmudin Z., Mangles SPD, Murphy C.D., Dangor A.E., Kamperidis C., Lancaster K.L., Mori W.B., Norreys P.A., Rozmus W., Kushelnick K., "Effect of laser-focusing conditions on propagation and monoenergetic electron production in laser-wakefield accelerators", Physical Review Letters, vol 98, no. 4 pp. 095004/1-4 2 March 2007.

F. S. Tsung et al J. Phys.: Conf. Ser., 78, 0120077 (2007)

Blumenfeld I., Clayton C.E., Decker F-J., Hogan M.J., Huang Chengkun, Ischebeck R., Iverson R., Joshi Chandrashekhar, Katsouleas T., Kirby N., Lu W., Marsh K.A., Mori W.B., Muggli P., Oz E., Siemann R.H., Walz D., Zhou M., Energy doubling of 42 GeV electrons in a metre-scale plasma wakefield accelerator, Nature, vol. 445 no. 7129, pp. 741-4 15 February 2007.

Lu W., Tzoufras M. , Joshi C., Tsung F.S.,.Mori W.B., Vieira J., Fonseca R.A., Silva L.O., "Generating Multi-GeV Electron Bunches Using Single Stage Laser Wakefield Acceleration in a 3D Nonlinear Regime," Physical Review Special Topics Acceleraors and Beams vol. 10, no. 6pp. 061301 June 2007.

**PI James Morris**

J. R. Morris, F. Jiang, P. Liaw, "A simple model for examining composition effects in eutectic nucleation," Mater. Trans. (JIM) 48, 1675-1679 (2007).

T. Egami, V. Levashov, R. S. Aga and J. R. Morris, "Atomic dynamics in metallic liquids and glasses," Mater. Trans. (JIM) 48, 1729-1733 (2007).

J. R. Morris, U. Dahlborg and M. Calvo-Dahlborg, "Recent developments and outstanding challenges in theory and modeling of liquid metals," J. Non-cryst. Sol 353, 3444-3453 (2007).

J. R. Morris, M. I. Mendelev and D. J. Srolovitz, "A comparison of crystal-melt interfacial free energies using different Al potentials," J. Non-cryst. Sol 353, 3565-3569 (2007).

C. L. Fu and Maja Krcmar, "First-principles study of the structural, defect, and mechanical properties of B2 FeCo alloys", Physical Review B74, 174108 (2006).

Maja Krcmar, C. L. Fu, and James R. Morris, "Structural transformations and improved ductility in ordered FeCo and ZrCo intermetallics", in Advanced Intermetallic-Based Alloys, MRS Symposium Proceedings, volume 980, 89 (2007).

James R. Morris, Yiying Ye, Maja Krcmar, and C. L. Fu, "The role of phase stability in ductile, ordered B2 intermetallics", in Advanced Intermetallic-Based Alloys, MRS Symposium Proceedings, volume 980, 113 (2007).

C. L. Fu and Maja Krcmar, G. S. Painter, and Xing-Qiu Chen, "The vacancy mechanism of high oxygen solubility and nucleation of stable oxygen-enriched clusters in Fe", Physical Review Letters (accepted).

**PI Shaul Muckerman**

"Many-body Effects in 2-D Optical Spectra of Semiconductor Quantum-Dot Pairs: TPHF and Beyond, R. Oszwaldowski, D. Abramavicius and S. Mukamel, J. Phys. Cond. Matt (Submitted, 2007)

## N

**PI Habib Najm**

J. Ray, C. A. Kennedy, S. Lefantzi and H. N. Najm, "Using high-order methods on adaptively refined block-structured meshes - derivatives, interpolations, and filters", SIAM Journal on Scientific Computing, 2007, 29(1):139-181.

N. Trebon, A. Morris, J. Ray, S. Shende and A. D. Malony, "Performance modeling using component assemblies", Concurrency and Computation: Practice and Experience, 2007, 19(5):685-696.

David E. Bernholdt, Benjamin A. Allan, Robert Armstrong and Felipe Bertrand, Kenneth Chiu, Tamara L. Dahlgren, Kostadin Damevski, Wael R. Elwasif, Thomas G. W. Epperly, Madhusudhan Govindaraju, Daniel S. Katz, James A. Kohl, Manoj Krishnan, Gary Kumfert, J. Walter Larson, Sophia Lefantzi, Michael J. Lewis, Allen D. Malony, Lois C. McInnes, Jarek Nieplocha, Boyana Norris, Steven G. Parker, Jaideep Ray, Sameer Shende, Theresa L. Windus, and Shujia Zhou, "A Component Architecture for High-Performance Scientific Computing", International Journal of High-Performance Computing Application, 2006, 20:162-202.

**PI John Negele**

QCD, C. Alexandrou, G. Koutsou, Th. Leontiou, J.W. Negele, A. Tsapalis. Accepted for publication in Phys. Rev. D. (2007) arXiv:0706.3011 [hep-lat]

The Axial N to Delta transition form factors from Lattice QCD.? C. Alexandrou, Th. Leontiou, J.W. Negele, A. Tsapalis, Phys.Rev.Lett.98:052003,2007, hep-lat/0607030

The Nucleon electromagnetic form factors from Lattice QCD.? C. Alexandrou, G. Koutsou, J.W. Negele, A. Tsapalis, Phys.Rev.D74:034508,2006, hep-lat/06050176

The Nucleon to Delta electromagnetic transition in full lattice QCD. C. Alexandrou, G. Koutsou, H. Neff, J.W. Negele, W. Schroers, A. Tsapalis, submitted to Phys. Rev. D

**PI Brian Nelson**

"Hall magnetohydrodynamics simulations of end-shorting induced rotation in field-reversed configurations", A. I. D. Macnab, R. D. Milroy, C. C. Kim, and C. R. Sovinec, Phys. Plasmas 14, 092503 (2007)

"Overview of the Plasma Science and Innovation Center (PSI - Center)" Jarboe, T.R.; Bayless, A.; Held, E.; Jeong-Young Ji; Kim, C.; Macnab, A.; Marklin, G.; Milroy, R.D.; Nelson, B.A.; Uri Shumlak; Sovenic, C.; Vadlamani, S.; Woodruff, S., Journal of Fusion Energy, v 26, n 1-2, June 2007, p 91-2

"The Plasma Science and Innovation Center Interfacing Group", Nelson, B.A.; Kim, C.C.; Cassidy, A.P.; Griffith, S.D.; Milroy, R.D.; Jarboe, T.R., Journal of Fusion Energy, v 26, n 1-2, June 2007, p 127-30

"Simulations of the field-reversed configuration with the NIMROD code", Macnab, A.I.D. ; Barnes, D.C.; Milroy, R.D.; Kim, C.C.; Sovinec, C.R. Journal of Fusion Energy, v 26, n 1-2, June 2007, p 113-17

"Preliminary Simulations of FLR Effects on RFP Tearing Modes", Charlson C. Kim and NIMROD Team, Journal of Fusion Energy, 0164-0313, (2007)

**PI Karoly Nemeth**

Karoly Nemeth, Baifei Shen, Yuelin Li, Robert Crowell, Katherine C. Harkay and John Cary: Laser-Driven Coherent Betatron Oscillation in a Laser-Wakefield Cavity, submitted to Physical Review Letters.

Baifei Shen, Yuelin Li, Karoly Nemeth, Hairong Sheng, Robert Soliday, Robert Crowell, Edward Frank, William Gropp and John Cary: Electron injection by a nanowire in the bubble regime, Physics of Plasmas 14, 053115 (2007).

**PI Gregory Newman**

Commer M. and Newman G. A., 2007, New advances in three-dimensional controlled- source electromagnetic inversion: Geophysical Journal International, In Press.

Commer M., Newman G., Carazzone, J., Dickens, T., Green, K., Wahrmund,L., Willen, D., and Shiu, J., 2007, Massively parallel eletrical imaging of hydrocarbons using the Blue Gene/L supercomputer: IBM Journal of Research and Development, 52,No. 1/2.

**PI Cheuk-Yiu Ng**

Juan Li, Jie Yang, Yuxiang Mo, K. C. Lau, X. M. Qian, Y. Song, Jianbo Liu, and C. Y. Ng, J. Chem. Phys., 126, 184304 (2007). "Combined Vacuum Ultraviolet Laser and Synchrotron Pulsed Field Ionization Study of CH2BrCl".

Xi Xing, Beth Reed, Kai-Chung Lau, C. Y. Ng, Xu Zhang, and G. Barney Ellis, J. Chem. Phys., 126, 171101 (2007). "Vacuum Ultraviolet Laser Pulsed Field Ionization-Photoelectron Study of Allyl Radical CH2CHCH2".

Xiaonan Tang, Cassidy Houchins, Kai-Chung Lau, C. Y. Ng, Rainer A. Dressler, Yu-hui Chiu, Tian-Shu Chu and Ke-Li Han, J. Chem. Phys., in press, (2007). "A time-dependent wave packet quantum scattering study of the reaction HD+(v=0-3; j0=1) + He -> HeH+ (HeD+) + D(H)".

K.-C. Lau and C. Y. Ng, Acc. Chem. Res., 39, 823 (2006). "Benchmarking state-of-the-art ab initio thermochemical predictions with accurate pulsed-field ionization photoion-photoelectron measurements".

**PI Esmond Ng**

P. Amestoy, X.S. Li, and E.G. Ng. "Diagonal Markowitz Scheme with Local Symmetrization", SIAM J. Matrix Analysis and Applications, Vol. 29, No. 1, pp. 228-244, 2007.

P. Amestoy, X.S. Li, and S. Pralet. "Unsymmetric Ordering Using a Constraint Markowitz Scheme", SIAM J. Matrix Analysis and Applications, Vol. 29, No. 1, pp. 302-327, 2007.

S. Chandrasekaran, M. Gu, X. S. Li, and J. Xia. "Some Fast Algorithms for Hierarchically Semiseparable Matrices", Submitted to SIAM J. Matrix Analysis and Applications. June, 2007.

S. Chandrasekaran, M. Gu, X. S. Li, and J. Xia. "Superfast Multifrontal Method for Structured Linear Systems of Equations", Submitted to SIAM J. Matrix Analysis and Applications. June, 2007.

W. Gao, X.S. Li, C. Yang, and Z. Bai. "An Implementation and Evaluation of the AMLS Method for Sparse Eigenvalue Problems", ACM Trans. on Math. Software, vol. 34, no. 4, 2007.

Laura Grigori, Michel Cosnard, and Esmond G. Ng. "On the Row Merge Tree for Sparse LU Factorization with Partial Pivoting". BIT Numer. Math, Vol. 47, No. 1, March 2007, pp. 45-76.

L. Grigori, J.W. Demmel, and X.S. Li. "Parallel Symbolic Factorization for Sparse LU with Static Pivoting", SIAM J. Scientific Computing, Vol. 29, Issue 3, 1289-1314, 2007.

L. Grigori and X.S. Li. "Towards an Accurate Performance Modeling of Parallel Sparse Factorization", Applicable Algebra in Engineering, Communication, and Computing, Vol. 18, No. 3, pp. 241-261, 2007.

X.S. Li, J. Demmel, L. Grigori, M. Gu, J. Xia, S. Jardin, C. Sovinec, L.-Q. Lee. "Enhancing Scalability of Sparse Direct Methods", Proceedings of SciDAC 2007, Scientific Discovery Through Advanced Computing, 24-28 June 2007, Boston. J. Physics: Conference Series 78 (2007) 012041, Institute of Physics Publishing.

K. Nakajima. "The Impact of Parallel Programming Models on the Linear Algebra Performance for Finite Element Simulations", Lecture Notes in Computer Science 4395, 334-348, Special Issue of VEPAR 2006, Rio de Janeiro, Brazil (2007).

K. Nakajima. "Parallel Multistage Preconditioners based on a Hierarchical Graph Decomposition for SMP Cluster Architectures with a Hybrid Parallel Programming Model", Lecture Notes in Computer Science 4782, 384-395, HPCC'07 (High-Performance Computation Conference 2007), Houston, Texas

Esmond G. Ng. "Parallel Sparse Solvers, Preconditioners, and Their Applications", in Parallel Processing for Scientific Computing, eds. Michael Heroux, Padma Raghavan, and Horst Simon, SIAM (2006).

**PI Jerry Nolen**

Wish-List for Large-Scale Simulations for Future Radioactive Beam Facilities http://cern.ch/AccelConf/ICAP06/PAPERS/WEMPMP02.PDF

"Application of a New Procedure for Design of 325 MHz RFQ" P. N. Ostroumov, V. N. Aseev, and A. A. Kolomiets Journal of Instrumentation, JINST 1 P04002

Physics Design of the 8-GeV H-Minus Linac P. N. Ostroumov New Journal of Physics, http://www.iop.org/EJ/njp Status: ACCEPTED FOR PUBLICATION

Parallelization of a Beam Dynamics Code TRACK and First Large Scale RFQ Simulations, J. Xu, B. Mustapha, V. N. Aseev, and P. N. Ostroumov, Phys. Rev. ST, Status: TIS

Computational Needs for the RIA Accelerator Systems P. N. Ostroumov, J. A. Nolen, and B. Mustapha Proceedings of the 8th International Computational Accelerator Physics Conference (ICAP-04), St. Petersburg, Russia, June 29-July 2, 2004; Nucl. Instrum. Methods A558, 25-31 (2006), Status: PUBLISHED

**PI Arthur Nozik**

S.-H. Lee, Y.-H. Kim, R. Deshpande, P. A. Parilla, K. M. Jones, B. To, E. Whitney, A. H. Mahan, S. B. Zhang, and A. C. Dillon, "Anomalous Reversible Lithium-Ion Intercalation in Molybdenum Oxide Nanoparticles", Submitted to Science (2007).

Y. Jiang, Y.-H. Kim, S. Yang, Z. Tang, K. Wu, P. Ebert, S. B. Zhang, and E. G. Wang, "Growing extremely thin bulklike metal film on a semiconductor surface: monolayer Al(111) on Si(111)", Appl. Phys. Lett., Accepted (2007).

T. J. McDonald, D. Svedruzic, Y.-H. Kim, J. L. Blackburn, S. B. Zhang, P. W. King, and M. J. Heben, "Wiring-up hydrogenase with single-walled carbon nanotubes", Nano Lett., Accepted (2007).

Y. Y. Sun, Y.-H. Kim, and S. B. Zhang, "Effect of Spin State on the Dihydrogen Binding Strength to Transition Metal Centers in Metal-organic Frameworks", J. Am. Chem. Soc., published online (Sep. 2007).

A. C. Dillon, E. Whitney, C. Engtrakul, C. J. Curtis, K. J. O'Neill, P. A. Parilla, L. J. Simpson, M. J. Heben, Y. Zhao, Y.-H. Kim, and S. B. Zhang, "Novel organometallic fullerene complexes for vehicular hydrogen storage", phys. stat. sol. (b), published online (Sep. 2007).

C. Engtrakul, Y.-H. Kim, J. M. Nedeljkovic, S. P. Ahrenkiel, K. E. H. Gilbert, J. L. Alleman, S. B. Zhang, O. I. Micic, A. J. Nozik, and M. J. Heben, "Self-Assembly of Linear Arrays of Semiconductor Nanoparticles on Carbon Single-Walled Nanotubes", J. Phys. Chem. B 110, 25153-25157 (2006).

**PI Peter Nugent**

E. Huff, A.E. Schulz, M. White, D.J. Schlegel, & M.S. Warren, "Simulations of Baryon Oscillations", Astroparticle Physics, 26, 351.

D.J. Eisenstein, H.-J. Seo, & M. White, "On the Robustness of the Acoustic Scale in the Low-Redshift Clustering of Matter," Astrophysical Journal, 664, 660.

N. Padmanabhan, M. White, & D.J. Eisenstein, "A Robust Estimator of the Small-Scale Galaxy Correlation Function," Monthly Notices of the Royal Astronomical Society, 376, 1702.

## O

**PI Grazyna Odyniec**

Longitudinal double-spin asymmetry for inclusive jet production in p+p collisions at sqrt(s)=200 GeV STAR Collaboration arXiv:0710.2048

Measurement of Transverse Single-Spin Asymmetries for Di-Jet Production in Proton-Proton Collisions at sqrt(s) = 200 GeV STAR COllaboration Phys. Rev. Lett. 99(2007)142003

Forward Lambda Production and Nuclear Stopping Power in d+Au Collisions at sqrt(sNN) = 200 GeV STAR Collaboration e-Print: 0706.0472

Partonic flow and phi-meson production in Au+Au collisions at sqrt(s) = 200 GeV STAR Collaboration Phys. Rev. Lett. 99 (2007) 112301

Enhanced strange baryon production in Au+Au collisions compared to p+p at sqrt(s)=200 GeV STAR Collaboration e-Print Archives (0705.2511)

Global polarization measurement in Au+Au collisions STAR Collaboration Phys. Rev. C 76(2007)024915

Strangelet Search in AuAu collisions at 200 GeV STAR Collaboration Phys. Rev. C 76 (2007)011901

Strange particle production in p+p collisions at sqrt(s) = 200 GeV STAR Collaboration Phys. Rev. C 75(2007)064901

Partonic flow and phi-meson production in Au+Au collisions at sqrt(s)=200 GeV STAR Collaboration Phys. Rev. Lett. 99(2007)112301

Charged particle distributions and nuclear modification at high rapidities in d+Au collisions at sqrt(s)=200 GeV STAR Collaboration e-Print nucl-ex/0703016

Mass, quark-number, and sqrt(s) dependence of the second and fourth flow harmonics in ultra-relativistic nucleus-nucleus collisions STAR Collaboration Phys. Rev. C 75(2007)054906

**PI Joseph Oefelein**

T. G. Drozda, G. Wang, V. Sankaran, J. R. Mayo, J. C. Oefelein and R. S. Barlow (2007). Scalar filtered mass density functions in nonpremixed turbulent jet flames. Submitted to Combustion and Flame.

T. C. Williams, R. W. Schefer, J. C. Oefelein and C. R. Shaddix (2007). Idealized gas turbine combustor for performance research and validation of large eddy simulations. Review of Scientific Instruments, 78(035114): 1-9.

J. C. Oefelein, V. Sankaran and T. G. Drozda (2007). Large eddy simulation of swirling particle-laden flow in a model axisymmetric combustor. Proceedings of the Combustion Institute, 31: 2291-2299.

