# 2005 Publications Resulting from the Use of NERSC Resources

On their Allocation Year 2006 ERCAP Request Forms Principal Investigators reported 1,448 refereed publications (published or submitted) for the preceding 12 months, based on using, at least in part, NERSC resources.

## A

**PI Musa Ahmed**

Ndome H, Hochlaf M, "Ab initio investigations of the C3S+ cation and of its role during the reactions of C-3(+) ions against atomic sulfur", PHYSICAL CHEMISTRY CHEMICAL PHYSICS 7 (7): 1568-1576 2005

Ben Houria A, Ben Lakhdar Z, Hochlaf M, et al., "Theoretical investigation of the SO2+ dication and the photo-double ionization spectrum of SO", JOURNAL OF CHEMICAL PHYSICS 122 (5): Art. No. 054303 FEB 1 2005

Hochlaf M, Pilcher-Clayton A, Eland JHD, "HCN2+ dication spectroscopy: theoretical and experimental investigations", CHEMICAL PHYSICS 309 (2-3): 291-301 MAR 14 2005

Eland JHD, Hochlaf M, King GC, et al., "Photo double ionization spectra of CO: comparison of theory with experiment", JOURNAL OF PHYSICS B-ATOMIC MOLECULAR AND OPTICAL PHYSICS 37 (15): 3197-3214 AUG 14 2004

**PI Mowfak Al-Jassim**

Y. Yan, M.M. Al-Jassim, M.F. Chisholm, L. Boatner, S.J. Pennycook, and M. Oxley [1-100]/(11-22) twin boundaries in wurzite ZnO and group-III-nitrides Phys. Rev. B71, 041309(R) (2005)

Y. Yan, G.D, Dalpin, M.M. Al-Jassim, and S.-H. Wei Energetics and electronic structure of stacking faults in ZnO Phys. Rev. B 70 , 193206 (2004)

Y. Yan, M.M. Al-Jassim, and K.M. Jones Passivation of double-positioning twin boundaries in CdTe J. Appl. Phys. 96, 320 (2004).

Y. Yan and M.M. Al-Jassim Inversion domain boundaries in ZnO: First-principles total-energy calculations Phys. Rev. B 69, 085204 (2004).

**PI Greg Aldering**

Garavini, G., et al. 2004, Spectroscopic Observations and Analysis of the Peculiar SN 1999aa, Astronomy & Astrophysics, 128, 387.

Blanc, G., et al. 2004, Type Ia supernova rate at a redshift of 0.1, Astronomy & Astrophysics, 423, 881.

Wood-Vasey, W.~M., Wang, L. and Aldering, G. 2004, Photometry of SN 2002ic and Implications for the Progenitor Mass-Loss History, Astrophysical Journal, 616, 339.

Lidman, S., et al. 2005 Spectroscopic confirmation of high-redshift supernovae with the ESO VLT, Astronomy & Astrophysics, 430, 843.

Nobili, S., et al. 2005 "Restframe I-band Hubble Diagram for Type Ia Supernovae up to Redshift z = 0.5," Astronomy & Astrophysics, 437, 789.

Garavini, G., et al. 2005 "Spectroscopic Observations and Analysis of the Unusual Type Ia SN 1999ac," astro-ph/0507288, Astronomical Journal, accepted.

Hook, I. M, et al. 2005 " Spectra of High-Redshift Type Ia Supernovae and a Comparison with their Low- Redshift Counterparts," Astronomical Journal, accepted

**PI Yoram Alhassid**

"The nuclear moment of inertia and spin distribution of nuclear levels," Y. Alhassid, G.F. Bertsch, L. Fang and S. Liu, nucl-th/0508027, submitted to Phys. Rev. C (2005).

"Disordered systems with interactions: induced two-body ensembles and the Hartree-Fock approach," Y. Alhassid, H.A. Weidenmuler, and A. Wobst, Phys. Rev. B 72, 045318 (2005).

**PI Paul Alivisatos**

F. J. Ribeiro, J. B. Neaton, S. G. Louie, and M. L. Cohen, Mechanism for bias-assisted indium mass transport on carbon nanotube surfaces, Phys. Rev. B 72, 075302 (2005).

J. B. Neaton, K. H. Khoo, C. Spataru, and S. G. Louie, Electronic transport and optical properties of carbon nanostructures from first principles, Comp. Phys. Comm. 169, 1 (2005).

**PI Thomas Antonsen**

Resonant heating of a cluster plasma by intense laser light, Thomas M. Antonsen, Jr., Toshihiro Taguchi, Ayush Gupta, John Palastro, and Howard M. Milchberg, Phys. Plasmas 12, 056703 (2005)

Effective coupling of ultraintense laser pulse to funnel-mouthed plasma waveguides, Jianzhou Wu, James H. Cooley, Thomas M. Antonsen, Jr., and Howard M. Milchberg, Phys. Plasmas 12, 043105 (2005)

**PI Jonathan Arons**

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

O. Skjaeraasen, A. Melatos, A. Spitkovsky, "Particle-In-Cell Simulations of a Nonlinear Transverse Electromagnetic Wave in a Pulsar Wind Termination Shock," 2005, ApJ accepted, astro-ph/0508192

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", ApJ, 615L, 137

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," ApJ, 613L, 137

**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.

## B

**PI Dmitri Babikov**

J. Barber, D. E. Hooks, D. J. Funk, R. D. Averitt, A. J. Taylor and D. Babikov, Temperature-dependent far-infrared spectra of single crystals of high explosives using terahertz time-domain spectroscopy, J. Phys Chem. A 109, pp. 3501-3505, 2005.

D. Babikov, Accuracy of gates in a quantum computer based on vibrational eigenstates, J. Chem. Phys. 121, pp. 7577-7585, 2004.

D. Babikov, B. Kendrick, P. Zhang, and K. Morokuma, Cyclic-N3: II. Large geometric phase effects in the vibrational spectra, J. Chem. Phys. 122, pp. 44315-44335, 2005.

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. 121, pp. 6743-6749, 2004.

**PI Ferdinand Baer**

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.

Wang, H., and G.-T. Yeh, 2005: A characteristic-based semi-Lagrangian method for hyperbolic systems of conservation laws. Chinese J. Atmos. Sci., (in English), Vol. 29, No. 1, 21-42.

Fournier, 2005: ``Instantaneous wavelet energetic transfers between atmospheric blocking and local eddies,'' Journal of Climate, 13, 2151-2171.

K. A. Maasch, R. J. Oglesby and A. Fournier, 2005: ``Barry Saltzman and the theory of climate,'' J. Climate, 13, 2141-2150.

J. M. Dennis, A. Fournier, W. Spotz, A. St.-Cyr, M. Taylor, S. J. Thomas and H. Tufo, 2005: ``High resolution mesh convergence properties and parallel efficiency of a spectral element atmospheric dynamical core,'' International Journal of High-Performance Computing Applications, accepted.

Rousseau, A., R.Temam and J. Tribbia, 2004: Boundary layers in an ocean related system. J. Scientific Comp., 21, 405 432.

Dubois, T., F. Jauberteau, R. Temam and J. Tribbia, 2005: Multilevel schemes for the shallow water equations. J. Comp. Phys., 207, 660-694.

Ji, L., J. Chen, D. Zhang, and H. Wang, 2005: Review on some numerical aspects of the dynamic framework of NWP model. Chinese J. Atmos. Sci., (in Chinese), 29, 120-130.

Rousseau, A., R.Temam and J. Tribbia, 2004: Boundary conditions for an ocean related system with a small parameter. Contemporary Mathematics, 371, 231-263.

**PI Mark Baertschy**

David Cardoza, Mark Baertschy, and Thomas Weinacht; "Interpreting Closed-Loop Learning Control of Molecular Fragmentation in Terms of Wave Packet Dynamics and Enhanced Molecular Ionization"; Journal of Chemical Physics}, 123, 074315.

David Cardoza, Mark Baertschy, and Thomas Weinacht; "Understanding learning control of molecular fragmentation"; Chemical Physics Letters, 411, 311-315.

Florian Langhojer, David Cardoza, Mark Baertschy, and Thomas Weinacht; "Gaining mechanistic insight from closed loop learning control: The importance of basis in searching the phase space"; Journal of Chemical Physics, 122, 014102.

C.W. McCurdy, M. Baertschy and T.N. Rescigno; "Solving the three-body Coulomb breakup problem using exterior complex scaling"; Journal of Physics B, 37, No 17, R137-R187.

**PI David Bailey**

David H. Bailey, "High-Precision Arithmetic in Scientific Computation", Computing in Science and Engineering, May/June, 2005, pg 54-61; LBNL-57487.

David H. Bailey and Michal Misiurewicz, "A Strong Hot Spot Theorem", Proceedings to the American Mathematical Society, to appear, 2005; LBNL-53656 Journal.

David H. Bailey and Jonathan M. Borwein, "Experimental Mathematics: Examples, Methods and Implications", Notices of the American Mathematical Society, May 2005; LBNL-57490.

David H. Bailey, "Review of The Siam 100-Digit Challenge: A Study in High-Accuracy Numerical Computing", Bulletin of the American Mathematical Society, to appear, 2005.

David H. Bailey and Alexei M. Frolov, "Positron annihilation in the bipositronium Ps sub

Thomas H. Dunigan, Jr., Jeffrey S. Vetter, James B. White III, and Patrick H. Worley, Performance Evaluation of the Cray X1 Distributed Shared Memory Architecture, IEEE Micro (in press).

**PI Ramesh Balakrishnan**

Balakrishnan, R., "An approach to entropy consistency in second-order hydrodynamic equations", Journal of Fluid Mechanics, Vol. 503, Cambridge University Press, pp. 201 - 245, March 25, 2004.

Agarwal, R. K., Yun, K. Y., and Balakrishnan, R., "Beyond navier-stokes: burnett equations for flow simulations in the continuum-transition regime", Annual Review of Computational Physics, Vol. IX, Edited by Dietrich Stauffer, World Scientific Press, pp. 211-251, 2001.

Agarwal, R. K., Yun, K. Y., and Balakrishnan, R., "Beyond Navier-Stokes: Burnett equations for flows in the continuum-transition regime", Physics of Fluids, Vol. 13, No. 10, American Institute of Physics, pp. 3061 - 3085, October 2001.

Balakrishnan, R., Agarwal, R. K., and Yun, K. Y.,"BGK-Burnett Equations for Flows in the Continuum--Transition Regime", Journal of Thermophysics and Heat Transfer, American Institute of Aeronautics and Astronautics, Vol. 13, No. 4, pp. 397-410, October - December, 1999.

Yun, K. Y., Agarwal, R. K., and Balakrishnan, R., "Augmented Burnett and Bhatnagar-Gross-Krook Burnett Equations for Hypersonic Flow", Journal of Thermophysics and Heat Transfer, American Institute of Aeronautics and Astronautics, Vol. 12, No. 3, pp. 328-335, July-September, 1998.

**PI Perla Balbuena**

Y. Wang and P. B. Balbuena, "Design of Oxygen Reduction Bimetallic Catalysts: Ab initio-Derived Thermodynamic Guidelines, J. Phys. Chem. B. Letter, accepted for publication.

J. M. Seminario, L. A. Agapito, L. Yan, and P. B. Balbuena, "Density Functional Theory Study of Adsorption of OOH on Pt-Based Bimetallic Clusters Alloyed with Cr, Co, and Ni, Chem. Phys. Lett., 410, 275-281, (2005).

Y. Wang and P. B. Balbuena, "Potential Energy Surface Profile of the Oxygen Reduction Reaction on a Pt Cluster: Adsorption and Decomposition of OOH and H2O2, J. Chem. Theory and Comp., accepted for publication.

Z. Gu and P. B. Balbuena, "Structural characterization of Pt nanoclusters deposited on graphite: Effects of substrate and surrounding medium, Cat. Today, 105, 152-161 (2005).

S. R. Calvo and P. B. Balbuena, "Molecular dynamics studies of phonon spectra in mono- and bimetallic nanoclusters, Surf. Sci, 581, 213-224, (2005).

Y. Wang and P. B. Balbuena, "Ab initio Molecular Dynamics Simulations of the Oxygen Reduction Reaction on a Pt(111) Surface in the Presence of Hydrated Hydronium (H3O) (H2O)2: Direct or Series Pathway?, J. Phys.Chem, accepted for publication.

P. B. Balbuena, E. J. Lamas, and Y. Wang "Molecular modeling studies of polymer electrolytes for power sources, Electrochimica Acta, 50, 3788-3795 (2005).

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).

S. Calvo, D. S. Mainardi, A. P. J. Jansen, J. J. Lukkien, and P. B. Balbuena, "Test of a Mechanism for O2 Electroreduction on Pt(111) via Dynamic Monte Carlo Simulations", in Power Sources Modeling, R. G. Jungst, J. W. Weidner, B. W. Liaw, and K. Nechev , Eds., Pennington, NJ, in press, 2005.

**PI Arun Bansil**

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

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

M. Lindroos, S. Sahrakorpi, V. Arpiainen, R.S. Markiewicz, and A. Bansil, "Role of kz-dispersion in Photoemission from Quasi-2D Cuprates", in press, Journal of Physics and Chemistry of Solids (2005).

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

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

S. Sahrakorpi, M. Lindroos, and A. Bansil, "Site and Orbital Selectivity Properties of Angle-resolved Photoemission from the Cuprates", in press, Journal of Physics and Chemistry of Solids (2005).

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).

Yinwan Li, P. A. Montano, J.F. Mitchell, B. Barbiellini, P. E. Mijnarends, S. Kaprzyk and A. Bansil, "Temperature dependent orbital degree of freedom in a bilayer manganite by magnetic Compton scattering", Phys. Rev. Lett. 93, 207206 (2004).

A.B. Denison, R. Meulenberg, S.W.H. Eijt, A. Van Veen, P.E. Mijnarends, B. Barbiellini, A. Bansil, C. Fischer, M.H. Weber, K.G. Lynn, "Radial Electron Momentum Densities of Colloidal CdSe Nanocrystals Determined by Positron Beam Analysis", Mat. Sci. Forum 445-446, 395 (2004).

X. Zuo, B. Barbiellini and C. Vittoria, "Calculation of exchange constants in manganese ferrite (MnFe2O4)", Journal of Magnetism and Magnetic Materials 272-276, 306 (2004).

B. Barbiellini, A. Bansil, "Dyson Orbitals, Quasi-Particle effects and Compton scattering", J. Phys. Chem. 65, 2031 (2004).

A. Bansil , D. Nissenbaum, B. Barbiellini, R. Saniz, "Electron correlations, spontaneous magnetization and momentum density in quantum dots", J. Phys. Chem. Solids 65, 2005 (2004).

Pedro A. Montano, Yinwan Li, J. F. Mitchell, B. Barbiellini, P.E. Mijnarends, S. Kaprzyk, and A. Bansil, "Inelastic Magnetic X-Ray Scattering from Highly Correlated Electron Systems: La1.2Sr1.8Mn2O7, La0.7Sr0.3MnO3 and Fe3O4", J. Phys. Chem. Solids 65, 1999 (2004).

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

B. Barbiellini, A. Bansil, "A spin-polarized scheme for obtaining quasi-particle energies within the density functional theory", Submitted to J. Phys. Chem. Solids (2005).

**PI Edward Baron**

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), 622, 991--1007.

D. Kasen and T. Plewa, "Spectral Signatures of Gravitationally Confined Thermonuclear Supernova Explosions, 2005, ApJ, 21, L41

**PI Don Batchelor**

"Integrated Simulation of Fusion Plasmas", D. B. Batchelor, Physics Today, (February, 2005)

"Nonthermal Particle and Full-Wave Diffraction Effects on Heating and Current Drive in the ICRF and LHRF Regimes", J. C. Wright, L.A. Berry, P.T. Bonoli, et.al., to be published in Nucl. Fusion 45 (2005).

"Monte-Carlo orbit/full wave simulation of ion cyclotron resonance frequency wave damping on resonant ions in tokamaks" M. Choi, V.S. Chan, R.I. Pinsker, S.C. Chiu, W.W. Heidbrink, Phys. Plasmas 12 072505 (2005).

"Electron Bernstein Wave-Bootstrap Current Synergy in NSTX", R.W. Harvey and G.Taylor, Phys. of Plasmas 12, 052509 (2005).

"Integrated Modeling of the Current Profile in Steady-State and Hybrid ITER Scenarios", W.A. Houlberg, C. Gormezano, J.F. Artaud, E. Barbato, V. Basiuk, A. Becoulet, P. Bonoli, R.V. Budny, L.G. Eriksson, D. Farina, Yu. Gribov, R.W. Harvey, J. Hobirk, F. Imbeaux, C.E. Kessel, V. Leonov, M. Murakami, A.Polevoi, E. Poli, R. Prater, H. St. John, F. Volpe, E. Westerhof, A. Zvonkov, to be published in Nucl. Fusion (2005)

"Progress Towards High Performance Plasmas in the National Spherical Torus Experiment (NSTX)," S.M. Kaye, ....,R. Harvey,..., to appear in Nucl. Fusion (2005).

"Dynamo free plasma in the Reversed Field Pinch: Advances in Understanding the RFP High Confinement Mode", J.K. Anderson, J. Adney, A. Almagri, A. Blair,.....,R.W. Harvey,...., Physics of Plasmas 12, 056118 (2005).

"Efficient generation of non-inductive, off-axis, Ohkawa current, driven by electron Bernstein waves in high beta, spherical torus plasmas", G. Taylor, P.C. Efthimion, C.E. Kessel, R.W. Harvey, A.P. Smirnov, N.M. Ershov, M.D. Carter, C.B. Forest, , Phys. of Plasmas 11, 4733 (2004).

**PI Victor Batista**

J. Phys. Chem. B 108, 6745-6749, 2004 Model Study of Coherent-Control of the Femtosecond Primary Event of Vision, by Samuel C. Flores and Victor S. Batista.

Biophys. J., 87(5), 2931-2941, 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.

J. Chem. Phys., 121,1676-1680, 2004 Quantum Tunneling in Multidimensional Systems: A Matching-Pursuit Description, by Yinghua Wu and Victor S. Batista.

Photosynthesis: Fundamental Aspects to Global Perspectives, vol. 1, (D. Bruce and A. van der Est, ed.) Allen Press Inc., Lawrence, Kansas, 278-280, 2005. Computational Structural Model of the Oxygen Evolving Complex in Photosystem II: Complete Ligation by Protein, Water and Chloride, by James P. McEvoy, Jose A. Gascon, Eduardo M. Sproviero, Victor S. Batista and Gary W. Brudvig.

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

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

J. Chem. Phys., 122, 084111, 2005 Is the Filinov integral conditioning technique useful in semiclassical IVR methods?, Michael Spanner, Victor S. Batista and Paul Brumer.

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

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

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

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

J. Phys. Chem. B 108, 6745-6749, 2004 Model Study of Coherent-Control of the Femtosecond Primary Event of Vision, by Samuel C. Flores and Victor S. Batista.

Biophys. J., 87(5), 2931-2941, 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.

J. Chem. Phys., 121,1676-1680, 2004 Quantum Tunneling in Multidimensional Systems: A Matching-Pursuit Description, by Yinghua Wu and Victor S. Batista.

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

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

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

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

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

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

J. Chem. Theor. Comput., submitted, 2005. A self-consistent space-domain decomposition method for QM/MM computations of protein electrostatic potentials, by Jose A. Gascon, Siegfried S.F. Leung, Enrique R. Batista and Victor S. Batista.

Acc. Chem. Res., submitted, 2005. Molecular Rearrangements and Spectroscopic Changes due to the Primary Photochemical Event in Rhodopsin, by Jose A. Gascon, Eduardo M. Sproviero and Victor S. Batista.

**PI Marco Battaglia**

M. Battaglia and M. Peskin, The Role of the ILC in the Study of Cosmic Dark Matter, to appear in the Proceedings of the Intl. Workshop on Physics and Detectors at the Linear Collider, LCWS05, Stanford, May 2005

M. Battaglia et al., Monolithic CMOS Pixel R&D for the ILC at LBNL, to appear in the Proceedings of the Intl. Workshop on Physics and Detectors at the Linear Collider, LCWS05, Stanford, May 2005.

**PI John Bell**

J. B. Bell, M. S. Day, I. G. Shepherd, M. Johnson, R. K. Cheng, J. F. Grcar, V. E. Beckner, M. J. Lijewski, "Numerical Simulation of a Laboratory-Scale Turbulent V-flame", Proc. Natl. Acad. Sci. USA, 102(29):10006-10011, 2005.

P. Schwartz, M. Barad, P. Colella, T. J. Ligocki, "A Cartesian grid embedded boundary method for the heat equation and Poisson's equation in three dimensions", LBNL report LBNL-56607, to appear, J. Comput. Phys., 2005.

D. F. Martin, P. Colella, M. Anghel, F. Alexander, "Adaptive mesh refinement for multiscale nonequilibrium physics", Comp. Sci. Eng., 7(3):24-31, 2005.

R. K. Crockett, P. Colella, R. Fisher, R. I. Klein, C. F. McKee, "An unsplit, cell-centered Godunov method for ideal MHD", J. Comput. Phys., 203:422-448, 2005.

J. B. Bell, M. S. Day, and J. F. Grcar, M. J. Lijewski, "Stochastic Algorithms for the Analysis of Numerical Flame Simulations", J. Comp. Phys., 202:262-280, 2004.

R. Samtaney, P. Colella, S. C. Jardin, D. F. Martin, "3D adaptive mesh refinement simulations of pellet injection in tokamaks", Comp. Phys. Commun., 164:220-228, 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", Astrophys. J., 608:883-906, 2004.

J. L. Vay, P. Colella, J. W. Kwan, P. McCorquodale, D. B. Serafini, A. Friedman, D. P. Grote, G. Westenskow, J. C. Adam, A. Heron, I. Haber, "Application of adaptive mesh refinement to particle-in-cell simulations of plasmas and beams", Physics of Plasmas, 11:2928-2934, 2004.

M. S. Day, J. B. Bell, J. F. Grcar, V. E. Beckner, "Numerical Control of 3D Turbulent Premixed Flame Simulations", 20th International Colloquium on the Dynamics of Explosions and Reactive Systems, July 31-August 5, 2005.

P. McCorquodale, P. Colella, G. Balls, S. B. Baden, "A scalable parallel Poisson solver with infinite domain boundary conditions", Proceedings of the 7th Workshop on High Performance Scientific and Engineering Computing, June 14-17, 2005.

M. Zingale, S. E. Woosley, C.A. Rendleman, M. S. Day, and J. B. Bell, "Three-dimensional Numerical Simulations of Rayleigh-Taylor Unstable Flames in Type Ia Supernovae", accepted, Astrophys. J., 2005.

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", Proc. Combust. Inst., 30:1193-1200, 2004.[4]

**PI Roy Benedek**

Dopant-induced stabilization of rhombohedral LiMnO2 against Jahn-Teller distortion - art. no. 134111 Prasad, R;Benedek, R;Thackeray, MM PHYSICAL REVIEW B, APR 2005, 7113, 13, pp. 4111-4111

**PI Amitava Bhattacharjee**

A. Bhattacharjee, K. Germaschewski, and C.S. Ng, Current singularities: Drivers of impulsive reconnection, Phys. Plasmas 12, 042305 (2005)

K. Germaschewski, A. Bhattacharjee, R. Grauer, D. Keyes, and B. Smith, Using Krylov-Schwarz methods in an adaptive mesh refinement environment in: Adaptive Mesh Refinement - Theory and Applications, Series : Lecture Notes in Computational Science and Engineering , Vol. 41 (2005) Plewa, Tomasz; Linde, Timur; Weirs, V. Gregory (Eds.)

**PI Julian Borrill**

P.R.Meinhold et al "A Map of the Cosmic Microwave Background from the BEAST Experiment," Ap.J.Sup. 158, 101-108 (2005)

I.O'Dwyer et al "The CMB Power Spectrum from the Background Emission Anisotropy Scanning Telescope (BEAST) Experiment," Ap.J.Sup. 158, 93-100 (2005)

J.Meja et al, "Galactic foreground contribution to the BEAST CMB Anisotropy Maps" Ap.J.Sup. 158, 109-117 (2005)

I.J.O'Dwyer et al "Bayesian Power Spectrum Analysis of the First-Year WMAP data," Ap.J. 617, L99-102 (2004)

H.K.Eriksen et al "Power spectrum estimation from high-resolution maps by Gibbs sampling," Ap.J.Sup. 155, 227-241 (2004)

**PI Marcia Branstetter**

Branstetter, M.L., David J. Erickson III, and Robert Oglesby, "Spatial resolution impacts on the magnitude and variability of continental runoff in the CCSM3 control simulation", submitted to Journal of Geophysical Research-Atmospheres, 2005.

**PI Dmitry Budker**

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

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

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

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

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

**PI Vasily Bulatov**

V. V. Bulatov, W. Cai, J. Fier, M. Hiratani, T. Pierce, M. Tang, M. Rhee, K. Yates, A. Arsenlis, Scalable line dynamics of ParaDiS, Supercomputing 2004, p.19.

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

M. Hiratani, and V.V. Bulatov "Solid Solution Hardening by Point-like Obstacles of Different Kinds", Phil. Mag. Lett. 2004, v 84, n 7, p 461-470

M. Hiratani, and V.V. Bulatov "Dynamical Effects on Dislocation Glide through Weak Obstacles", 2005 MRS spring meeting proceeding, San Francisco CA, EE4.4.

W. Cai, V. V. Bulatov, J. Chang, J. Li, and S. Yip, Dislocation Core Effects on Mobility, in F. R. N. Nabarro and J. P. Hirth, ed. Dislocations in Solids, North-Holland Pub. vol. 12, p. 1 (2004).

Ju Li, Cai-Zhuang Wang, Jin-Peng Chang, Wei Cai, Vasily V. Bulatov, Kai-Ming Ho, Sidney Yip, Core energy and Peierls stress of a screw dislocation in bcc molybdenum: A periodic-cell tight-binding study, Phys. Rev. B, 70 104113 (2004).

N. Sekimura, K. Morishita, E. Kuramoto, N. Soneda, T. Okita, and M. Hiratani Theory and Modeling of Radiation Damange Processees in Materials, J. Plasma and Fusion Research (Japan), 2004, v 80, n 3, p228-235

N. Soneda, T. Okita, K. Morishita, E. Kuramoto, M. Hiratani, and N. Sekimura How Can We Bridge the Multiple Timescale Models of Radiation Damage Processes? , J. Plasma and Fusion Research (Japan), 2004, v 80, n 4, p318-324

E. Kuramoto, M. Hiratani, T. Okita, K. Morishita, N. Sekimura, and N. Soneda How Can We Bridge the Multiple Lengthscale Models of Radiation Damage Processes? , J. Plasma and Fusion Research (Japan), 2004, v 80, n 6, p492-499.

## C

**PI Philip Cameron-Smith**

Lamarque, J.-F., P. Cameron-Smith, and 18 other authors, "Assessing Nitrogen Deposition and Carbon Cycle Feedback using a Multi-Model approach. Part 1: Analysis of Nitrogen Deposition", J.G.R. Atmospheres, accepted 2005.

Lamarque, J.-F., J. T. Kiehl, P. G. Hess, W. D. Collins, L. K. Emmons, P. Ginoux, C. Luo, and X. X. Tie (2005), Response of a coupled chemistryclimate model to changes in aerosol emissions: Global impact on the hydrological cycle and the tropospheric burdens of OH, ozone, and NOx, Geophys. Res. Lett., 32, L16809, doi:10.1029/2005GL023419.

**PI Andrew Canning**

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

Non-free-electron momentum- and thickness-dependent evolution of quantum well states in the Cu/Co/Cu(001) system E. Rotenberg, Y. Z Wu, J. M. An, M.A. van Hove, A. Canning et al. Physics Rev. B. (In press) (2005)

Comparison of Nonlinear Conjugate-Gradient Methods for Computing the Electronic Properties of Nanostructure Architectures S. Tomov, J. Langou, A. Canning, L-W Wang and J. Dongarra, Proceedings of International Conference on Computer Science CNST05 Atlanta, May 2005.

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

X. Cartoixa, L.W. Wang, "Microscopic dieletric response functions in semiconductor quantum dots", Phys. Rev. Lett. 94, 236804 (2005)

**PI Paola Cessi**

Gallego, B. and P. Cessi and J.C.McWilliams, 2004. The Antarctic Circumpolar Current in equilibrium. J. Phys. Oceanogr., 34, 1571-1587.

Cessi, P. and M. Fantini, 2004. The eddy-driven thermocline. J. Phys. Oceanogr., 34, 2642-2658.

**PI Yuen-Dat Chen**

B. Aharmim et al. (the SNO Collaboration), Electron Energy Spectra, Fluxes, and Day-Night Asymmetries of 8B Solar Neutrinos from the 391-Day Salt Phase SNO Data Set, submitted to Phys. Rev. C, arXiv:nucl-ex/0502021 (2005)

B. Aharmim et al. (the SNO Collaboration), Electron Antineutrino Search at the Sudbury Neutrino Observatory, Phys. Rev. D70, 093014 (2004)

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

**PI Choong-Seock Chang**

S. Hahn, G. Park, C. S. Chang, C. K. Choi, "Diffusion in a two dimensional anisotropic web map by extrinsic noise applied to the intrinsically perturbed quantity," Phys. Rev. E 69, 017202 (2004).

R. Maingi, C. S. Chang, Seunghoe Ku, etc, "Effect of gas fueling location on H-mode Access in NSTX," Plasma Phys. Cont. Fusion 46, A305-A313 (2004).

H. Weitzner and C. S, Chang, Phys. Plasmas 11, 3060 (2004).

C. S. Chang, Seunghoe Ku, and H. Weitzner, "Numerical study of neoclassical plasma pedestal in a tokamak geometry," Phys. Plasmas APS Invited Issue 11, 2649 (2004).

S.H. Ku and C. S. Chang, "Property of an X-point generated velocity space hole in a diverted tokamak plasma edge," Phys. Plasmas 11, 5626 (2004).

Harold Weitzner and C.S. Chang, "Extension of adiabatic invariant theory for a charged particle," Phys. Plasmas 12, 012106 (2005).

S. Hahn, S.H. Ku, and C.S. Chang, "Wall striking of ion orbits induced by fast transport of pedestal plasma over an electrostic potential hill in a tokamak plasma edge," Phys. Plasmas, Accepted (2005).

Hoyul Baik and C.S. Chang, "Poloiization drift in a sheared electric field," Phys. Plasmas, submitted.

H. Strauss, A. Pletzer, W. Park, S. Jardin, J. Breslau, L. Sugiyama, E0V0 MHD simulations with resistive wall and magnetic separatrix, E0\3 Comp. Phys. Comm. 164, 40 (2004)

**PI James Chelikowski**

L. Kronik, M. Jain, and J.R. Chelikowsky: Electronic structure and spin-polarization of MnGaP, Applied Phys. Lett. 85, 2014 (2004).

G. Nesher, L. Kronik and J.R. Chelikowsky: Ab initio absorption spectra of Ge nanocrystals, Phys. Rev. B 71, 035344 (2005).

X. Huang, E. Lindgren and J.R. Chelikowsky: Surface passivation method for semiconductor nanostructures, Phys. Rev. B 71, 165328 (2005).

S. Li, M.M.G. Alemany, and J.R. Chelikowsky: Ab initio calculations of the photoelectron spectra of transition metal clusters, Phys. Rev. B 71, 165433 (2005).

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

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

E. Ko, M.M.G. Alemany, J. J. Derby and J.R. Chelikowsky: Ab Initio Simulations of Non-Stoichiometric Cd_x Te_1-x Liquids,'' J. Chem. Phys. (in press).

C. Bekas, Y. Saad, M.L. Tiago and J.R. Chelikowsky: Computing Charge Densities with Partially Reorthogonalized Lanczos, Comp. Phys. Commun. (in press).

M. Lopez del Puerto, M.L. Tiago, I. Vasiliev and J.R. Chelikowsky: Real Space Pseudopotential Calculations of the Ground State and Excited State Properties of the Water Molecule, Phys. Rev. A (in press.)

**PI Jacqueline Chen**

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

E. R. Hawkes and J. H. Chen, "Evaluation of Models for Flame Stretch in the Thin Reaction Zones Regime," Proceedings of the Combustion Institute, 30, pp. 647-655. (2004).

J. C. Sutherland, P. J. Smith, and J. H. Chen, "Quantification of Differential Diffusion in Nonpremixed Systems," to appear in Combust. Theory and Modeling, (2005).

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," Proceedings of the Combustion Institute, 30, pp. 875-882. (2004).

R. Seiser, J. H. Frank, S. Liu, J. H. Chen, R. J. Sigurdsson, and K. Seshadri, "Ignition of Hydrogen in Unsteady Nonpremixed Flows," Proceedings of the Combustion Institute, 30, pp. 423-430. (2004).

**PI Liu Chen**

"Role of nonlinear toroidal coupling in electron temperature gradient turbulence", Z. Lin, L. Chen and F. Zonca; Physics of Plasmas, 12 (2005).

"A gyrokinetic electron and fully kinetic ion plasma simulation model", Y. Lin, X. Wang, Z. Lin, and L. Chen; Plasma Phys. Control. Fusion, 47 (2005).

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

**PI Yang Chen**

Y. Chen and S.E. Parker, "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

Srinath Vadlamani, Scott E. Parker, Yang Chen and Charlson Kim, ``The particle-continuum method: an algorithmic unification of particle-in-cell and continuum methods,'' Computer Physics Communications, 164, Issue 1-3, 1-15 Dec., 2004.

"Hybrid Kinetic-MHD simulation in general geometry," C.Kim, C.R. Sovenic and S.E. Parker, Comp. Phys. Comm., Vol. 164, p. 448 (2004).

"Modeling of field-aligned electron bursts by dispersive Alfven waves in the dayside auroral region," Y.J. Su, S.T. Jones, R.E. Ergun and S.E. Parker, J. Geophysical Research}, Vol. 109, p. A11201 (2004).

"Electromagnetic gyrokinetic simulations," S. Parker,Y. Chen, W.~Wan, B.I.~Cohen, W.M.~Nevins, Phys. Plasmas., Vol. 11, p. 2494 (2004).

**PI Hai-Ping Cheng**

First-principles investigation of one monolayer of C60 on h-BN/Ni(111), Jingguang Che and Hai-Ping Cheng, Phys. Rev. B (accepted).

Energy Transfer in the Nanostar: The Role of Coulombic Coupling and Dynamics Wilfredo Ortiz,Brent P. Krueger, Valeria D. Kleiman, Jeffrey L. Krause,and Adrian E. Roitberg, J. Phys Chem B109, 11512 (2005).

Adsorption and non-adiabatic processes in the photodesorption of molecular oxygen from the reduced TiO2 (110) surface, M. P. de Lara-Castells, A. O. Mitrushenkov, O. Roncero and J. L. Krause, Israel J. Chem. 45, 59 (2005)

Multiple-Steering QM-MM Calculation of the Free Energy Profile in Chorismate Mutase, Alejandro Crespo, Marcelo A. Mart?, Dario A. Estrin, and Adrian E. Roitberg, 127, 6940 (2005)

Free Energy calculations with non-equilibrium methods. Applications ofthe Jarzynski Relationshipn. Hui Xiong, Alejandro Cresp, Marcelo Marti, Dario Estrin and Adrian E. Roitberg. Accepted Theoretical Chemistry Accounts. April 2005

Non-Equilibrium Approaches to Free Energy Calculationsn. Adrian E. Roitberg. Annual Reports in Computational Chemistry. Chapter 8, page 103. Elsevier (2005)

Suppressing the spreading of continuum wave packets via chirped laser pulse, C. Manescu, J. L. Krause, K. B. Mvller and N. E. Henriksen, J. Phys. Chem. A108, 8840 (2004).

**PI Wai-Yim Ching**

S. Leitch, A. Moewes, L. Ouyang, W.Y. Ching, T. Sekine, "Propoerties of non-equivalent sites and band gap of spinel-phase silicon nitride using soft X-ray spectroscopy", J. Phys.: Condens. Matter 16, 6469-6476 (2004).

Paul Rulis, Lizhi Ouyang, and W.Y. Ching, "Electronic Structure and Bonding in Calcium Apatite Crystals: Hydroxyapatite, Fluorapatite, Chlorapatite, and Bromapatite", Phys. Rev. B70, 155104 (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. 87[11], 1996-2013 (Feature article, 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, 085105-118 (2004)

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

Lizhi Ouyang, P. Rulis, W.Y. Ching, M. Slouf, G. Nardin and L. Randaccio, "Electronic structure and bonding in Hydroxl-cobalamin", Spectrochimica Acta A, 61(7), 1647-1652 (2005).

Lizhi Ouyang and W.Y. Ching, "Prediction of a high-density phase of SiO2 with a high dielectric constant", Physica Status Solidi(b): Rapid Research Letters, 242[7], R64-R66 (2005).

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

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

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

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

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

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

**PI Mei-Yin Chou**

"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 70, 165105/1-7 (2004).

"Alternative Low-Symmetry Structure for 13-Atom Metal Clusters", C. M. Chang and M. Y. Chou, Phys. Rev. Lett. Phys. 93, 133401/1-4 (2004).

"Hydrogenation-Induced Insulating State in the Intermetallic Compound LaMg2Ni", K. Yvon, G. Renaudin, C. M. Wei and M. Y. Chou, Phys. Rev. Lett. 94, 066403/1-4 (2005).

**PI Daryl Chrzan**

A. M. Minor, E. T. Lilleodden, M. Jin, E. A. Stach, D. C. Chrzan and J. W. Morris, Jr. Room temperature dislocation plasticity in silicon. Philosophical Magazine 85, 323-330 (2005).

I. D. Sharp, D. O. Yi, Q. Xu, C. Y. Liao, J. W. Beeman, Z. Liliental-Weber, K. M. Yu, D. N. Zakharov, J. W. Ager, III, D. C. Chrzan and E. E. Haller. Mechanism of stress relaxation in Ge nanocrystals embedded in SiO2. Applied Physics Letters 86, 063107/1-3 (2005).

E. Ertekin, P. A. Greaney, D. C. Chrzan and T. D. Sands. Equilibrium limits of coherency in strained nanowire heterostructures. Journal of Applied Physics 97, 114325/1-10 (2005).

M. H. Jhon, A. M. Glaeser and D. C. Chrzan. Computational study of stacking faults in sapphire using total energy methods. Physical Review B 71, 214101/1-5 (2005).

I. D. Sharp, Q. Xu, C. Y. Liao, D. O . Yi, J. W. Beeman, S. Liliental-Weber, K. M. Yu, D. N. Zakharov, J. W. Ager, III, D. C. Chrzan and E. E. Haller. Stable free standing Ge nanocrystals. Journal of Applied Physics 97, 124316/1-4 (2005).

E. Ertekin and D. C. Chrzan. Ideal torsional strengths and stiffnesses of carbon nanotubes. Physical Review B 72, 045425/1-5 (2005).

P. A. Greaney and D. C. Chrzan. Irreversible island growth in the presence of anisotropic surface diffusion with long jumps. Accepted for publication in Physical Review B, 2005.

X. Xu, S. P. Beckman, P. Specht, E. R. Weber, D. C. Chrzan, R. P. Erni, I. Arslan, N. Browning, A. Bleloch and C. F. Kisielowski. Distortion and segregation in a dislocation core region at atomic resolution. Accepted for publication in Physical Review Letters, 2005.

**PI Catherine Chuang**

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.

Phillips, T.J., et al., and S.C. Xie, 2004: The CCPP-ARM Parameterization Testbed (CAPT): Where climate simulation meet with weather prediction, Bulletin of the American Meteorological Society, 85, 1903-1915.

Xie, S.C., M.H. Zhang, J.S. Boyle, R.T. Cederwall, G.L. Potter, and W.Y. Lin, 2004: Impact of a revised convective triggering mechanism on CAM2 model simulations: results from short-range weather forecasts, J. Geophys. Res., 109, D14102, doi:10.1029/2004JD004692.

Chin, H.-N.S., M.J. Leach, G.A. Sugiyama, J.M. Leone Jr., H. Walker, J.S. Nasstrom, and M.J. Brown, 2005: Evaluation of an urban canopy parameterization in a mesoscale model using VTMX and URBAN 2000 data, Mon. Wea. Rev., in press.

**PI Bruce Cohen**

James C. Kniep, Jean-Noel G. Leboeuf, and Viktor K. Decyk,"Gyrokinetic Particle-In-Cell Calculations of Ion Temperature Gradient Driven Turbulence with Parallel Nonlinearity and Strong Flow Corrections", Comp. Phys. Comm. 164/1-3, 98-102(2004).

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

Simulation of turbulence in the divertor region of tokamak edge plasma, M.V.Umansky, T.D.Rognlien,X.Q.Xu, Journal of Nuclear Materials, VOL. 337-339, 266-270 (2005).

Simulation of plasma fluxes to material surfaces with self-consistent edge turbulenceand transport for tokamaks, T.D.Rognlien, M.V.Umansky, X.Q.Xu, R.H.Cohen, L.L.LoDestro, Journal of Nuclear Materials, VOL. 337-339, 327-331 (2005).

J. Candy and R.E. Waltz, "Smoothness of Turbulent Transport Across a Minimum-q Surface", Phys. Plasmas 11 (2004) pp 1879-1891

F.L. Hinton, R.E. Waltz, and J. Candy, "Effect of Electromagnetic Turbulence in the Neoclassical Ohm's Law", Phys. Plasmas 11 (2004) pp2433-2440

C. Estrada-Mila, J. Candy, and R.E. Waltz, "Gyrokinetic Simulations of Ion and Impurity Transport", Phys. Plasmas 12 (2005) pp 22305-22318

J.E. Kinsey, R.E. Waltz, and J. Candy, "Nonlinear Gyrokinetic Turbulence Simulations of ExB Shear Quenching of Transport", Phys. Plasma 12 (2005) pp 062302-062310

R.E. Waltz and J. Candy, "Heuristic Theory of Nonlocally Broken Gyro-Bohm Scaling", Phys. Plasmas 12 (2005) pp 072303-072310

R.E. Waltz, J. Candy, F.L. Hinton, C. Estrada-Mila, and J.E. Kinsey, "Advances in Comprehensive GyroKinetic Simulations of Transport in Tokamaks", Nucl. Fusion 45 (2005) 741-750

R. E. Waltz, Rho-star Scaling and Physically, "Realistic Gyrokinetic Simulations of Transpiort in DIII-D", Fusion Science and Tecjhnology 48 (2005) pp 1051-1059

J. Candy, "Beta scaling of transport in microturbulence simulations", Phys. Plasmas 12 (2005) pp. 072307_

R. V. Bravenec and W. M. Nevins, A System for Direct Comparisons of Nonlinear Simulations of Turbulence with Measurements, to be published in Rev. Sci. Instrum. (2005).

"Studies of Improved Electron Confinement on NSTX," D. Stutman, K. W. Hill, S. M. Kaye, M. H. Redi, E. J. Synakowski, M. G. Bell, R. E. Bell, C. Bourdelle, W. Dorland, M. Finkenthal, S. Kubota, B. P. LeBlanc, F. Levinton, J. E. Menard, D. R. Mikkelsen, K. Tritz, and the NSTX Team,submitted to Nuclear Fusion, early version is available as paper EX/P2-8, IAEA Fusion Energy Conference, 1-6 November 2004, Vilamoura, Portugal.

"Transport modelling and gyrokinetic analysis of advanced high performance discharges", J.E. Kinsey, F. Imbeaux, G.M. Staebler, R. Budny, C. Bourdelle, A. Fukuyama, X. Garbet, T. Tala, V. Parail, for the ITPA Topical Group on Transport Physics and the ITB Database Working Group Nucl. Fusion 45 (2005) 450-458

B.I. Cohen, E.B. Hooper, R.H. Cohen, D.N. Hill, H.S. McLean, R.D. Wood, and S. Woodruff, C.R. Sovinec and G.A. Cone, Simulation of Spheromak Evolution and Energy Confinement, Phys. Plasmas 12, 056106 (2005)

E. B. Hooper, T. A. Kopriva, B. I. Cohen, D. N. Hill, H. S. McLean, R. D. Wood, S. Woodruff, C. R. Sovinec, A Magnetic Reconnection Event in a Driven Spheromak, accepted by Phys. Plasmas (Aug. 2005).

R.D. Wood, B.I. Cohen, D.N. Hill, S. Woodruff, H.S. McLean, E.B. Hooper, L.L. LoDestro, L.D. Pearlstein, D.D. Ryutov, B.W. Stallard, M.V. Umansky, C.T. Holcomb, T. Jarboe, C.R. Sovinec, and G.A. Cone, Improved Operation and Modeling of the SSPX Spheromak, 20th IAEA Fusion Energy Conference, Vilmoura, Portugal (Nov. 1-6, 2004), EX/C1-3.

D.D. Ryutov, B.I Cohen, R.H. Cohen, E.B. Hooper, The effect of artificial diffusivity on the flute instability, Phys. Plasmas 12, 084504 (2005).

Simulation of plasma fluxes to material surfaces with self-consistent edge turbulence and transport for tokamaks, T.D.Rognlien, M.V.Umansky, X.Q.Xu, R.H.Cohen, L.L.LoDestro, Journal of Nuclear Materials, Vol. 337-339, 327-331 (2005).

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, Physical Review Letters, Vol. 93, 265001-4 (2004).

Density Effects on Tokamak Edge Turbulence and Transport with Magnetic X-points, X.Q. Xu, R.H. Cohen, W.M. Nevins, T.D. Rognlien, D.D. Ryutov, M.V. Umansky, L.D. Pearlstein, R.H. Bulmer, D.A. Russell, J.R. Myra, D.A. D'Ippolito, M. Greenwald, P.B. Snyder, M.A. Mahdavi, 20th IAEA Fusion Energy Conference Vilamoura, Portugal, 1-6 November 2004, IAEA-CN-116/TH/1-5, (2004).

Convective Transport in Tokamaks, D. A. D'Ippolito, J. R. Myra, D. A. Russell, S. I. Krasheninnikov, A. Yu. Pigarov, G. Q. Yu, X. Q. Xu, and W. M. Nevins, 20th IAEA Fusion Energy Conference Vilamoura, Portugal, 1-6 November 2004, IAEA-CN-116/TH/P6-2, (2004).

Correlation of Density Pedestal Width and Neutral Penetration Length, X. Q. Xu, W. M. Nevins, R. H. Cohen, T. D. Rognlien, and M. V. Umansky, Contributions to Plasma Physics, Vol. 44, 105 - 110 (2004).

Turbulence in the Divertor Region of Tokamak Edge Plasma, M. V. Umansky, , T.D.Rognlien, X.Q.Xu, R.H.Cohen, and W. M. Nevins, Contributions to Plasma Physics , Vol. 44, 182 - 187 (2004).

Self-consistent simulation of turbulence and transport in tokamak edge plasmas, T. D. Rognlien, M.V.Umansky, X.Q.Xu, and R. H. Cohen, Contributions to Plasma Physics, Vol. 44, 188 - 193 (2004).

**PI Marvin Cohen**

R.B. Capaz, C.D. Spataru, P. Tangney, M.L. Cohen, and S.G. Louie, "Hydrostatic pressure effects on the structural and electronic properties of carbon nanotubes", Physica Status Solidi (b) 241, 3352 (2004).

A. Trave, F.J. Ribeiro, S.G. Louie and M.L. Cohen, "Energetics and structural characterization of C60 polymerization in BN and carbon Nanopeapods", Phys. Rev. B 70, 205418 (2004).

W.D. Luo, W.H. Duan, S.G. Louie and M.L. Cohen, "Structural and electronic properties of n-doped and p-doped SrTiO3", Phys. Rev. B 70, 214109 (2004).

P.H. Zhang, W.D. Luo, V.H. Crespi, M.L. Cohen and S.G. Louie, "Doping effects on the electronic and structural properties of CoO2 An LSDA U study", Phys. Rev. B 70, 085108 (2004)

V. Brouet, W.L. Yang, X.J. Zhou, H.J. Choi, S.G. Louie, M.L. Cohen, A. Goldoni, F. Parmigiani, Z. Hussain and Z.X. Shen, "Orientation- dependent C60 electronic structures revealed by photoemission spectroscopy", Phys. Rev. Lett. 93, 197601 (2004).

M. Ishigami, J.D. Sau, S. Aloni, M.L. Cohen, and A. Zettl, "Observation of the giant stark effect in boron nitride nanotubes", Phys. Rev. Lett. 94, 56804 (2005).

P.H. Zhang, S.G. Louie, and M.L. Cohen, "Nonlocal screening, electron-phonon coupling, and phonon renormalization in metals", Phys. Rev. Lett. 94, 225502 (2005).

P.H. Zhang, R.B. Capaz, M.L. Cohen, and S.G. Louie, "Theory of sodium ordering in NaxCoO2", