Publications Resulting from Computations at NERSC

As Reported on the Allocation Year 2005 Request Forms

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

PI Musa Ahmed

M. Hochlaf. "Theoretical spectroscopy of tetratomic molecules". Trends in Chemical Physics, (2004), in press (invited review).

M. Hochlaf, J. Palaudoux and A. Ben Houria. "Theoretical spectroscopy of molecular dications". Transworld Research World. In press (invited review).

M. Hochlaf. "Ab initio investigations of CS2+ for internal energies lower than 10 eV". J. Phys. B 37, 595 (2004).

F. Richter, M. Hochlaf, P. Rosmus, F. Gatti and H.-D. Meyer. "A study of the mode-selective trans-cis isomerisation in HONO using ab initio methodology". J. Chem. Phys. 120, 1306 (2004).

M. Hochlaf and J. H. D. Eland. "A theoretical and experimental study of the SO22+ dication". J. Chem. Phys. 120, 6449 (2004).

J. H. D. Eland, M. Hochlaf, G. C. King, P. S. Kreynin, R. LeRoy, I. R. McNab and J. M. Robbe. "Photo double ionization of CO: comparison of theory with experiment". J. Phys. B 37, 3197 (2004).

M. Hochlaf, K.-M. Weitzel and C. Y. Ng. "Vacuum ultraviolet pulsed field ionization-photoelectron study of H2S in the energy range of 10-17 eV". J. Chem. Phys.120, 6944 (2004).

X.-M. Qian, K.-C. Lau, G. Z. He, C. Y. Ng and M. Hochlaf. "Vacuum Ultraviolet Pulsed field ionization study of ND3: accurate thermochemistry for the ND2/ND2+ and ND3/ND3+ system". J. Chem. Phys. 120, 8476 (2004).

P. Palaudoux and M. Hochlaf. "Theoretical investigations of the N2H2+ cation and of its reactivity" J. Chem. Phys. 121, 1782 (2004). M. Hochlaf. "Ion-molecule reactions: Theoretical studies of the [N2 + CO]+ system". J. Phys. Chem. A, (2004) (in press)

PI Mowfak Al-Jassim

Y. Yan and M.M. Al-Jassim Adsorption of water molecules on the CdTe(001) surface Surface Science (submitted).

Y. Yan, M.M. Al-Jassim, and K.M. Jones Atomic structure and effects of double-positioning twins in CdTe J. Appl. Phys. (accepted).

Y. Yan, G.M. Dalpian, M.M. Al-Jassim, and Su-Huai Wei Energetics and electronic structure of stacking faults in ZnO Phys. Rev. B (submitted). Y. Yan and M.M. Al-Jassim Water adsorption on ZnO (11-20) surfaces. Surface Science (to be submitted).

PI Robert Albers

"Modeling Solid-Solid Phase Transformations: From Single Crystal to Polycrystal Behavior,'' R. C. Albers, R. Ahluwalia, T. Lookman, and A. Saxena, accepted for publication in Computational and Applied Mathematics.

"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, Submitted to Nature.

"Extended X-Ray Absorption Fine Structure Measurements of Laser-Shocks in Ti and V and Phase Transformation in Ti,'' B. Yaakobi, D. D. Meyerhofer, T. R. Boehly, J. J. Rehr, B. A. Remington, P. G. Allen, S. M. Pollaine, and R. C. Albers, Phys. Rev. Lett. 92, 95504 (2004).

"Charge and Dimensional Effects on the Properties of CaNiN,'' Michael Springborg and R. C. Albers, Phys. Rev. B. 69, 235115 (2004).

"Thermal Stabilization of the HCP Phase in Titanium,'' Sven P. Rudin, M. D. Jones, and R. C. Albers, Phys. Rev. B 69, 94117 (2004).

"New Pseudo-Phase Structure for Alpha-Pu,'' J. Bouchet, R. C. Albers, M. D. Jones, and G. Jomard, Phys. Rev. Lett. 92, 95503 (2004).

"Landau Theory for Shape Memory Polycrystals,'' R. Ahluwalia, T. Lookman, A. Saxena, and R. C. Albers, Acta Materialia 52, 209 (2004).

"Constitutive Response of Polycrystalline Shape Memory Alloys,'' A. Saxena, R. Ahluwalia, T. Lookman, and R. C. Albers, Materials Science Forum 426-432, 2255 (2003).

"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, Phys. Rev. Lett. 91, 025701, 2003.

PI Greg Aldering

"Photometry of SN~2002ic and Implications for the Progenitor Mass-Loss History" Wood-Vasey, W. M, Aldering, G., & Wang,~L. (2004), Astrophys. J., accepted for publication

"Type Ia supernova rate at a redshift of ~ 0.1,'' Blanc, G., Afonso, C., Alard, C., Albert, J.N., Aldering, G., Amadon, A., Andersen, J., Ansari, R., Aubourg, E., Balland, C., Bareyre, P., Beaulieu, J.P., Charlot, X., Conley, A., Coutures, C., Dahlen, T., Derue, F., Fan, X., Ferlet, R., Folatelli, G., Fouque, P., Garavini, G., Glicenstein, J.F., Goldman, B., Goobar, A., Gould, A., Graff, D., Gros, M., Haissinski, J., Hamadache, C., Hardin, D., Hook, I.M., deKat, J., Kent, S., Kim, A., Lasserre, T., LeGuillou, L., Lesquoy, E., Loup, C., Magneville, C., Marquette, J.B., Maurice, E., Maury, A., Milsztajn, A., Moniez, M., Mouchet, M., Newberg, H., Nobili, S., Palanque-Delabrouille, N., Perdereau, O., Prevot, L., Rahal, Y.R., Regnault, N., Rich, J., Ruiz-Lapuente, P., Spiro, M., Tisserand, P., Vidal-Madjar, A., Vigroux, L., Walton, N.A., Zylberajch, S. (2004), Astronomy & Astrophysics, 423, 881.

"Spectroscopic Observations and Analysis of the Peculiar SN~1999aa,'' Garavini, G., Folatelli, G., Goobar, A., Nobili,~S., Aldering, G. , Amadon, A., Amanullah, R., Astier, P., Balland, C., Blanc, G., Burns, M.~S., Conley, A., Dahlen, T., Deustua, S. E., Ellis, R., Fabbro, S., Fan, X., Frye, B., Gates, E. L., Gibbons, R., Goldhaber, G., Goldman, B., Groom, D. E., Haissinski, J., Hardin, D., Hook, I. M., Howell, D. A., Kasen, D., Kent, S., Kim, A. G., Knop, R. A., Lee, B. C., Lidman, C., Mendez, J., Miller, G. J., Moniez, M., Mourao, A., Newberg, H., Nugent, P. E., Pain, R., Perdereau, O., Perlmutter, S., Prasad, V., Quimby, R., Raux, J., Regnault, N., Rich, J., Richards, G. T., Ruiz-Lapuente, P., Sainton, G., Schaefer, B. E., Schahmaneche, K., Smith, E., Spadafora, A. L., Stanishev, V., Walton, N. A., Wang, L., Wood-Vasey., W. M. (2004), Astronomical. Journal, 128, 387.

"New Constraints on Omega_M, Omega_Lambda, and w from an Independent Set of 11 High-Redshift Supernovae Observed with the Hubble Space Telescope'', Knop, R. A., Aldering, G., Amanullah, R., Astier, P., Blanc, G., Burns, M. S., Conley, A., Deustua, S. E., Doi, M., Ellis, R., Fabbro, S., Folatelli, G., Fruchter, A. S., Garavini, G., Garmond, S., Garton, K., Gibbons, R., Goldhaber, G., Goobar, A., Groom, D. E., Hardin, D., Hook, I., Howell, D. A., Kim, A. G., Lee, B.~C., Lidman, C., Mendez, J., Nobili, S., Nugent, P. E., Pain, R., Panagia, N., Pennypacker, C. R., Perlmutter, S., Quimby, R., Raux, J., Regnault, N., Ruiz-Lapuente, P., Sainton, G., Schaefer, B., Schahmaneche, K., Smith, E., Spadafora, A. L., Stanishev, V., Sullivan, M., Walton, N. A., Wang, L., Wood-Vasey, W. M., & Yasuda, N., (2003), Astrophysical. Journal, 598, 102.

PI Yoram Alhassid

"Nuclear level statistics: extending the shell model theory to higher temperatures," Y. Alhassid, G.F. Bertsch, and L. Fang, Phys. Rev. C 68, 044322 (2003).

"Effects of spin and exchange interaction on the Coulomb-blockade peak statistics in quantum dots," Y. Alhassid and T. Rupp, Phys. Rev. Lett. 91, 056801 (2003).

"A universal Hamiltonian for a quantum dot in the presence of spin-orbit interaction," Y. Alhassid and T. Rupp, cond-mat/0312691 (2003).

"Spin of a quantum dot and conductance peak motion in parallel magnetic field," D. Huertas-Hernando and Y. Alhassid, cond-mat/0404619 (2004). "Disordered systems with interactions: induced two--body ensembles and the Hartree--Fock approach," Y. Alhassid, H.A. Weidenmuller, and A. Wobst, cond-mat/0406495 (2004).

PI Paul Alivisatos

Manna, L., Wang, L. W., Cingolani, R. & Alivisatos, A. P. First-principles Calculations of Unpassivated and Surfactant-passivated Bulk Surfaces of Wurtzite CdSe: a Model System for Studying the Anisotropic Growth of CdSe Nanocrystals. Physical Review B submitted (2004).

Puzder, A., Williamson, A. J., Zaitseva, N., Galli, G., Manna, L. & Alivisatos, A. P. First-Principles Simulations of the Interaction between CdSe Nanoparticles and Organic Molecules: Effects on Nanoparticle Growth. Nano Letters submitted (2004).

Milliron, D. J., Hughes, S. M., Cui, Y., Manna, L., Li, J. B., Wang, L. W. & Alivisatos, A. P. Colloidal nanocrystal heterostructures with linear and branched topology. Nature 430, 190-195 (2004).

J. B. Neaton, K. H. Khoo, C. D. Spataru, and S. G. Louie, "Electron transport and optical properties of nanostructures from first principles", submitted.

PI David Alumbaugh

Tompkins, M., Alumbaugh, D. L., Stanley, D., and Lu, X., 2004, Numerical analysis of near-borehole and anisotropic effects on the response of a new multi-component induction logging tool; Geophysics, 69, 140-151.

PI Thomas Antonsen

"Further developments for a particle in cell code for efficientlty modeling wakefield acceleration schemes" J. H. Cooley, T. M. Antonsen Jr., C. Huang, V. Decyk, S. Wang, E. S. Dodd, C. Ren, W. B. Mori, and T. Katsouleas, AIP Conference Proceedings 647, 232 (2002).

"Resonant heating of a cluster plasma by intense laser light", T. Taguchi, T. M. Antonsen Jr. H. M. Milchberg , Physical Review Letters 92 (20): Art. No. 205003 May 21 2004

PI Jonathan Arons

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

P. Demorest, R. Ramachandran, D.C. Backer, S. M. Ransom, V. Kaspi, J. Arons, A. Spitkovsky, 2004, "Orientations of Spin and Magnetic Dipole Axes of Pulsars in the J0737--3039

Binary Based on Polarimetry Observations at the Green Bank Telescope", submitted to ApJ Letters, astro-ph/0402025

V.M. Kaspi, S. M. Ransom, D.C. Backer, R. Ramachandran, P. Demorest, J. Arons, A. Spitkovsky, 2004, "Green Bank Telescope Observations of the Eclipse of Pulsar "A" in the Double Pulsar Binary PSR J0737-3039," accepter to ApJ Letters, astro-ph/0401614

PI Cynthia Atherton

Rotman, D.A., C.S. Atherton, D.J. Bergmann, P.J. Cameron-Smith, C.C.Chuang, P.S. Connell, J.E. Dignon, A. Franz, K.E. Grant, D.E. Kinnison, C.R. Molenkamp, D.D. Proctor, J.R. Tannahill, 2004: IMPACT, the LLNL 3D global atmospheric chemical transport model for the combined troposphere and stratosphere: Model description and analysis of ozone and other trace gases, J. Geophys. Res., 109 doi:10.1029/2002JD003155.

Marcy, T.P., D.W. Fahey, R.S. Gao, P.J. Popp, E.C. Richard, T.L. Thompson, K.H. Rosenlof, E.A. Ray, R.J. Salawitch, C.S. Atherton, D.J. Bergmann, B.A. Ridley, A.J. Weinheimer, M. Loewenstein, E.M. Weinstock, and M.J. Mahoney, 2004: Quantifying stratospheric ozone in the upper troposphere using in situ measurements of HCl, Science, 304, 261-265.

Penner, J.E., S.Y. Zhang, and C.C. Chuang, 2003: Soot and smoke aerosol may not warm climate, J. Geophys. Res., 108, 4657, doi:10.1029/2003JD003409.

Douglass, A.R., P.S. Connell, R.S. Stolarski, and S.E. Strahan,, 2004: Radicals and Reservoirs in the GMI Chemistry and Transport Model: Comparison to Measurements, J. Geophys. Res., Vol. 109, No. D16, doi:10.1029/2004JD004632, 17 August 2004

Considine, D., P.S. Connell, D.J. Bergmann, D.A. Rotman, and S.E. Strahan,, 2004: Sensitivity of Global Modeling Initiative CTM predictions of Antarctic ozone recovery to GCM and DAS generated meteorological fields, J. Geophys. Res., Vol. 109, No. D15, D1530110.1029/2003JD004487 03 August 2004

PI Robert Averback

Ion beam smoothening of metal surfaces Zhong Y, Ashkenazy Y, Albe K, et al. JOURNAL OF APPLIED PHYSICS 94 (7): 4432-4439 OCT 1 2003

Mayr SG, Samwer K, Averback RS Surface kinetics during growth and ion irradiation of glassy metal films SCRIPTA MATERIALIA 49 (10): 961-967 NOV 2003

Simulations of the inert gas condensation processes Krasnochtchekov P, Albe K, Averback RS ZEITSCHRIFT FUR METALLKUNDE 94 (10): 1098-1105 OCT 2003 Effect of ion bombardment on stress in thin metal films Mayr SG, Averback RS PHYSICAL REVIEW B 68 (21): Art. No. 214105 DEC 2003

Evolution of thin-film morphologies in metals during ion beam bombardment Mayr SG, Ashkenazy Y, Averback RS NUCLEAR INSTRUMENTS & METHODS IN PHYSICS RESEARCH SECTION B-BEAM INTERACTIONS WITH MATERIALS AND ATOMS 212: 246-252 DEC 2003

Molecular dynamics simulations of void and helium bubble stability in amorphous Si during heavy ion bombardment M. Okuniewski, Y. Ashkenazy, B.J. Heuser, and R.S. Averback J. Appl. Phys. 96 (2004)

Molecular dynamics simulations of cluster nucleation during inert gas condensation Pavel Krasnochtchekov and R.S. Averback J. Phys. Chem. (in press)

Strings and interstitials in liquids, glasses and crystals K. Nordlund, Y. Ashkenazy, R.S. Averback and A.V. Granato submitted to Phys. Rev. Lett. Shock induced amorphization as the onset to spall Y. Ashkenazy and R.S. Averback submitted to Appl. Phys. Lett.

PI Dmitri Babikov

D. Babikov, B. Kendrick, P. Zhang, and K. Morokuma, Cyclic-N3: II. Large geometric phase effects in the vibrational spectra, J. Chem. Phys. (submitted).

R. D. Averitt, D. E. Hooks, D. Babikov, J. Barber, A. J. Taylor, and D. J. Funk, Temperature-dependent far-infrared spectra of single crystals of high explosives using terahertz time-domain spectroscopy, J. Phys Chem. A. (submitted).

D. Babikov, Accuracy of gates in a quantum computer based on vibrational eigenstates, J. Chem. Phys. (accepted, to appear in Oct. 2004)

D. Babikov, P. Zhang, and K. Morokuma, Cyclic-N3: I. An accurate potential energy surface for the ground doublet electronic state up to the energy of the 2A2/2B1 conical intersection, J. Chem. Phys. (accepted, to appear in Sept. 2004).

D. Babikov, Entrance channel localized states in ozone: possible application to helium nanodroplet isolation spectroscopy, J. Chem. Phys. 119, pp. 6554-6559, 2003.

D. Babikov, B. Kendrick, R. B. Walker, and R. T Pack, Formation of ozone: scattering resonances and anomalous isotope effect, J. Chem. Phys.119, pp. 2577-2589, 2003.

D. Babikov, B. Kendrick, R. B. Walker, R. Schinke, and R. T Pack, Quantum origin of an anomalous isotope effect in ozone formation, Chem. Phys. Let. 372, pp. 686-691, 2003.

D. Babikov, B. Kendrick, R. B. Walker, R. T Pack, P. Fleurat-Lesard and R. Schinke, Metastable states of ozone calculated on an accurate potential energy surface, J. Chem. Phys. 118, pp. 6298-6308, 2003.

PI Diana Bacon

Bacon DH, and BP McGrail. 2003. Lessons Learned From Reactive Transport Modeling of a Low-Activity Waste Glass Disposal System. Computers and Geosciences, 29(3):361-370.

Bacon DH, and BP McGrail. 2003. Waste Form Release Calculations for Performance Assessment of the Hanford Immobilized Low-Activity Waste Disposal Facility Using a Parallel, Coupled Unsaturated Flow and Reactive Transport Simulator. Scientific Basis for Nuclear Waste Management XXVI. Materials Research Society, Warrendale, PA. Freedman VL, P Saripalli,

DH Bacon, and PD Meyer. 2003. "Modeling changes in the hydraulic properties of subsurface media using film depositional models. Part 1. Application to mineral precipitation and dissolution reactions in saturated porous media." Vadose Zone Journal. [In Press]

McGrail BP, DH Bacon, PD Meyer, MI Ojovan, DM Strachan, and IV Startceva. 2003. New Developments in Field Studies of Low Activity Waste Glass Corrosion and Contaminant Transport. Scientific Basis for Nuclear Waste Management XXVI. Materials Research Society, Warrendale, PA.

PI Scott Baden

Gregory T. Balls, Scott B. Baden, and Phillip Colella, SCALLOP: A Highly Scalable Parallel Poisson Solver in Three Dimensions, Conf. Proc., SC '03, Phoenix AZ, November 2003.