J. C. Oefelein, T. G. Drozda and V. Sankaran (2006). Large Eddy Simulation of Turbulence-Chemistry Interactions in Reacting Flows: The Role of High-Performance Computing and Advanced Experimental Diagnostics. Journal of Physics, 46: 16-27.

J. C. Oefelein (2006). Large eddy simulation of turbulent combustion processes in propulsion and power systems. Progress in Aerospace Sciences, 42: 2-37.

**PI Serdar Ogut**

Juan C. Idrobo, Mingli Yang, Koblar Jackson, and Serdar Ogut,"First Principles Absorption Spectra of Si_n (n=20-28) Clusters: Time-Dependent Local-Density Approximation versus Predictions from Mie Theory", Phys. Rev. B 74, 153410 (2006).

Serdar Ogut, Juan C. Idrobo, Julius Jellinek, and Jinlan Wang, "Structural, Electronic, and Optical Properties of Noble Metal Clusters from First Principles", J. Cluster Sci. 17, 609 (2006).

Juan C. Idrobo, Serdar Ogut, Karoly Nemeth, Julius Jellinek, and Riccardo Ferrando, "First Principles Isomer-Soecific Absorption Spectra of Ag_11", Phys. Rev. B 75, 233411 (2007).

Hakim Iddir, Serdar Ogut, Peter Zapol, and Nigel Browning, "Diffusion Mechanisms of Native Point Defects in Rutile TiO2", Phys. Rev. B 75, 072303 (2007).

Juan C. Idrobo, Weronika Walkosz, Shing Fan Yip, Serdar Ogut, Jinlan Wang, and Julius Jellinek, "Static Polarizabilities and Optical Absorption Spectra of Gold Clusters (Au_n, n = 2 - 14 and 20) from First Principles", to appear in Phys. Rev. B.

**PI Leonid Oliker**

L. Oliker, A. Canning, J. Carter, C. Iancu, M. Lijewski, S. Kamil, J. Shalf, H. Shan, E. Strohmaier, S. Ethier, T. Goodale,"Scientific Application Performance on Candidate PetaScale Platforms", International Parallel & Distributed Processing Symposium (IPDPS) 2007. LBNL-62952. WINNER: Best paper application track.

L. Oliker, R. Biswas, R. Wijngaart, D. Bailey, A. Snavely. Chapter 5: Performance Evaluation and Modeling of Ultra-Scale Systems, In Frontiers of Parallel Processing for Scientific Computing, M. A. Heroux, P. Raghavan, and H. D. Simon Eds. SIAM Software, Environments and Tools. Society for Industrial and Applied Mathematics, Philadelphia, PA, USA, pages 233-247, 2006 LBNL-58054.

L. Oliker, J. Shalf, J. Carter, A. Canning, S. Kamil, M. Lijewski, S. Ethier Performance Characteristics of Potential Petascale Scientific Applications , Petascale Computing: Algorithms and Applications, Chapman & Hall / CRC Press, in press, LBNL # pending.

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, LBNL 60800, in press.

J. Borrill, L. Oliker. J. Shalf, H. Shan, Investigation Of Leading HPC I/O Performance Using A Scientific- Application Derived Benchmark, SC07: International Conference for High-Performance Computing, Networking, Storage, and Analysis, 2007, in press, LBNL #63314.

J. Carter, L. Oliker, J. Shalf, "Performance Evaluation of Scientific Applications on Modern Parallel Vector Systems ", High Performance Computing for Computational Science - VECPAR 2006 7th International Conference, Rio de Janeiro, Brazil, June 10-13, 2006, Revised Selected and Invited Papers, Lecture Notes in Computer Science, LNCS 4395, 2007. LBNL 58004.

S. Kamil, A. Pinar, D. Gunter, M. Lijewski, L. Oliker, J. Shalf, "Reconfigurable Hybrid Interconnection for Static and Dynamic Scientific Applications", ACM International Conference on Computing Frontiers, 2007, LBNL-60060.

## P

**PI Bahram Parvin**

B. Parvin, Q. Yang, H. Chang, J. Han, M.H. Barcellos-Hoff, "Iterative Voting for Inference of Structural Saliency and Characteriztion of Subcellular Events ", IEEE Trans. on Image Processing, 2007

H. Chang, Q. Yang, and B. Parvin, "Segmentation of Heterogeneous Blob Objects through Voting and Level Set Formulation ", Pattern Recognition Letters, 2007

J. Han, H. Chang, M.H. Barcellos-Hoff, and B. Parvin, "Segmentation of Mammosphere Structures from Volumetric Data ," IEEE Int. Symp. on Biomedical Imaging, 2007

Andarawewa KL, Erickson AC, Chou WS, Costes SV, Gascard P, Mott JD, Bissell MJ, Barcellos-Hoff MH, " Ionizing radiation predisposes nonmalignant human mammary epithelial cells to undergo transforming growth factor beta induced epithelial to mesenchymal transition," Cancer Research, 2007.

**PI Martin Pattison**

Martin J. Pattison, Kannan N. Premnath, Neil B. Morley and Mohamed A. Abdou. Progress in Lattice Boltzmann Methods for Magnetohydrodynamic Flows relevant to Fusion Applications. In press Fusion Eng Des (2007), doi:10.1016/j.fusengdes.2007.10.005

Sanjoy Banerjee, Kannan N. Premnath and Martin J. Pattison, “Turbulence Simulation using the Generalized Lattice Boltzmann Equation on Massively Parallel Architectures”, 3rd Asian-Pacific Conference on Computational Mechanics (APCOM ‘07) in conjunction with 11th International Conference on Enhancement and Promotion of Computational Methods in Engineering and Science (EPMESC XI), Kyoto, Japan, Dec. 2007.

Martin J. Pattison, Kannan N. Premnath and Neil B. Morley (2007) Lattice Boltzmann Methods for Magnetohydrodynamic Flows in Fusion Applications. Fusion Science and Technology, Vol. 52, 812-816

**PI Joyce Penner**

Guo, H., J. E. Penner, M. Herzog, and S. Xie: 2007, Investigation of the first and second aerosol indirect effects using data from the May 2003 Intensive Operational Period at the Southern Great Plains, J. Geophys. Res., 112, D15206, doi:10.1029/2006JD007173.

Feng, Y. and J.E. Penner, 2007: Global Modeling of Nitrate and Ammonium: Interaction of Aerosols and Tropospheric Chemistry, J. Geophys. Res., 112, D01304, doi:10.1029/2005JD006404.

Penner, J.E., N. Andronova, R. C. Oehmke, J. Brown, Q. F. Stout, C. Jablonowski, B.van Leer, K G. Powell, and M. Herzog, Three Dimensional Adaptive Mesh Refinement on a Spherical Shell for Atmospheric Models with Lagrangian Coordinates, Proceedings of the SciDac Conference, Journal of Physics: Conference Series, 78, 012072, doi:10.1088/1742-6596/78/1/012072, http://www.iop.org/EJ/toc/1742-6596/78/1.

Ito, A., S. Sillman, and J. E. Penner, 2007: Effects of additional nonmethane volatile organic compounds, organic nitrates, and direct emissions of oxygenated organic species on global tropospheric chemistry, J. Geophys. Res., 112, D06309, doi:10.1029/2005JD006556.

Guo, H. J. E. Penner, M. Herzog, H. Pawlowska, 2007: Examination of the aerosol indirect effect under contrasting environments during the ACE-2 experiment, Atmos. Chem. Phys., 7, 535-548, http://www.atmos-chem-phys.net/7/535/2007/acp-7-535-2007.pdf.

H. Guo, Y. Liu, and J E. Penner, 2007: Does the threshold representation associated with the autoconversion process matter?, Geophys. Res. Lett., submitted.

Jablonowski, C., M. Herzog, J.E. Penner, R.C. Oemke, Q.F. Stout, B. van Leer, and K.G. Powell, 2005: Block-Structured Adaptive Grids on the Sphere: Advection Experiments, Mon. Weath. Rev., Volume 134, pp. 3691-3713, DOI: 10.1175/MWR3223.1.

**PI Stephen Pennycook**

W. Luo, A. Franceschetti, M. Varela, J. Tao, S.J. Pennycook, and S.T. Pantelides, Orbital-Occupancy versus Charge Ordering and the Strength of Electron Correlations in Electron-Doped CaMnO3, Physical Review Letters 99, 036402 (2007).

W. Luo, S. J. Pennycook, and S. T. Pantelides, s-Electron Ferromagnetism in Gold and Silver Nanoclusters, Nano Letters 7, 3134 (2007).

S. Ho Oh, K. van Benthem, S.I. Molina, A.Y. Borisevich, W. Luo, P. Werner, N.D. Zakharov, D. Kumar, S.T. Pantelides, and S.J. Pennycook, Point Defect Configurations of Supersaturated Au Atoms Inside Si Nanowires, submitted to Nano Letters.

K.G. Roberts, M. Varela, S. Rashkeev, S.T. Pantelides, S.J. Pennycook, and K.M. Krishnan, Defect- mediated ferromagnetism in insulating Co-doped anatase TiO2 thin films, submitted to Physical review Letters.

J.C. Idrobo, A. Halabica, R. H. Magruder III, R.F. Haglund Jr., S.J. Pennycook, and S.T. Pantelides, Optical Properties of Embedded Nanoparticles: Size Does Not Always Matter, work to be submitted to Physical Review Letters November 2007.

A. G. Marinopoulos, K. van Benthem, S. N. Rashkeev, S. J. Pennycook and S. T. Pantelides, Impurity segregation and ordering in Si/SiO/HfO structures, Physical Review B 76, 035438 (2007).

A. Halabica, J. C. Idrobo, S. T. Pantelides, and R. F. Haglund Jr., R. H. Magruder III, S.J. Pennycook, Pulsed infrared laser annealing of gold nanoparticles embedded in a silica matrix, submitted to Applied Physics Letters.

S. J. Pennycook, A. R. Lupini, M. Varela, A. Y. Borisevich, Y. Peng, M. P. Oxley and M. F. Chisholm Scanning Transmission Electron Microscopy for Nanostructure Characterization, pp. 152-191 in Scanning Microscopy for Nanotechnology: Techniques and Applications, ed. by W. Zhou and Z. L. Wang, Springer, 2006.

A. R. Lupini, S. N. Rashkeev, M. Varela, A. Y. Borisevich, M. P. Oxley, K. van Benthem, Y. Peng, N. de Jonge, G. M. Veith, M. F. Chisholm and S. J. Pennycook, Scanning Transmission Electron Microscopy, in Nanocharacterization, edited by the Royal Society of Chemistry, United Kingdom, in press (2007).

**PI Saul Perlmutter**

Kuznetsova, N., et al., A New Determination of the High Redshift Type Ia Supernova Rates with the Hubble Space Telescope Advanced Camera for Surveys, ArXiv e-prints, 710, arXiv:0710.3120 (2007). Accepted for publication in Astrophysical Journal.

Kuznetsova, N. V. & B. M. Connolly, A Probabilistic Approach to Classifying Supernovae Using Photometric Information, Astrophysical Journal, 659, 530 (2007).

Cosmology: The Universe's skeleton sketched Authors: Linder, Eric V. Publication: Nature, Volume 445, Issue 7125, pp. 273 (2007)

Separating dark physics from physical darkness: Minimalist modified gravity versus dark energy Authors: Huterer, Dragan; Linder, Eric V. Publication: Physical Review D, vol. 75, Issue 2, id. 023519

Snapping supernovae at z > 1.7 Authors: Aldering, Greg; Kim, Alex G.; Kowalski, Marek; Linder, Eric V.; Perlmutter, Saul Publication: Astroparticle Physics, Volume 27, Issue 2-3, p. 213-225.

Cosmic variance of weak lensing surveys in the non-Gaussian regime Authors: Semboloni, Elisabetta; van Waerbeke, Ludovic; Heymans, Catherine; Hamana, Takashi; Colombi, Stephane; White, Martin; Mellier, Yannick Publication: Monthly Notices of the Royal Astronomical Society: Letters, Volume 375, Issue 1, pp. L6-L10.

Simulations of baryon oscillations Authors: Huff, Eric; Schulz, A. E.; White, Martin; Schlegel, David J.; Warren, Michael S. Publication: Astroparticle Physics, Volume 26, Issue 6, p. 351-366.

K-Corrections and Spectral Templates of Type Ia Supernovae Authors: Hsiao, E. Y.; Conley, A.; Howell, D. A.; Sullivan, M.; Pritchet, C. J.; Carlberg, R. G.; Nugent, P. E.; Phillips, M. M. Publication: The Astrophysical Journal, Volume 663, Issue 2, pp. 1187-1200.

**PI Steven Pieper**

Flavor Evolution of the Neutronization Neutrino Burst from an O-Ne-Mg Core-Collapse Supernova, Huaiyu Duan (INT, Univ of Washington), George M. Fuller (UCSD), J. Carlson (LANL), Yong-Zhong Qian (UMN) preprint arXiv:0710.1271, submitted to Phys. Rev. Lett.

Analysis of Collective Neutrino Flavor Transformation in Supernovae, Huaiyu Duan (UCSD), George M. Fuller (UCSD), J. Carlson (LANL), Yong-Zhong Qian (UMN), Phys. Rev. D75, 125005 (2007).

Coherent Development of Neutrino Flavor in the Supernova Environment Huaiyu Duan (UCSD), George M. Fuller (UCSD), J. Carlson (LANL), Yong-Zhong Qian (UMN), Phys.Rev.Lett. 97 (2006) 241101.

**PI Ali Pinar**

Vaibhav Donde, Vanessa Lopez, Bernard Lesieutre, Ali Pinar, Chao Yang, and Juan Meza, Severe multiple contingency screening in electric power systems, to appear in IEEE Transactions on Power Systems.

A. Pinar J. Meza, V. Donde, B. Lesieutre, Optimization Strategies for the vulnerability analysis of the electric power grid, to be submitted to SIAM Optimization, available as an LBNL technical report LBNL-63473.

B. Lesieutre, A. Pinar, and S. Roy, Power system extreme event detection: the vulnerability frontier, to appear in Proc. 40th Hawaii international conference on system sciences.

A. Pinar, Y. Fogel, and B. Lesieutre, The Inhibiting Bisection Problem, to be submitted to ACM 20th Symposium Parallel Algorithms and Architectures (SPAA) 2007, available as an LBNL technical report LBNL-62142.

Shoaib Kamil, Ali Pinar, Dan Gunter, Michael Lijewski, Leonid Oliker, and John Shalf, Reconfigurable hybrid interconnection for static and dynamic scientific applications, in Proc. 2007 ACM International Conference on Computing Frontiers.

Ali Pinar, Adam Reichert, and Bernard Lesieutre, Computing Criticality of Lines in a Power System, to appear in Proc. 2007 IEEE International Symposium on Circuits and Systems, New Orleans, LA, May 2007.

B. Lesieutre, S. Roy, V. Donde, and A. Pinar, Power system extreme event analysis using graph partitioning, Proc. of the North American Power Symposium, Carbondale, IL, October 2006.

**PI Michael Pindzola**

Electron-impact ionization of highly excited hydrogen-like ions in a co-linear s-wave model, T Topcu, M S Pindzola, C P Ballance, D C Griggin, and F J Robicheaux, Physical Review A 74, 062708 (December 2006).

Charge dependent effects in the double photoionization of He-like ions, M Foster and J P Colgan, Journal of Physics B 39, 5067 (December 2006).

Electron-impact excitation of W+44 and W+45, C P Ballance and D C Griffin, Journal of Physics B 40, 247 (January 2007).

Electron-impact ionization of argon using the R-matrix with pseudostates method C P Ballance D C Griffin, M S Pindzola, and S D Loch, Journal of Physics B 40, F27 (February 2007).

Capture and transport of electronic states of fast ions penetrating solids: an open quantum system approach with sources and sinks, M Seliger, C O Reinhold, T Minami, D R Schultz, M S Pindzola, S Yoshida, J Burgdorfer, E Lamour, J P Rozet, and D Vernhet, Physical Review A 75, 032714 (March 2007).

Electron-impact excitation of neutral boron using the R-matrix with pseudostates method, C P Ballance, D C Griffin, K A Berrington, and N R Badnell, Journal of Physics B 40, 1131 (March 2007).

Triple differential cross sections for the double photoionization of H_2, J P Colgan, M S Pindzola, and F J Robicheaux, Physical Review Letters 98, 153001 (April 2007).

Electron-impact ionization of metastable excited states of Li+, J C Berengut, S D Loch, C P Ballance, and M S Pindzola, Journal of Physics B 40, 1331 (April 2007).

Double ionization of helium by fast bare ion collisions, M S Pindzola, F J Robicheaux, and J P Colgan, Journal of Physics B 40, 1695 (May 2007).

Angular distributions from photoionization of H+_2 M Foster, J P Colgan, O Al-Hagan, J L Peacher, D H Madison, and M S Pindzola, Physical Review A 75, 062707 (June 2007)

Electron-impact double ionization of helium at high energies, M S Pindzola, F J Robicheaux, and J P Colgan, Physical Review A 76, 024704 (August 2007)

Numerical study of charge transfer in H+ + H+ and H+2 + Li+2 collisions, T Minami, M S Pindzola, T G Lee, and D R Schultz, Journal of Physics B 40, 3629 (September 2007)

**PI Tomasz Plewa**

Zhang, J., Messer, O. E. B., Khokhlov, A. M., and Plewa, T., On the Evolution of Thermonuclear Flames on Large Scales, 2007, ApJ, 656, 347

Plewa, T., Detonating Failed Deflagration Model of Thermonuclear Supernovae. I. Explosion Dynamics, 2007, ApJ, 657, 942

Kasen, D., and Plewa, T., Detonating Failed Deflagration Model of Thermonuclear Supernovae. II. Comparison to Observations, 2007, ApJ, 662, 459

**PI Gerald Potter**

Climate Model Forecast Experiments for TOGA-COARE.J. Boyle,S. Klein,G. Zhang,S. Xie,X. Wei. Accepted by Monthly Weather Review.

On the deep convection, high clouds and the upper troposphere relative humidity in the Multi-scale Modeling Framework, Yunyan Zhang, Stephen A. Klein, Chuntao Liu, Baijun Tian, Roger Marchand, John Haynes, Renata McCoy and Yuying Zhang to be submitted to JGR

Simulations of Arctic mixed-phase clouds in forecasts with CAM3 and AM2 for M-PACE" by Xie et al. Accepted and currently under revision

**PI Larry Pratt**

Lawrence M. Pratt Modeling Lithium Dialkylamides in Ethereal Solvents: A Test of the Microsolvation Model Theochem, 2007, 811, 191

Lawrence M. Pratt, Diep Huong Phan Tran, Phung Thao Thi Tran, Ngan Van Nguyen Basis set and Electron Correlation Effects on Lithium Carbenoid Dimerization Energies Bull. Chem. Soc. Japan, 2007, 80, 1587

**PI Joel Primack**

Berrier, Bullock, Barton, Guenther, Zentner, and Wechsler, Close Galaxy Counts as a Probe of Hierarchical Structure Formation, ApJ 652, 56 (2006).

Ceverino and Klypin, Resonances in Barred Galaxies, MNRAS 379, 1155 (2007).

Conroy, Wechsler, and Kravtsov, The Hierarchical Build-Up of Massive Galaxies and Intracluster Light since z=1, ApJ 668, 826 (2007).

Cox, Jonsson, Primack, and Somerville, Feedback in simulations of disc-galaxy major mergers, MNRAS 373, 1013 (2006).

Cox, Jonsson, Somerville, Primack, and Dekel The effect of Mass Ratio on Merger Driven Starbursts, submitted to MNRAS, arXiv:0709.3511 (2007).

Flores, Allgood, Kravtsov, Primack, Buote, and Bullock, The shape of galaxy cluster dark matter haloes: systematics of its imprint on cluster gas and comparison to observations, MNRAS 377, 883 (2007).

Rocha, Jonsson, Primack, and Cox, Dust Attenuation in Hydrodynamic Simulations of Spiral Galaxies, MNRAS in press, arXiv:astro-ph/0702513 (2007).

Wechsler, Zentner, Bullock, Kravtsov, and Allgood, The Dependence of Halo Clustering on Halo Occupation History, Concentration, and Occupation, ApJ 652, 71 (2006).

**PI Fritz Prinz**

X. Wang, H. Huang, T. Holme, X. Tian, F. Prinz, J. Power Sources. In press (accepted).

T. Holme, H. Huang, F. Prinz, Phys. Rev. B, submitted, under review.

H. Huang, T. Holme, F. Prinz, ECS Trans. In press (accepted).

## Q

**PI Eliot Quataert**

Sharma, P. Quataert, E. & Stone, J. M., "Faraday Rotation in Global Accretion Disk Simulations: Implications for Sgr A*", 2007, ApJ, 671, 1696 Sharma, P. Quataert, E., Hammett, G. W., & Stone, J. M., "Electron Heating in Hot Accretion Flows", 2007, ApJ, 667, 714

## R

**PI Abhay Ram**

Plasma 2010 Committee, Plasma Science Committee, National Research Council, Plasma Science: Advancing Knowledge in the National Interest, National Academies Press, 2007.

"Microturbulent drift mode suppression as a trigger mechanism for internal transport barriers on Alcator C-Mod," K. Zhurovich et al., Nucl. Fusion 47 (2007) 1220-1231.

"Identification of TEM Turbulence through Direct Comparison of Nonlinear Gyrokinetic Simulations with Phase Contrast Imaging Density Fluctuation Measurements," D. R. Ernst, N. Basse, W. Dorland, C. L. Fiore, L. Lin, A. Long, M. Porkolab, K. Zeller, and K. Zhurovich, IAEA Fusion Energy Conference Chengdu, China, 16-21 October (2006), oral paper IAEA-CN-149/TH/1-3.

"Role of trapped electron mode turbulence in internal transport barrier control in the Alcator C-Mod Tokamakak", D. R. Ernst, P. T. Bonoli, P. J. Catto, W. Dorland, C. L. Fiore, R. S. Granetz, M. Greenwald, A. E. Hubbard, M. Porkolab, M. H. Redi, J. E. Rice, K. Zhurovich, and the Alcator C-Mod Group, Phys. Plasmas, 11(5) 2637 (2004).

D. R. Ernst, N. Basse, P. T. Bonoli, P. J. Catto, W. Dorland, C. L. Fiore, M. Greenwald, A. E. Hubbard, E. S. Marmar, M. Porkolab, J. E. Rice, K. Zeller and K. Zhurovich, "Mechanisms for ITB Formation and Control in Alcator C-Mod Identified Through Gyrokinetic Simulations of TEM Turbulence," Proc. 20th Int'l. Atomic Energy Agency Fusion Energy Conference, Vilamoura, Portugal, 1-6 November 2004, oral paper IAEA-CN-116/TH/4-1. http://www-naweb.iaea.org/napc/physics/fec/fec2004/datasets/TH_4-1.html

C L Fiore, P T Bonoli, D R Ernst, M J Greenwald, E S Marmar, M H Redi, J E Rice, S J Wukitch and K Zhurovich, "Internal transport barrier production and control in Alcator C-Mod," Plasma Phys. Control. Fusion 46 B281-B291. EPS Invited Oral 2004.

C. L. Fiore, D. R. Ernst, J. E. Rice, N. Basse, P. T. Bonoli, M. J. Greenwald, E. S. Marmar, S. J. Wukitch, K. Zhurovich, "Internal Transport Barriers in Alcator C-Mod," submitted to C-Mod Special Issue, Fusion Science and Tecnology, Augst, 2005.

N. P. Basse et al., "Characterization of core and edge turbulence in L- and enhanced D-alpha H-mode Alcator C-mod plasmas," Physics of Plasmas, 12(5) May 2005, p 52512-1-14.

C. L. Fiore et al., "Control of internal transport barriers on Alcator C-mod," Physics of Plasmas 11(5), May 2004, p 2480-7.

J. C. Wright, L. A. Berry, D. B. Batchelor P. T. Bonoli, E. F. Jaeger, E. D Azevedo M. D. Carter, C. K. Phillips, R. W. Harvey H. Okuda, D. N. Smithe, D. A. D Ippolito J. R. Myra, M. Brambilla, and R. J. Dumont, ``Nonthermal particle and full-wave diffraction effects on heating and current drive in the ICRF and LHRF regimes,'' Nucl. Fusion, 45(9), September 2005.

Y. Lin, S. J.Wukitch, A. Parisot, J. C. Wright, N. Basse, P. Bonoli, E. Edlund, L. Lin, M. Porkolab, S.Wolfe, G. Schilling, and P. Phillips, ``Ion cyclotron range of frequencies wave phenomena in the mode conversion region in Alcator C-Mod,'' Plasma Phys. Controlled Fusion, 47(-1):0, 2005.

J. C. Wright, P. T. Bonoli, M. Brambilla, E. Azevedo, L. A. Berry, D. B. Batchelor, E. F. Jaeger, M. D. Carter, C. K. Phillips, H. Okuda, R. .W. Harvey, J. R.Myra, D. A. D Ippolito, and D. N. Smithe, ``Full-wave electromagnetic field simulations of lower hybrid waves in tokamaks,'' In P. Bonoli and S. Wukitch, editors, 16th Topical Conference on Radio Frequency Power in Plasmas and, number to be published, page 1, New York, 2005. American Institute of Physics.

**PI David Randall**

Benedict, J., and D. A. Randall, 2007: An analysis of the MJO based on TRMM rainfall data. J. Atmos. Sci., 64, 2332-2354.

DeMott, C. A., D. A. Randall, and M. Khairoutdinov, 2007: Convective precipitation variability as a tool for general circulation model analysis. J. Climate, 20, 91-112.

Jung, J.-H., and A. Arakawa, 2007: A three-dimensional anelastic model based on the vorticity equation. Mon. Wea. Rev., in press.

Khairoutdinov, M., C. A. DeMott, and D. A. Randall, 2007: Evaluation of the simulated interannual and subseasonal variability in an AMIP-style simulation using the CSU Multiscale Modeling Framework. J. Climate (in press).

Konor, C. S., and A. Arakawa, 2007: Multi-point explicit differencing (MED) for time integrations of the wave equation. Mon. Wea. Rev., in press.

Toy, M., and D. A. Randall, 2007: Comment on the article Vertical discretizations for compressible Euler equation atmospheric models giving optimal representation of normal modes by Thuburn and Woolings. J. Comp. Phys., 223, 82-88.

Tulich, S. N., D. A. Randall, and B. E. Mapes, 2007: Vertical-mode and cloud decomposition of large- scale convectively coupled gravity waves in a two-dimensional cloud-resolving model. J. Atmos. Sci., 64, 1220-1229.

Yamaguchi, T., and D. A. Randall, 2007: Large-eddy simulation of evaporatively driven entrainment in cloud-topped mixed layers. J. Atmos. Sci. (in press).

**PI Sergey Rashkeev**

S.N.Rashkeev, D.M.Ginosar, L.M.Petkovic, and H.H.Farrell. Catalytic activity of supported metal particles for sulfuric acid decomposition reaction. Catalysis Today (submitted 10/17/2007).

A.G.Marinopoulos, K.van Benthem, S.N.Rashkeev, S.J.Pennycook, and S.T.Pantelides. Impurity segregation and ordering in Si/SiO2/HfO2 structures. Phys. Rev. Lett. (submitted 07/23/2007).

K.Griffin Roberts, M.Varela, S.Rashkeev, S.T.Pantelides, S.J.Pennycook, and Kannan M. Krishnan. The origin of ferromagnetism in insulating CoxTi1-xO2 anatase thin films. Phys. Rev. Lett. (submitted 03/16/07).

A.Y.Borisevich, S.Wang, S.N.Rashkeev, M.Glazoff, S.J.Pennycook, and S.T.Pantelides. Dual nanoparticle/substrate control of catalytic dehydrogenation. Advanced Materials 19, N 16, 2129-2133 (2007).

S.N.Rashkeev, A.R.Lupini, S.H.Overbury, S.J.Pennycook, and S.T.Pantelides. The role of the nanoscale in catalytic CO oxidation by supported Au and Pt nanostructures. Phys. Rev. B 76, N 3, 035438 (2007); Virtual Journal of Nanoscience & Technology, 16, N 7, (August 13, 2007).

S.N.Rashkeev, K.W.Sohlberg, S.Zhuo, and S.T.Pantelides. Hydrogen-induced initiation of corrosion in aluminum. The Journal of Physical Chemistry C 111, N 19, 7175-7178 (2007).

**PI Lawrence Rauchwerger**

Associative Parallel Containers In STAPL, Gabriel Tanase, Chidambareswaran (Chids) Raman, Mauro Bianco, Nancy M. Amato, Lawrence Rauchwerger, In Wkshp. on Lang. and Comp. for Par. Comp. (LCPC), Oct 2007.

The STAPL pArray, Gabriel Tanase, Mauro Bianco, Nancy M. Amato, Lawrence Rauchwerger, In Proc. of Workshop MEDEA, Sep 2007.

Design and Use of htalib a Library for Hierarchically Tiled Arrays, Ganesh Bikshandy, Jia Guo, Christoph von Praun, Gabriel Tanase, Basilio Fraguela, Maria Jesus Garzaran, David Padua, Lawrence Rauchwerger, In Wkshp. on Lang. and Comp. for Par. Comp. (LCPC), Nov 2006.

ARMI: A High Level Communication Library for STAPL, Nathan Thomas, Steven Saunders, Tim Smith, Gabriel Tanase, Lawrence Rauchwerger, Parallel Processing Letters, 16(2):261-280, Jun 2006.

Sensitivity analysis for automatic parallelization on multi-cores, Silvius Rus and Maikel Pennings and Lawrence Rauchwerger, ICS '07: Proceedings of the 21st annual international conference on Supercomputing, Seattle , 2007.

**PI Asok Ray**

R. Atta-Fynn and A. K. Ray, Atomic Adsorptions on the (020) Surface of α-Pu: A Density Functional Study, submitted for publication (2007).

R. Atta-Fynn and A. K. Ray, An Ab Initio Relativistic Study of Adsorption and Dissociation of H2O on δ-Pu (111) Surface, submitted for publication (2007).

P. Dholabhai and A. K. Ray, A Density Functional Study of Atomic Hydrogen and Oxygen Chemisorption on the Relaxed (0001) Surface of Double Hexagonal Close Packed Americium, submitted for publication (2007)

**PI Fernando Reboredo**

"Anomalous photoluminescence in CdSe quantum dot solids at high pressure due to non-hydrostatic stress", C. D. Grant, J.C. owhurst, S. Hamel, A. Williamson and N. Zaitseva, submitted to Nano Letters.

"First-principles calculations of mechanical properties of Si <001> nanowires and comparison to nanomechanical theory", B. Lee and R. E. Rudd, Phys. Rev. B 75, 195328 (2007).

"First-principles study of the Young's modulus of Si <001> nanowires", B. Lee and R. E. Rudd, Phys. Rev. B 75, 041305(R) (2007).

**PI John Rehr**

Theoretical X-Ray Absorption Debye-Waller Factors, Fernando D. Vila, J. J. Rehr, H. H. Rossner, H. J. Krappe, Phys. Rev. B 76, 014301 (2007).

Losses and Multi-Electron Excitations in X-Ray Spectra, J. J. Rehr, J. J. Kas, M. P. Prange, A. P. Sorini, L. W. and F. D. Vila, AIP Conf. Proc. 882, 85 (2007).

Real time time-dependent density functional theory approach for frequency-dependent non-linear optical response in c molecules, Y. Takimoto, F. D. Vila and J. J. Rehr, J. Chem. Phys. 127, 154114 (2007).

Many-pole model of inelastic losses in x-ray absorption spectra, J.J. Kas, A. P. Sorini, M. P. Prange, L. W. Cambell, and J. A. Soininen, Phys. Rev. B (in press, 2007).

Dynamic structure in supported Pt nanoclusters, F. Vila, J.J. Rehr, J. Kas, R.G. Nuzzo, A.I. Frenkel, Submitted Oct, 2007.

**PI Chuang Ren**

G. Li, R. Yan, C. Ren, T.-L. Wang, J. Tonge, and W. B. Mori, 'Laser channeling in millimeter-scale underdense plasmas of fast ignition targets'

**PI Tony Rollett**

J. R. Morris, F. Jiang, P. Liaw, "A simple model for examining composition effects in eutectic nucleation," Mater. Trans. M) 48, 1675-1679 (2007).

T. Egami, V. Levashov, R. S. Aga and J. R. Morris, "Atomic dynamics in metallic liquids and glasses," Mater. Trans. (JIM) 1729-1733 (2007).

J. R. Morris, U. Dahlborg and M. Calvo-Dahlborg, "Recent developments and outstanding challenges in theory and modeling of quid metals," J. Non-cryst. Sol 353, 3444-3453 (2007).

J. R. Morris, M. I. Mendelev and D. J. Srolovitz, "A comparison of crystal-melt interfacial free energies using different Al potentials," J. Non-cryst. Sol 353, 3565-3569 (2007).

Z. G. Xia, D. Y. Sun, M. Asta and J. J. Hoyt, "Molecular Dynamics Calculations of the Crystal-Melt Interfacial Mobility for exagonal-Close-Packed Mg," Phys. Rev. B 75, 012103 (2007).

C. A. Becker, D. Buta, J. J. Hoyt and M. Asta, "Crystal-Melt Interface Stresses: Atomistic Simulation Calculations for a ard-Jones Alloy, Stillinger-Weber Si, and Embedded Atom Method Ni," Phys. Rev. E 75, 061610 (2007).

D. Buta, M. Asta and J. J. Hoyt, "Kinetic Coefficient of Steps at the Si(111) Crystal-Melt Interface from Molecular Dynamics Simulations," J. Chem. Phys. 127, 074703 (2007).

R. B. Godiksen, Z. T. Trautt, M. Upmanyu, J. Schixtz, S. Schmidt and D. Juul Jensen, Simulations of boundary migration recrystallisation using molecular dynamics, Acta Materialia, accepted, 2007.

R. B. Godiksen, Z. T. Trautt, M. Upmanyu, S. Schmidt and D. Juul Jensen, Simulation of recrystallization using molecular mics: Effects of the interatomic potential, Materials Science Forum 558-559 , pp 1081-1086, 2007.

Z. T. Trautt, M. Upmanyu and A. Karma, "Interface mobility from interface random walk ", Science 27, pp 632-635, 2006.

M. Upmanyu, D. J. Srolovitz, A. Lobkovsky, J. A. Warren and W. C. Carter, Simultaneous Grain Rotation and Grain Boundary ation, Acta Materialia 54(7), pp 1707-1719, 2006.

**PI Barbara Romanowicz**

Romanowicz, B., A. Cao, A. Kim, M. Panning, M. Pasyanos and D. Dreger (2007) CALIBRATION OF 3D UPPER MANTLE STRUCTURE IN EURASIA USING REGIONAL AND TELESEISMIC FULL WAVEFORM SEISMIC DATA, extended abstract, Monitoring Research Review, NEMRE.

**PI Edward Rubin**

The JGI has been able to produce over 70 publications to date in 2007; these were all based on data from the pipeline which was enabled by NERSC resources.

http://www.jgi.doe.gov/News/pubs.html

Key Papers/Reports Published in Nature in 2007 are listed here:

Pandit, B; Sarkozy, A; Pennacchio, LA; et al. Gain-of-function RAF1 mutations cause Noonan and LEOPARD syndromes with hypertrophic cardiomyopathy NATURE GENETICS, 39 (8): 1007-1012 AUG 2007

Romeo, S; Pennacchio, LA; Fu, YX; et al. Population-based resequencing of ANGPTL4 uncovers variations that reduce triglycerides and increase HDL NATURE GENETICS, 39 (4): 513-516 APR 2007

Jeffries, TW; Grigoriev, IV; Grimwood, J; et al. Genome sequence of the lignocellulose-bioconverting and xylose-fermenting yeast Pichia stipitis NATURE BIOTECHNOLOGY, 25 (3): 319-326 MAR 2007

Lo, I; Denef, VJ; VerBerkmoes, NC; et al. Strain-resolved community proteomics reveals recombining genomes of acidophilic bacteria NATURE, 446 (7135): 537-541 MAR 29 2007

McHardy, AC; Martin, HG; Tsirigos, A; et al. Accurate phylogenetic classification of variable-length DNA fragments NATURE METHODS, 4 (1): 63-72 JAN 2007

Tartaglia, M; Pennacchio, LA; Zhao, C; et al. Gain-of-function SOS1 mutations cause a distinctive form of Noonan syndrome NATURE GENETICS, 39 (1): 75-79 JAN 2007

Key Papers/Reports Published in Science in 2007 are listed here:

Merchant, SS; Prochnik, SE; Vallon, O; et al. The Chlamydomonas genome reveals the evolution of key animal and plant functions SCIENCE, 318 (5848): 245-251 OCT 12 2007

Putnam, NH; Srivastava, M; Hellsten, U; et al. Sea anemone genome reveals ancestral eumetazoan gene repertoire and genomic organization SCIENCE, 317 (5834): 86-94 JUL 6 2007

McPherson, R; Pertsemlidis, A; Kavaslar, N; et al. A common allele on chromosome 9 associated with coronary heart disease SCIENCE, 316 (5830): 1488-1491 JUN 8 2007

Giraud, E; Moulin, L; Vallenet, D; et al. Legumes symbioses: Absence of Nod genes in photosynthetic bradyrhizobia SCIENCE, 316 (5829): 1307-1312 JUN 1 2007

Rubin, EM; Noonan, JP Comparing neanderthal and human genomes - Response SCIENCE, 315 (5819): 1664-1664 MAR 23 2007

von Mering, C; Hugenholtz, P; Raes, J; et al. Quantitative phylogenetic assessment of microbial communities in diverse environments SCIENCE, 315 (5815): 1126-1130 FEB 23 2007

Newton, ILG; Woyke, T; Auchtung, TA; et al. The Calyptogena magnifica chemoautotrophic symbiont genome SCIENCE, 315 (5814): 998-1000 FEB 16 2007

**PI Robert Ryne**

M. Borland et al., "Potential and Challenges of an Energy Recovery Upgrade to the APS," NIM A 582 (2007) 54-56.

M. Borland, ``A super-bright storage ring alternative to an energy recovery linac,'' NIM A 557 (2006) 230-235.

M. Borland, ``Evaluation of the possibility of upgrading the Advanced Photon Source to an energy recovery linac,'' NIM A 557 (2006) 224-229.

J. Qiang, S. Lidia, R. D. Ryne, and C. Limborg-Deprey, "A Three-Dimensional Quasi-Static Model for High Brightnees Beam ics simulation," Phys. Rev. ST Accel. Beams 9, 044204 (2006).

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

J. Qiang, M. A. Furman, R. D. Ryne, W. Fischer, K. Ohmi, "Recent advaces of strong-strong beam-beam simulation," Nuclear ruments & Methods in Physics Research A558, 351, (2006).

J. Amundson, P. Spentzouris, J.Qiang and R. Ryne, "Synergia: An accelerator modeling tool with 3-D space charge," J. Comp. ys. vol. 211, 229 (2006).

H. Shan, J. Qiang, K. Yelick and E. Strohmaier, "Performance analysis of a high energy colliding beam simulation code on high-performance computing architectures," to appear in the 35th International Conference on Parallel Processings. (peer reviewed).

## S

**PI Yousef Saad**

H.R. Fang and Y. Saad: "Two Classes of Multisecant Methods for Nonlinear Acceleration," Numerical Linear Algebra with tions (submitted).

**PI Roman Samulyak**

R. Samulyak, T. Lu, P. Parks, A magnetohydrodynamic simulation of pellet ablation in the electrostatic approximation, Nuclear Fusion, 47 (2007), 103-118.

R. Samulyak, J. Du, J. Glimm, Z. Xu, A numerical algorithm for MHD of free surface flows at low magnetic Reynolds numbers, J. Comput. Phys., 226 (2007), 1532 - 1549.

J. Du, T. Lu, R. Samulyak, Algorithms for magnetohydrodynamics of ablated materials, Journal of Nanoscience and Nanotechnology, 8 (2008). In press

**PI Richard Saykally**

D. Prendergast and G. Galli; Phys. Rev. Lett. 96, 215502, 2006.

**PI Henry Schaefer**

"π and σ-phenylethynyl radicals and their isomers o-, m- and p-ethynylphenyl: Structures, energetics, and electron ties", Raj K. Sreeruttun, Ponnadurai Ramasami, Chaitanya S. Wannere, Andrew C. Simmonett, and Henry F. Schaefer III, dubmittee

"Synthesis and Characterization of Hydroxymethylene", Peter R. Schreiner, Hans Peter Reisenauer, Frank Pickard, Andrew C. monett, Wesley D. Allen, Edit Matyus, and Attila G. Csaszar, Submitted.

"In Search of Definitive IR Signatures of the Elusive NCCO Radical", A. C. Simmonett, F. A. Evangelista, W. D. Allen and H. . Schaefer III, J. Chem. Phys. 127 014306 (2007).

"Model Systems for Probing Metal Cation Hydration: The V+(H2O) and ArV+(H2O) Complexes", V. Kasalova, W. D. Allen, H. F. efer, E. D. Pillai, and M. A. Duncan,, Journal of Physical Chemistry A 111, 7599 (2007).

"Anchoring the Absolute Proton Affinity Scale", Veronika Kasalova, Andrew C. Simmonett, Wesley D. Allen, Henry F. Schaefer I, Gabor Czaks and Attila G. Csaszar, Submitted.

"High Precision Energetics of the C2H3 + O2 Reaction", Jeremiah J. Wilke, Wesley D. Allen, and Henry F. Schaefer, Submitted.

**PI Rocco Schiavilla**

"Isospin Mixing in the Nucleon and 4He and the Nucleon Strange Electric Form Factor" M. Viviani, R. Schiavilla, B. Kubis, R. Lewis, L. Girlanda, A. Kievsky, L. E. Marcucci, and S. Rosati, Phys. Rev. Lett. 99, 12002 (2007)

"Relativistic Calculation of Deuteron Threshold Electrodisintegration at Backward Angles" A. Arriaga and R. Schiavilla, Phys. Rev. C 76, 014007 (2007).

"Tensor Forces and the Ground-State Structure of Nuclei" R. Schiavilla, R. B. Wiringa, Steven C. Pieper, and J. Carlson, Phys. Rev. Lett. 98, 132501 (2007)

"Correlations in Nuclei: a Review" R. Schiavilla, proceedings of the "9th International Spring Seminar on Nuclear Physics: Changing Facets of Nuclear , A. Covello, ed., Vico Equense, Italy, May 20-24, 2007, World Scientific in press

**PI David Schultz**

Generalized collisional-radiative model for light elements: Data for the Li isonuclear sequence, S D Loch, J P Colgan, M C Witthoeft, M S Pindzola, C P Ballance, D M Mitnik, D C Griffin, M G O'Mullane, N R Badnell, and H P Summers, Atomic Data and Nuclear Data Tables 92, 813 (November 2006).

Dielectronic recombination of Fe+13: benchmarking the M-shell, N R Badnell, Journal of Physics B 39, 4825 (December 2006).

Steps toward dielectronic recombination of argon-like ions: a revisited theoretical investigation of Sc+3 and Ti+4, D Nikolic, T W Gorczyca, J Fu, D W Savin, and N R Badnell, Nuclear Instruments and Methods in Physics Research B 261, 145 (April 2007).

Dielectronic recombination data for dynamic finite-density plasmas: XII The helium isoelectronic sequence, M A Bautista and N R Badnell, Astronomy and Astrophysics 466, 755 (May 2007).

Atomic data from the IRON project: LXIII Electron-impact excitation of Fe+19 up to n=4, M C Witthoeft, G D Zanna, and N R Badnell, Astronomy and Astrophysics 466, 763 (May 2007).

Line ratio diagnostics in helium and helium seeded argon plasmas, R F Boivin, S D Loch, C P Ballance, D Branscomb, and M S Pindzola Plasma Sources Science Technology 16, 470 (May 2007).

Electron-impact ionization of diatomic molecules using the configuration-average distorted-wave method, M S Pindzola, F J Robicheaux, J P Colgan, and C P Ballance, Physical Review A 76, 012714 (July 2007).

R-matrix electron-impact excitation calculations along the F-like isoelectronic sequence, M C Witthoeft, A D Whiteford, and N R Badnell, Journal of Physics B 40, 2969 (August 2007).

Dielectronic recombination of Fe+14 forming Fe+13: Laboratory measurements and theoretical calculations, D V Lukic, M Schnell, D W Savin, C Brandau, E W Schmidt, S Bohm, A Muller, S Schippers, M Lestinsky, F Sprenger, A Wolf, Z Altun, and N R Badnell, Astrophysical Journal 664, 1244 (August 2007).

Electron-impact ionization and recombination of M-shell atomic ions in the argon isonuclear sequence, S D Loch, S A Abdel-Naby, C P Ballance, and M S Pindzola, Physical Review A 76, 022706 (August 2007).

**PI Ryoichi Seki**

"Lattice Calculation of Thermal Properties of Low-Density Neutron Matter with NN Effective Field Theory" by T. Abe and R. Seki, submitted to Phys.Rev. C; arXiv nucl/th 0708.2523 (2007).

"From Low-Density Neutron Matter to the Unitary Limit" by T. Abe and R. Seki, submitted to Phys.Rev. C; arXiv nucl/th .2424 (2007).

**PI Shunli Shang**

S. L. Shang, Y. Wang, and Z. K. Liu. First-principles elastic properties of alpha- and theta-Al2O3, Applied Physics rs, Vol. 90 (2007) 101909.

S. L. Shang, Y. Wang, H. Zhang, and Z. K. Liu. Lattice dynamics and anomalous bonding in rhombohedral As: First-s supercell method, Physical Review B, Vol. 76 (2007) 052301.

S. L. Shang, A. J. Böttger, and Z. K. Liu, The influence of interstitial distribution on phase stability and properties of hexagonal epsilon-Fe6Cx, epsilon-Fe6Ny, and epsilon-Fe6CxNy phases: a first-principles calculation, Acta Materialia, Vol. 55 (2007) in Press. http://dx.doi.org/10.1016/j.actamat.2007.10.018

S. L. Shang, Y. Wang, Z. K. Liu, C. E. Yang, S. Z. Yin, Band structure of FeBO3: Implications for tailoring the band gap of nanoparticles, Applied Physics Letters, Submitted in Oct-2007.

**PI Marjorie Shapiro**

Measurement of the Top-Quark Mass using Missing E(t) + Jets Events with Secondary Vertex b-tagging at CDF II T. Aaltonen et al., The CDF Collaboration, Phys. Rev. D75, 111103 (2007).

Measurement of the Top Quark Mass in p anti-p Collisions at s**(1/2) = 1.96 TeV using the Decay Length Technique A. Abulencia et al., The CDF Collaboration, Phys. Rev. D75, 071102 (2007)

Precise Measurement of the Top Quark Mass in the Lepton+Jets Topology at CDF II A. Abulencia et al., The CDF Collaboration, FERMILAB-PUB-07-070-E. Submitted to Phys. Rev. Lett. March 29, 2007.

Observation of B0(s)-B-bar0_s Oscillations A. Abulencia et al., The CDF Collaboration, Phys. Rev. Lett. 97, 242003 (2006).

**PI Michael Shay**

Shay, M. A., J. F. Drake, and M. Swisdak, "Two-scale structure of the electron dissipation region during collisionless magnetic reconnection," Physical Review Letters, Vol. 99, 155002, 2007.

P. A. Cassak and M. A. Shay, ``Scaling of Asymmetric Magnetic Reconnection: General Theory and Collisional Simulations'', In Press, Phys. Plasmas (2007).

Shay, M. A., J. F. Drake, and B. Dorland, "Equation free projective integration: A multiscale method applied to a plasma ion acoustic wave," Journal of Computational Physics, Vol. 226, p.571, 2007.

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

Cassak, P. A., D. J. Mullan, and M. A. Shay, "A Physical Mechanism for Self-Organization in Solar and Stellar Coronae: Theory and Observations," Astrophysical Journal Letters, submitted, 2007.

Eastwood, J., T. D. Phan, F. S. Mozer, M. A. Shay et al., "Multipoint observations of the Hall electromagnetic field and secondary island formation during magnetic reconnection," Journal of Geophysical Research, Vol. 112, A06235, 2007.

P. A. Cassak, J. F. Drake, M. A. Shay and B. Eckhardt, ``Onset of Fast Magnetic Reconnection'', Phys. Rev. Lett., 98, 215001 (2007).

P. A. Cassak, J. F. Drake, and M. A. Shay, ``Catastrophic Onset of Fast Magnetic Reconnection with a Guide Field'', Phys. Plasmas, 14, 054502 (2007)

Drake, J. F., M. Swisdak, H. Che, and M. A. Shay, "Electron acceleration from contracting magnetic islands during reconnection," Nature, Vol. 443, p. 553, doi:10.1038/nature05116, 2006.

**PI Junko Shigemitsu**

`$B Meson Semileptonic Form Factors from Unquenched Lattice QCD'', E.Gulez, A.Gray, M.Wingate, C.Davies, P.Lepage, J.Shigemitsu; Phys. Rev. D\underbar{73}:074502 (2006).

``Unquenched Determination of the Kaon Parameter B_K from Improved Staggered Fermions'', E.Gamiz, S.Collins, C.Davies, P.Lepage, J.Shigemitsu, M.Wingate; Phys. Rev. D\underbar{73}:114502 (2006).

``Highly-Improved Staggered Quarks on the Lattice with Applications to Charm Physics'', E.Follana, Q.Mason, C.Davies, K.Hornbostel, P.Lepage, J.Shigemitsu, H.Trottier and K.Wong; Phys. Rev. D\underbar{75}:054502 (2007).

``B0 Mixing Parameters from Unquenched Lattice QCD'', E.Dalgic, A.Gray, E.Gamiz, C.Davies, P.Lepage, J.Shigemitsu, H.Trottier and M.Wingate, Phys. Rev. D\underbar{76}:011501(R) (2007).

``High Precision Determination of the pi, K, D and D(s) Decay Constants from Lattice QCD''; [arXiv:0706.1726] E.Follana, C.Davies, P.Lepage, J.Shigemitsu, submitted for publication

**PI Donald Sinclair**

J.B.Kogut and D.K.Sinclair, Argonne preprint, ANL-HEP-PR-07-81 (2007).

J.B.Kogut and D.K.Sinclair, ``The RHMC algorithm for theories with unknown spectral bounds,'' Phys. Rev. D 74, 114505 (2006), [arXiv:hep-lat/0608017].

J.B.Kogut and D.K.Sinclair, ``Quantization and simulation of Born-Infeld non-linear electrodynamics on a lattice,'' Phys. Rev. D 73, 114508 (2006), [arXiv:hep-lat/0603017].

J.B.Kogut and D.K.Sinclair, ``Evidence for O(2) universality at the finite temperature transition for lattice QCD with 2 flavours of massless staggered quarks,'' Phys. Rev. D 73, 074512 (2006), [arXiv:hep-lat/0603021].

**PI George Smoot**

Jeong, E.; Smoot, G. F., "Probing Non-Gaussianity In The Cosmic Microwave Background Anisotropies: One Point Distribution ction", arXiv:0710.2371 (2007).

Jeong, E.; Smoot, G. F., "The Validity of the Cosmic String Pattern Search with the Cosmic Microwave Background", ApJL. 661, L1, 2007.

**PI Randall Snurr**

Sung, C., Broadbelt, L.J., Snurr, R.Q. "A DFT study of adsorption of intermediates in the NOx reduction pathway over BaNaY olites", Catalysis Today, Submitted.

**PI Philip Snyder**

D.P. Brennan, A.D. Turnbull, M.S. Chu, R.J. La Haye, L.L. Lao, T.H. Osborne and S.A. Galkin, "Resistive Stability of 2/1 Modes Near 1/1 Resonance," Phys. Plasmas 14, 056108 (2007).

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

J. Candy, R.E. Waltz, M.R. Fahey, and C. Holland, "Plasma Microturbulence Simulations of Instabilities at Highly Disparate Scales", J. Phys. Conf. Ser. 78 (2007) 012008.

M.S. Chu, V.S. Chan, P.A. Politzer, D.P. Brennan et al, "Kinetic Alfven Wave and Associated Current Drive at the Center of Tokamaks," Phys. Plasmas 13 114501 (2006).

M.S. Chu, D.P. Brennan, V.S. Chan et al, "Maintaining the Quasi-Steady State Central Current Density Profile in Hybrid Discharges," Nucl. Fusion 47 434 (2007).

C. Estrada-Mila, J. Candy and R.W. Waltz, "Turbulent Transport of Alpha Particles in Reactor Plasmas," Phys. Plasmas 13 112303 (2006).

F.L. Hinton and R.E. Waltz, "Gyrokinetic Turbulent Heating," Phys. Plasmas 13 102301 (2006).

C. Holland, G.R. Tynan et al, "Zonal-flow-driven Nonlinear Energy Transfer in Experiment and Simulation," Phys. Plasmas 14 056112 (2007).

J.E. Kinsey, R.E. Waltz, J. Candy, The Effect of Plasma Shaping on Turbulent Transport and ExB Shear Quenching in Nonlinear Gyrokinetic Simulations, accepted for publication in Phys. Plasmas.

E.A. Lazarus, T.C. Luce, M.E. Austin, D.P. Brennan et al, "Sawtooth Oscillations in Shaped Plasmas," Phys. Plasmas 14 055701 (2007).

W.M. Nevins, J. Candy et al, "Characterizing ETG Turbulence via Numerical Simulation," Phys. Plasmas 13 122306 (2006).

W.M. Nevins, S.E. Parker, Y. Chen, J. Candy et al, "Verification of Gyrokinetic df Simulations of Electron Temperature Gradient Turbulence," Phys. Plasmas 14 084501 (2007).

A.Y. Pankin, G. Bateman, D.P. Brennan et al, "Modeling of ELM Dynamics for DIII-D and ITER," Plasma Phys. Control. Fusion 49 S63 (2007).

P.B. Snyder, K.H. Burrell, H.R. Wilson et al, "Stability and Dynamics of the Edge Pedestal in the Low Collisionality Regime: Physics Mechanisms for Steady-State ELM-Free Operation," Nucl. Fusion 47 961 (2007).

G.M. Staebler, J.E. Kinsey and R.E. Waltz, A Theory Based Transport Model with Comprehensive Physics, Phys. Plasmas 14, 0055909 (2007)

R.E. Waltz, J. Candy, and M. Fahey, Coupled Ion Temperature Gradient and Trapped Electron Mode to Electron Temperature Gradient Mode Gyrokinetic Simulations, APS06 Issue Phys. Plasmas 14, 0056116 (2007)

R.E. Waltz, G. M. Staebler, J. Candy, and F. Hinton, "Gyrokinetic Theory and Simulation of Toroidal Angular Momentum Transport", submitted to Phys. Plasmas

R.E. Waltz, G. M. Staebler, and J. Candy, "Gyrokinetic Theory and Simulation of Turbulent Energy Exchange", to be submitted Phys. Plasmas

**PI Masha Sosonkina**

M. Sosonkina, F. Liu, and R. Bramley, Usability levels for sparse linear algebra components, Concurrency and Computation: Practice and Experience, in press 2007.

J. Jones, M. Sosonkina, and Y. Saad, Component-based iterative methods for sparse linear systems, Concurrency and Computation: Practice and Experience, 19 (2007) pp. 625--635.

M. Sosonkina, Scalable dynamic adaptations for electronic structure calculations, Parallel Computing 2007 ParCo'07, Aachen--Juelich, Germany, Sep. 2007.

M. Sosonkina, B. Ucar, and Y. Saad, Hypergraph partitioning for parallel iterative solution of general sparse linear systems, Parallel Computing, submitted Dec. 2006.

**PI Carl Sovinec**

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).

A. I. D. Macnab, R. D. Milroy, C. C. Kim, C. R. Sovinec, Hall magnetohydrodynamic simulations of end- shorting induced rotation in field-reversed configurations, Phys. Plasmas 14, 092507 (2007).

C. R. Sovinec, D. C. Barnes, R. A. Bayliss, D. P. Brennan, E. D. Held, S. E. Kruger, A. Y. Pankin, D. D. Schnack, and the NIMROD Team, Two-fluid studies of edge relaxation events in tokamaks, J. Physics: Conf. Series 78, 012070 (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).

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).

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

**PI Panagiotis Spentzouris**

Volkan Akcelik, Kwok Ko, Lie-Quan Lee, Zenghai Li, Cho-Kuen Ng, and Liling Xiao, Shape Determination for Deformed Electromagnetic Cavities, Journal of Computational Physics, to be published.

Blumenfeld I., Clayton C.E., Decker F-J., Hogan M.J., Huang Chengkun, Ischebeck R., Iverson R., Joshi Katsouleas T., Kirby N., Lu W., Marsh K.A., Mori W.B., Muggli P., Oz E., Siemann R.H., Walz D., Zhou M., Energy doubling 42 GeV electrons in a metre-scale plasma wakefield accelerator, Nature, vol. 445 no. 7129, pp. 741-4 15 February 2007.

Oz E., Deng S., Katsouleas T, Muggli P., Barnes C.D., Blumenfeld I., Decker F.J., Emma P., Hogan M.J., Ishchebeck Iverson R.H., Kirby N., Krejcik P., Oonnell C., Siemann R.h., Walz D., Auerbach D., Clayton D.E., Huang C., Johnson D.K., shi C., Lu W., Marsh K.A., Mori W.B., Zhou M., Ionization-induced electron trapping in ultra-relativistic plasma wakes, cal Review Letters, vol 98, no. 8 pp. 084801/1-4 23 February 2007.

Thomas AGR, Najmudin Z., Mangles SPD, Murphy C.D., Dangor A.E., Kamperidis C., Lancaster K.L., Mori W.B., Norreys ., Rozmus W., Kushelnick K., Effect of laser-focusing conditions on propagation and monoenergetic electron production in r-wakefield accelerators, Physical Review Letters, vol 98, no. 4 pp. 095004/1-4 2 March 2007.

A. V. Fedotov, D. L. Bruhwiler, A. O Sidorin, D. T. Abell, I. Ben-Zvi, R. Busby, J. R. Cary, and V. N. Litvinenko, Study of the Magnetized Friction Force," Phys. Rev. ST/AB 9, 074401 (2006). G. R. Werner and J. R. Cary, "A Stable FDTD Algorithm for Non-diagonal, Anisotropic Dielectrics," J. Comp. Phys. 226, 01 (2007), doi:10.1016/j.jcp.2007.05.008.

Baifei Shen, Yuelin Li, Karoly Nemeth, Hairong Shang, Robert Soliday, Robert Crowell, Edward Frank, William Gropp, and John ary, "Triggering wave breaking in a laser plasma bubble by a nanowire," Phys. Plasmas 14, 053115 (2007).

D. A. Dimitrov, D. L. Bruhwiler, J. R. Cary, C. G. R. Geddes, R. E. Giacone, E. Esarey and W. P. Leemans, "Particle-in-cell imulations of Laser Pulse Propagation in Plasma Channels," Phys. Plasmas, 14, 043105 (2007).

Baifei Shen, Yuelin Li, M. Y. Yu, and John Cary, "Bubble regime for ion acceleration in a laser driven plasma," Phys. Rev. E accepted (2007).

Lu W., Tzoufras M. , Joshi C., Tsung F.S.,.Mori W.B., Vieira J., Fonseca R.A., Silva L.O., "Generating Multi-GeV Electron unches Using Single Stage Laser Wakefield Acceleration in a 3D Nonlinear Regime," Physical Review Special Topics Acceleraors and Beams vol. 10, no. 6pp. 061301 June 2007.

"An Experimentally Robust Technique For Halo Measurement Using The IPM At The Fermilab Booster," J. Amundson, W. Pellico, P. Spentzouris, T. Sullivan, and L. Spentzouris, Nucl. Instrum. Meth. A570, (2007).

C. Huang, V.K. Decyk, C. Ren, M. Zhou, W. Lu, W.B. Mori, J.H. Cooley, T.M. Antonsen, Jr. and T. Katsouleas, Journal of Computational Physics, 217, pp 658-679 (2006).

**PI Frank Spera**

Thermal diffusivity of orthoclase glasses and single-crystals at high temperature, M. Pertermann, A. Whittington, A. Hofmeister, F. Spera, in press, Contributions to Mineralogy and Petrology, 2007

Accurate computation of shear viscosity from equilibrium molecular dynamics simulations, Journal of Molecular Simulation, in press, 2007, Nevins, D., Spera, F.J.

Molecular Dynamics Studies of MgSiO3 Liquid to 150 GPa: An Equation of State (EOS), Tracer Diffusivities, and a Detailed Analysis of Changes in Atomic Coordination Statistics as a Function of Temperature and Pressure, Ghiorso, M S; Nevins, D; Spera, F J, EOS Transactions, American Geophysical Union. Vol. 87, no. 52, Suppl. 26 Dec. 2006

Thermodynamic and Structural Properties of liquid Mg2SiO4 at high temperatures and pressure in the range 0-150 GPa from Molecular Dynamics Simulation, Martin, B; Spera, F; Nevins, D.; EOS Transactions, American Geophysical Union. Vol. 87, no. 52, Suppl. 26 Dec. 2006

Partitioning of trace elements among coexisting crystals, melt and supercritical fluid during isobaric crystallization and melting, American Mineralogist, In Press, 2007, Frank J. Spera, Wendy A. Bohrson, Christy B. Till, Mark S. Ghiorso

Tradeoffs in chemical and thermal variations in the post-perovskite phase transition: Mixed phase regions in the deep lower mantle, Physics of The Earth and Planetary Interiors, 159, 2006, 234-246, Frank J. Spera, David A. Yuen and Grace Giles

Phase Equilibria Impetus For Large-Volume Explosive Volcanic Eruptions Fowler, S J; Spera, F J; Bohrson, W A; Ghiorso, M S EOS Transactions, American Geophysical Union. Vol. 87, no. 52, Suppl. 26 Dec. 2006

The Magma Chamber Simulator: A Comprehensive Tool for Modeling the Evolution of Magmatic Systems Bohrson, W A; Spera, F J; Ghiorso, M S; Fowler, S J, EOS Transactions, American Geophysical Union. Vol. 87, no. 52, Suppl. 26 Dec. 2006

**PI Don Spong**

Sheared plasma flow generation: A new measure for stellarator optimization, Spong, D. A., FUSION SCIENCE AND TECHNOLOGY, Volume: 50, Issue: 3, Pages: 343-351 (2006).

"Shear flow generation in stellarators - configurational variations," Spong, D. A., Harris, J. H., Ware, A. S., Hirshman, S. P., Berry, L. A., Nucl. Fusion, Vol. 47, Pages 626-633 (2007).

Compression of magnetohydrodynamic simulation data using singular value decomposition, del-Castillo-Negrete, D., Hirshman, S. P., Spong, D. A., D'Azevedo, E. F., JOURNAL OF COMPUTATIONAL PHYSICS, Volume: 222, Issue: 1, Pages: 265-286 (2007).

Assessment of transport in NCSX, Mikkelsen, D. R., Maassberg, H., Zarnstorff, M. C., Beidler, C. D., Houlberg, W. A., Kernbichler, W., Mynick, H., Spong, D. A., Strand, P., Tribaldos, V., FUSION SCIENCE AND TECHNOLOGY, Volume: 51, Issue: 2, Pages: 166-180 (2007).

Power and particle handling and wall conditioning in NCSX, Mioduszewski, P. K., Owen, L. W., Spong, D. A., Fenstermacher, M. E., Koniges, A. E., Rognlien, T. D., Umansky, M. V. FUSION SCIENCE AND TECHNOLOGY, Volume: 51, Issue: 2, Pages: 238-260 (2007).

Simulational study on losses of neutral beam-injected energetic ions via collisional ripple transport in the low aspect ratio helical system CHS, Isobe, M., Spong, D. A., Shimizu, A., Toi, K., Matsushita, H., Nagaoka, K., Nishiura, M., Matsuoka, K., Okamura, S., Murakami, S., JOURNAL OF PLASMA PHYSICS, Volume: 72, Pages: 1189-1192, Part: Part 6 (2006).

Studies of fast-ion transport induced by energetic particle modes using fast-particle diagnostics with high time resolution in CHS, Isobe, M., Toi, K., Matsushita, H., Goto, K., Suzuki, C., Nagaoka, K., Nakajima, N., Yamamoto, S., Murakami, S., Shimizu, A., Yoshimura, Y., Akiyama, T., Minami, T., Nishiura, M., Nishimura, S., Darrow, D. S., Spong, D. A., Shinohara, K., Sasao, M., Matsuoka, K., Okamura, S., NUCLEAR FUSION, Volume: 46, Issue: 10, Pages: S918-S925 (2006).

**PI Garrison Sposito**

Kwon K.D., Refson K., and Sposito G. (2007) Defect-induced photoconductivity in layered manganese oxides, Physical Review ters (submitted).

Bourg I.C., and Sposito G. (2007). Isotopic fractionation of noble gases by diffusion in liquid water. 1. Molecular dynamics simulations, Geochimica et Cosmochimica Acta (submitted).

Bourg I.C., and Sposito G. (2007). Isotopic fractionation of noble gases by diffusion in liquid water. 2. Hydrologic ions, Geochimica et Cosmochimica Acta (submitted).

Bourg I.C., and Sposito G. (2007). Molecular dynamics simulations of kinetic isotope fractionation during the diffusion of onic species in liquid water, Geochimica et Cosmochimica Acta (in press).

**PI Philip Sprangle**

D.F. Gordon, "Improved Ponderomotive Guiding Center Algorithm," accepted for publication in IEEE Trans. Plasma Sci.

**PI Malcolm Stocks**

Y. Q. Cai, P. C. Chow, O. D. Restrepo, Y. Takano, K. Togano, H. Kito, H. Ishii, C. C. Chen, K. S. Liang, C. T. Chen, S. Tsuda, S. Shin, C. C. Kao, W. Ku, and A. G. Eguiluz, Low-Energy Charge-Density Excitations in MgB2: Striking Interplay ween Single-Particle and Collective Behavior for Large Momenta, Phys. Rev. Lett. 97, 176402 (2006). Eisenbach, M., Stocks, G. M., Nicholson, D. M., Noncollinear magnetism in permalloy, J. Appl. Phys. 101 (9) 09G503 007).

Etz, C., Lazarovits, B., Zabloudil, J., et al. Magnetic properties of FeCo nanoclusters on Cu(100): Ab initio tions, Phys. Rev. B: 75 (24) 245432 (2007).

Fishman, Randy S.; Fernando A. Reboredo, Alex Brandt, and Juana Moreno, Nature of Perpendicular-to-Parallel Spin ientation in a Mn-doped GaAs Quantum Well: Canting or Phase Separation? Phys. Rev. Lett. 98, 267203 (2007).

H. Yang, Q. Sun, Z. Zhang, Y. Jia, Upward self-diffusion of adatoms and small clusters on facets of fcc metal (110) urfaces, Phys. Rev. B 76, 115417 (2007).

Huang L.; Gong, X. G., Gergert, E., Forster, F., Bendounan, A., Reinert, F., Zhang, Zhenyu, Evolution of a symmetry ap and synergetic quantum well states in ultrathin Ag films on Au(111) substrates Europhys. Lett. 78, 57003 (2007).

Liu, Shudun, Jayanthi, C. S., Zhang, Zhenyu, Wu, S. Y., Stability and mechanical properties of silicon nanowires, J. Comput. Theor. Nanosci. 4 (2): 275-281 (2007).

Liu, W. L., Zhang, K. W., Xiao, H. P., et al. Surface reconstruction and core distortion of silicon and germanium owires, Nanotechno 18 (21) 215703 (2007).

Melko, R. G.; R. S. Fishman, and F. A. Reboredo, Single layer of Mn in a GaAs quantum well: A ferromagnet with m fluctuations Phys. Rev. B 75, 115316 (2007).

Meng, S., Kaxiras, E., Zhang, Z., Metal-diboride nanotubes as high-capacity hydrogen storage media, Nano Letters: 7 3): 663-667 (2007).

Namilae, S., Fuentes-Cabrera, M., Radhakrishnan, B., Sarma, G. B., Nicholson, D. M., Energetics of hydrogen storage n organolithium nanostructures, Chem. Phys. Lett. 436 (1-3): 150-154 (2007).

Nicholson, D. M. C., Barabash, R. I. , Ice, G. E., et al. Relationship between pair and higher-order correlations in solid solutions and other Ising systems, J. Phys. Condens Mat.18 (50): 11585-11594 (2006).

Oezer, M. M., Jia, Yu, Zhang, Z., Thompson, J. R., Weitering, H. H., Tuning the quantum stability and ty of ultrathin metal alloys, Science 316 (5831): 1594-1597 (2007).

Petit, L, Stocks, G. M., Egami, T., Szotek, Z. and Temmerman, W. M., Ground state valency and spin configuration of the Ni ions in nickelates, Phys. Rev. Lett. 97 (14) 146405 (2006).

Seletskaia, T.; Osetskiy, Y. N., Stoller, R. E., Stocks, G. M., Development of a FeHe interatomic potential based on electronic structure calculations, J Nucl. Mat. 355-360, 367 (2007).

Stocks, G. M., Eisenbach, M., Ujfalussy, B., et al. On calculating the magnetic state of nanostructures, Prog. Sci. 52 (2-3) 371-387 (2007).

Yoon, M.; Ho Nyung L., Wei Hong, H. M. Christen, Z. Zhang, and Z. Suo, Dynamics of Step Bunching in Heteroepitaxial rowth on Vicinal Substrates, Phys. Rev. Lett. 99, 055503 (2007).

Yoon, M., Howe, J., Tibbetts, G., Eres, Gyula, Zhang, Z., Polygonization and anomalous graphene interlayer spacing multi-walled carbon nanofibers,Phys. Rev. B 75 (16): 165402 (2007).

Yoon, M.; S. Y. Yang, E. G. Wang, and Z. Y. Zhang, Charged fullerenes as high capacity hydrogen storage media, Nano. Lett. 9, 2578 (2007).

Zhang, K. W., Stocks, G. M., Zhong, J. X. Melting and premelting of carbon nanotubes, Nanotechno 18 (28) 285703 ).0077

Zhong, J. X., Stocks, G. M. Persistent mobility edges and anomalous quantum diffusion in order-disorder separated ntum films, Phys. Rev. B 75 (3) 033410 (2007).

**PI Alberto Striolo**

N.R. Tummala and A. Striolo, The Influence of Counter-Ion Condensation on the Self-Assembly of SDS Surfactants at the hite-Water Interface, Journal of Physical Chemistry C, submitted.

A. Striolo, Water Self Diffusion Through Narrow Oxygenated Carbon Nanotubes, Nanotechnology, 18 (2007) 475704.

B.H. Morrow and A. Striolo, Morphology and Diffusion Mechanism of Platinum Nanoparticles Supported on Carbon Nanotube les, Journal of Physical Chemistry B, (2007) in press.

E.R. Chan, A. Striolo, C. McCabe, S.C. Glotzer, and P.T. Cummings, A Coarse-Grained Force Field for Simulating Polymer-hered Silsesquioxane Self-Assembly in Solution, Journal Chemical Physics, 127 (2007) 114102. Also featured on the Virtual rnal of Nanoscale Science & Technology, Vol. 16, Issue 14, October 1st, 2007.

A. Striolo, C. McCabe, P. T. Cummings, E. R. Chan, and S. C. Glotzer, Aggregation of POSS Monomers in Liquid Hexane: A ecular-Simulation Study, Journal of Physical Chemistry B, 111 (2007) 12248.

H.-C. Li, C.Y. Lee, C. McCabe, A. Striolo, and M. Neurock, Ab Initio Analysis of the Structural Properties for Alkyl-ituted Polyhedral Oligomeric Silsesquioxanes, Journal of Physical Chemistry A, 111 (2007) 3577.

A. Striolo, Controlled Assembly of Spherical Nanoparticles: Nanowires and Spherulites, Small, 3 (2007) 628.

A. Striolo and S.A. Egorov, Sterical Stabilization of Colloidal Particles: Implicit and Explicit Solvent, Journal of cal Physics, 126 (2007) 014902.

A. Striolo, Colloidal Brushes in Complex Solutions: Existence of a Weak Mid-Range Attraction Due To Excluded-Volume s, Physical Reviews E, 74 (2006) 041401. Also featured on the Virtual Journal of Nanoscale Science & Technology, Vol. 14, ue 18, October 30th, 2006.

**PI Erich Strohmaier**

E. Strohmaier and H. Shan, Apex-Map: A Parameterized Scalable Memory Access Probe for High-Performance Systems, ncurrency and Computation: Practice and Experience , 2007; 19:1-21, January 2007

H. Shan, E. Strohmaier, and J. Qiang, Performance Analysis of leading HPC Architectures with BeamBeam3D International nal of High Performance Computing Applications (IJHPCA), in Press, LBNL-61134

C. C. Iancu and E. Strohmaier, 2007. Optimizing Communication Overlap for High-Speed Networks. In Proceedings of he 12th ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming (San Jose, California, USA, March 14 - 17, 007). PPoPP '07. ACM Press, New York, NY, 35-45.

L. Oliker, A. Canning, J. Carter, C. Iancu, M. Lijewski, S. Kamil, J. Shalf, H. Shan, E. Strohmaier, S. Ethier, T. , "Scientific Application Performance on Candidate PetaScale Platforms", International Parallel & Distributed Processing osium (IPDPS) 2007, LBNL-62952.

E. Strohmaier, Performance and it Complexity on Petascale Systems, book chapter in Petascale Computing: and Applications, D.A. Bader editor, in Press.

M. M. Tikir, L. Carrington, E. Strohmaier, A. Snavely, A Genetic Algorithms Approach to Modeling the Performance f Memory-bound Computations, to appear in Proceedings of SC2007,

**PI Maxim Sukharev**

M. Besbes, J.P. Hugonin, P. Lalanne, S. van Haver, O. T. A. Jansse, A.M. Nugrowati, M. Xu, S. F. Pereira, H. P. Urbach, A. S. van de Nes, P. Bienstman, G. Granet, S. Helfert, M. Sukharev, T. Seideman, F. I. Baida, B. Guizal, D. Van Labeke, "Numerical analysis of a slit-groove diffraction problem", Journal of the European Optical Society: Rapid Publications 2, 07022 (2007).

Maxim Sukharev and Tamar Seideman, "Light trapping and guidance in plasmonic nanocrystals", Journal of Chemical Physics 126, 204702 (2007).

Maxim Sukharev and Tamar Seideman (invited review paper), "Coherent Control of Light Propagation via Nanoparticle Arrays", Journal of Physics B: Atomic, Molecular & Optical Physics 40, S283 (2007).

G. Gay, O. Alloschery, J. Weiner, H. J. Lezec, C. O'Dwyer, M. Sukharev, T. Seideman, "Surface quality and surface waves on subwavelength-structured silver films" Physical Review E 75, 016612 (2007)

## T

**PI Xianzhu Tang**

Driven resonance in partially relaxed plasmas, X.Z. Tang, Phys. Rev. Lett. 98, 175001 (2007).

Proposed experiment to study relaxation formation of a spherical tokamak with a plasma center column, S.C. Hsu and X.Z. Tang, Journal of Fusion Energy 26, 85 (2007).

Self-organization of radio lobe magnetic fields via driven-relaxation submitted to Astrophysical Journal, X.Z.Tang (2007).

Scale-up of spherical tokamak solenoid-free startup by co-axial helicity injection accepted for publication, Physics of Plasmas, X.Z. Tang and A.H. Boozer (2007).

L. Chacon, A. N. Simakov, A. Zocco, "Steady state properties of magnetic reconnection in 2D EMHD," Phys. Rev. Lett., submitted (2007)

G. L. Delzanno, L. Chacon, J. M. Finn, "Electrostatic mode associated with the pinch velocity in Reversed Field Pinch simulations," Plasma Physics and Controlled Fusion, submitted (2007)

B. Philip, M. Pernice, and L. Chacon, "Solution of reduced resistive magnetohydrodynamics using implicit adaptive mesh refinement," Lecture Notes in Computational Science and Engineering, accepted (2007).

G. Lapenta, J.U. Brackbill, P. Ricci, Kinetic Approach to microscopic-macroscopic coupling in space and laboratory plasmas, Physics of Plasmas, 13, 055904, 2006.

G. Lapenta, D. Krauss-Varban, H. Karimabadi, J.D. Huba, L.I. Rudakov, P. Ricci, Kinetic Simulations of X-line Propagation in 3D Reconnection, Geophysical Research Letters, 33, L10102, doi:10.1029/2005GL025124, 2006.

K. Noguchi, C. Tronci, G. Zuccaro, G. Lapenta, Formulation of the relativistic moment implicit particle-in-cel l method, Physics of Plasmas, 14, 042308, 2007.

W. Wan, G. Lapenta, Micro-Macro Coupling in Plasma Self-Organization Processes During Island Coalescence, Physical Review Letters, submitted.

**PI Dave Thirumalai**

D. L. Pincus, Changbong Hyeon, and D. Thirumalai, "Effects of Trimethylamine N-Oxide (TMAO) and Crowding Agents on the Stability of RNA Hairpins", J. Am. Chem. Soc. (submitted).

**PI Robin Tokmakian**

Tokmakian, R., 2007, How stationary is the ocean component of the climate signal?, submitted, Jrnl. of Climate.

**PI Owen Toon**

Fridlind, A.M., A.S. Ackerman, G. McFarquhar, G. Zhang, M.R. Poellot, P.J. DeMott, A.J. Prenni, and A.J. Heymsfield, 2007: Ice properties of single-layer stratocumulus during the Mixed-Phase Arctic Cloud Experiment (M-PACE): Part II, Model results. J. Geophys. Res., in press.

Charlson, R.J., A.S. Ackerman, F.A.-M. Bender, T.L. Anderson, and Z. Liu, 2007: On the climate forcing consequences of the albedo continuum between cloudy and clear air. Tellus, 59B, 715-727, doi:10.1111/j.1600-0889.2007.00297.x.

Jensen, E.J., A.S. Ackerman, and J.A. Smith, 2007: Can overshooting convection dehydrate the tropical tropopause layer? J. Geophys. Res., 112, D11209, doi:10.1029/2006JD007943.

Senocak, I, A.S. Ackerman, M.P. Kirkpatrick, D.E. Stevens, and N.N. Mansour, 2007: Study of near-surface models for large-eddy simulations of a neutrally stratified atmospheric boundary layer. Bound.-Lay. Meteorol., 124, 405-424, doi:10.1007/s10546-007-9181-x.

Barth, M.C., S.-W. Kim, C. Wang, K.E. Pickering, L.E. Ott, G. Stenchikov, M. Leriche, S. Cautenet, J.-P. Pinty, C. Barthe, C. Mari, J. Helsdon, R. Farley, A.M. Fridlind, A.S. Ackerman, V. Spiridonov, and B. Telenta, 2007: Cloud-scale model intercomparison of chemical constituent transport in deep convection. Atmos. Chem. Phys., 7, 4709-4731.

**PI Doug Toussaint**

QCD thermodynamics with 2+1 flavors at nonzero chemical potential, C. Bernard, C. DeTar, Steven Gottlieb, U.M. Heller, J.E. Hetrick, L.Levkova, R. Sugar, D. Toussaint, submitted to Physical Review D

QCD equation of state with 2+1 flavors of improved staggered quarks, C. Bernard, T. Burch, C. DeTar, Steven Gottlieb, L. Levkova, U.M. Heller, J.E. Hetrick, R. Sugar, D. Toussaint, Phys. Rev. D75 (2007) 094505

## U

## V

**PI George Vahala**

B. Keating, G. Vahala, J. Yepez, M. Soe and L. Vahala, "Entropic Lattice Boltzmann Representations Required to Recover Navier-Stokes Flows", Phys. Rev. E75, 036712 (2007)

G. Vahala, J. Yepez, M. Soe, L. Vahala and S. Ziegeler, "Lattice Boltzmann Algorithms for Fluid Turbulence", IEEE Transactions (to be published, 2007)

G. Vahala, B. Keating, M. Soe, L. Vahala, J. Yepez, S. Ziegeler, J. Carter, "MHD Turbulence Studies - using Lattice Boltzmann algorithms", submitted to Communications in Computational Physics (Oct. 2007)

**PI James Vary**

A. Negret, T. Adachi, B.R. Barrett, C. Baumer, A.M. van den Berg, G.P.A. Berg, P. von Brentano, D. Frekers, D. De Frenne, H. Fujita, K. Fujita, Y. Fujita, E.-W. Grewe, P. Haefner, M.N. Harakeh, K. Hatanaka, K. Heyde, M. Hunyadi, E. Jacobs, Y. Kalmykov, A. Korff, K. Nakanishi, P. Navratil, P. von Neumann-Cosel, L. Popescu, S. Rakers, A. Richter, N. Ryezayeva, Y. Sakemi, A. Shevchenko, Y. Shimbara, Y. Shimizu, Y. Tameshige, A. Tamii, M. Uchida, J. Vary, H.J. Woertche, M. Yosoi, L. Zamick, Gamow-Teller Strengths in the A = 14 Multiplet: A Challenge to the Shell Model, Phys. Rev. Lett. 97, 062502 (2006); UCRL-JRNL-223644.

A.M. Shirokov, J.P. Vary, A.I. Mazur and T.A. Weber, Realistic Nuclear Hamiltonian: Ab exitu approach, Phys. Letts. B 644, 33(2007), ArXiv nucl-th/0512105, UCRL-JRNL-217903, SLAC-PUB-11614.

S.J. Brodsky, D. Chakrabarti, A. Harindranath, A. Mukherjee, J. P. Vary, Hadron Optics in Three-Dimensional Invariant Coordinate Space from Deeply Virtual Compton Scattering, Phys. Rev. D 75, 14003 (2007). ArXiv hep-ph/0611159 (SLAC-PUB-12096, UCRL-JRNL-226236).

K. D. Sviratcheva, J. P. Draayer, and J.P. Vary, Global Properties of fp-Shell Interactions in Many-nucleon Systems, accepted for publication in Nuclear Physics A; (ArXiv nucl-th/0703076, SLAC-PUB-11903, UCRL-JRNL-222549).

Tomas Dytrych, Kristina D. Sviratcheva, Chairul Bahri, Jerry P. Draayer and James P. Vary, Evidence for Symplectic Symmetry in Ab Initio No-Core Shell Model Results for Light Nuclei, Phys. Rev. Lett. 98, 162503 (2007).

P. Navratil, V.G. Gueorguiev, J. P. Vary, W. E. Ormand and A. Nogga, Structure of A = 10-13 nuclei with two- plus three-nucleon interactions from chiral effective field theory, Phys. Rev. Lett. 99, 042501(2007); UCRL-JRNL-227256, ArXiV: nucl-th 0701038.

T. Dytrych, K. D. Sviratcheva, C. Bahri, J. P. Draayer and J.P. Vary, Dominant role of symplectic symmetry in the ab-initio no-core shell model results for light nuclei, Phys. Rev. C 76, 014315 (2007).

J.P. Vary, P. Navratil, V.G. Gueorguiev, W. E. Ormand A. Nogga, P. Maris and A. Shirokov, Ab initio and ab exitu no core shell model, Proceedings of the Vico Equense Conference, A. Covello, Ed., World Scientific (Singapore, 2008), to appear.

## W

**PI Haobin Wang**

H. Wang, D.E. Skinner, and M. Thoss, "Calculation of reactive flux correlation functions for systems in a model condensed phase environment: a multilayer multi-configuration time-dependent Hartree approach'', J.Chem.Phys., 125, 174502 (2006).

H. Wang, and M. Thoss, "Quantum dynamical simulation of electron-transfer reactions in an anharmonic environment", J. Phys. Chem. A, 111, 10369 (2007).

I. Kondov, M. Cizek, C. Benesch, H. Wang, and M. Thoss, "Quantum dynamics of photoinduced electron-transfer reactionsin dye-semiconductor systems: First principles description and application to coumarin 343-TiO2", J. Phys. Chem. A, 111, 11970 (2007).

I. R. Craig, M. Thoss, and H. Wang, "Proton transfer reactions in model condensed-phase environments: Accurate quantum dynamics using multilayer multiconfiguration time-dependent Hartree approach", J. Chem. Phys., 127, 144503 (2007).

M. Thoss, I. Kondov, and H. Wang, "Correlated electron-nuclear dynamics in ultrafast photoinduced electron-transfer reactions at dye-semiconductor interfaces", Phys. Rev. B, 76, xx (2007).

H. Wang and M. Thoss, "Nonperturbative quantum simulation of time-resolved nonlinear spectra: Methodology and application to electron transfer reactions in the condensed phase", Chem. Phys., accepted.

**PI Lin-Wang Wang**

Z. Zhao, L.W. Wang, F. Wu, "Wavefunction localizations in bulged CdSe nanowires", J. Theor. Comp. NanoSci. 4, 247 (2007) [LBNL-60841].

C. Yang, J. Meza, L.W. Wang, "A trust region direct constrained minimization algorithm for the Kohn-Sham equation", 29, 1854 (2007) [LBNL-59841].

C. Voemel, J. Dongarra, O. Marques, S. Tomov, L.W. Wang, "The use of bulk states to accelerate the band edge state calculation of a semiconductor quantum dot", J. Comp. Phys. 223, 774 (2007) [LBNL-60147].

L.W. Wang, X. Cartoixa, "Motif-based polarization model: Calculations of the dielectric function and polarization in large nanostructures", Phys. Rev. B 75, 205334 (2007) [LBNL--63027].

Z. Yang, L.W. Wang, A. Mascarenhas, "Quantum coaxial cables for solar energy harvesting", Nanolett. 7, 1264 (2007) [LBNL-63026].

L. Fang, J.Y. Park, Y. Cui, P. Alivisatos, J. Schrier, B. Lee, L.W. Wang, M. Salmeron, "Mechanical and electrical properties of CdTe tetrapods studied by atomic force microscopy", J. Phys. Chem. (in press).

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

R. D. Robinson, B. Sadtler, D. Demchenko, C. K. Erdonmez, L.W. Wang, A. P. Alivisatos, "Spontaneous superlattice formation in nanorods through partial cation exchange", Science, 317, 355 (2007) [LBNL-62650].

B. Lee, L.W. Wang, C. D. Sparatus, S. G. Louie, "Nonlocal exchange-correlation in screened exchange density functional methods", Phys. Rev. B (in press) [LBNL-61337].

J. Schrier, D. O. Demchenko, L.W. Wang, A.P. Alivisatos, "Optical properties of ZnO/ZnS and ZnO/ZnTe heterostructures for solar cell applications" Nanolett. 7, 2377 (2007)[LBNL-62616].

J. Schrier, B. Lee, L.W. Wang, "Mechanical and electronic structure properties of compressed CdSe tetrapod nanocrystals", J. Nanosci. Nanotech. (in press) [LBNL-62312].

D. O. Demchenko, L.W. Wang, "Localized electron states near a metal-semiconductor nanocontact", Nanolett. 7, 3219 (2007).

Q. Zhao, P. A. Craf, W. B. Jones, A. Franceschetti, J. Li, L.W. Wang, K. Kim, "Shape dependence of band edge exciton fine structure in CdSe nanocrystals", Nanolett. (in press).

F. Wang, H. Yu, J. Li, Q. Hang, D. Zemlyanov, P. C. Gibbons, L.W. Wang, D. B. Janes, W. E. Buhro, "Spectroscopic properties of colloidal indium phosphide quantum wires", J. Phys. Chem. B (submitted).

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

D. Demchenko, R.D. Robinson, B. Sadtler, C.J. Erdonmex, A.P. Alivisatos, L.W. Wang, "Formation mechanism and properties of CdS-Ag2S nanorod superlattices", ACS Nano (submitted).

C. Vomel, S.Z. Tomov, O.A. Marques, A. Canning, L.W. Wang, J.J. Dongarra, "State-of-the-art eigensolvers for electronic structure calculations of large scale nano-systems", J. Comp. Phys. (submitted).

**PI Warren Washington**

Alexander, L.M. and J.M. Arblaster, Assessing trends in observed and modelled climate extremes over Australia in relation to future projections, Int. J. Climatology, submitted.

Meehl, G., C. Tebaldi, H. Teng, and T.C. Peterson, 2007b: Current and future U.S. weather extremes and El Niqo. Geophysical Research Letters, in press.

Meehl, G. J. Arblaster, and W. Collins, 2007c: Effects of black carbon aerosols on the Indian monsoon. J. Climate, in press. Meehl, G., J. Arblaster, G. Branstator, and H. van Loon, 2007d: A coupled air sea response mechanism to solar forcings in the Pacific region. J. Climate, in press.

Osborne, T.M., D.M. Lawrence, A.J. Challinor, J.M. Slingo, T.R. Wheeler, 2007: Development and assessment of a coupled crop-climate model. Glob. Change Biol., 13, 169-183.

Santer, B.D., C. Mears, F.J. Wentz, K.E. Taylor, P.J. Gleckler, T.M.L. Wigley, T.P. Barnett, J.S. Boyle, W. Bruggemann, N.P. Gillett, S.A. Klein, G.A. Meehl, T. Nozawa, D.W. Pierce, P.A. Stott, W.M. Washington, and M.F. Wehner, 2007: Identification of human-induced changes in atmospheric moisture content. Proc. Nat. Acad. Sci., 104, 15248-15253.

**PI William Weber**

R. Devanathan, L. R. Corrales, W. J. Weber, A. Chartier and C. Meis, "Molecular dynamics simulation of energetic uranium recoil damage in zircon", Molecular Simulations 32 (2006) 1069-1077.

J. Du, R. Devanathan, L. R. Corrales, W. J. Weber and A. N. Cormack, "Short-and medium-range structure of amorphous zircon from molecular dynamics simulations", Physical Review B 74 (2006) 214204.

R. Devanathan, P. Durham, J. Du, L. R. Corrales and E. M. Bringa, "Molecular dynamics simulation of amorphization in forsterite by cosmic rays", Nuclear Instruments and Methods B 255 (2007) 172-176.

R. Devanathan and W. J. Weber, "Radiation Effects in a Model Ceramic for Nuclear Waste Disposal", JOM 59(4) (2007) 32-35.

R. Devanathan, F. Gao and W. J. Weber, "Atomistic modeling of amorphous silicon carbide using a bond-order potential", Nuclear Instruments and Methods B 255 (2007) 130-135.

F. Gao, Y. Zhang, R Devanathan, M. Posselt, and W. J. Weber, "Atomistic Simulations of Epitaxial Recrystallization in 4H-SiC along the [0001] Direction", Nuclear Instruments and Methods B 255 (2007) 136-140.

F. Gao, J. Du, E. J. Bylaska, M. Posselt, and W. J. Weber, "Ab Initio Atomic Simulations of Antisite Pair Recovery in Cubic Silicon Carbide", Applied Physics Letters 90 (2007) 221915.

R. Devanathan and W. J. Weber, "Self-healing in irradiated zirconia-based ceramics", J. Materials Research (submitted).

H. Xiao, F. Gao, L. M. Wang, X. T. Zu, Y. Zhang and W. J. Weber, "Ab initio molecular dynamics determination of phase transformation pathways and mechanism", Nature Materials (submitted).

H. Xiao, L. M. Wang, F. Gao, X. T. Zu, W. J. Weber, J. Lian and R. C. Ewing, "Radiation resistance of A2Ti2O7 (A=Dy, Y, and Ho) Pyrochlores: Role of f electrons", Physical Review Letters (submitted).

N. Li, H. Xiao, X. Zu, L. M. Wang, R C Ewing, J. Lian and F. Gao, "First-principles study of electronic properties of La2Hf2O7 and Gd2Hf2O7", Journal of Applied Physics (Submitted)

Z. J. Chen, H. Y. Xiao, X. Zu, L. M Wang, F. Gao, J. Lian and R. C. Ewing, "Structural and bonding properties of stannate pyrochlores: a density functional theory investigation", Computational Materials Science (submitted).

**PI Suhai Wei**

S. Limpijumnong, M. F. Smith, and S. B. Zhang, "Characterization of As-doped, p-type ZnO by x-ray absorption near-edge structure spectroscopy: Theory", Appl. Phys. Lett. 89, 222113 (2006).

M.-H. Du, H. M. Branz, R. S. Crandall, S. B. Zhang, "Bistability-mediated carrier recombination at light-induced boron-oxygen complexes in silicon", Phys. Rev. Lett. 97, 256602 (2006).

Engtrakul C, Kim YH, Nedeljkovic JM, Ahrenkiel SP, Gilbert KEH, Alleman JL, Zhang SB, Micic OI, Nozik AJ, Heben MJ, "Self-assembly of linear arrays of semiconductor nanoparticles on carbon single-walled nanotubes", JOURNAL OF PHYSICAL CHEMISTRY B 110 (50): 25153-25157 DEC 21 2006.

Y. Qi, X. Ma, P. Jiang, S. Ji, Y. Fu, J.-F. Jia, Q.-K. Xue, and S. B. Zhang, "Atomic-layer-resolved local work functions of Pb thin films and their dependence on quantum well states", APPLIED PHYSICS LETTERS 90, 013109 (2007).

M.-H. Du, J. Feng, S. B. Zhang, "Photo-Oxidation of Polyhydroxyl Molecules on TiO2 Surfaces: From Hole Scavenging to Light-Induced Self-Assembly of TiO2-Cyclodextrin Wires", Phys. Rev. Lett. 98, 066102 (2007).

H. X. Yang, L. F. Xu, C. Z. Gu, and S. B. Zhang, "First-principles study of oxygenated diamond (001) surfaces with and without hydrogen", APPLIED SURFACE SCIENCE 253, 4260 (2007).

X. Ma, P. Jiang, Y. Qi, J. Jia, Y. Yang, W. Duan, W.-X. Li, X. Bao, S. B. Zhang, Q.-K. Xue, "Experimental observation of quantum oscillation of surface chemical reactivities", PNAS 104, 9204-9208 (2007).

Y. Zhao, M. J. Heben, A. C. Dillon, L. J. Simpson, J. L. Blackburn, H. C. Dorn, and S. B. Zhang, "Nontrivial Tuning of the Hydrogen-Binding Energy to Fullerenes with Endohedral Metal Dopants", J. Phys. Chem. C 2007, 111, 13275.

A. Allenic, W. Guo, Y. B. Chen, M. B. Katz, G. Y. Zhao, Y. Che, Z. D. Hu and B. Liu, S. B. Zhang, X. Q. Pan, "Amphoteric phosphorus doping for stable p-type ZnO", Advanced Materials, DOI: 10.1002/adma.200700083.

Sun, Y. Y.; Kim, Y.-H.; Zhang, S. B., "Effect of Spin State on the Dihydrogen Binding Strength to Transition Metal Centers in Metal-Organic Frameworks", J. Am. Chem. Soc.; (Communication); 2007; ASAP Article; DOI: 10.1021/ja0740061.

Y. Jiang, Y.-H. Kim, S. Yang, Z. Tang, K. Wu, P. Ebert, S. B. Zhang, and E. G. Wang, "Growing extremely thin bulklike metal film on a semiconductor surface: monolayer Al(111) on Si(111)", Appl. Phys. Lett. (MS #L07-08059RFIXR1, accepted for publication).

S. Chen, X. G. Gong, and S.-H. Wei, "Superhard pseudocubic BC2N superlattices", Phys. Rev. Lett. 98, 015502 (2007).

C.-H. Moon, S.-H. Wei, Y. Z. Zhu, and G. D. Chen, "Band gap bowing coefficients in large size-mismatched II-VI alloys: first-principles calculations", Phys. Rev. B 74, 233202 (2006).

C.-Y. Moon, J. Li, S.-H. Wei, A. T.-L. Lim, and Y. P. Feng, "Ordering induced direct and indirect transitions in semiconductor alloys", Phys. Rev. B 74, 205203 (2006).

Shiyou Chen, X. G. Gong and S.-H. Wei, "Band structure anomaly of chalcopyrite semiconductors CuGaX2 versus AgGaX2 (X=S and Se) and their alloys", Phys. Rev. B 75, 205209 (2007).

F. Wang, S.-S. Li, J.-B. Xia, H. X. Jiang, J. Y. Lin, J. Li, and S.-H. Wei, "Effects of the wavefunction localization in AlxInyGa1-x-yN quaternary alloys", Appl. Phys. Lett. 91, 061125 (2007).

A. Walsh and S.-H. Wei, "Filling the green gap: A first-principles study of the LiMgZnN alloy system", Phys. Stat. Sol. (b) (in press).

Y. Yan, J. Li, S.-H. Wei, and M. M. Al-Jassim, "Possible approach to overcome the doping polarity in wide-band-gap semiconductors", Phys. Rev. Lett. 98, 135506 (2007).

Y. Yan, M. M. Al-Jassim, and S.-H. Wei, "Doping of ZnO by group-Ib elements", Appl. Phys. Lett. 89, 181912 (2006).

Q. Xu, J.-W. Luo, S.-S. Li, J.-B. Xia, J. Li and S.-H. Wei, "Chemical Trends of defect formation in Si quantum dots: The case of group-III and group-V dopants", Phys. Rev. B 75, 235304 (2007).

**PI Michael Weinert**

Magnetic instability and meta-magentism on the surface of the bulk paramagnetic intermetallic compound YCo$_{2}$. S. Khmelevskyi, P. Mohn, J. Redinger, and M. Weinert, Physica B 378-380, 109 (2006).

Unusual adsorption site of hydrogen on the unreconstructed Ir(100) surface. D. Lerch, A. Klein, A. Schmidt, S. M\"uller, L. Hammer, K. Heinz, and M. Weinert, Phys. Rev. B 73, 075430 (2006).

Atomistic view of the autosurfactant effect during GaN epitaxy. S. T. King, M. Weinert, and L. Li, Phys. Rev. Lett. 98, 206106 (2007).

YCo$_2$: Intrinsic Magnetic Surface of a Paramagnetic Bulk Material. Yu. S. Dedkov, C. Laubschat, S. Khmelevskyi, J. Redinger, P. Mohn, and M. Weinert, Phys. Lett. 99, 047204 (2007).

**PI Harold Weitzner**

G. Park and C.S. Chang, A 5-1/2 dimensional theory for fast and accurate evaluation of the cyclotron resonance heating using spatial waverepresentation, Phys. Plasmas 14, 052503 (2007) H. Strauss, L. Sugiyama, C.S. Chang, G.Y. Park, S. Ku, W. Park, J. Breslau, S. Jardin ``ELM Simulations with M3D,"21st IAEA Fusion Energy Conference, Chengdu, China, TH/P8-6 (2006)

G. Y. Fu, W. Park, H. Strauss, J. Breslau, J. Chen, S. Jardin, and L. E. Sugiyama, "Global hybrid simulations of energetic particle effects on n = 1 mode in tokamaks: internal kink and fishbone instability", Phys. Plasmas 2006.

Zaslavsky G.M., Guzdar P.N., Edelman M., et al., Selfsimilarity and fractional kinetics of solar wind-magnetosphere coupling Physica A 373: 11-20 (2007).

Courbage M. Edelman M., Saberi S.M., Fathi Zaslavsky G.M.., The problem of transport in billiards with infinite horizon, PRE (submitted)

Zaslavsky G.M., Edelman M., Stochastic Web as a Generator of Three-Dimensional Quasicrystal Symmetry, Chaos, 17, 023127 (2007).

G. M. Zaslavsky, A. A. Stanislavsky, and M. Edelman, "Chaotic and pseudochaotic attractors of perturbed fractional oscillator", Chaos 16, 013102 (2006).

G.M. Zaslavsky, M. Edelman, "Stickiness of trajectories in a perturbed Anosov system", Regular & Chaotic Dynamics 11 (2): 329-336 (2006).

P. Garabedian, Bifurcated equilibria and magnetic islands in tokamaks and stellarators, Comm. Appl. Math. Comp. Sci. 1 (2006) 79-90.

L.-P. Ku and P. Garabedian, New classes of quasi-axisymmetric stellarator configurations, Fusion Sci. Technol. 50 (2006) 207-215.

P. Garabedian, Three-dimensional equilibria in axially symmetric tokamaks, Proc. Natl. Acad. Sci. USA 103 (2006) 19232-19236.

R. Alexander and P. Garabedian, Choice of coils for a fusion reactor, Proc. Natl. Acad. Sci. USA 104 (2007) 12250-12252.

**PI Don Werthimer**

Stanimirovic, Putnam, Heiles, Peek, Goldsmith, Koo, Krco, Lee, Mock, Muller, Pandian, Parsons, Tang, Werthimer First Results from the Arecibo Galactic HI Survey: The Disk/Halo Interface Region In The Outer Galaxy accepted for publication in ApJ

**PI Martin White**

Conroy, Charlie, Ho, Shirley, and White, Martin, Constraints on the merging time-scale of luminous red galaxies, or, where do all the haloes go?, 2007, Monthly Notices of the Royal Astronomical Society, 379, 1497

Eisenstein, Daniel J., Seo, Hee-Jong, and White, Martin, On the Robustness of the Acoustic Scale in the Low-Redshift Clustering of Matter, 2007, Astrophysical Journal, 664, 674

Heitmann, Katrin, Lukic, Zarija, Fasel, Patricia, Habib, Salman, Warren, Michael S., White, Martin, Ahrens, James, Ankeny, Lee, Armstrong, Ryan, O'Shea, Brian, Ricker, Paul M., Springel, Volker, Stadel, Joachim, and Trac, Hy, The Cosmic Code Comparison Project, 2007, ArXiv e-prints, 706,

Cohn, J. D., Evrard, A. E., White, M., Croton, D., and Ellingson, E., Red Sequence Cluster Finding in the Millennium Simulation, 2007, ArXiv e-prints, 706,

Cohn, J. D. and White, Martin, Dark matter halo abundances, clustering and assembly histories at high redshift, 2007, ArXiv e-prints, 706,

Semboloni, Elisabetta, van Waerbeke, Ludovic, Heymans, Catherine, Hamana, Takashi, Colombi, Stephane, White, Martin, and Mellier, Yannick, Cosmic variance of weak lensing surveys in the non-Gaussian regime, 2007, Monthly Notices of the Royal Astronomical Society, 375, L10

Evrard, A. E., Bialek, J., Busha, M., White, M., Habib, S., Heitmann, K., Warren, M., Rasia, E., Tormen, G., Moscardini, L., Power, C., Jenkins, A. R., Gao, L., Frenk, C. S., Springel, V., White, S. D. M., and Diemand, J., Virial Scaling of Massive Dark Matter Halos: Why Clusters Prefer a High Normalization Cosmology, 2007, ArXiv Astrophysics e-prints,

Wetzel, Andrew R., Cohn, J. D., White, Martin, Holz, Daniel E., and Warren, Michael S., The Clustering of Massive Halos, 2007, Astrophysical Journal, 656, 147

White, Martin, Zheng, Zheng, Brown, Michael J. I., Dey, Arjun, and Jannuzi, Buell T., Evidence for Merging or Disruption of Red Galaxies from the Evolution of Their Clustering, 2007, Astrophysical Journal, 655, L72

Huff, Eric, Schulz, A. E., White, Martin, Schlegel, David J., and Warren, Michael S., Simulations of baryon oscillations, 2007, Astroparticle Physics, 26, 366

**PI John Wilkins**

From compact point defects to extended structures in silicon. Y. A. Du, R. G. Hennig, T. J. Lenosky and J. W. Wilkins. Eur. Phys. J. B 57 229 (2007).

Alleviation of the Fermion-Sign Problem by Optimization of Many-Body Wave Functions. C. J. Umrigar, J. Toulouse, C. Filippi, S. Sorella and R. G. Hennig. Phys. Rev. Lett. 98, 110201 (2007).

Comparison of screened hybrid density functional theory to diffusion Monte Carlo in calculations of total energies of silicon phases and defects. E. R. Batista, J. Heyd, R. G. Hennig, B. P. Uberuaga, R. L. Martin, G. E. Scuseria, C. J. Umrigar, and J. W. Wilkins. Phys. Rev. B 74, 121102(R) (2006).

Questioning the existence of a unique ground state structure for Si clusters. W. Hellmann, R. G. Hennig, S. Goedecker, C. J. Umrigar, B. Delley, T. Lenosky. submitted to Phys. Rev. Lett. (2006).

Impurities block the alpha to omega martensitic transformation in titanium. R.G. Hennig, D.R. Trinkle, J. Bouchet, S.G. Srinivasan, R.C. Albers, and J.W. Wilkins. Nature Materials 4, 129 (2005).

Systematic pathway generation and sorting in martensitic transformations: Titanium alpha to omega. D.R. Trinkle, D.M. Hatch, H.T. Stokes, R.G. Hennig and R.C. Albers. Physical Review B 72, 014105 (2005).

A new mechanism for the alpha to omega martensitic transformation in pure titanium. D.R. Trinkle, R.G. Hennig, S.G. Srinivasan, D.M. Hatch, M.D. Jones, H.T. Stokes, R.C. Albers, and J.W. Wilkins. Physical Review Letters 91, 025701 (2003).

Complexity of Small Silicon Self-Interstitial Defects. D.A. Richie, J. Kim, S.A. Barr, K.R. A. Hazzard, R.G. Hennig, and J.W. Wilkins. Physical Review Letters 92, 45501 (2004).

**PI Simon Woodruff**

S. Woodruff et al. J. Fusion Energy, 26, 0164-0313 (2007). "Physics of Formation, Acceleration, Reconnection and Compression of Two Field Reversed Configurations"

S. Woodruff et al. J. Fusion Energy, Adiabatic Compression of a Doublet Field Reversed Configuration (FRC). J. Fusion Energy, Curretnly available online (to appear in print) (2007)

Macnab et al. Phys. Plasmas, 14 092503 (2007) Hall magnetohydrodynamics simulations of end-shorting induced rotation in field-reversed configurations.

S. Woodruff, Proceedings of IEEE ICOPS June 2007. Application of Pulsed Power to the Compression of Magnetized Plasmas.

**PI Stan Woosley**

``Multi-Dimensional Radiation/Hydrodynamic Simulations of Protoneutron Star Convection," (Luc Dessart, Adam Burrows, Christian D. Ott, & Eli Livne), ApJ, 645, 534, 2006.

``Multi-Dimensional Simulations of the Accretion-Induced Collapse of White Dwarfs to Neutron Stars," (L. Dessart, A. Burrows, C.D. Ott, E. Livne, S.-Y. Yoon, & N. Langer), Astrophys. J., 644, 1063, 2006

``Features of the Acoustic Mechanism of Core-Collapse Supernova Explosions," (A. Burrows, E. Livne, L. Dessart, C.D. Ott, & J. Murphy), ApJ, 655, 416, 2007

``A Two-Dimensional Magnetohydrodynamics Scheme for General Unstructured Grids," (E. Livne, L. Dessart, A. Burrows, & C.A. Meakin), ApJ. Suppl., 170, 187, 2007

``Simulations of Magnetically-Driven Supernova and Hypernova Explosions in the Context of Rapid Rotation," (A. Burrows, L. Dessart, E. Livne, C.D. Ott, & J. Murphy), ApJ, 664, 416, 2007

``Magnetically-Driven Explosions of Rapidly-Rotating White Dwarfs Following Accretion-Induced Collapse," (L. Dessart, A. Burrows, E. Livne, & C.D. Ott), accepted to ApJ, 2007 (http://arxiv.org/abs/0705.3678).

``3D Collapse of Rotating Stellar Iron Cores in General Relativity Including Deleptonization and a Nuclear Equation of State," Ott et al., Phys. Rev. Lett. 98, 261101 (2007)

``Rotating collapse of stellar iron cores in general relativity ," Ott et al., Class. Quant. Grav. 24, S139 (2007).

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

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

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

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

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

**PI Jianzhong Wu**

''Osmotic pressure and packaging structure of caged DNA,'' Z. Li, J. Wu, Z. G. Wang, Biophysical Journal, in press, 2007

''Melting kinetics of thermally responsive microgel crystals,'' S. Tang, Z. Hu, B. Zhou, Z. Cheng J. Wu, M. Marquez, Macromolecules, in press, 2007

''Towards a quantitative theory of ultra-small liquid droplets and vapor/liquid nucleation,'' Z. Li, J. Wu, Industrial & Engineering Chemistry Research, in press, 2007

''Dynamic control of protein folding pathway with a polymer of tunable hydrophobicity,'' D. Lu, J. Wu, Z. Liu, The Journal of Physical Chemistry B, in press, 2007. (Invited contribution)

''Density functional theory for liquid structure and thermodynamics,'' J. Wu, Molecular Thermodynamics of Complex Systems, Springer, X. Lu, Y. Hu (Eds), 106 m.s. pages, 2007. (Invited contribution)

''Isotropic-nematic phase transition in athermal solutions of rod/coil diblock copolymers,'' J. Jiang, J. Wu, Journal of Chemical Physics, 127, Article# 034902, 2007.

"Density functional theory for complex fluids", J. Wu and Z. Li, Annual Review of Physical Chemistry, 58:85-112 (2007).

"Structure and swelling of grafted polyelectrolytes: Predictions from a non-local density functional theory,'' T. Jiang, Z. Li and J. Wu, Macromolecules, 40(2), 334-343 (2007).

"Potential distribution theorem for the polymer-induced depletion between colloidal particles," Z. Li and J. Wu, Journal of Chemical Physics, 126, Article# 144904 (2007) )Appeared also in April 15, 2007 issue of Virtual Journal of Biological Physics Research).

"Density functional theory for a primitive model of nanoparticle-block copolymer mixtures", D. Cao and J. Wu, Journal of Chemical Physics 126, Article# 144912 (2007).

''Density Functional Theory for Chemical Engineering: From Capillarity to Soft Materials,'' J. Wu, AIChE Journal, 52(3), 1169-1193 (2006).

''Density Functional Theory for Polyelectrolytes near Oppositely Charged Surfaces,'' Z. Li and J. Wu, Physical Review Letters, 96 Article# 048302 (2006) (Appeared also in February 15, 2006 issue of Virtual Journal of Biological Physics Research)

''A hybrid method for predicting the micro-structure of polymers with complex architecture: Combination of single-chain simulation with density functional theory'', D. Cao, T. Jiang and J. Wu, Journal of Chemical Physics, 124 (16), 164904 (2006).

"Density Functional Theory for Planar Electric Double Layers: Closing the Gap between Simple and Polyelectrolytes,'' Z. Li and J. Wu, Journal of Physical Chemistry B, 110, 7473-7484, (2006).

''Molecular Thermodynamics for Charged Biomacromolecules,'' J. Wu and D. Morikis, Fluid Phase Equilibria, 241, 317-333, 2006. (Invited Contribution)

**PI Meng-Shiou Wu**

M.-S. Wu, J. Bentz, F. Peng, M. Sosonkina, M. S. Gordon, R. A. Kendall. Integrating Performance Tools with Large-Scale Scientific Software, in The 8th IEEE International Workshop on Parallel and Distributed Scientific and Engineering Computing (PDSEC-07), in conjunction with The 21st International Paralleland Distributed Processing Symposium (IPDPS-07), Long Beach, California, March 2007.

F. Peng, M.-S. Wu, M. Sosonkina, J. Bentz, T.Windus, M.S. Gordon, J. Kenny, C. Janssen. Tackling Component Interoperability in Quantum Chemistry Software, in the Workshop on Componentand Framework Technology in High-Performance and Scientific Computing, held in conjunction withooPLSA 2007, Montreal, Canada, October 21-22, 2007.

"Components for Integral Evaluation in Quantum Chemistry", J.P. Kenny, C.L. Janssen, E.F. Valeev, andT.L. Windus, J. Comp. Chem., in press, 10.1002/jcc.20815.

**PI Ruqian Wu**

S.C. Hong. J.I. Lee and R.Q. Wu, Ferromagnetism in Pd thin films induced by quantum well states, Phys. Rev. B 75, 172402 (2007).

J.X. Cao, X.G. Gong, and R.Q. Wu, Giant piezoresistance and its origin in Si(111) nanowires: First-principles calculations, Phys. Rev. B 75, 233302 (2007).

D.X. Wu, Q.M. Zhan, J.P. Liu, D.W. Yuan and R.Q. Wu, On the Thermostability and Magnetism of FeCo Alloys: A First-Principles Study, Applied Phys. Lett. submitted.

J.H. Wang, C.S. Jo, R.Q. Wu, Magnetic Properties of Fe-5d (Os, Ir, and Pt) Nanowires Encapsulated in Carbon Nanotubes, Appl. Phys. Lett. Submitted.

D.W. Yuan, X.G. Gong, and R.Q. Wu, Atomic configurations of Pd atoms in PdAu(111) bimetallic surfaces investigated using the first-principles pseudopotential plane wave approach, Phys. Rev. B 75, 085428 (2007).

D.L. Mills, J.X. Cao and R.Q. Wu, "Interaction of adsorbates with electric-field fluctuations near surfaces: Nonradiative lifetimes and energy-level shifts", Phys. Rev. B 75, 205439 (2007).

D.W. Yuan, X.G. Gong, and R.Q. Wu, "Ensemble effects on ethylene dehydrogenation on PdAu(001) surfaces investigated with first-principles calculations and nudged-elastic-band simulations," Phys. Rev. B 75, 233401 (2007).

D.W. Yuan, X.G. Gong, and R.Q. Wu, "Origin of high activity and selectivity of PdAu(001) bimetallic surfaces toward vinyl acetate synthesis", J. Phys. Chem. submitted.

D.W. Yuan, X.G. Gong, and R.Q. Wu, "Methanol dehydrogenation on PtAu(111) bimetallic surfaces", J. Chem. Phys. submitted.

C.S. Jo, A.A. Shinde, R. Ragan, and R.Q. Wu, First Principles Studies of Adsorption of Pd, Ag, Pt, and Au on YSi2 Nanowires, Phys. Rev. B submitted.

## X

## Y

**PI Yanfo Yan**

K.-S. Ahn, Y. Yan, and M. Al-Jassim,Band gap narrowing of ZnO:N films by varying rf sputtering power in O2/N2 mixtureJ. Vac. Sci. Technol. B 25, L23 (2007)

Aron Walsh, Yanfa Yan, Mowafak Al-Jassim and Su-Huai WeiAn electronic structure study of the Co-Fe-Al oxide spinel systemPhys. Rev. B (in press)

M. N. Huda, Yanfa Yan, Su-Huai Wie and Mowafak M. Al-JassimA density functional theory study of the effects of atomic doping on the band edges of monoclinic WO3Phys. Rev. B (submitted)

**PI Chao Yang**

M. Hohn, G. Tang, G. Goodyear, P. R. Baldwin, Z. Huang, P. A. Penczek, C. Yang, R. M. Glaeser, P. D. Adams, S. J. Ludtke. "SPARX, a new environment for Cryo-EM image processing". Journal of Struct. Biology , vol. 157, pages 47-55, 2007

Baldwin, P.R. and P.A. Penczek, "The Transform Class in SPARX and EMAN2", J. Structure Biology, vol. 157, pages 250-61, 2007

**PI Katherine Yelick**

Jimmy Su and Katherine Yelick, "Automatic Performance Debugging in Partitioned Global Address Space Programs" 20th International Workshop on Languages and Compilers for Parallel Computing (LCPC), Urbana, Illinois, October 2007. To appear in Springer Lecture Notes in Computer Science.

Parry Husbands and Katherine Yelick, "Multithreading and One-Sided Communication in Parallel LU Factorization." Proceedings of Supercomputing (SC07), Reno, NV, November, 2007.

Tong Wen, Jimmy Su, Phillip Colella, Katherine Yelick and Noel Keen, "An Adaptive Mesh Refinement Benchmark for Modern Parallel Programming Languages." Proceedings of Supercomputing (SC07), Reno, NV, November 2007.

Amir Kamil and Katherine Yelick, "Hierarchical Pointer Analysis for Distributed Programs," Static Analysis Symposium (SAS), Kongens Lyngby, Denmark, August 22-24, 2007.

Katherine Yelick, Paul Hilfinger, Susan Graham, Dan Bonachea, Jimmy Su, Amir Kamil, Kaushik Datta, Phillip Colella, and Tong Wen, "Parallel Languages and Compilers: Perspective from the Titanium Experience." Journal of High Performance Computing Applications, August 2007, vol. 21, pp. 266-290.

K. Yelick, D. Bonachea, W.-Y. Chen, P. Colella, K. Datta, J. Duell, S. Graham, P. Hargrove, P. Hilfinger, P. Husbands, C. Iancu, A. Kamil, R. Nishtala, J. Su, M. Welcome, T. Wen, "Productivity and Performance Using Partitioned Global Address Space Languages," Proceedings of Parallel Symbolic Computation (PASCO), London, Ontario, July 27-28, 2007.

Ewing Lusk and Katherine Yelick, "Languages for High-Productivity Computing: The DARPA HPCS Language Project," Parallel Processing Letters, Vol. 17, No. 1 (2007) 89-102.

Wei Chen, Dan Bonachea, Costin Iancu, and Katherine Yelick, "Automatic Nonblocking Communication for Partitioned Global Address Space Programs," Proceedings of the International Conference on Supercomputing (ICS), Seattle, Washington, June 16-17, 2007.

] Alfredo Buttari, Jack Dongarra, Parry Husbands, Jakub Kurzak and Katherine Yelick, "Multithreading for synchronization tolerance in matrix factorization," The proceedings of the SciDAC 2007 Conference, Boston, Massachusetts, July 24-28, 2007. Published in the Journal of Physics: Conference Series. To appear.

**PI Pui-kuen Yeung**

Donzis, D.A., Yeung, P.K. \& Sreenivasan, K.R. (2007) "Energy dissipation rate and enstrophy in isotropic turbulence: resolution effects and scaling in direct numerical simulations". Physics of Fluids (under revision).

## Z

**PI Peter Zapol**

Shape of Platinum Nano-Particles Supported on SrTiO3: Experiment and Theory, H. Iddir, V. Komanicky, S. Ogut, H. You, P. Zapol, J. Phys. Chem. C 111, 40, 14782 - 14789, 2007

Electron density mapping and molecular simulations of triblock copolymers associated with model biomembranes: Insights into conformational states and effect on bilayer structure B. Lee, S. P. Adiga, P. Zapol, M. A. Firestone (submitted)

**PI Bin Zhang**

Ruipeng Li, Hai Jiang, Hung-Chi Su, Bin Zhang, and Jeff Jenness Speculative and distributed simulation of many-particle collisions systems Proceedings of ICPADS 2007, the 13th international conference on parallel and distributed systems, Dec 5-7, 2007, Hsinchu, Taiwan (accepted)

Ruipend Li, Hai Jiang, Hung-Chi Su, Bin Zhang, and Jeff Jenness Coordination schemes in distributed simulation of relativistic particle transport Proceedings of SAC08, the 23rd annual ACM symposium on applied computing, March 16-20, 2008, the beach at Vila Gal\'e in Fortaleza, Cear\'a, Brazil (accepted)

**PI Guoping Zhang**

Manifestation of electron-electron interactions in time-resolved ultrafast pump-probe spectroscopy in C60: Theory, G. P. Zhang and T. F. George, Physical Review B, Vol. 76, 085410 (2007).

High harmonic generation in atoms, molecules and nanostructures, G. P. Zhang, (INVITED), Internal Journal of Modern Physics B, (in press, 2007)

Parallel block tridiagonalization of real symmetric matrices, Yihua Bai and Robert C. Ward, submitted to Journal of Parallel and Distributed Computing, June (2007).

Understanding laser-induced ultrafast magnetization inferromagnets: First-principles investigation G. P. Zhang, Yihua Bai, W. Hubner,Georg Lefkidis, and Thomas F. George, Submitted to Journal of Applied Physics (2007)

**PI Keni Zhang**

Zhang K., C. Doughty, YS Wu, and K. Pruess, 2007, Efficient Parallel Simulation of CO2 Geologic Sequestration in Saline Aquifers, Submitted to SPE Journal.

**PI Zhenyu Zhang**

Optimal doping control of magnetic semiconductors via subsurfactant epitaxyC. Zeng, Z. Y. Zhang,K. van Benthem,M. F. Chisholm,and H. H. Weitering Submitted to Phys. Rev. Lett.

Dopant-assisted Concentration Enhancement of Substitutional Mn in Si and Ge, W. Zhu, Z. Y. Zhang, and E. KaxirasPhys. Rev. Lett., in press.

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

Schottky barrier formation at a carbon nanotube -metal junction W. Zhu and E. Kaxiras Appl. Phys. Lett. 89, 243107 (2006).

The nature of contact between Pd leads and semiconducting carbon nanotubes W. Zhu and E. KaxirasNano Letters 6, 1415 (2006).

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

Dynamics of step bunching in heteroepitaxial growth on vicinal substrates, Yoon M, Lee HN, Hong W, Christen HM, Zhang ZY, and Suo ZG, Phys. Rev. Lett. 99, 055503(2007).

Concerted diffusion, clustering, and magnetic properties of Mn dopants on a 2$\times$2-$T_{4}$ GaN(0001) substrate by Shiqiang Hao and Zhenyu Zhang, Phys Rev. Lett. 99, 166101 (2007).

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

Charged Fullerenes as High-Capacity Hydrogen Storage Media, Mina Yoon, Shenyuan Yang, Enge Wang, and Zhenyu Zhang, Nano Lett. 9, 2578 (2007).

Interplay between elastic interactions and kinetic processes in stepped Si (001) homoepitaxy, Hong W, Zhang ZY, and Suo ZG, Phys. Rev. B 74, 235318 (2006).

Polygonization and anomalous graphene interlayer spacing of multi-walled carbon nanofibers, Yoon M, Howe J, Tibbetts G, Eres G, and Zhang ZY, Phys. Rev. B 75, 165402 (2007).

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

Evolution of a symmetry gap and synergetic quantum well states in ultrathin Ag films on Au(111) substrates Author(s): Li Huang, X. G. Gong, E. Gergert, F. Forster, A. Bendounan, F. Reinert, and Z. Y. Zhang, Europhys. Lett. 78 (5), 57003 (2007).

Stability and mechanical properties of silicon nanowires, Liu SD, Jayanthi CS, Zhang ZY, and Wu SY, Journal of Computational and Theoretical Nanoscience 4 (2), 27

Water wettability of close-packed metal surfaces, S. Meng, E. Kaxiras, and Z. Y. Zhang, J of Chem. Phys. (accepted).

**PI Ping Zhu**

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).

**PI Alex Zunger**

J. Osorio-Guillen, S. Lany, S.V. Barabash, and A. Zunger "Nonstoichiometry as a source of magnetism in otherwise nonmagnetic oxides: Magnetically interacting cation vacancies and their percolation" Phys. Rev. B 75, 184421 (2007)

J. Osorio-Guillen, S. Lany, and A. Zunger "Atomic-control of conductivity vs. ferromagnetism in wide-gap oxides via selective doping: V, Nb, and Ta in anatase TiO2" Phys. Rev. Lett., in press (2007)

J.M. Osorio-Guillen, S. Barabash, S. Lany, and A. Zunger "Magnetism Without Magnetic Ions: Percolation, Exchange and Formation Energies of Magnetism-Promoting Intrinsic Vacancies in CaO" Phys. Rev. Lett. 96, 107203 (2006)

A. Franceschetti, S.V. Barabash, J. Osorio-Guillen, A. Zunger, and M. van Schilfgaarde "Enhancement of interactions between magnetic ions in semiconductors due to declustering" Phys. Rev. B 74, 241303(2006)

A. Franceschetti, A. Zunger, and M. van Schilfgaarde "Design rules to achieve high-Tc ferromagnetism in (Ga,Mn)As alloys" J. Phys. Cond. Matter 19, 242203 (2007)

H. Raebiger, S. Lany, and A. Zunger "Impurity clustering and ferromagnetic interactions that are not carrier-induced in dilute magnetic semiconductors: The case of Cu2O:Co" Phys. Rev. Lett. 99, 167203 (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)

J.M. An, A. Franceschetti, and A. Zunger "Pauli blocking versus electrostatic attenuation of optical transition intensities in PbSe quantum dots" Phys. Rev. B (Rapid Communications), in press (2007)

G. Trimarchi and A. Zunger "Global space-group optimization problem: Finding the stablest crystal structure without constraints" Phys. Rev. B 75, 104113 (2007)

G. Bester, D. Reuter, L. He, A. Zunger, P. Kailuweit, A.D. Wieck, U. Zeitler, J.C. Maan, O. Wibbelhoff, and A. Lorke "Experimental imaging and atomistic modeling of electron and hole quasiparticle wave functions in InAs/GaAs quantum dots" Phys. Rev. B 76, 075338 (2007)

L. He, G. Bester, Z. Su, and A. Zunger "Calculation of near-field scanning optical images of exciton, charged-exciton, and multiexciton wave functions in self-assembled InAs/GaAs quantum dots" Phys. Rev. B 76, 035313 (2007)

L. He and A. Zunger "Electronic structures of (In,Ga)As/GaAs quantum dot molecules made of dots with dissimilar sizes" Phys. Rev. B 75, 075330 (2007)

G.A. Narvaez and A. Zunger "Calculation of conduction-to-conduction and valence-to-valence transitions between bound states in (In,Ga)As/GaAs quantum dots" Phys. Rev. B 75, 085306 (2007)

M. Ediger, G. Bester, A. Badolato, P.M. Petroff, K. Karrai, A. Zunger, and R. J. Warburton "Peculiar Many-Body Effects Revealed in the Spectroscopy of Heavily Charged Quantum Dots" Nature Physics, in press (2007)

M. Ediger, G. Bester, B.D. Gerardot, A. Badolato, P.M. Petroff, K. Karrai, A. Zunger, and R.J. Warburton "Fine Structure of Negatively and Positively Charged Excitons in Semiconductor Quantum Dots: Electron-Hole Asymmetry" Phys. Rev. Lett. 98, 036808 (2007)

M. Califano, A. Franceschetti, and A. Zunger "Lifetime and polarization of the radiative decay of excitons, biexcitons, and trions in CdSe nanocrystal quantum dots" Phys. Rev. B 75, 115401 (2007)

G.A. Narvaez, G. Bester, A. Franceschetti, and A. Zunger "Excitonic exchange effects on the radiative decay time of monoexcitons and biexcitons in quantum dots" Phys. Rev. B 74, 205422 (2006)

G. Bester, A. Zunger, X. Wu, and D. Vanderbilt "Effects of linear and nonlinear piezoelectricity on the electronic properties of InAs/GaAs quantum dots" Phys. Rev. B 74, 081305 (2006)