PI Ferdinand Baer

Baer, F., and J. J. Tribbia, 2004: Sensitivity of atmospheric prediction models to amplitude and phase. Submitted to Tellus.

Fournier, A., 2003: Atmospheric energetics in the wavelet domain. Part II: Time-averaged observed atmospheric blocking, J. Atmos. Sci., 60, 319-338.

Fournier, A., 2004: Instantaneous wavelet energetic transfers between atmospheric blocking and local eddies, J. Climate, in press.

Fournier, A., Mark A. Taylor and Joseph J. Tribbia, 2004: The Spectral Element Atmospheric Model: High-resolution parallel computation and response to regional forcing, Mon. Wea. Rev., 132, 726-748.

Schneider, E., D. DeWitt, A. Rosati, B. Kirtman, M. Ji, and J. Tribbia 2004: Retrospective ENSO forecasts: sensitivity to atmospheric model and ocean resolution, to appear, Mon Wea. Rev.

Wang, H., and G.-T. Yeh, 2004: A characteristic-based semi-Lagrangian method for hyperbolic systems of conservation laws. (Submitted to Adv. In Atmos. Sci.).

Temam, R and J. Tribbia, 2004: Open Boundary Conditions for the Primitive and Boussinesq Equations, Accepted, J. Atmos. Sci.

PI Mark Baertschy

"Solving the three-body Coulomb breakup problem using exterior complex scaling"; C. W. McCurdy, M. Baertschy, and T. N. Rescigno; J. Phys. B: At. Mol. Opt. Phys. 37 (2004) R137-R187.

"Toward Gaining Mechanistic Insight From Closed Loop Learning Control: the Importance of Basis in Searching the Phase Space"; Florian Langhojer, David Cardoza, Mark Baertschy, and Thomas Weinacht; submitted to J. Chem. Phys, July 2004.

PI David Bailey

David H. Bailey and Xiaoye S. Li, "A Comparison of Three High-Precision Quadrature Programs", Proceedings of the Real Numbers and Computing Conference, Lyon, France, Sept 2003.

David H. Bailey, Karthik Jeyabalan and Xiaoye S. Li, "A Comparison of Three High-Precision Quadrature Programs", [signifiantly revised from #1], submitted to Experimental Mathematics.

David H. Bailey, Jonathan M. Borwein, Vishall Kapoor and Eric Weisstein, "Ten Problems in Experimental Mathematics: A Challenge", Aug. 2004, to be submitted to American Mathematical Monthly.

Laura Carrington, Nicole Wolter, Allan Snavely, and Cynthia Bailey Lee, "Applying an Automated Framework to Produce Accurate Blind Performance Predictions of Full-Scale HPC Applications", DOD HPCMOD Users Group Conference, Williamsburg, VA, June 2004.

A. Snavely, X. Gao, C. Lee, L. Carrington, N. Wolter, J. Labarta, J. Gimenez, P. Jones, "Performance Modeling of HPC Applications", Parallel Computing Europe, Sept. 1993.

P. K. Agarwal, R. A. Alexander, E. Apra, S. Balay, A. S. Bland, J. Colgan, E. F. D'Azevedo, J. J. Dongarra, T. H. Dunigan, Jr., M. R. Fahey, R. A. Fahey, A. Geist, M. Gordon, R. J. Harrison, D. Kaushik, M. Krishnakumar, P. Lusczek, A. Mezzacappa, J. A. Nichols, J. Nieplocha, L. Oliker, T. Packwood, M. S. Pindzola, T. C. Shulthess, J. S. Vetter, J. B. White III, T. L. Windus, P. H. Worley, T. Zacharia, "ORNL Cray X1 Evaluation Status Report", Proceedings of the 46th Cray User Group Conference, Knoxville, TN, May 17-21, 2004.

G. Mahinthakumar, M. Sayeed, J. Blondin, P. Worley, W. Hix, A. Mezzacappa, "Performance Evaluation and Modeling of a Parallel Astrophysics Application", in Proceedings of the High Performance Computing Symposium 2004, p. 27-33, ed. Joerg Meyer.

P. H. Worley, J. Levesque, "The Performance Evolution of the Parallel Ocean Program on the Cray X1", in Proceedings of the 46th Cray User Group Conference, Knoxville, TN, May 17-21, 2004.

PI Perla Balbuena

Y. Wang and P. B. Balbuena, "Combined ab initio quantum mechanics and classical molecular dynamics studies of polymer electrolytes: Competitive solvation of Li+ and LiCF3SO3, J. Phys. Chem. B, in press.

P. B. Balbuena, D. Altomare, N. Vadlamani, S. Bingi, L. A. Agapito, and J. M. Seminario, "Adsorption of O, OH, and H2O on Pt-based bimetallic clusters alloyed with Co, Cr, and Ni, J. Phys. Chem. A, 108, 6378, (2004).

Y. Wang and P. B. Balbuena, Roles of proton and electric field in the electroreduction of O2 on Pt(111) surfaces: Results of an ab initio molecular dynamics study , J. Phys. Chem. B, 108, 4376-4384, (2004).

D. S. Mainardi and P. B. Balbuena, "Hydrogen and Oxygen Adsorption on Rhn (n =1-6) Clusters, J. Phys. Chem. A., 107, 10370-10380, (2003).

D. S. Mainardi, S. Calvo, A. P. J. Jansen, J. J. Lukkien, and P. B. Balbuena, "Dynamic Monte Carlo Simulations of O2 Adsorption and Reaction on Pt (111), Chem. Phys. Lett., 382, 553-560, (2003).

P. B. Balbuena, D. Altomare, L. A. Agapito, and J. M. Seminario, "Theoretical analysis of oxygen adsorption on Pt-based clusters alloyed with Co, Ni, or Cr embedded in a Pt matrix, J. Phys. Chem. B, 107, 13671-13680, (2003).

E. J. Lamas and P. B. Balbuena, "Adsorbate effects on structure and shape of supported nanoclusters: A molecular dynamics study, J. Phys. Chem. B, 107, 11682-11689, (2003).

S-P. Huang, D. S. Mainardi, and P. B. Balbuena, "Structure and dynamics of graphite-supported nanoclusters, Surf. Sci., 545, 163-179, (2003).

PI Arun Bansil

M. Samsel-Czekala, G. Kontrym-Sznajd, G. Doring, W. Schulke, J. Kwiatkowska, F. Maniawski, S. Kaprzyk, and A. Bansil: ``Electron Momentum Density in Cu0.9Al0.1", Applied Physics A 76, 87 (2003).

R. Saniz, B. Barbiellini, A. B. Denison, and A. Bansil: "Spontaneous Magnetization and Electron Momentum Density in 3D Quantum Dots", Phys. Rev. B 68, 165326 (2003).

I. G. Kaplan, B. Barbiellini, and A. Bansil: "Compton scattering beyond the impulse approximation", Phys. Rev. B 68, 235104 (2003).

M. C. Asensio, J. Avila, L. Roca, A. Tejeda, G. D. Gu, M. Lindroos, R. S. Markiewicz, and A. Bansil: ``Emergence of multiple Fermi surface maps in angle-resolved photoemission from Bi2212", Phys. Rev. B 67, 014519 (2003).

S. Sahrakorpi, M. Lindroos and A. Bansil: "Site selectivity properties of the ARPES matrix element in Bi_2Sr_2CaCu_2O_8", Phys. Rev. B 68, 054522 (2003).

Y. -D. Chuang, A. D. Gromko, A.V. Fedorov, Y. Aiura, K. Oka, Yoichi Ando, M. Lindroos, R. S. Markiewicz, A. Bansil and D.S. Dessau: "Bilayer Splitting and Coherence Effects in Optimal and Underdoped Bi_2Sr_2CaCu_2O_(8+\delta)", Phys. Rev. B 69, 094515 (2004).

M. Lindroos, R.S. Markiewicz, and A. Bansil: "Special Photon Energies for Extracting the Bosonic Spectral Function Mediating Superconductivity in Bi2212 via ARPES", Phys. Rev. B 69, 140505 (2004).

A. Bansil, R.S. Markiewicz, C. Kusko, M. Lindroos, and S. Sahrakorpi: "Matrix Element and Strong Electron Correlation Effects in ARPES from Cuprates", J. Phys. Chem Solids 65, 1417 (2004).

A. Bansil, D. Nissenbaum, and B. Barbiellini: "Spontaneous Spin Magnetization in Quantum Dots", J. Phys. Chem Solids (2004, in press).

A. Bansil, M. Lindroos, S. Sahrakorpi and R. S. Markiewicz: "Influence of the Third Dimension of Quasi-Two-Dimensional Cuprate Superconductors on Angle-Resolved Photoemission Spectra", submitted to Phys. Rev. Letters (2004).

S. Sahrakorpi, M. Lindroos, R.S. Markiewicz, and A. Bansil: "Evolution of Mid-gap States and Residual 3-Dimensionality in La_2-xSr_xCuO_4", submitted to Nature (2004).

PI Don Batchelor

"Nonlinear Fluxes and Forces from Radio-frequency Waves with Application to Driven Flows in Tokamaks", J. R. Myra, L. A. Berry, D. A. D'Ippolito, and E. F. Jaeger, Phys. Plasmas 11, 1786 (2004).

"Full Wave Simulations of Fast Wave Mode Conversion and Lower Hybrid Wave Propagation in Tokamaks", J. C. Wright, P. T. Bonoli, M. Brambilla, F. Meo, E. D'Azevedo, D. B. Batchelor, E. F. Jaeger, L. A. Berry, C. K. Phillips and A. Pletzer, Phys. Plasmas 11, 2473 (2004).

"Fast Ion Absorption of the High Harmonic Fast Wave in the National Spherical Torus Experiment," A. L. Rosenberg, J. E. Menard, J. R. Wilson, S. Medley, R. Andre, D. Darrow, R. Dumont, B. P. LeBlanc, C. K. Phillips, M. Redi, T. K. Mau, E. F. Jaeger, P. M. Ryan, D. W. Swain, R. W. Harvey, J. Egedal, and the NSTX Team, Phys. Plasmas 11, 2441 (2004).

"Effects of Non-Maxwellian Species on Electromagnetic Wave Propagation and Absorption in Magnetically Confined Plasmas", R. J. Dumont, C. K. Phillips, and D. N. Smithe, Submitted to Phys. Rev. Lett. (2004).

"Sheared Poloidal Flow Driven by Mode Conversion in Tokamak Plasmas", E. F. Jaeger, L. A. Berry, J. R. Myra, D. B. Batchelor, E. D'Azevedo, P. T. Bonoli, C.K. Phillips, D. N. Smithe, D. A. D'Ippolito, M. D. Carter, R. J. Dumont, J. C. Wright, R. W. Harvey, Phys. Rev. Lett. 90, 195001-1 (2003).

PI Victor Batista

J. Phys. Chem. B 108, 6745, 2004. Model Study of Coherent-Control of the Femtosecond Primary Event of Vision, by Samuel C. Flores and Victor S. Batista.

Biophys. J., in press, 2004. QM/MM Study of Energy Storage and Molecular Rearrangements due to the Primary Event in Vision, by Jose A. Gascon and Victor S. Batista.

PNAS, submitted , 2004. Molecular Quantum Entanglement in Functionalized Semiconductor Nanostructures, by Luis G.C. Rego, Sabas Abuabara and Victor S. Batista.

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

J. Chem. Phys. 121, 1676, 2004. Quantum Tunneling in Multidimensional Systems: A Matching-Pursuit Description, by Yinghua Wu and Victor S. Batista.

J. Am. Chem. Soc. 125, 7989, 2003. Quantum Dynamics Simulations of the Interfacial Electron Transfer in Sensitized TiO2 semiconductors by Luis G.C. Rego and Victor S. Batista

J. Chem. Phys. 118, 6720 (2003). Matching Pursuit for Simulations of Quantum Processes, by Yinghua Wu and Victor S. Batista.

J. Chem. Phys. 119, 7606 (2003). Erratum: Matching Pursuit for Simulations of Quantum Processes [J. Chem. Phys. 118, 6720, 2003], by Yinghua Wu and Victor S. Batista.

Center Recherches Mathematiques CRM Proceedings and Lecture Notes. Volume 33 (2003) Coherent Control: Principles and Semiclassical Implementations, by Victor S. Batista and Paul Brumer.

PI John Bell

J.B. Bell, M.S. Day, J.F. Grcar, and M.J. Lijewski, "Stochastic Algorithms for the Analysis of Numerical Flame Simulations", Report LBNL-49326-Journal, J. Comp. Phys, in press, 2004.

J.F. Grcar, P. Glarborg, J.B. Bell, M.S. Day, A. Loren, and A.D. Jenson, "Effects of Mixing on Ammonia Oxidation in Combustion Environments at Intermediate Temperatures", Report LBNL-54187, Proceedings of the Combustion Institute, v. 30, in press, 2004.

J.B. Bell, M.S. Day, C.A. Rendleman, S.E. Woosley, and M.A. Zingale, "Direct Numerical Simulations of Type Ia Supernovae Flames II: The Rayleigh-Taylor Instability", LBNL Report LBNL-54300, Astrophysical Journal, v. 608, pp. 883-906, 2004.

J.B. Bell, M.S. Day, C.A. Rendleman, S.E. Woosley, and M.A. Zingale, "Direct Numerical Simulations of Type Ia Supernovae Flames I: The Landau-Darrieus Instability", Report LBNL-54088, Astrophysical Journal, v. 606, pp. 1029-1038, 2004.

J.B. Bell, M.S. Day, C.A. Rendleman, S.E. Woosley, and M.A. Zingale, "Adaptive low Mach number simulations of nuclear flame microphysics", Report LBNL-52395, J. Comp. Phys, v. 195, pp. 677-694, 2004.

P. McCorquodale, P. Colella, D.P. Grote and J.-L. Vay, "A node-centered local refinement algorithm for Poisson's equation in complex geometries," Report LBNL-54138, J. Comp. Phys, in press, 2004.

D. Trebotich, P. Colella, and G. Miller, "A stable and convergent scheme for viscoelastic flow in contraction channels," Report LBNL-55880, J. Comp. Phys, in review, 2004.

R.K. Crockett, P. Colella, R.T. Fisher, R.I. Klein, and C.F. McKee, "An unsplit, cell-centered Godunov method for ideal MHD," Report LBNL-55881, J. Comp. Phys, in review, 2003.

PI Roy Benedek

Dopant-induced Stabilization of Rhombohedral LiMnO2 against Jahn-Teller Distortion, R. Prasad, R. Benedek, and M. M. Thackeray, Physical Review B, submitted (2004).

Effect of Co on the magnetism and phase stability of lithiated manganese oxides, R. Prasad, R. Benedek, and M. M. Thackeray, vol. 26, 147 (2003).

Structural considerations of intermetallic electrodes for lithium batteries, M. M. Thackeray, J. T. Vaughey, C. S. Johnson, A. J. Kropf, R. Benedek, L. M. L. Fransson, K. Edstrom, Journal of Power Sources vol 113, 124 (2003).

Divalent dopant criterion for the suppression of Jahn-Teller distortion in Mn oxides: First-principles calculations and x-ray spectroscopy measurements for Co in LiMnO2, vol 68, article 012101.

PI Amitava Bhattacharjee

Anisotropic weak whistler wave turbulence in electron magnetohydrodynamics, S. Galtier and A. Bhattacharjee, Physics of Plasmas 10, 3065 (2003).

Wave driven magnetic reconnection in the Taylor problem, R. Fitzpatrick, A. Bhattacharjee, Z.-W. Ma, and T. Linde, Physics of Plasmas 10, 4284 (2003).

WIND observations pertaining to current disruptions and ballooning instabilities during substorms, L.-J. Chen, A. Bhattacharjee, K. Sigsbee, M. Fillingim, G. Parks and R. Lin, Geophysical Research Letters 30, 1335, doi:10.1029/2002GL016317 (2003).

Sufficient condition for finite-time singularity and tendency towards self-similarity in a high- symmetry Euler flow, C. S. Ng and A. Bhattacharjee, in Tubes, Sheets and Singularities in Fluid Dynamics, edited by K. Bajer and H. K. Moffatt, IUTAM Symposium Series (Kluwer Academic Publishers 2003), Vol. 71, pp. 317-328.

P. Zhu, A. Bhattacharjee, and Z. W. Ma, Finite-ky Ballooning Instability in the Near-Earth Magnetotail, to appear in Journal of Geophysical Research.

K. Germaschewski, A. Bhattacharjee, Rainer Grauer, David Keyes, and Barry Smith, Using Krylov-Schwarz methods in an adaptive mesh refinement environment, in Adaptive Mesh Refinement - Theory and Applications, Lecture Notes in Computational Sciences and Engineering (LNCSE) series, editors Tomasz Plewa, Timur Linde and V. Gregory Weirs, Springer 2004

PI Julian Borrill

"High-Resolution Observations of the Cosmic Microwave Background Power Spectrum with ACBAR", C-L Kuo et al, 2004, ApJ, 600, 32

"Asymmetries in the CMB anistropy field", Eriksen, H. K., Hansen, F. K., Banday, A. J., Gsrski, K. M. and Lilje, P. B., 2004, ApJ, 605, 14, [astro-ph/0307507]

"Testing for non-Gaussianity in the WMAP data: Minkowski functionals and the length of the skeleton", Eriksen, H. K., Novikov, D. I., Lilje, P. B., Banday, A. J. and Gsrski, K. M., 2004, ApJ, in press, [astro-ph/0401276].

"Foreground removal by an Internal Linear Combination method: limitations and implications", Eriksen, H. K., Banday, A. J., Gsrski, K. M. and Lilje, P. B., 2004, ApJ, in press, [astro-ph/0403098].

"Bayesian power spectrum analysis of the first-year WMAP data", O'Dwyer, I. J., Eriksen, H. K., Wandelt, B. D., Jewell, J. B., Larson, D. L., Gsrski, K. M., Banday, A. J., Levin, S. and Lilje, P. B., 2004, ApJL, submitted, [astro-ph/0407027].

"Power spectrum estimation from high-resolution maps by Gibbs sampling", Eriksen, H. K., O'Dwyer, I. J., Jewell, J. B., Wandelt, B. D., Larson, D. L., Gsrski, K. M., Banday, A. J., Levin, S. and Lilje, P. B., 2004, ApJS, in press, [astro-ph/0407028].

"The N-point correlation functions of the first-year Wilkinson Microwave Anisotropy Probe sky maps", Eriksen, H. K., Banday, A. J., Gsrski, K. M. and Lilje, P. B., 2004, ApJ, submitted, [astro-ph/0407271].

E. Keihdnen, H. Kurki-Suonio, T. Poutanen, D. Maino, and C. Burigana: "A maximum likelihood approach to the destriping technique", accepted for publication in A&A.

T. Poutanen, D. Maino, H. Kurki-Suonio, E. Keihdnen, E. Hivon: "Cosmic microwave background power spectrum estimation with the destriping technique", MNRAS 353, 43 (2004)

O'Dwyer et al. "The CMB Power Spectrum from the Background Emission Anisotropy Scanning Telescope (BEAST)". Astro-ph/0312610, accepted for publication in ApJ Supplement Series.

PI Virginia Brown

V.R.Brown, B.F.Gibson, J.A.Carlson,and R.Schiavilla, Eur. Phys. J. A. 18,289-29 (2003)

PI Suse Broyde

"Simulating structural and thermodynamic properties of carcinogen-damaged DNA", S. Yan, M. Wu, D. J. Patel, N. E. Geacintov and S. Broyde, Biophys. J. 84, 1-12 (2003).

"Role of Base Sequence Context in Conformational Equilibria and Nucleotide Excision Repair of Benzo[a]pyrene Diol Epoxide Adenine Adducts", S. Yan, M. Wu, T. Buterin, H. Naegli, N. E. Geacintov, and S. Broyde, Biochemistry 42, 2339-2354 (2003).

"Extending the Understanding of Mutagenicity: Structural Insights into Primer Extension Past a Benzo[a]pyrene Diol Epoxide-DNA Adduct", R. Perlow and S. Broyde, J. Mol. Biol. 327, 797-818 (2003).

"Conformations of Stereoisomeric Base Adducts to 4-Hydrooxyequilenin", S. Ding, R. Shapiro, N. E. Geacintov and S. Broyde, Chem. Res. Tox. 16, 695-707 (2003).

"Human RNA Polymerase II is partially blocked by DNA Adducts Derived from Tumorigenic Benzo[c]phenanthrene Diol Epoxides: relating biological consequences to biological preferences Bypass", T. M. Schinecker, R. A. Perlow, S. Broyde, N. E. Geacintov and D. A. Scicchitano, Nuc. Acids Res. 31, 6004-6015 (2003).

"Solution Structure of an O6-[4-oxo-4(3-pyridyl)butyl]guanine adduct in an 11mer DNA duplex: evidence for formation of a base 'triplex'", L. A. Peterson, C. Vu, B. E. Hingerty, S. Broyde and M. Cosman, Biochemistry 42, 13134-13144 (2003).

"Substrate discrimination by formamidopyrimidine-DNA glycosylase - A Mutational analysis", E. I. Zaika, R. A. Perlow, E. Matz, S. Broyde, R. Gilboa, A. P. Grollman and D. O. Zharkov, J. Biol. Chem, 279, 4849-4861 (2004).

"Conformational searches elucidate effects of sterochemistry on structures of deoxyadenosine covalently bound to tumorigenic metabolites of benzo[c]phenanthrene", M. Wu, S. Yan, J. Tan, D. J. Patel, N. E. Geacintov and S. Broyde, Frontiers in Bioscience 9, 2807-2818 (2004).

"Structural and stereoisomer effects of model estrogen quinone-derived DNA adducts: N6-(2-hydroxyestron-6(alpha,beta)-yl)-2'-deoxyadenosine and N2-(2-hydroxyestron-6(alpha,beta)-yl)-2'-deoxyguanosine", L. Wang, B. E. Hingerty, R. Shapiro and S. Broyde, Chem. Res. in Tox. 3, 311-324 (2004).

PI Vasily Bulatov

V. Bulatov, W. Cai, J. Fier, M. Hiratani, T. Pierce, M. Tang, M. Rhee, K. Yates, T. Arsenlis, ParaDiS on BlueGene/L: scalable line dynamics, SuperComputing 2004 (2004 in press).

M. Hiratani, and V. V. Bulatov, Solid-Solution Hardening by Point-Like Obstacles of Different Kinds: Discrete Dislocation Dynamics, Philosophical Magazine Letters (2004 in press)

J. Marian, W. Cai and Vasily V. Bulatov, Dynamic Transitions in Dislocation Motion: from smooth to rough to twinning, Nature Materials, 3, 158 (2004).

A.Athanasios, B.Wirth, and M.Rhee, Polycrystal-Plasticity-Based Plasticity Model for Irradiated Copper, Philosophical Magazine A (2004 in press) W. Cai, V. V. Bulatov, J. Chang, J. Li, and S. Yip, Periodic Image Effects in Dislocation Modeling, Philosophical Magazine A, 83, 539 (2003).

M. de Koning, W. Cai and V. V. Bulatov, A Mechanism for Anomalous Dislocation Multiplication in FCC Metals, Physical Review Letters, 91, 022503 (2003).

M. Hiratani, and H.M.Zbib, On Dislocation Interactions and Patterning: Stochastic Discrete Dislocation Dynamics, Journal Nuclear Materials, 323, 290 (2003)

PI Philip Cameron-Smith

"IMPACT, the LLNL 3-D global atmospheric chemical transport model for the combined troposphere and stratosphere: Model description and analysis of ozone and other trace gases", D. A. Rotman, C. S. Atherton, D. J. Bergmann, P. J. Cameron-Smith, C. C. Chuang, P. S. Connell, J. E. Dignon, A. Franz, K. E. Grant, D. E. Kinnison, C. R. Molenkamp, D. D. Proctor, and J. R. Tannahill, J. GEOPHYS. RES., VOL. 109, D04303, doi:10.1029/2002JD003155, 2004.

PI Andrew Canning

L.W. Wang, Calculating quantum transports using periodic boundary conditions, Phys. Rev. B (submitted).

NMR chemical shifts in amino acids: effects of environments in the condensed phase, Y. Yoon, B.G. Pfrommer, S.G. Louie and A. Canning, Solid State Communications, Vol 131, pp 15-19 (2004)

Atomistic simulation of fcc Pt75Ni25 and Pt75Re25 Cubo-octahedral nanoparticles, G. Wang, M.A. Van Hove, P.N. Ross and M.I. Baskes, to appear in Bull. Mat. Res. Soc.

The Grassman-metal all band iterative diagonalization method for total energy calculations of metallic systems , D. Raczkowski, L.W. Wang and A. Canning. submitted to Phys. Rev. B.

PI Joseph Carlson

`Quantum Monte Carlo Studies of Superfluid Fermi Gases', S. Y. CHang, J. Carlson, V. R. Pandharipande, and K. E. Schmidt, accepted by Phys. Rev. A.

'Superfluid Fermi Gases with Large Scattering Length', J. Carlson, S-Y. Chang, V. R. Pandharipande, and K. E. Schmidt, Phys. Rev. Lett. 91, 050401 (2003).

'Parity-Violating Interaction Effects in the np System', R. Schiavilla, J. Carlson, and M. Paris, submitted to Phys. Rev. C.

Quantum Monte Carlo Calculations of Excited States in A=6-8', S. C. Pieper, R. B. Wiringa, and J. Carlson, submitted to Phys. Rev. C, LA-UR-04-5712.

PI Yuen-Dat Chen

Measurement of the Total Active 8B Solar Neutrino Flux at the Sudbury Neutrino Observatory with Enhanced Neutral Current Sensitivity, S.N. Ahmed et al. (The SNO Collaboration), Phys. Rev. Lett. 92, 181301 (2004), LBNL 55219

Constraints on Nucleon Decay via Invisible Modes from the Sudbury Neutrino Observatory S.N. Ahmed et al. (the SNO Collaboration), Phys.Rev.Lett. 92 (2004) 102004, LBNL 53918

PI James Chelikowski

D.V. Melnikov and J.R. Chelikowsky: "Ab Initio Absorption Spectra of Germanium Nanocrystals," Solid State Comm. 127, 361 (2003).

C. Troparevsky, L. Kronik, and J.R. Chelikowsky: "Optical Excitations in CdSe Quantum Dots,'' J. Chem. Phys. 119, 2284 (2003).

S. Ogut , R. Burdick, Y. Saad, and J.R. Chelikowsky: "Ab Initio Calculations for the Large Dielectric Matrices of Confined Systems," Phys. Rev. Lett. 90, 127401 (2003).

L. Kronik, R. Fromherz, E. Ko, G. Gantefor, and J.R. Chelikowsky: "Photoemission spectra of deuterated silicon clusters: experiment and theory,'' Euro. Phys. J. D 24, 33 (2003).

M.M.G. Alemany and James R. Chelikowsky: "Edge-sharing tetrahedra: Precursors of the E$^\prime_\gamma$ defects in amorphous silica,'' Phys. Rev. B 68, 054206 (2003).

D.V. Melnikov and J.R. Chelikowsky: "Quantum confinement in phosphorus-doped silicon nanocrystals,'' Phys. Rev. Lett. 92, 046802 (2004).

S. Ogut and J.R. Chelikowsky: "Charge State Dependence Jahn-Teller Distortions of the E- center Defect in Crystalline Silicon,'' Phys. Rev. Lett. 91, 235503 (2003).

F.-C. Chuang, C.Z. Wang, S. Ogut, J.R. Chelikowsky and K.M. Ho: "Melting of small Sn clusters by ab initio molecular dynamics simulations,'' Phys. Rev. B 69, 165408 (2004).

G. Nesher, L. Kronik and J.R. Chelikowsky: "Ab initio absorption spectra of Ge nanocrystals,'' Phys. Rev. B, (submitted).

S. Li, M.M.G. Alemany and J.R. Chelikowsky: "Ab initio calculations for the photoelectron spectra of vanadium clusters,'' J. Chem. Phys. (in press).

PI Liu Chen

"Parallel Data Streaming Implemented for Gyrokinetic Toroidal Code", S. Klasky, S. Either, Z. Lin, K. Martins, D. McCune, and R. Samtangey, Proceedings of the ACM/IEEE Conference on Supercomputing, (November 2003).

"Turbulence Spreading and Transport Scaling in Global Gyrokinetic Particle Simulation", Z. Lin and T. S. Hahm, Phys. Plasmas 11, 1099-1108 (March 2004).

"Turbulence Spreading into Linearly Stable Zone and Transport Scaling", T. S. Hahm, P. H. Diamond, Z. Lin, K. Itoh, and S.-I. Itoh, Plasma Phys. Contr. Fusion 46, A323-A333 (May 2004).

"Porting the 3D Gyrokinetic Particle-in-Cell Code GTC to the NEC SX-6 Vector Architecture: Perspectives and Challenges, S. Ethier and Z. Lin, to appear in Computer Physics Communications, 2004.

"A Gyrokinetic Electron and Fully Kinetic Ion Particle Simulation Model", Y. Lin, X. Y. Wang, Z. Lin, and L. Chen, submitted to Phys. Plasmas, 2004.

"Calculating the Thermal Structure of Solar Active Region in Three Dimension", Y. Mok, R. Lionello, Z. Mikic and J. Linker, Astrophys. J., accepted. "Discrete Alfven Eigenmode in High-Beta Toroidal Plasma", S. Hu and L. Chen, Phys. Plasma, 11, 1, 2004.

PI Jacqueline Chen

T. Echekki and J. H. Chen, Direct Numerical Simulation of Autoignition in Non-homogeneous Hydrogen-Air Mixtures, Combust. Flame, 134:169-191. (2003).

E. R. Hawkes and J. H. Chen, "Direct Numerical Simulation of Hydrogen Enriched Lean Premixed Methane/Air Flames," Combust. Flame 138:242-258, (2004b).

S. Liu, J. C. Hewson, J. H. Chen, and H. Pitsch, "Effects of Strain Rate on High-Pressure Nonpremixed N-Heptane Autoignition in Counterflow," Combust. Flame, 137:320-339 (2004).

E. R. Hawkes and J. H. Chen, "Evaluation of Models for Flame Stretch in the Thin Reaction Zones Regime," to appear in Proceedings of the Combustion Institute, 30, (2004c).

E. R. Hawkes and J. H. Chen, "Comparison of Direct Numerical Simulations of Lean Premixed Flames with Strained Laminar Flame Calculations," submitted to Combust. Flame, (2004b).

J. C. Sutherland, P. J. Smith, and J. H. Chen, "A Generalized Method for A Priori Evaluation of Combustion Reaction Models," submitted to Combust. Flame, (2004a).

J. C. Sutherland, P. J. Smith, and J. H. Chen, "Quantification of Differential Diffusion in Nonpremixed Systems," submitted to Combust. Theory and Modeling, (2004b).

J. H. Chen, E. R. Hawkes, J. C. Hewson, R. Sankaran, H. G. Im, and S. D. Mason, and P. Pebay "Ignition Front Propagation in a Constant Volume With Temperature Inhomogeneities," submitted to Combust. Flame, (2004).

R. Sankaran, H. G. Im, E. R. Hawkes, and J. H. Chen, "The Effects of Nonuniform Temperature Distribution on the Ignition of a Lean Homogeneous Hydrogen-Air Mixture," to appear in Proceedings of the Combustion Institute, 30, (2004).

R. Seiser, J. H. Frank, S. Liu, J. H. Chen, R. J. Sigurdsson, and K. Seshadri, "Ignition of Hydrogen in Unsteady Nonpremixed Flows," to appear in Proceedings of the Combustion Institute, 30, (2004).

PI Yang Chen

Y. Chen and S.E. Parker, "A delta-f particle method for gyrokinetic simulaitons with kinetic electrons and electromagnetic perturbations," J. Comp. Phys. 189 (2003) 463-475

S.T. Jones and S.E. Parker,"Including electron inertia without advancing electron flow," Journal of Computational Physics 191(2003) 322-327

Y. Chen, S.E. Parker, B.I. Cohen, A.M, Dimits, W.M. Nevins, D. Shumaker, V.K. Decyk and J.N. Leboeuf, "Simulations of turbulent transport with kinetic electrons and electromagnetic effects," Nuc. Fusion 43 (2003) 1121-1127

S.E. Parker, Y. Chen, W. Wan, B.I. Cohen and W.M. Nevins, "Electromagnetic gyrokinetic simulations," Phys. Plasmas 11(5) (2004) 2594-2599

S. Vadlamani, S.E. Parker, Y. Chen and C.C. Kim, "The particle-continuum method: an algorithmic unification of particle-in-cell and continuum methods," Computer Physics Communications, prn. 23/07/2004 available online at www.sciencedirect.com

C.C Kim, C.R. Sovinec, S.E. Parker and the NIMROD Team, "Hybrid kinetic-MHD simulations in general geometry," Computer Physics Communication, prn. 09/08/2004, available online at www.sciencedirect.com

Y. Su, S. Jones, R. Ergun, S. Parker, "Modeling of field-aligned electron bursts by dispersive Alfven waves in the dayside auroral region," accepted Journal of Geophysical Research - Space Physics, August 2004

W. Wan, Y. Chen and S.E. Parker, "Gyrokinetic delta-f simulation of the collisionless and semi-collisional tearing mode instability," submitted to Phys. plasmas.

W. Wan, Y. Chen and S.E. Parker, "delta-f simulation of the collisionless tearing mode instability with kinetic ion response," submitted to IEEE Transactions on Plasma Science.

PI Hai-Ping Cheng

Density functional study of the adsorption of a C60 monolayer on Ag(111) and Au(111) surfaces, Lin-Lin Wang and Hai-Ping Cheng Phys. Rev. B 69, 165417 [12 pages] (2004).

Coherent electron transport through an azobenzene molecule: A light driven molecular switch, C. Zhang, M.-H. Du, Hai-Ping Cheng, X.-G. Zhang, A.E. Roitberg, and J.L. Krause, Phys. Rev. Lett. 92, 158301 [4 pages] (2004).

Electronic structure and spin-dependent tunneling conductance under finite bias, Chun Zhang, Xiao-Guang Zhang, P.S. Krstic, Hai-Ping Cheng, and W.H. Butler, Phys. Rev. B 69, 134406 [12 pages] (2004).

Rotation, translation, charge transfer, and electronic structure of C60 on Cu (111) surface, Lin-Lin Wang and Hai-Ping Cheng, Phys. Rev. B 69, 40404 [7 pages] (2004).

Hydrolysis of a Two-Membered Silica Ring on the Amorphous Silica surface: A Computational Study that Combines Quantum Mechanics and Classical Interatomic Potential Functions, Mao-Hua Du, Andrew Kolchin and Hai-Ping Cheng, J. Chem. Phys. 120, 1044-1054 (2004).

Bulk separative enrichment in metallic or semiconducting single-walled carbon nanotubes, Z.-H. Chen, X. Du, M.-H. Du, C.D. Rancken, H.-P. Cheng, and A.G. Rinzler, Nano Lett. 3, 1245-1249 (2003).

Manipulation of fullerene-induced impurity states in carbon peapods, Mao-Hua Du and Hai-Ping Cheng, Phys. Rev. B 68, 113402 [4 pages] (2003).

Stability of free and oxidized silver clusters, M. Schmidt, Ph. Cahuzac, C. Brichignac and Hai-Ping Cheng, J. Chem. Phys. 118, 10956-10962 (2003).

Molecular dynamics simulation of potential energy sputtering on LiF surface by slow highly charged ions, Lin-Lin Wang, Ajith Perera, and Hai-Ping Cheng, Phys. Rev. B 68 115409 [13 pages] (2003)

Water-silica surface interactions: A combined quantum-classical molecular dynamic study of energetics and reaction pathways, Mao-Hua Du, Andrew Kolchin, and Hai-Ping Cheng, J. Chem. Phys. 119, 6418-6422 (2003).

Water-silica interactions in clusters, Mao-Hua Du, Lin-Lin Wang, Andrew Kolchin, and Hai-Ping Cheng, Euro Phys. J D 24, 323-326 (2003).

PI Wai-Yim Ching

L. Ouyang, H. Yao, S. Richey, Y.-N. Xu and W.Y. Ching, "On the crystal structure and optical Properties of YSiO2N", Phys. Rev. B69, 094112-1-6 (2004).

L. Ouyang, P. Rulis, W.Y. Ching, G. Nardin, and L. Randaccio, "Electronic Structure and Bonding in Adenosylcobalamin", Inorg. Chem. 43 (4), 1235-1241 (2004).

Lizhi Ouyang and W.Y. Ching," Electronic structure and dielectric properties of gate material: (ZrO2)x(SiO2)1-x", J. Appl. Phys, 95 (12) 7918-7924 (2004).

P. Rulis, W.Y. Ching and M. Kohyama, "ab-initio ELNES/XANES spectral calculation of polar and non-polar grain boundary models in b-SiC", Acta Materials, 52[10], 30009-30018 (2004).

T. Mizoguchi, I. Tanaka, S. Yoshioka, M. Kunisu, T. Yamamoto, and W.Y. Ching, "First-principles calculations of ELNES/XANES of selected wide gap materials: dependence on crystal structure and orientation", Phys. Rev. B70, 045103 (2004).

W.Y. Ching, L. Ouyang, Hongzhi Yao and Y.-N. Xu, "Electronic Structure and Bonding in the Y-Si-O-N quaternary Crystals", Phys. Rev. B70., (July 15, 2004)

W.Y. Ching, "The electronic structure and bonding of all crystalline phases in the SiO2-Y2O3-Si3N4 phase equlibrium diagram", J. Amer. Ceram. Soc. (invited feature article, November, 2004).

Paul Rulis, Lizhi Ouyang, and W.Y. Ching, "Electronic Structure and Bonding in Calcium Apatite Crystals: Hydroxyapatite, Fluorapatite, Chlorapatite, and Bromapatite", Phys. Rev. B. (accepted, 2004).

Jun Chen, Yong-Nian Xu, Paul Rulis, Lizhi Ouyang, and W.Y. Ching "Ab-initio tensor experiments on Y-doped S=3 grain boundary in a-Al2O3", submitted to Acta Materials.

Paul Rulis, Jun Chen, Lizhi Ouyang and W.Y. Ching, Xiaotao Su, S.H. Garofalini, "Electronic structure and bonding of the intergranular glassy films (IGF) in polycrystalline Si3N4: Ab-initio studies and classical MD simulations", submitted to Advanced Materials.

PI Mei-Yin Chou

"Effects of the Substrate on Quantum Well States: A First-Principles Study for Ag/Fe(100) ", C. M. Wei and M. Y. Chou, Phys. Rev. B 68, 125406/1-5 (2003).

"Quantum Confinement and Electronic Properties of Silicon Nanowires", X. Zhao, C. M. Wei, L. Yang, and M. Y. Chou, Phys. Rev. Lett. 92, 236805/1-4 (2004).

"Thermal Stability and Electronic Structure of Pb Films on Si(111)", M. H. Upton, C. M. Wei, M. Y. Chou, T. Miller, and T.-C. Chiang, Phys. Rev. Lett. 93, 026802/1-4 (2004).

"First-Principles Study of NaAlH4 and Na3AlH6 Complex Hydrides", A. Peles, J. A. Alford, Zhu Ma, Li Yang, and M. Y. Chou, Phys. Rev. B (in press).

"Alternative Low-Symmetry Structure for 13-Atom Metal Clusters", C. M. Chang and M. Y. Chou, Phys. Rev. Lett. (in press).

PI Daryl Chrzan

Tianshu Li, J.W. Morris, Jr., and D.C. Chrzan, "Ideal tensile strength of B2 transition-metal aluminides", Physical Review B 70, 54107(2004)

Yi DO, Sharp ID, Xu Q, Liao CY, Ager JW III, Beeman JW, Liliental-Weber Z, Yu KM, Zakharov D, Haller EE, and Chrzan, DC, "Modeling the stress evolution of Ion Beam Synthesized Nanocrystals," Materials Research Society, Spring Meeting, 2004.

J. Deslippe, R. Tedstrom, M. S. Daw, D. C. Chrzan, T. Neeraj and M. J. Mills, "Dynamic Scaling in a Simple One-Dimensional Model of Dislocation Activity," Philosophical Magazine 84, 2445-2454 (2004).

PI Catherine Chuang

Penner, J.E., S.Y. Zhang, and C.C. Chuang, 2003: Soot and smoke aerosol may not warm climate, J. Geophys. Res., 108, 4657, doi:10.1029/2003JD003409.

Rotman, D.A., C.S. Atherton, D.J. Bergmann, P.J. Cameron-Smith, C.C. Chuang, and others, 2004: IMPACT, the LLNL 3D global atmospheric chemical transport model for the combined troposphere and stratosphere: Model description and analysis of ozone and other trace gases, J. Geophys. Res., 109, doi:10.1029/2002JD003155.

Chin, H.-N.S., M.J. Leach, G.A. Sugiyama, J.M. Leone Jr., H. Walker, J.S. Nasstrom, and M.J. Brown, 2004: Evaluation of an urban canopy parameterization in a mesoscale model using VTMX and URBAN 2000 data, submitted to Mon. Wea. Rev.

Duffy, P.B., B. Govindasamy, J. Milovich, K. Taylor, and S. Thompson, 2003: High resolution simulations of global climate, Part 1: Present climate, Clim. Dyn., 21, 371-390.

Wickett, M.E., K. Caldeira, and P.B. Duffy, 2003: Effect of horizontal grid resolution on simulations of oceanic CFC-11 uptake and direct injection of anthropogenic CO2, J. Geophys. Res. (Oceans), 108, 10.1029/2001JC001130.

Govindasamy, B., P.B. Duffy, and J. Coquard 2003: High resolution simulations of global climate, Part 2: Effects of increased greenhouse gases, Clim. Dyn., 21, 391-404.

Iorio, J., P.B. Duffy. M. Khairoutdinov, and D. Randall, 2004: Effect of model resolution and subgrid scale physics on daily precipitation in the continental United States, Clim. Dyn., in press.

Coquard, J., P.B. Duffy, and K.E. Taylor, 2004: Present and future surface climate in the western U.S. as simulated by 15 global climate models, Clim. Dyn., in press.

Marcy, T.P., D.W. Fahey, R.S. Gao, P.J. Popp, E.C. Richard, T.L. Thompson, K.H. Rosenlof, E.A. Ray, R.J. Salawitch, C.S. Atherton, and others, 2004: Quantifying stratospheric ozone in the upper troposphere using in situ measurements of HCl, Science, 304, 261-265.

PI Bruce Cohen

Y. Chen, S.E. Parker, B.I. Cohen, A.M. Dimits, W.M. Nevins, D. Shumaker, V.K. Decyk, and J.-N. Leboeuf, Simulations of Turbulence with Kinetic Electrons and Electromagnetic Effects from the Summit Framework, November, 2002, Nucl. Fusion 43, 1121 (2003).

S. E. Parker, Y. Chen, W. Wan, B.I. Cohen, and W.M. Nevins, Electromagnetic Gyrokinetic Simulations, (APS DPP Annual Meeting, October 2003, Invited Paper), Phys. Plasmas. 11, 231 (2004).

S. Woodruff, B. W. Stallard, H. S. McLean, E. B. Hooper, R. Bulmer, B. I. Cohen, D. N. Hill, C.T. Holcomb, J. Moller, R. D. Wood, Increasing the magnetic helicity content of a plasma by pulsing a magnetized source, February 2004, submitted to Phys. Rev. Lett.

S. Woodruff, B.I. Cohen, E.B. Hooper, H.S. Mclean, C.T. Holcomb, B.W. Stallard, D.N. Hill, L.L. Smith, R.D. Wood, G. Cone, C.R. Sovinec, Controlled and Spontaneous Magnetic Field Generation in a Gun-Driven Spheromak, February 2004, submitted to Phys. Plasmas.

W.M. Nevins, et al., A Statistical Analysis of ITG Turbulence, in preparation, Feb. 2004. Pigarov, A.Y., Krasheninnikov, S.I., Rognlien, T.D., et al., Multi-fluid code simulations including anomalous non-diffusive transport of plasma and impurities in the tokamak SOL, accepted for publication in Contrib. Plasma Phys. (2004).

T.D. Rognlien, M.V. Umansky, X.Q. Xu, and R.H. Cohen, Self-consistent simulation of turbulence and transport in tokamak edge plasmas, Contrib. Plasma Phys. 44 (2004) 188.

Xu, X.Q., Nevins, W.M., Cohen, R.H., Rognlien, T.D., and Umansky, M.V., Correlation of density pedestal width and neutral penetration length, Contrib. Plasma Phys. 44 (2004) 105.

Xu, X.Q., Nevins, W.M., Cohen, R.H., Myra, J.R., and Snyder, P.B., Dynamical simulations of boundary physics turbulence in divertor geometry, New Journal of Physics 4 (53), 1-15 (2003).

Xu, X.Q., Nevins, W.M., Rognlien, T.D., Bulmer, R.H., Greenwald, M., Mahdavi, A., Pearlstein, L.D., and Snyder, P., Transitions of turbulence in Plasma density limits, Phys. Plasmas 10 (5), 1773-1781 (2003).

Holland, C., Diamond, P.H., Champeaux, S., Kim, E., Rosenbluth, M.N., Tynan, G.R., Crocker, N., Nevins, W.M., and Candy, J., Investigations of the role of nonlinear couplings in structure formation and transport regulation: experiment, simulation, and theory, Nuclear Fusion 43 (8), 761-780 (2003).

T. D. Rognlien, and M. V. Umansky, X. Q. Xu, R. H. Cohen, Self-Consistent Simulation of Turbulence and Transport in Tokamak Edge Plasmas, Contrib. Plasma Phys. 44, No. 1-3, 188 193 (2004)

M. V. Umansky, T. D. Rognlien, X. Q. Xu, R. H. Cohen, and W. M. Nevins, Turbulence in Divertor region of Tokamak Edge Plasma, Contrib. Plasma Phys. 44, No. 1-3, 182 187 (2004)

Snyder PB, Wilson HR, Ferron JR, Lao LL, Leonard AW, Mossessian, D, Murakami M, Osborne TH, Turnbull AD, Xu XQ, ELMs and constraints on the H-mode pedestal: peeling-ballooning stability calculation and comparison with experiment, Nuclear Fusion, 44 (2): 320-328 FEB 2004

"Role of trapped electron mode turbulence in internal transport barrier control in the Alcator C-Mod Tokamak", 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) (2004) 2637.

Gyrokinetic Simulations of Ion and Impurity Transport, C. Estrada-Mila, J. Candy and R.E. Waltz, submitted to Phys. Plasmas. Smoothness of Turbulent Transport Across a Minimum-q Surface, J. Candy, R.E. Waltz and M.N. Rosenbluth, Phys. Plasmas 11, 1879 (2004)

The Local Limit of Global Gyrokinetic Simulations, J. Candy , R.E. Waltz and W. Dorland, Phys. Plasmas 11, L25 (2004)

Effects of Electromagnetic Turbulence in the Neoclassical Ohm's Law, F.L. Hinton, R.E. Waltz and J. Candy, Phys. Plasmas 11, 2433 (2004)

Anomalous Transport Scaling in the DIII-D Tokamak Matched by Supercomputer Simulation, J. Candy and R.E. Waltz, Phys. Rev. Lett. 91, 045001 (2003)

Burning Plasma Confinement Projections and Renormalization of the GLF23 Driftwave Transport Model, J.E. Kinsey and G. Staebler and R.E. Waltz, Fusion Sci. and Tech 44, 763 (2003).

PI Marvin Cohen

F. J. Ribeiro, M. L. Cohen, Phys. Rev. B 69, 212507 (2004)

H. Sun, F. J. Ribeiro, J.-L. Li, D. Roundy, M. L. Cohen, S. G. Louie, Phys. Rev. B 69, 024110 (2004)

P. Tangney, S. G. Louie, and M. L. Cohen, Phys. Rev. Lett 93, 065503 (2004).

P. Zhang, W. Luo, V. H. Crespi, M. L.Cohen, and S. G. Louie, Phys. Rev. B 70, 085109 (2004)

R. B. Capaz, C. D. Spataru, P. Tangney, M. L. Cohen, and S. G. Louie, Phys. Stat. Solid (b), (2004).

J. W. Morris, D.M. Clatterbuck, D.C. Chrzan, C.R. Krenn , W. Luo, M. L. Cohen, Materials Science Forum 426-432, 4429-4434 (2003).

A. Trave, F.J. Ribeiro, S.G. Louie and M.L. Cohen, "Energetics and Structural Characterization of C60 Polymerization in BN and Carbon Nano-peapods", submitted to Phys. Rev. B

W. Luo, W. Duan, S. G. Louie, and M. L. Cohen, "Structural and electronic properties of n-doped and p-doped SrTiO3", submitted to Phys. Rev. B

R. B. Capaz, C. D. Spataru, P. Tangney, M. L. Cohen, and S. G. Louie, "Temperature Dependence of the Band Gap of Semicondcting Carbon Nanotubes", submitted to Phys. Rev. Lett.

PI John Cooke

A. Franceschetti, S.J. Pennycook, and S.T. Pantelides, "Oxygen chemisorption on Au nanoparticles", Chem. Phys. Lett. 374, 471 (2003).

A. Franceschetti and S.T. Pantelides, "Excited-state relaxations and Franck-Condon shift in Si quantum dots", Phys. Rev. B 6803, 3313 (2003).

S.W. Wang, A.Y. Borisevich, S.N. Rashkeev, M.V. Glazoff, K. Sohlberg, S.J. Pennycook, and S.T. Pantelides, "Dopant adsorbed as single atoms prevent degradation of catalysts" Nature Materials 3, 274 (2004).

H.S. Baik, M. Kim, G.S. Park, S.A. Song, M. Varela, A. Franceschetti, S.T. Pantelides, and S.J. Pennycook, "Interface structure and non-stoichiometry in HfO2 dielectrics", Appl. Phys. Lett. 85, 672 (2004).

J.P. Buban, A. Franceschetti, J.C. Idrobo, N.D. Browning, X. Song, G. Daniels, A. Gurevich, D.C. Larbalestier, S.T. Pantelides, and S.J. Pennycook, "Cooperative Doping Mechanisms at Grain Boundaries in Ca-Doped YBCO", submitted to Phys. Rev. Lett.

M. Varela, A. Franceschetti, A.R. Lupini, W. Tian, R. Jin, B.C. Sales, D.G. Mandrus, S.J. Pennycook, and S.T. Pantelides, "Ordered phases in doped manganites - atomic-resolution spectroscopy and density-functional calculations", submitted to Science.

PI Silvia Crivelli

S. Crivelli, O. Kreylos, B. Hamann, N. Max, and W. Bethel (2004). ProteinShop: A Tool for Interactive Protein Manipulation. Journal of Computer-Aided Molecular Design Vol. 18, pp. 271-285.

S. Crivelli and T. Head-Gordon (2004). A New Load Balancing Strategy for the Solution of Dynamical Large Tree Search Problems Using a Hierarchical Approach, IBM Journal of Research and Development.

PI Peter Cummings

Rivera, J. L., McCabe, C., and Cummings, P. T., "Oscillatory behavior of double nanotubes under extension: A simple nanoscale damped spring," Nano Letters, 3, 1001-1005 (2003).

Leng YS, Keffer DJ, Cummings PT Structure and dynamics of a benzenedithiol monolayer on a Au(111) surface, Journal Of Physical Chemistry B 107 (43): 11940-11950 2003

Z. Zhang, P. Fenter, L. Cheng, N. C. Sturchio, M. J. Bedzyk, M. Predota, A. Bandura, J. Kubicki, N. Lvov, P. T. Cummings, A. A. Chialvo, M. K. Ridley, P. Binizeth, L. Anovitz, D. A. Palmer, M. L. Machesky, D. J. Wesolowski, "Ion Adsorption at the Oxide-Water Interface: Linking Molecular and Macroscopic Properties," Langmuir, 20(12); 4954-4969 (2004).

M. Predota, A. V. Bandura, P. T. Cummings, J. D. Kubicki, D. J. Wesolowski, A. A. Chialvo, M. L. Machesky, "Electric Double Layer at Rutile Surfaces. I. Structure Of Water From Molecular Dynamics Using Ab Initio Potentials," Journal of Physcial Chemistry B 108(32), 12049-12060 (2004).

M. Predota, Z. Zhang, P. Fenter, D. J Wesolowski and P. T. Cummings, "Electric double layer at rutile surfaces. II. Adsorption of ions from molecular dynamics," Journal of Physcial Chemistry B 20(12); 4954-4969 (2004).

C. McCabe, D. Bedrov, O. Borodin, G. D. Smith and P. T. Cummings, "A Molecular Dynamics Study of The Rheology of Perfluoroalkanes: Comparing A Fully Atomistic and United Atom Model," Ind. Eng. Chem. Res., 42, 6956-6961 (2003).

S. Bair and C. McCabe, A Study of Mechanical Shear Bands in Liquids at High-Pressure, Tribology International, 37 783-789 (2004).

C. McCabe, S. C. Glotzer, J. Kieffer, M. Neurock and P. Cummings, Multiscale Simulation of the Synthesis, Assembly and Properties of Nanostructured Organic/Inorganic Hybrid Materials, Journal of Theoretical and Computational Nanoscience, in press (2004).

A. Striolo, C. McCabe, and P.T. Cummings, "Thermodynamic and Transport Properties of Polyhedral Oligomeric Silsesquioxanes in Poly(Dymethyl Siloxane)", Nano Letters, submitted (2004).

A. Striolo, A. A. Chialvo, P. T. Cummings PT, "Water adsorption in carbon-slit nanopores" Langmuir, 19 (20): 8583-8591 2003.

PI Larry Curtiss

O. Borodin, G. D. Smith, R. Bandyopadhyaya, P. Redfern, L. A. Curtiss Molecular dynamics study of nanocomposite polymer electrolyte based on poly(ethylene oxide)/LiBF4, Modelling and Simulation in Material Science and Engiennering 12 (3): S73-S89 May 2004

Y. Duan, J. W. Halley, L. Curtiss, and P. Redfern, Mechanisms of Lithium Transport in Amorphous Polyethylene Oxide, J. Chem. Phys., submitted.

A. S. Barnard and P. Zapol A model for the phase stability of arbitrary nanoparticles as a function of size and shape. J. Chem. Phys. 121(9) 4276 (2004)

Effects of particle morphology and surface hydrogenation on the phase stability of TiO₂, A. S. Barnard and P. Zapol Phys Rev B, 2004 (in press)

A. Barnard , P. Zapol Predicting the Energetics, Phase Stability and Morphology Evolution of Faceted and Spherical Anatase Nanocrystals, J. Phys. Chem. (submitted)

Modeling the morphology and phase stability of TiO2 nanocrystals in water, A. S. Barnard, P. Zapol and L.A. Curtiss, J. Theo. Chem. Comp. (2004) submitted

Shaping Nanoscale Architecture Through Surface Chemistry, Z. V. Saponjic, D. Tiede, L. Chen, N. Dimitrijevic, A. Goshe, A. S. Barnard, P. Zapol, L. Curtiss, and T. Rajh, Advanced Materials (2004) submitted

PI Daniel D'Ippolito

"Blob Dynamics in 3D BOUT Simulations of Tokamak Edge Turbulence," D. A. Russell, D. A. D'Ippolito, J. R. Myra, W. M. Nevins, and X. Q. Xu, submitted to Phys. Rev. Lett. (2004).

PI Ronald Davidson

Drift Compression and Final Focus Options for Heavy Ion Fusion, H. Qin, R. C. Davidson, J. J. Barnard and E. P. Lee, Nuclear Instruments and Methods in Physics Research, in press (2004).

Chaotic Particle Trajectories in High-Intensity Finite-Length Charge Bunches, S. T. Hudson, H. Qin, and R. C. Davidson, Nuclear Instruments and Methods in Physics Research, in press (2004).

Survey of Collective Instabilities and Beam-Plasma Interactions in Intense Heavy Ion Beams, R. C. Davidson, I. D. Kaganovich, H. Qin, et al, Nuclear Instruments and Methods in Physics Research, in press (2004).

Three-Dimensional Simulation Studies of the Temperature Anisotropy Instability in Intense Charged Particle Beams, E. A. Startsev, R. C. Davidson, and H. Qin, Nuclear Instruments and Methods in Physics Research, in press (2004).

The Electromagnetic Darwin Model for Intense Charged Particle Beams, W. W. Lee, R. C. Davidson, E. A. Startsev, and H. Qin, Nuclear Instruments and Methods in Physics Research, in press (2004).

Drift Compression and Final Focus of Intense Heavy Ion Beams, H. Qin, R. C. Davidson, J. J. Barnard and E. P. Lee, submitted to Physical Review Special Topics on Accelerators and Beams (2004).

Electromagnetic Weibel Instability in Intense Charged Particle Beams With Large Temperature Anisotropy, E. A. Startsev and R. C. Davidson, Physics of Plasmas 10, in press (2003).

Wall-Impedance-Driven Collective Instability in Intense Charged Particle Beams, R. C. Davidson, H. Qin and G. Shvets, Physical Review Special Topics on Accelerators and Beams 6, 104402 (2003).

Analytical Theory and Nonlinear Delta-f Perturbative Simulations of Temperature Anisotropy Instability of Intense Charged Particle Beams, E. A. Startsev, R. C. Davidson and H. Qin, Physical Review Special Topics on Accelerators and Beams 6, 084401 (2003).

Nonlinear Delta-f Simulations of Collective Effects in Intense Charged Particle Beams, H. Qin, Physics of Plasmas 10, 2708 (2003).

Belova, E. V., R. C. Davidson, H. Ji, M. Yamada, Kinetic effects on the stability properties of field-reversed configurations: II. Nonlinear evolution, Phys. Plasmas v.11, 2523 (2004).

N. N. Gorelenkov, E. V. Belova, H. L. Berk, C. Z. Cheng, E. Fredrickson, W. Heidbrink, S. Kaye, G. Kramer, Beam Ion Driven Instabilities in NSTX, Phys. Plasmas v.11, 2586 (2004).

Belova, E. V., N. N. Gorelenkov, C. Z. Cheng, Self-consistent equilibrium model of low aspect ratio toroidal plasma with energetic beam ions, Phys. Plasmas v.10, 3240 (2003).

PI Murray Daw

"Dynamic scaling in a simple one-dimensional model of dislocation activity" Phil Mag 84 p2445-2454 (2004). J. Deslippe, R. Tedstrom, M. Daw, D. Chrzan, T. Neeraj, and M. Mills

PI Eric DeWeaver

DeWeaver, E., and S. Nigam, 2004: On the forcing of ENSO teleconnections by anomalous heating and cooling. J. Climate, 17, 3225-3235.

PI David Dean

Coupled-cluster approach to nuclear physics, D. J. Dean and M. Hjorth-Jensen Phys. Rev. C 69, 054320 (2004)

Coupled Cluster Calculations of Ground and Excited States of Nuclei K. Kowalski, D. J. Dean, M. Hjorth-Jensen, T. Papenbrock, and P. Piecuch Phys. Rev. Lett. 92, 132501 (2004)

Solution of large scale nuclear structure problems by wave function factorization, T. Papenbrock, A. Juodagalvis, and D. J. Dean Phys. Rev. C 69, 024312 (2004)

Systematic study of deformed nuclei at the drip lines and beyond M. V. Stoitsov, J. Dobaczewski, W. Nazarewicz, S. Pittel, and D. J. Dean Phys. Rev. C 68, 054312 (2003)

Consequences of Nuclear Electron Capture in Core Collapse Supernovae W. R. Hix, O. E. B. Messer, A. Mezzacappa, M. Liebendvrfer, J. Sampaio, K. Langanke, D. J. Dean, and G. Martmnez-Pinedo Phys. Rev. Lett. 91, 201102 (2003)

Free energy and criticality in the nucleon pair breaking process M. Guttormsen, R. Chankova, M. Hjorth-Jensen, J. Rekstad, S. Siem, A. Schiller, and D. J. Dean, Phys. Rev. C 68, 034311 (2003)

Electron Capture Rates on Nuclei and Implications for Stellar Core Collapse, K. Langanke, G. Martmnez-Pinedo, J. M. Sampaio, D. J. Dean, W. R. Hix, O. E. B. Messer, A. Mezzacappa, M. Liebendvrfer, H.-Th. Janka, and M. Rampp, Phys. Rev. Lett. 90, 241102 (2003)

Factorization of shell-model ground states, T. Papenbrock and D. J. Dean, Phys. Rev. C 67, 051303 (2003)

How magic is the magic Ni-68 nucleus?, K. Langanke, J. Terasaki, F. Nowacki, D. J. Dean, and W. Nazarewicz, Phys. Rev. C 67, 044314 (2003)

Neutral-current neutrino-nucleus cross sections for A~50-65 nuclei, A. Juodagalvis, K. Langanke, G. Martinez-Pinedo, W.R. Hix, D.J. Dean, and J.M. Sampaio, in press, Nucl. Phys. A (2004)

PI Tomas Diaz de la Rubia

B.D. Wirth and E.M. Bringa, "A Kinetic Monte Carlo Model for Helium Diffusion and Clustering in Fusion Environments", Physica Scripta, T108 (2004) 80.

B.D. Wirth, G.R. Odette, J. Marian, L. Ventelon, J.A. Young and L.A. Zepeda-Ruiz, "Multiscale Modeling of Radiation Damage in Fe-based Alloys in the Fusion Environment", Journal of Nuclear Materials 329-333 (2004) 103.

L. A. Zepeda-Ruiz, J. Rottler, S. Han, G. J. Ackland, R. Car, and D. J. Srolovitz, "Strongly Non-Arrhenius Interstitial Diffusion in Vanadium", Physical Review B - Rapid Communication, in press.

L. A. Zepeda-Ruiz, J. Marian, and B. D. Wirth, "On the Character of Self-Interstitial Dislocation Loops in Vanadium", accepted for publication in Philosophical Magazine.

B. Remington et al., "Materials science under extreme conditions of pressure and strain rate", , Met. Mat. Trans. A 35, 2587 (2004).

L. Davila, P. Erhart, E.M. Bringa, M.A. Meyers, V.A. Lubarda, M. Schneider, R. Becker and M. Kumar, "Shock-induced void collapse in fcc metals" submitted to Applied Physics Letters.

P. Erhart, E. Bringa and M. Kumar, "Atomistic simulation of shocks in porous metals", submitted to Phys. Rev. Letters.

"A new model for cosmic ray erosion of volatiles from grains in the inter-stellar medium". E. M. Bringa and R. E. Johnson, Astrophysical Journal 603, 159 (2004).

"Molecular dynamics simulation of sputtering from a cylindrical track: EAM vs. pair potentials", O.J. Tucker, D. Ivanov, R.E. Johnson, L. Zhigilei and E.M. Bringa, submitted to Nucl. Instr. and Meth. Phys. Res. B.

"High-Energy Ion Tracks in Thin Films", David M. Follstaedt, Adam K. Norman, Paolo Rossi, Barney L. Doyle, Floyd D. McDaniel and Eduardo M. Bringa, submitted to Nucl. Instr. and Meth. in Phys. Res. B.

"Atomistic simulations of threshold displacement energies in SiO2", F.Mota, M.-J.Caturla, J.M.Perlado, E.Dominguez, A. Kubota Journal of Nuclear Materials accepted for publication 2004

"Differences in deformation processes in nanocrystalline nickel with low and high angle boundaries from atomistic simulations", M.J. Caturla, T. G. Nieh, J. S. Stolken, Applied Physics Letters 84 (2004) 598-600

"Transformations in the medium-range order of fused silica under high pressure", L. P. Davila, M.-J. Caturla, A. Kubota, B. Sadigh, T. Diaz de la Rubia, J. F. Shackelford, S. H. Risbud, S. H. Garofalini, Physical Review Letters 91 (2003) 205501-4.

"Molecular dynamics simulations of energy deposition in solids" M. J. Caturla, A. Gras Marti, J. J. Jimenez-Rodriguez, J.C. Jimenez Saez, M.C. Perez-Martin, Advances in Quantum Chemistry 45 (2004) 79-98.

"Temperature dependent defect properties from ion-irradiation in Pu(Ga)" J. Fluss, B. D. Wirth, M. Wall, M. J. Caturla, T. Diaz de la Rubia, and T. E. Felter, Journal of Alloys and Compounds 368 (2004) 62-74

"Modeling microstructure evolution of f.c.c. metals under irradiation in the presence of He", M. J. Caturla, T. Diaz de la Rubia, M. Fluss Journal of Nuclear Materials 323 (2003) 163-168

"Fused Silica Final Optics For Inertial Fusion Energy: Radiation Studies And System-Level Analysis", Jeffery F. Latkowski,* Alison Kubota, Maria J. Caturla, Sham N. Dixit, Joel A. Speth, And Stephen A. Payne, Fusion Science and Technology 43 (2003) 540 - 558.

PI Dimitre Dimitrov

C. Nieter and J. R. Cary, "VORPAL: a versatile plasma simulation code", J. Comput. Phys, vol. 196, pp. 448-473 (2004).

PI Chris Ding

MPH: a Library for Distributed Multi-Component Environment. Chris Ding and Yun He. Submitted to Int'l Journal of High Performance Computing.

ZioLib: a Parallel I/O Library, Woo-Sun Yang and Chris Ding, Oct 2003, LBNL Tech Report, LBNL-53521

PI Julie Ditri

V. I. Kovalchuk, J. L. d'Itri, "Catalytic Chemistry of Chloro- and Chlorofluorocarbon Dehalogenation: From Macroscopic Observations to Molecular Level Understanding." Applied Catalysis A: General, 271 (2004) 13-25.

V. Yu. Borovkov, D. R. Luebke, V. I. Kovalchuk, J. L. d'Itri, "Hydrogen-Assisted 1,2-Dichloroethane Dechlorination Catalyzed by Pt-Cu/SiO2: Evidence for Different Functions of Pt and Cu Sites." Journal of Physical Chemistry B, 107 (2003) 5568-5574.

PI Jianjun Dong

D. Hatch, H. Stokes, Jianjun Dong, J. Gunter, H. Hao, and J. Lewis, "SiC transition paths between the zinc-blend and rocksalt structure types", submitted

(H. Stokes, D. Hatch, Jianjun Dong, and J. Lewis, "Mechanisms of phase transition between the B1 and B2 structure types in NaCl and PbS", Phys. Rev. B 69, 174111 (2004).

Jianjun Dong, A.A. Kinkhabwala, and P.F. McMillan, "High-pressure polymorphism in phosphorus nitrides", Phys. Stat. Solid. B 241, 2319 (2004).

P.F. McMillan, S.K. Deb, and Jianjun Dong, "High pressure phase transition in beta-Ge3N4: a Raman scattering study", J. Raman Spectroscopy 28, 885 (2003).

PI Sebastian Doniach

J. Lipfert, J. Franklin, F. Wu and S. Doniach, Protein Misfolding and Amyloid Formation for the Peptide GNNQQNY from Yeast Prion Protein Sup35: Simulation by Reaction Path Annealing submitted fro publication

PI William Dorland

B. D. Jemella, M. A. Shay, J. F. Drake and B. N. Rogers, Impact of Frustrated Singularities on Magnetic Island Growth, Phys. Rev. Lett. 91, 125002, 2003.

M. A. Shay, J. F. Drake, M. Swisdak and B. N. Rogers, The scaling of embedded collisionless reconnection, Phys. Plasmas 11, 2199, 2004.

M. A. Shay and M. Swisdak, Three species collisionless reconnection: Effect of O+ on magnetotail reconnection, Phys. Rev. Lett. (in press 2004).

B. D. Jemella, J. F. Drake, and M. A. Shay, Singular Structure of Magnetic Islands Resulting from Reconnection, Phys. Plasmas (in press 2004).

C. Cattell, J. Dombeck, J. Wygant, J. F. Drake, M. Swisdak, et al., Cluster observations of electron holes in association with magnetotail reconnection and comparison to simulations, J. Geophys. Res. (in press 2004).

M. Swisdak, J. F. Drake, J. G. McIlhargey and M. A. Shay, The trnasition from anti-parallel to component magnetic reconnection, J. Geophys. Res. (submitted 2004).

J. F. Drake, M. A. Shay, M. Swisdak, W. Thongthai, Electron energization during magnetic reconnection, Phys. Rev. Lett. (submitted 2004).

PI Philip Duffy

J. Coquard, P.B. Duffy, and K.E. Taylor, 2004: Present and future surface climate in the western U.S. as simulated by 15 global climate models, Climate Dynamics, in press.

P.B. Duffy, B. Govindasamy, J. Iorio, J. Milovich, K. Taylor, M. Wehner, and S. Thompson, 2003: High Resolution Simulations of Global Climate, Part 1: Present Climate. Climate Dynamics, 21, 371-390.

B. Govindasamy, and P.B. Duffy, 2003: High Resolution Simulations of Global Climate, Part 2: Effects of Increased Greenhouse Gases. Climate Dynamic, 21, 391-404.

Iorio, J. P.Duffy, B. Govindasamy, S. Thompson, 2004: Effects of increased resolution on the simulation of daily precipitation statistics in the US, Climate dynamics (in press)

PI Barry Dunietz

Dunietz, B.D. and Markovic, N. and Ross, P.H. and Head-Gordon, M., The initiation of Electro-oxidation of CO on Pt based electrodes at full coverage conditions simulated by ab-initio electronic structure calculations, J.Phys.Chem B, 108, (2004), 9888.

Ugalde, J.M. and Dunietz, B.D and Dreuw, A. and Head-Gordon, M. and Boyd, R.J., The size of Fe(II) spin states and the spin dependence of the structure of Fe(II)-porphyrins, J.Phys.Chem B, 108, (2004), 4653.

PI Charlotte Elster

"Three-Body Scattering at Intermediate Energies" H. Liu, Ch. Elster, W. Gloeckle nucl-th/0410051 and submitted to Phys Rev C

The Operator form of 3H (3He) Wave Function and its Spin Structure, I. Fachruddin, W. Gloeckle, Ch. Elster, A. Nogga, Phys. Rev. C69, 064002 (2004).

Model Study of Three-Body Forces in the Three-Body Bound State, H. Liu, Ch. Elster, W. Gloeckle, Few-Body Systems 33, 241 (2003).

The Nd Break-Up Process in Leading Order in a Three-Dimensional Approach, I. Fachruddin, Ch. Elster, W. Gloeckle, Phys. Rev. C68, 054003 (2003).

Lorentz Boosted NN Potentials for Few-Body Systems: Application to the three-nucleon bound state, H. Kamada, W. Gloeckle, J. Golak, Ch. Elster, Mod. Phys. Lett. A18, 124-127 (2003).

PI Eric Esarey

C. Nieter and J.R. Cary, "VORPAL: a versatile plasma simulation code", J. Comp. Phys. 196 (2004), p. 448.

R.M.G.M. Trines, L.P.J. Kamp, T.J. Schep, W.P. Leemans, E.H. Esarey and F.W. Sluijter, "Enhancement of high-energy electron production through suppression of Raman backscattering," Europhys. Lett. 66 (2004), p. 492.

C.G.R. Geddes, Cs. Toth, J. van Tilborg, E. Esarey, C.B. Schroeder, D.L. Bruhwiler, C. Nieter, J. Cary and W.P. Leemans, "High quality electron beams from a laser wakefield accelerator using plasma channel guiding," Nature (2004), accepted.

M.S. Hur, G. Penn, R. Lindberg and J.S. Wurtele, "Slowly varying envelope kinetic simulations of pulse amplification by Raman Backscattering," Phys. Plasmas (2004), accepted.

P. Messmer and D.L. Bruhwiler, "A parallel electrostatic solver for the VORPAL code," Comp. Phys. Comm. (2004), in press.

R.E. Giacone, J.R. Cary, C. Nieter, D.L. Bruhwiler, E.H. Esarey and W.P. Leemans, "Formation of clean single beams in laser wake field acceleration", Phys. Rev. Lett (2004), submitted.

R.R. Lindberg, A.E. Charman, J.S. Wurtele and L. Friedland, "Robust autoresonant excitation in the plasma beat-wave accelerator: A theoretical study," Phys. Rev. Lett. 93, 055001 (2004).

PI William Fawley

Zholents, A.A. and Fawley, W.M., ``Proposal for Intense Attosecond Radiation from an X-Ray Free-Electron Laser'', Phys. Rev. Lett., 92, 224801 (2004).

PI Andrew Felmy

Rosso KM and Dupuis M (2004) Reorganization energy associated with small polaron mobility in iron oxide JOURNAL OF CHEMICAL PHYSICS 120 (15): 7050-7054.

Rosso KM, Smith DMA, and Dupuis M (2004) Aspects of aqueous iron and manganese (II/III) self-exchange electron transfer reactions JOURNAL OF PHYSICAL CHEMISTRY A 108 (24): 5242-5248.

Rustad JR, Loring JS, Casey WH (2004) Oxygen-exchange pathways in aluminum polyoxocations GEOCHIMICA ET COSMOCHIMICA ACTA 68 (14): 3011-3017 JUL 2004

Rustad JR, Rosso KM, Felmy AR (2004) Molecular dynamics investigation of ferrous-ferric electron transfer in a hydrolyzing aqueous solution: Calculation of the pH dependence of the diabatic transfer barrier and the potential of mean force JOURNAL OF CHEMICAL PHYSICS 120 (16): 7607-7615 APR 22 2004

E.J. Bylaska, D.A. Dixon, A.R. Felmy, T.L. Windus, E. Apra, C.-G. Zhan, and P.G. Tratnyek (2004),The Energetics of the Hydrolysis, Dehydrohalogenation, and Reductive Dehalogenation of 4,4-Dichloro-diphenyl-trichloroethane, Journal of Physical Chemistry, A , vol. 108, pages 5883-5893.

E. Apr`, E. J. Bylaska, D. J. Dean, A. Fortunelli, F. Gao, P. S. Kristi?, J. C. Wells, and T. L. Windus (2003) NWChem for Material Science, Computational Materials Science, vol. 28, pages 209-221.

M. Valiev, E. J. Bylaska, and J. H. Weare (2003), Bonding Structure of 3d Transition Metal Dimers With the Projector Augmented Plane Wave Method, Journal of Chemical Physics ), vol. 119, pages 5955-5964.

PI Paul Fischer

J.W. Lottes and P.F. Fischer "Hybrid Multigrid/Schwarz Algorithms for the Spectral Element Method,", J. Sci. Comp. To appear. (2004).

S. J. Thomas, J. M. Dennis, H. M. Tufo, and P. F. Fischer, ``A Schwarz Preconditioner for the Cubed-Sphere," SIAM J. Sci. Comp., Vol. 25, No. 2, pp 442-453 (2003).

F. X. Giraldo, J. B. Perot and P. F. Fischer, ``A spectral element semi-Lagrangian (SESL) method for the spherical shallow water equations,'' J. of Comp. Phys., 190 2, pp. 623-650 (2003).

J. D. Scheel, M. R. Paul, M. C. Cross, and P. F. Fischer ``Traveling waves in rotating Rayleigh-Binard Convection: Analysis of modes and mean flow,'' Phys. Rev. E (to appear). K.-H. Chiam, M. C. Cross, H. S. Greenside, and P. F. Fischer ``Transport of Passive Scalars by Spiral Defect Chaos in Rayleigh-Binard Convection,'' submitted (Aug. 2003).

T. Iliescu and P.F. Fischer ``Backscatter in the Rational LES Model," Computers and Fluids (to appear).

P.F. Fischer and J.W. Lottes, "Hybrid Schwarz-Multigrid Methods for the Spectral Element Method: Extensions to Navier-Stokes,", Proc. of the 15th Int. Conf. on Domain Decomposition Methods, Berlin, 2003.

Paul Fischer, Frederic Hecht, and Yvon Maday, "A Parareal in Time Semi-implicit Approximation of the Navier-Stokes Equations," Proc. of the 15th Int. Conf. on Domain Decomposition Methods, Berlin, 2003.

PI Graham Fleming

Energy transfer pathways in Photosystem I studied by one and two color photon echo spectroscopy, H. M. Vaswani, J. Stenger, M. Yang, P. Fromme, G. R. Fleming, In press.

The Mechanism of Energy Transfer and Trapping in Photosystem I., H. M. Vaswani, M. Yang, A. Damjanovic, and G. R. Fleming. In Proceedings of Femtochemistry VI, Ultrafast Molecular Events in Chemistry and Biology, pp.401-408 Elsevier, (2004).

Chlorophyll Fluorescence Quenching by Xanthophylls, A. Dreuw, G.R. Fleming and M. Head-Gordon. Phys. Chem. Chem. Phys., 5, 3247-3256, (2003).

PI Ching-Yao Fong

C. Y. Fong, L. H. Yang, J. E. Pask, and S. Dag, 'Electronic and magnetic properties in zincblende structure half-metal superlattices', Appl. Phys. Letts. 84, 239 (2004). b.

C. Y. Fong and M. C. Qian, 'New spintronic superlattices composed of half-metallic compounds with zinc-blende structure', J. Phys.: Condens. Matter 16, 1, (2004). c.

M. C. Qian, C. Y. Fong, W. E. Pickett, J. E. Pask, L. H. Yang and S. Dag, 'Spin-polarized ballistic transport in a thin superlattice of zincblende half metallic compounds', submitted to Physical Review B. d.

M. C. Qian, C. Y. Fong, W. E. Pickett, and Huai-Yu Wang, 'An ab inito investigation on the zinc-blende MnAs nanocrystallite', J. Appl. Phys. 95, 7459 (2004). e.

M. C. Qian, C. Y. Fong, and L. H. Yang, 'Coexistence of a localized majority spin moment and an itinerant minority spin channel in MnC', Phys. Rev. B (Brief report) 70, 1 (2004).

PI Alberto Franceschetti

Lin-Wang Wang, Marco Califano, Alex Zunger, and Alberto Franceschetti, "Pseudopotential Theory of Auger Processes in CdSe Quantum Dots", Phys. Rev. Lett. 91, 056404 (2003).

M. Califano, A. Zunger, and A. Franceschetti, "Efficient Inverse Auger Recombination at Threshold in CdSe Nanocrystals", Nano Letters (Communication) 4(3), 525-531 (2004).

Marco Califano, Alex Zunger, and Alberto Franceschetti, "Direct carrier multiplication due to inverse Auger scattering in CdSe quantum dots", Appl. Phys. Lett. 84, 2409 (2004).

Marco Califano, Alex Zunger, and Alberto Franceschetti, "Radiative decay of bright and dark excitons in CdSe nanocrystal quantum dots", submitted to Phys. Rev. Lett.

Marco Califano, Alex Zunger, and Alberto Franceschetti, "Lifetime and polarization of the radiative decay of excitons, trions and biexcitons in CdSe nanocrystal quantum dots", submitted to Phys. Rev. B.

PI Joachim Frank

P.S. Umesh Adiga, Ravi Malladi, William Baxter, and Rober M. Glaeser A binary segmentation approach for boxing ribosome particles in cryo EM micrographs, Journal of structural biology 145(2004) 142-151.

PI Stuart Freedman

A High Sensitivity Search for Anti-Neutrino's from the Sun and other Sources at KamLAND", KamLAND Collaboration, Phys. Rev. Lett. 92, 021802 (2003).

"Measurement of Neutrino Oscillation with KamLAND: Evidence for Spectral Distortion", KamLAND Collaboration, Submitted to Phys. Rev. Lett.

PI Arthur Freeman

Screened-exchange determination of the optical properties of large gap insulators: CaF2, (M. Kim, Y.-J. Zhao, A.J. Freeman, and W. Mannstadt) Appl. Phys. Lett., 84, 3579 (2004).

Electronic structure and light-induced conductivity in a transparent refractory oxide, (J.E. Medvedeva, A.J. Freeman, M.I. Bertoni, and T.O. Mason) Phys. Rev. Lett., 93, 016408 (2004).

Hopping versus bulk conductivity in transparent oxides: 12CaO.7Al2O3, (J.E. Medvedeva, and A.J. Freeman) Appl. Phys. Lett., 85, 955 (2004).

Combining high conductivity with complete optical transparency: A band-structure approach, (J.E. Medvedeva, and A.J. Freeman), submitted to Phys. Rev. B.

Electronic structure properties and BCS superconductivity in beta-pyrochlore oxides: KOs2O6, (R. Saniz, J. E. Medvedeva, Lin-Hui Ye, T. Shishidou, and A. J. Freeman), accepted to Phys. Rev. B.

PI Alex Friedman

A. Friedman, "Simulation of Intense Beams for Heavy Ion Fusion," Proc. 15th International Symposium on Heavy Ion Inertial Fusion, Princeton, NJ, 7-11 June 2004 (in press).

D.P Grote, "Simulation of Integrated Beam Experiment Design," Proc. 15th International Symposium on Heavy Ion Inertial Fusion, Princeton, NJ, 7-11 June 2004 (in press).

S.M. Lund, D.P. Grote, E. P. Lee and R.C. Davidson, "Simulations of Beam Emittance Growth from the Collective Relaxation of Space-Charge Non-uniformities," Proc. 15th International Symposium on Heavy Ion Inertial Fusion, Princeton, NJ, 7-11 June 2004 (in press); submitted to Nuclear Instruments and Methods in Physics Research A (2004).

W. M. Sharp, J. J. Barnard, D. P. Grote, C. M. Celata, S. S. Yu, D. V. Rose and D.R. Welch, "Simulation of Drift-Compression for Heavy-Ion-Fusion," Proc. 15th International Symposium on Heavy Ion Inertial Fusion, Princeton, NJ, 7-11 June 2004 (in press).

J.-L. Vay, P. Colella, J. W. Kwan, P. McCorquodale, D. B. Serafini, A. Friedman, D. P. Grote, G. Westenskow, J.-C. Adam, A. Hiron, and I. Haber, "Application of Adaptive Mesh Refinement to Particle- In-Cell Simulations of Plasmas and Beams," Phys. Plasmas 11, 2928 (2004).

E. Henestroza, S. Eylon, P. K. Roy, S. S. Yu, A. Anders, F. M. Bieniosek, W. G. Greenway, B. G. Logan, R. A. MacGill, D. B. Shuman, D. L. Vanecek, W. L. Waldron, W. M. Sharp, T. L. Houck, R. C. Davidson, P. C. Efthimion, E. P. Gilson, A. B. Sefkow, D. R. Welch, D. V. Rose, and C. L. Olson, "Design and characterization of a neutralized-transport experiment for heavy-ion fusion," Phys. Rev. ST Accel. Beams 8, 083501 (2004).

S. M. Lund and B. Bukh, "Influence of conducting plate boundary conditions on the transverse envelope equations describing intense ion beam transport," Phys. Rev. ST Accel. Beams 7, 064201 (2004).

D. P. Grote, E. Henestroza, and J. W. Kwan, "Design and simulation of a multibeamlet injector for a high-current accelerator,'' Phys. Rev. ST Accel. Beams 6, 014202 (2003).

D. R. Welch, T. C. Genoni, D. V. Rose, B. V. Oliver, R. E. Clark, C. L. Olson, and S. S. Yu, "Assisted pinched transport of heavy ion beams in a fusion chamber," Phys. Plasmas 10, 2442 (2003).

W. M. Sharp, D. A. Callahan, M. Tabak, S. S. Yu, P. F. Peterson, D. R. Welch, D. V. Rose, and C. L. Olson, "Modeling Chamber Transport for Heavy-Ion Fusion," Fusion Science & Technology 43, 393 (2003).

PI Charlotte Froese-Fischer

C. Froese Fischer and G. Tachiev, Breit-Paul energy levels, lifetimes, and transition probabilities for beryllium-like to neon-like sequences, in Atomic Data and Nuclear Data Tables, Vol. 87, No.1 pp 1-184 (2004).

PI Miguel Furman

Ji Qiang, Miguel A. Furman and Robert D. Ryne (LBNL), "Parallel Particle-In-Cell Simulation of Colliding Beams in High Energy Accelerators," LBNL-52600, Nov. 2003; Proc. SC2003, Phoenix, AZ, Nov. 15-21, 2003; http://www.sc-conference.org/sc2003/inter_cal/inter_cal_detail.php?eventid=10694#2

Y. Cai, M. Pivi (SLAC), M.A. Furman (LBNL), "Buildup of Electron Cloud in the PEP-II Particle Accelerator in the Presence of a Solenoid Field and with Different Bunch Pattern," SLAC-PUB-10164, LBNL-54689, Sep 2003; http://prst-ab.aps.org/PRSTAB/v7/i2/e024402.

R. Cimino (LNF-INFN-Frascati and CERN), I. R. Collins (CERN), M. A. Furman (LBNL), M. Pivi (SLAC), F. Ruggiero (CERN), G. Rumolo (GSI Darmstadt), and F. Zimmermann (CERN), "Can Low Energy Electrons Affect High Energy Physics Accelerators?," CERN-AB-2004-012 (ABP), LBNL-54594, SLAC-PUB-10350, February 9, 2004; Phys. Rev. Lett. 93, 014801 (2004). http://scitation.aip.org/getpdf/servlet/GetPDFServlet?filetype=pdf&id=PRLTAO000093000001014801000001&idtype=cvips

Ji Qiang, Miguel A. Furman and Robert D. Ryne (LBNL), "A Parallel Particle-In-Cell Model for Beam-Beam Interaction in High Energy Ring Colliders," LBNL-54598, May 2004. J. Comp. Phys. 198, Issue 1, 20 July 2004, Pages 278-294. http://dx.doi.org/doi:10.1016/j.jcp.2004.01.008

PI Alan Garfinkel

Omichi, C, Lamp, ST, Lin, SF, Yang, J, Baher, A, Zhou, S, Attin, M, Lee, MH, Karagueuzian, HS, Kogan, B, Qu, Z, Garfinkel, A, Chen, PS and Weiss, JN (2004). "Intracellular Ca Dynamics in Ventricular Fibrillation." Am J Physiol Heart Circ Physiol. 286: H1836-44

Weiss, JN, Chen, PS, Wu, TJ, Siegerman, C and Garfinkel, A (2004). "Ventricular Fibrillation: New Insights into Mechanisms." Ann N Y Acad Sci 1015: 122-132.

Xie, F, Qu, Z, Yang, J, Baher, A, Weiss, JN and Garfinkel, A (2004). "A simulation study of the effects of cardiac anatomy in ventricular fibrillation." J Clin Invest 113(5): 686-93.

PI Bruce Garrett

J.E. Jaffe, M. Dupuis, M. Gutowski, First-Principle Study of Band Offsets in alpha- Cr2O3/alpha-Fe2O3(0001) Interfaces, Phys. Rev. B, 69, 205106, (2004).

I.N. Yakovkin, M. Gutowski, The SrTiO3/Si(001) Epitaxial Interface: A Density Functional Theory Study, Phys. Rev. B, accepted for publication.

Sotiris S. Xantheas and Edoardo Apr`, J. Chem. Phys. 120, 823 (2004).

PI Ahmed Ghoniem

M. Marzouk and A. F. Ghoniem. K-means clustering for partition and dynamic load balance of parallel hierarchical N-body simulation. Submitted to Journal of Computational Physics.

Y. M. Marzouk. Vorticity structure and evolution in a transverse jet with new algorithms for scalable particle simulation. PhD Thesis, MIT. 2004.

Y. M. Marzouk, and A. F. Ghoniem, Vorticity transformation mechanisms and mixing in a transverse jet. To appear at the 57th APS Annual Meeting of the Division of Fluid Dynamics, Seattle, WA, November 2004.

D. Wee, Y. Marzouk, and A. F. Ghoniem, K-means clustering and diffusive interpolation for high-resolution vortex particle methods. To appear at the 57th APS Annual Meeting of the Division of Fluid Dynamics, Seattle, WA, November 2004.

D. Wee, Y. M. Marzouk, and A. F. Ghoniem, Lagrangian simulation of a jet in crossflow at a finite Reynolds number. To appear at the 43rd AIAA Aerospace Sciences Meeting and Exhibit, Reno, NV, Jan 2005.

Y. M. Marzouk and A. F. Ghoniem, Vorticity formulation for an actuated jet in crossflow. 42nd AIAA Aerospace Sciences Meeting, Reno, NV, January 2004

PI Robert Glaeser

C. Yang, E. G. Ng, and P.A. Penczek, "Matrix-free Constructions of Circulant and Block Circulant Preconditioners". To appear in Numerical Linear Algebra and Applications (2004).

C. Yang, E. G. Ng and P. A. Penczek, "Unified 3-D Structure and Projection Orientation Refinement Using Quasi-Newton Algorithm". To appear in Journal of Structure Biology (2004).

PI James Glimm

S. Dutta, E. George, J. Glimm, J. Grove, H. Jin, T. Lee, X. Li, D. H. Sharp, K. Ye, Y. Yu, Y. Zhang, and M. Zhao. Shock wave interactions in spherical and perturbed spherical geometries. Nonlinear Analysis, Elsevier 2004.

S. Dutta, E. George, J. Glimm, X. L. Li, A. Marchese, Z. L. Xu, Y. M. Zhang, J. W. Grove and D. H. Sharp. Numerical methods for the determination of mixing. Laser and Particle Beams, 21: 437-442, 2003.

L. Li, J. Glimm, and X.-L. Li. All isomorphic distinct cases for multi-component interfaces in a block. J. Comp. Appl. Mathematics, 152: 236-276, 2003.

J. Glimm, J. W. Grove, Y. Kang, T. Lee, X. Li, D. H. Sharp, Y. Yu, K. Ye and M. Zhao. Errors in numerical solutions of spherically symmetric shock physics problems. Contemporary Mathematics, 2004. University at Stony Brook Preprint Number SB-AMS-04-03, Los Alamos National Laboratory number LA-UR-04-0713.

J. Glimm, H. Jin, M. Laforest, F. Tangerman, and Y. Zhang. A two pressure numerical model of two fluid mixing. SIAM J. Multiscale Model. Simul., 1: 458-484, 2003.

S. Dutta, J. Glimm, J. W. Grove, D. H. Sharp, and Y. Zhang. Error comparison in tracked and untracked spherical simulations. Computers and Mathematics with Applications, 2003, accepted. University at Stony Brook Preprint Number AMS-03-10.

E. George and J. Glimm. Self similarity of Rayleigh-Taylor mixing rates. Phys. Fluids, 2004, submitted. University at Stony Brook Preprint Number AMS-04-05.

J. Glimm, J. W. Grove, Y. Kang, T. Lee, X. Li, D. H. Sharp, Y. Yu, K. Ye and M. Zhao. Statistical riemann problems and a composition law for errors in numerical solutions of shock physics problems. SISC, 2003, In Press. University at Stony Brook Preprint Number SB-AMS-03-11, Los Alamos National Laboratory number LA-UR-03-2921.

H. Jin, X. F. Liu, T. Lu, B. Cheng, J. Glimm, and D. H. Sharp. Rayleigh-Taylor mixing rates for compressible flow. Phys. Fluids, 2004, submitted. University at Stony Brook Preprint Number AMS-04-06, Los Alamos National Laboratory number LA-04-1384.

Y. Zhang, P. Drake, J. Glimm, J. Grove, and D. H. Sharp. Radiation coupled front tracking simulations for laser driven shock experiments. J. Nonlinear Analysis, 2004, submitted. Los Alamos National Laboratory number LA-UR-04-2381.

PI Balasubraman Govindasamy

P.B. Duffy, B. Govindasamy, J. Iorio, J. Milovich, K. Taylor, M. Wehner, and S. Thompson, 2003: High Resolution Simulations of Global Climate, Part 1: Present Climate. Climate Dynamics, 21, 371-390.

B. Govindasamy, and P.B. Duffy, 2003: High Resolution Simulations of Global Climate, Part 2: Effects of Increased Greenhouse Gases. Climate Dynamic, 21, 391-404.

Iorio, J. P.Duffy, B. Govindasamy, S. Thompson, 2004: Effects of increased resolution on the simulation of daily precipitation statistics in the US, Climate dynamics (in press)

PI Stephen Gray

Theoretical study of dielectrically coated metallic nanowires J. M. Oliva and S. K. Gray, Chem. Phys. Lett. 379, 325-331 (2003).

Optical scattering from isolated metal nanoparticles and arrays G. A. Wurtz, J. S. Im, S. K. Gray, and G. P. Wiederrecht, J. Phys. Chem. B 107, 14191- 14198 (2003).

The equilibrium constants for molecular hydrogen adsorption in carbon nanotubes based on iteratively determined nano-confined bound states T. Lu, E. M. Goldfield, and S. K. Gray, J. Theor. Comp. Chem. 2, 621-626 (2003).

Quantum states of molecular hydrogen and its isotopes in single-walled carbon nanotubes T. Lu, E. M. Goldfield, and S. K. Gray, J. Phys. Chem. B 107, 12989-12995 (2003).

Quantum wave packet and quasiclassical trajectory studies of OH + CO: Influence of the reactant channel well on thermal rate constants D. M. Medvedev, S. K. Gray, E. M. Goldfield, M. J. Lakin, D. Troya, and G. C. Schatz, J. Chem. Phys. 120, 1231-1238(2004).

A new expression for the direct quantum mechanical evaluation of the thermal rate constant D. M. Medvedev and S. K. Gray, J. Chem. Phys. 120, 9060-9070 (2004).

Quantum dynamics of vibrationally activated OH-CO reactant complexes Y. He, E. M. Goldfield, and S. K. Gray, J. Chem. Phys., in press (2004).

Surface plasmons at single nanoholes in Au-films L. Yin, V. K. Vlasko-Vlasov, A. Rydh, J. Pearson, U. Welp, S.-H. Chang, S. K. Gray, G. C. Schatz, D. E. Brown, and C. W. Kimball, Appl. Phys. Lett., 85, 467 (2004).

Controlled spatiotemporal excitation of metal nanoparticles with femtosecond pulses T.W. Lee and S.K. Gray, Phys. Rev. B, submitted (2004).

PI Chris Greene

"Photofragmentation of the H3 molecule, including Jahn-Teller coupling effects" V. Kokoouline, C.H. Greene Phys. Rev. A 69 (3): Art. No. 032711 MAR 2004

"Dissociative recombination of polyatomic molecules: a new mechanism" C. H. Greene, V. Kokoouline Phys. Scripta T1110, 178 (2004)

"Triatomic dissociative recombination theory: Jahn-Teller coupling among infinitely many Born-Oppenheimer surfaces" V. Kokoouline and C.H. Greene Faraday Discussion 127, 413 (2004). Two Body:

"Atom-Molecule Laser Fed by Stimulated Three-Body Recombination" B. Borca, J.W. Dunn, V. Kokoouline, C.H. Greene Phys. Rev. Lett. 91, 070404 (2003) R-Matrix:

Tonzani S., Greene C.H. "Electron-molecule scattering calculations in a 3D finite element R-matrix approach" S. Tonzani, C.H. Greene J. Chem. Phys., in press, (2004)

PI Keith Gubbins

F. R. Hung, G. Dudziak, M. Sliwinska-Bartkowiak and K.E. Gubbins, Freezing/Melting Behavior within Carbon Nanotubes, Mol. Phys. 102 (2004), 223-234

M. Sliwinska-Bartkowiak, F. R. Hung, E. E. Santiso, B. Coasne, F. R. Siperstein and K. E. Gubbins, Effect of Confinement on Freezing in Cylindrical Pores Adsorption, accepted (2004)

B. Coasne, K. E. Gubbins, F. R. Hung and M. Sliwinska-Bartkowiak, Freezing and Melting of Binary Mixtures Confined in a Nanopore Mol. Phys., accepted (2004)

B. Coasne, K. E. Gubbins, F. R. Hung, J. Czwartos and M. Sliwinska-Bartkowiak, Freezing of Mixtures Confined in a Slit Nanopore Adsorption, submitted (2004)

Thermodynamic and transport properties of water confined in carbon nanopores A. Striolo, A. A. Chialvo, P. T. Cummings, and K. E. Gubbins, Water Adsorption in Carbon-Slit Nanopores, Langmuir, 19 (2003) 8583-8591.

A. Striolo, K. E. Gubbins, A. A. Chialvo, and P. T. Cummings, Simulated Water Adsorption Isotherms in Carbon Nanopores, Molecular Physics, 102 (2004) 243.

A. Striolo, K. E. Gubbins, A. A. Chialvo, and P. T. Cummings, Effect of Pore Connectivity on Water Adsorption Isotherms in Non-Activated Graphitic Nanopores, Adsorption, accepted (2004).

A. Striolo, P. K. Naicker, A. A. Chialvo, P. T. Cummings, and K. E. Gubbins, Simulated Water Adsorption Isotherms in Hydrophilic and Hydrophobic Cylindrical Nanopores, Adsorption, submitted (2004).

PI Rajan Gupta

Mass dependence of the hairpin vertex in quenched QCD. Stephen R. Sharpe, Phys.Rev. D69 (2004) 034504

Perturbative matching of staggered four-fermion operators with hypercubic fat links. Weonjong Lee, Stephen Sharpe, Phys.Rev. D68 (2003) 054510

Unphysical Operators in Partially Quenched QCD. Stephen R. Sharpe, Ruth S. Van de Water. Phys.Rev. D69 (2004) 054027

The phase diagram of twisted mass lattice QCD. Stephen R. Sharpe, Jackson M. S. Wu hep-lat/0407025

Light pseudoscalar decay constants, quark masses, and low energy constants from three-flavor lattice QCD. MILC Collaboration: C. Aubin, C. Bernard, C. DeTar, Steven Gottlieb, E.B. Gregory, U.M. Heller, J.E. Hetrick, J. Osborn, R. Sugar, D. Toussaint. hep-lat/0407028

PI Maciej Gutowski

S.A. Chambers, T. Droubay, T.C. Kaspar, M. Gutowski, Experimental Determination of the Valence Band Maximum for SrTiO3 and TiO2 Anatase by X-ray and Ultraviolet Photoemission, J. Vac. Sci. Technol. B (Proceedings of the 31st Conference on the Physics and Chemistry of Semiconductor Interfaces (PCSI)), 22, 2205, (2004).

S.A. Chambers, T. Droubay, T.C. Kaspar, M. Gutowski, M. van Schilfgaarde, Accurate Valence Band Maximum Determination for SrTiO3(001), Surf. Sci. Lett., 554, 81, (2004).

J.E. Jaffe, M. Gutowski, Differences and Similarities between ZrO2 and HfO2 from the Monoclinic to the Cotunnite Phase, Phys. Rev. B, submitted for publication.

J.E. Jaffe, M. Dupuis, M. Gutowski, First-Principle Study of Band Offsets in alpha-Cr2O3/alpha-Fe2O3(0001) Interfaces, Phys. Rev. B, 69, 205106, (2004).

I.N. Yakovkin, M. Gutowski, The SrTiO3/Si(001) Epitaxial Interface: A Density Functional Theory Study, Phys. Rev. B, accepted for publication.

M. Gutowski, T. Autrey, Computational Studies of Boron/Nitrogen and Aluminum/Nitrogen Compounds for Chemical Hydrogen Storage, Prepr. Pap. - Am. Chem. Soc., Div. Fuel Chem. 49, 275, (2004).

T. Autrey, A. Gutowska, L. Li, J. Linehan, M. Gutowski, Chemical Hydrogen Storage in Nanostructured Materials. Control of Hydrogen Release and Reactivity from Ammonia Borane Complexes, Prep. Pap. - Am. Chem. Soc., Div. Fuel Chem. 49, 150, (2004).

M. Haranczyk, M. Gutowski, Fluorine-Substituted Phenols as Probes to Study Intermolecular Proton Transfer Induced by Excess Electron Attachment to Uracil-Phenol Complexes, Internet Electronic Journal of Molecular Design (IEJMD), 3, 368, (2004), http://www.biochempress.com

I. Dabkowska, J. Rak, M. Gutowski, J.M. Nilles, S.T. Stokes, K.H. Bowen, Barrier-Free Intermolecular Proton Transfer Induced by Excess Electron Attachment to the Complex of Alanine with Uracil, J. Chem. Phys., 120, 6064, (2004).

M. Haranczyk, I. Dabkowska, J. Rak, M. Gutowski, J.M. Nilles, S.T. Stokes, D. Radisic, K.H. Bowen, Excess Electron Attachment Induces Barrier-Free Proton Transfer in Anionic Complexes of Thymine and Uracil with Formic Acid, J. Phys. Chem. B, 108, 6919, (2004).

I. Dabkowska, J. Rak, M. Gutowski, J.M. Nilles, S.T. Stokes, D. Radisic, K.H. Bowen, Barrier-Free Proton Transfer in Anionic Complex of Thymine with Glycine, Phys. Chem. Chem. Phys., 6, 4351, (2004).

M. Haranczyk, J. Rak, M. Gutowski, D. Radisic, S.T. Stokes, J.M. Nilles, K.H. Bowen, Effect of Hydrogen Bonding on Barrier-Free Proton Transfer in Anionic Complexes of Uracil with Weak Acids: (U?HCN)- versus (U?H2S)-, Isr. J. Chem. (Joshua Jortner special issue), 44, issue no. 1-2 (2004).

I. Dabkowska, M. Gutowski, J. Rak, Interaction with Glycine Increases the Stability of a Mutagenic Tautomer of Uracil. A Density Functional Theory Study, J. Am. Chem. Soc., submitted for publication.

J.H. Miller, A. Aceves-Gaona, M.B. Ernst, M. Haranczyk, M.S. Gutowski, E.R. Vorpagel, M. Dupuis, Molecular Energetics of Clustered Damage Sites, Radiat. Res., special issue on the 3rd International Workshop on Space Radiation Research, 2004, Port Jefferson, NY, submitted for publication.

M. Haranczyk, M Gutowski, Valance and Dipole-Bound Anions of the Most Stable Tautomers of Guanine, J. Am. Chem. Soc., submitted for publication.

R.Bachorz, M. Haranczyk, I. Dabkowska, J. Rak, M. Gutowski, Anion of the Formic Acid Dimer as a Model for Intermolecular Proton Transfer Induced by Excess Electron Attachment, J. Chem. Phys., submitted for publication.

PI Stephan Haas

"Quantum Antiferromagnetism in Quasicrystals", S. Wessel, A. Jagannathan, and S. Haas, Phys. Rev. Lett. 90, 177205 (2003).

"Adaptive Design of Nano-Scale Dielectric Structures for Photonics", Y. Chen, Y. Rong, W. Li, S. Haas, and A.F.J. Levi, to be published in J. Appl. Phys 94, 6065 (2003)

JAP 95, 1420 (2004)

PRL 92, 157202 (2004)

PRB accepted (2004) cond-mat/0311397

PRL accepted (2004) cond-mat/0403375

APL accepted (2004) cond-mat/0402346

PI Salman Habib

The Semiclassical Regime of the Chaotic Quantum-Classical Transition, Benjamin D. Greenbaum, Salman Habib, Kosuke Shizume, and Bala Sundaram, Phys. Rev. Lett. (submitted) quant-ph/0401174

PI Edward Hamilton

Nonadiabatic alignment of asymmetric top molecules: Rotational revivals M. Poulsen, E. Peronne, H. Stapelfeldt, C. Bisgaard, S. Viftrup, E. Hamilton, and T. Seideman, J. Chem. Phys. 121, 783 (2004).

Nonadiabatic laser induced alignment of iodobenzene molecules M. Poulsen, E. Peronne, H. Stapelfeldt, C. Bisgaard, E. Hamilton, and T. Seideman, Phys. Rev. A, submitted.

PI Bruce Harmon

"Structure and Stability of the Si(105) surface", C. V. Ciobanu, V. B. Shenoy, C. Z. Wang, and K. M. Ho, Surf. Sci. Lett. 544, L715 (2003).

"Self-assembly of steps on Si(113) surfaces: an atomistic perspective", C. V. Ciobanu, D. T. Tambe, V. B. Shenoy, C. Z. Wang, and K. M. Ho, Phys. Rev. B 68 (Rapid Commun.), 201302 (2003).

"Heat-induced transformation of nanodiamond into a tube-shaped fullerence: A molecular dynamics simulation", Gun-Do Lee, C.Z. Wang, Jaejun Yu, Euijoon Yoon, K.M. Ho, Phys. Rev. Lett. 91, 265701 (2003).

"Medium-Sized silicon oxide clusters by Si3O3-ring assembly", W.C. Lu, C.Z. Wang and K.M. Ho, Chem. Phys. Lett. 378, 225 (2003).

"Melting of small Sn clusters by ab initio molecular dynamics simulations", F.-C. Chuang, C. Z. Wang, S. Ogut, James. R. Chelikowsky, and K. M. Ho, Phys. Rev. B 69, 165408 (2004).

"Core energy and peierls stress of screw dislocation in Molybdenum: a periodic cell tight-binding study", Ju Li, C. Z. Wang, J.-P. Chang, W. Cai, V. Bulatov, K. M. Ho, and S. Yip Phys. Rev. B (to appear)

"Impact of Interface Relaxation on Nanoscale corrugation in Pb/Si(111) Islands", Z. L. Chan, C. Z. Wang, M. Hupalo, M. C. Tringides, W. C. Lu, and K. M. Ho, Phys. Rev. Lett. (submitted)

"Ab initio Molecular Dynamics Simulation of liquid Al_xGe_1-x Alloys", Songyou Wang, C. Z. Wang, F. C. Chuang, J. R. Morris, and K. M. Ho, Phys. Rev. B (submitted).

"An ab initio calculation of the structure and energies of {1012} twin boundaries in Zr, Ti, and Mg," J. R. Morris, Y. Y. Ye and M. H. Yoo, to appear in Phil. Mag.

"Ab initio calculation of bulk and defect properties of ductile rare-earth intermetallic compounds," J. R. Morris, Y. Y. Ye, Y. B. Lee, B. N. Harmon, K A. Gschneidner, Jr., and Alan M. Russell, Acta Mat.52, 4849-4857 (2004).

Fabrication of photonic band gap crystals using microtransfer molded templates, W. Y. Leung, H. Kang, K. Constant, D. Cann, C.-H. Kim, R. Biswas, M. M. Sigalas, and K.-M. Ho, J. Appl. Phys. 93, 5866 (2003).

Enhanced complete photonic band gap in the optimized planar diamond structure, R. Biswas, I. El-Kady, and K.-M. Ho, Photonics and Nanostructures 1, 15 (2003).

Lattice symmetry applied in transfer matrix methods for photonic crystals. L.L. Lin, Z-Y. Li, K.-M. Ho, J. Appl. Physics. 94, 811 (2003).

Application of structural symmetries in the plane-wave based transfer matrix method for three dimensional photonic crystal waveguides. Phys Rev B 68, 245117 (2003).

PI Robert Harrison

G. G. Maisuradze, D. L. Thompson, A. F. Wagner, and M. Minkoff, "Interpolating Moving Least Squares Methods for Fitting Potential Energy Surfaces: Detailed Analysis of One-Dimensional Applications," Journal of Chemical Physics, (also MCS Preprint No. 1083), Vol. 119, No. 19, 10002-10014, November 15, 2003.

Kawano, Y. Guo, D. L. Thompson, A. F. Wagner, and M. Minkoff, "Improving the Accuracy of Interpolated Potential Energy Surfaces by Using an Analytical zeroth-Order Potential Function," Journal of Chemical Physics,, (also MCS Preprint No. 1137) Vol 120, No. 14, 6414-6422, April 8, 2004.

Y. Guo, A. Kawano, D. L. Thompson, A. F. Wagner, and M. Minkoff, "Interpolating moving least-squares methods for fitting potential energy surfaces: Applications to classical dynamics calculations," Journal of Chemical Physics (also MCS Preprint No. 1188), to appear, Vol 121, No. 9, Sept. 1, 2004.

G. G. Maisuradze, A. Kawano, D. L. Thompson, A. F. Wagner, and M. Minkoff, "Interpolating Moving Least-Squares Methods for Fitting Potential Energy Surfaces: Analysis of an Application to a Six-Dimensional System," Journal of Chemical Physics, (also MCS Preprint No. 1188), resubmitted with revisions.

Kurt Sattelmeyer, "Use of 2h and 3h-p-like Coupled-Cluster Tamm-Danncoff Approaches for the Equilibrium Properties of Ozone", in press, Chem. Phys. Lett.

R. Olson, M.S. Gordon, K. Christe and D. Dixon, "[N5]+[N5]-, ...," J. Phys. Chem., submitted for publication.

Michael Schuurman, et al. "The heats of formation of HNCO and NCO revisited: Definitive ab initio results via focal point analysis", submitted.

PI Wick Haxton

M. Bender, G.F. Bertsch and P-H. Heenen, "Correlation energies by the generator coordinate mathod: computational aspects for quadrupolar deformations," Physical Review C69 034340 (2004).

K. Hagino, G.F. Bertsch and P-G. Reinhard, "Quadrupole correlation energy by the generator coordinate method," Physical Review C68 024306 (2003).

PI Martin Head-Gordon

Are both symmetric and buckled dimers on Si(100) minima? Density functional and multireference perturbation theory calculations, Y. Jung, Y. Shao, M.S. Gordon, D.J. Doren and M. Head-Gordon, J. Chem. Phys 119, 10917-10923 (2003).

Failure of time-dependent density functional theory for long-range charge-transfer excited states: the zincbacteriochlorin-bateriochlorin and bacteriochlorophyll-spheroidene complexes, A. Dreuw and M. Head-Gordon, J. Am. Chem. Soc. 126, 4007-4016 (2004).

Aromaticity of 4-membered ring 6?-electron systems: N2S2 and Li2C4H4, Y. Jung, T. Heine, P.v.R. Schleyer and M. Head-Gordon, J. Am. Chem. Soc. 126, 3132-3138 (2004).

The spatial size of Fe(II) spin states and the spin-dependence of the structure of Fe(II)-porphyrins, J.M. Ugalde, B. Dunietz, A. Dreuw, M. Head-Gordon and R.J. Boyd, J. Phys. Chem. B 108, 4653-4657 (2004)

What is the nature of the long bond in the (TCNE)2(2?) ? dimer?, Y. Jung and M. Head-Gordon, Phys. Chem. Chem. Phys. 6, 2008-2011 (2004).

Initiation of electro-oxidation of CO on Pt-based electrodes at full coverage conditions simulated by ab initio electronic structure calculations, B.D. Dunietz, N. Markovic, G. Somorjai, P.N. Ross and M. Head-Gordon, J. Phys. Chem B 108, 9888-9892 (2004)

Antes, I., D. Chandler, H. Wang and G. Oster, "The unbinding of ATP from F1-ATPase," Biophys. J., 85, 695-706 (2003).

Maibaum, L. and D. Chandler, "A coarse-grained model of water confined in a hydrophobic tube," J. Phys. Chem. B, 107, 1189-1193 (2003).

Maibaum, L. , A. R. Dinner and D. Chandler. "Micelle Formation and the Hydrophobic Effect, " J. Phys. Chem. B 108, 6778-6781 (2004).

Jung, Y., J.P. Garrahan and D. Chandler. "Excitation lines and the breakdown of Stokes-Einstein relations in super-cooled liquids," Phys. Rev. E, 69, 061205.1-061205.7 (2004).

PI Teresa Head-Gordon

N. Fawzi, V. Chubukov, L.A. Clark, S. Brown & T. Head-Gordon (2004). Influence of denatured and intermediate states of folding on protein aggregation. Protein Science, submitted.

S. Brown & T. Head-Gordon (2004). Intermediates in the folding of proteins L and G. Protein Sci. 13, 958-970.

S. Crivelli & T. Head-Gordon (2004). A new load balancing strategy for the solution of dynamical large tree search problems using a hierarchical approach. IBM R&D Journal 48, 153-160.

S. Brown & T. Head-Gordon (2003). Cool-walking: a new markov chain monte carlo sampling method. J. Comp. Chem. PAK Symposium 24, 68-76.

T. Head-Gordon & S. Brown (2003). Minimalist models for protein folding and design. Curr. Opin. Struct. Biol. 13, 160-167.

S. Brown, N. Fawzi, & T. Head-Gordon (2003). Coarse-grained sequences for protein folding and design. Proc. Natl. Acad. Sci 100, 10712-10717

E. Eskow, B. Bader, R. Byrd, S. Crivelli, T. Head-Gordon, V. Lamberti and R. Schnabel (2003). An optimization approach to the problem of protein structure prediction. Submitted to Math Programming series B.

PI Eric Held

Free-boundary simulations of DIII-D plasmas with the NIMROD code, S.E. Kruger, C.R. Sovinec, D.D. Schnack, E.D. Held, accepted in Computer Physics Communications, 2004.

Nonlocal Closures for Plasma Fluid Simulations, E.D. Held, J.D. Callen, C.C. Hegna, C.R. Sovinec, T.A. Gianakon, and S.E. Kruger, Physics of Plasmas, 11 (2419) May 2004.

Unified Form for Parallel Ion Viscous Stress in Magnetized Plasmas, E.D. Held, Physics of Plasmas, 10 (4708) December 2003.

Conductive Electron Heat Flow along an Inhomogeneous Magnetic Field, E.D. Held, J.D. Callen, and C.C. Hegna, Physics of Plasmas, 10 (3933) October 2003.

PI Brian Hingerty

"Solution Structure of an O6-[4-oxo-4-(3-Pyridyl)butyl]guanine Adduct in an 11mer DNA Duplex: Evidence for Formation of a Base Triplex", L. A. Peterson, C. Vu, B. E. Hingerty, S. Broyde and M. Cosman, Biochemistry 42, 13134-13144 (2003).

"Structural and Stereoisomer Effects of Model Estrogen Quinone-Derived DNA Adducts: N6-(2-Hydroxyestron-6(alpha,beta)-yl)-2'-deoxyadenosine and N2-(2-Hydroxyestron-6(alpha,beta)- yl)-2'deoxyguanine", L. Wang, B. E. Hingerty, R. Shapiro and S. Broyde, Chemical Res. in Tox, 17, 311-324 (2004).

PI Justin Hnilo

Boyle, J., D. Williamson, R. Cederwall, M. Fiorino, J. Hnilo, J. Olsen, T. Phillips, G. Potter, S. Xie, 2004: Diagnosis of CAM2 in NWP configureation, J. Geophys. Res., submitted.

Phillips, T. J., G. Potter, D. L. Williamson, R. Cederwall, J. Boyle, M. Fiorino, J. Hnilo, J. Olson, J. J. Yio, and S. Xie, 2004: Evaluating parameterizations in general circulation models: Climate simulation meets weather prediction. Bull. Amer. Meteor. Soc., 84, accepted.

Xie, S., M. Zhang, J. Boyle, R. T. Cedarwall, G. L. Potter, and W. Lin, 2004: Impact of a revised convection triggering mechanism on cam2 model simulations: Results from short-range forecasts. J. Geophys. Res., in press.

Williamson, D. L., J. Boyle, R. Cederwall, M. Fiorino, J. Hnilo, J. Olson, T. Phillips, G. Potter, and S. Xie, 2004: Moisture and temperature budgets at the ARM Southern Great Plains site in forecasts with the CAM2. J. Geophys. Res., 84, submitted.

PI Hong Im

Wang, Y. and Trouve, A. (2004), "Artificial acoustic stiffness reduction in fully compressible, direct numerical simulation of combustion," Combust. Theory Modelling, v. 8, pp. 633-660.

Wang, Y. and Rutland, C. J. (2004), "Effects of temperature and equivalence ratio on the ignition of n-heptane fuel droplets in turbulent flow," Proc. Combust. Inst., v. 30, in press.

Yoo, C. S. and Im, H (2004), "Transient dynamics of edge flames in a laminar nonpremixed hydrogen-air counterflow," Proc. Combust. Inst., v. 30, in press.

Sankaran, R., Im, H. G., Hawkes, E. R. & Chen, J. H. (2004), "The effects of nonuniform temperature distribution on the ignition of a lean homogeneous hydrogen-air mixture," Proc. Combust. Inst., v. 30, in press

PI Bing Jap

P.J. Walian and B.K. Jap (2003) "A new era in membrane channel biology" Structure 11, 1467-1468.

P.J. Walian, T.A. Cross and B.K. Jap (2004) "Structural genomics of membrane proteins" Genome Biology 5, 215.

Y.D. Kwon, I. Nagy, P.D. Adams, W. Baumeister and B.K. Jap (2004) "Crystal structures of the Rhodococcus proteasomes with and without its pro-peptide: Implications for the role of the pro-peptide in proteasome assembly" J. Mol. Biol. 335, 233.

PI Stephen Jardin

E. A. Lazarus et al., "Simulation of A Discharge for the NCSX Stellarator," Fusion Science and Tech, 46, 209 (2004).

P. R. Garabedian et al., "Reactors with Stellarator Stability and Tokamak Transport," to appear in Fusion Science and Tech.

L. P. Ku et al., "A Compact Quasi-axisymmetric Stellarator Reactor," Proc. of 20th IEEE/NPSS Symposium on Fusion Engineering, San Diego, CA (2003).

L. P. Ku et. al., " Development of Compact Quasi-Axisymmetric Stellarator Configurations," 14th International Stellarator Workshop, Greifswald, Germany (2003).

J. Lyon et al., "Optimization of Stellarator Reactor Parameters," to appear in Fusion Science and Tech.

R. Samtaney. Suppression of the Richmyer-Meshkov instability in the presence of a magetic field. Physics of Fluids, Volume 15, No. 8, pp: L53-56, 2003.

R. Samtaney, S. C. Jardin, P. Colella and D. F. Martin. 3D Adaptive mesh refinement simulation of pellet injection in tokamaks. Computers Physics Communications, to appear 2004. Also PPPL Report No. 3891, October 2003.

V. Wheatley, D. I. Pullin and R. Samtaney, Regular refraction of a MHD shock at an oblique planar density interface. Journal of Fluid Mechanics, to appear 2004.

J. A. Breslau, S. C. Jardin, and W. Park, Simulation Studies of the Role of Reconnection in the Current Hole experiments in JET, Phys. Plasmas, 10, 1665 (2003)

W. Park, J. A. Breslau, J. Chen, et al, Nonlinear Simulation Studies of Tokamaks and STs, Nuclear Fusion, 43, 483 (2003)

S.Jardin, "A Triangular Finite Element with First-Derivative Continuity Applied to Fusion MHD Applications", J. Comp. Phys, 2004

H.R.Strauss, "Nonlinear magnetohydrodynamics in the Dag confinement configuration", Phys. Plasmas 11(3): 1236-1239 Mar 2004

G.W. Hammett, S.C. Jardin, and BC Stratton, "Non-existence of normal tokamak equilibria with negative central current", Physics of Plasmas 10 4048-4052 Oct 2003

V.S. Lukin and S.C.Jardin, "Magnetohydrodynamic modeling of two-dimensional reconnection in the Magnetic Reconnection Experiment", Physics of Plasmas, 10 : 3131-3138 Aug 2003

PI Julius Jellinek

THEORETICAL DETERMINATION OF ELECTRON BINDING ENERGY SPECTRA OF ANIONIC MAGNESIUM CLUSTERS P. H. Acioli and J. Jellinek Eur. Phys. J. D 24, 27-32 (2003)

COLLISIONLESS FRAGMENTATION OF NON-ROTATING Nin (n=4-14) CLUSTERS: A MOLECULAR DYNAMICS STUDY H. Avci, M. Civi, Z. B. Guvenc, and J. Jellinek J. Phys. B: At. Mol. Opt. Phys. 36, 3487-3507 (2003)

METAL CLUSTERS AND METALLICITY: THE PARADIGM OF MAGNESIUM J. Jellinek and P. H. Acioli Metal-Ligand Interactions in Molecular-, Nano-, Micro-, and Macro-Systems in Complex Environments, N. Russo, D. R. Salahub, and M. Witko, Eds., Kluwer Academic Publishers, Dordrecht, 2003, pp. 121-152

REACTIVITY OF THE Nin(T) (n=54,55,56) CLUSTERS WITH D2 (v,j) MOLECULE: MOLECULAR DYNAMICS SIMULATIONS S. Ozcelik, Z.B. Guvenc, P. Durmus, and J. Jellinek Surf. Sci. 566-568, 377-382 (2004)

STRUCTURAL AND ELECTRONIC PROPERTIES OF SMALL BERYLLIUM CLUSTERS: A THEORETICAL STUDY S. Srinivas and J. Jellinek J. Chem. Phys. (in press)

PI Chueng-Ryong Ji

Electromagnetic structure of the rho meson in the light front quark model, H.-M.Choi and C.-R.Ji, Phys. Rev. D, in press (2004); hep-ph/0402114.

Investigating the parity of the exotic Theta baryon from the kaon photoproduction, B.-G.Yu,T.-K.Choi and C.-R.Ji, Phys. Rev. C, in press (2004); nucl-th/0312075.

Radiative scalar meson decays in the light-front quark model, M.A.DeWitt, H.-M.Choi and C.-R.Ji, Phys. Rev. D68, 054026(2003).

Trnasition form factors between pseudoscalar and vector mesons in light-front dynamics, B.Bakker, H-M.Choi and C.-R.Ji, Phys. Rev. D67, 113007(2003).

Molar mass estimate of dark matter from the dark mass distribution measurements, Y.Mishchenko and C.-R.Ji, Phys. Rev. D68, 063503(2003).

PI Donald Johnson

Schaack, T. K., T. H. Zapotocny, A. J. Lenzen and D. R. Johnson, 2004: Global climate simulation with the University of Wisconsin global hybrid isentropic coordinate model. J. Climate, 17, 2998-3016.

PI Sidney Kahana

A. Pastorello, L. Zampieri, M. Turatto, E. Cappellaro, S. Benetti, W. P. S. Meikle, D. Branch, E. Baron, F. Patat, M. Armstrong, G. Altavilla, M. Salvo, and M. Riello, Low Luminosity Type II Supernovae: Spectroscopic and Photometric Evolution, MNRAS, (2004), 347, 74--94.

R. C. Thomas, David Branch, E. Baron, Ken'ichi Nomoto, Weidong Li, Alexei V. Filippenko On the Geometry of the High-Velocity Ejecta of the Peculiar Type Ia Supernova 2000cx, Ap. J. (2004), 601, 1019--1030.

P. Hauschildt and E. Baron, Improved discretization of the wavelength derivative term in CMF operator splitting numerical radiative transfer, A&A (2004), 417, 317--324.

David Branch, R. C. Thomas, E. Baron, D. Kasen, K. Hatano, Ken'ichi Nomoto, Weidong Li, Alexei V. Filippenko, R. Rudy, Direct Analysis of Spectra of the Peculiar Type Ia Supernova 2000cx, ApJ, (2004), in press.

E. Baron and P. Hauschildt, Co-moving frame radiative transfer in spherical media with arbitrary velocity fields, A&A (2004), in press.

C. Fransson, P. M. Challis, R. A. Chevalier, A. V. Filippenko, R. P. Kirshner, C. Kozma, D. C. Leonard, T. Matheson, E. Baron, P. Garnavich, B. Leibundgut, P. Lundqvist, R. McCray, N. Panagia, M. M. Phillips, C. S. J. Pun, B. Schmidt, G. Sonneborn, N. B. Suntzeff, L. Wang, and J. C. Wheeler, Hubble Space Telescope and Ground-Based Observations of SN 1993J and SN 1998S: CNO Processing in the Progenitors, Ap. J., (2004), submitted.

D. Branch, E. Baron, R. C. Thomas, D. Kasen, W. Li, and A. V. Filippenko Reading the Spectra of the Most Peculiar Type Ia Supernova 2002cx, PASP, (2004), in press.

Travis S. Barman, Peter H. Hauschildt, France Allard, Model Atmospheres for Irradiated Stars in pre- Cataclysmic Variables, ApJ (2004), in press.

E. Baron, P. Nugent, D. Branch, and P. Hauschildt, Type II Supernovae as Cosmological Probes: A SEAM Distance to SN 1999em, PRL, submitted.

PI Martin Karplus

R. Bitetti-Puzer, W. Yang, and M. Karplus, Generalized ensembles serve to improve the convergence of free energy simulations, Chem. Phys. Lett. 377, 633-641 (2003).

Q. Cui, G. Li, J. Ma, and M. Karplus, A normal mode analysis of structural plasticity in the biomolecular motor F1-ATPase, J. Mol. Biol. 340, 345-372 (2004).

W. Yang, R. Bitetti-Putzer, and M. Karplus, Free energy simulations: Use of reverse cumulative averaging to determine the equilibrated region and the time required for convergence, J. Chem. Phys. 120, 2618-2628 (2004).

W. Yang, R. Bitetti-Putzer, and M. Karplus, Chaperoned alchemical free energy simulations: A general method for QM, MM, and QM/MM potentials, J. Chem. Phys. 120, 9450-9453 (2004).

A. van der Vaart, J. Ma, and M. Karplus, the Unfolding Action of GroEL on a Protein Substrate, Biophys. J. 87, 562-573 (2004).

Y. Q. Gao, W. Yang, R. A. Marcus, and M. Karplus, A model for the cooperative free energy transduction and kinetics of ATP hydrolysis by F1-ATPase, Proc. Natl. Acad. Sci. USA 100, 11339-11344 (2003).

R. J. Petrella, and M. Karplus, The role of carbon-donor hydrogen bonds in stabilizing tryptophan conformations, Proteins: Struc. Func. Bio. 54, 716-726 (2004).

A. Banerjee, W. Yang, M. Karplus, and G. L. Verdine, Disulfide trapping of a repair enzyme interrogating undamaged DNA elucidate recognition of damaged DNA, submitted to Nature.

PI Thomas Katsouleas

Plasma wakefield acceleration in self-ionized gas or plasmas, Phys. Rev. E 68, 047401, 2003

Meter-Scale Plasma-Wakefield Accelerator Driven by a Matched Electron Beam, Rev. Lett. 93 , 014802 (2004)

Plasma Accelerators at the Energy Frontier and on Tabletops, Physics Today 56, 47 (2003).

On the Possibility of a Multi-bunch Plasma Afterburner for Linear Colliders, submitted to Phys. Rev. Special Topics Acc. & Beams, 2004.

PI Ricky Kendall

M.-S. Wu, R. A. Kendall, S. Aluru, ``A Tunable Collective Communication Framework on Cluster of SMPs,'' Procedings of the IASTED International Conference on Parallel and Distributed Computing and Networks (PDCN 2004), Innsbruck, Austria, February 17-19, pp. 56-63 2004.

J. Bentz and R. A. Kendall, ``Parallelization of general matrix multiply routines using OpenMP,'' in the Proceedings of the Workshop on OpenMP Applications and Tools, WOMPAT 2004, Houston, TX, May 17-18, 2004.

M.S. Wu, R. A. Kendall, and S. Aluru, ``Exploring Collective Communications on a Cluster of SMPs,'' in the Proceedings of 7th International Conference on High Performance Computing and Grid in Asia Pacific Region, HPCAsia2004, Omiya Sonic City, Tokyo Area, Japan, July 20-22, pp. 114-117, 2004.

J. Bentz and R. A. Kendall, ``Parallelization of general matrix multiply routines using OpenMP,'' submitted to Lecture Notes in Computer Science.

PI Davd Keyes

S. Bhowmick,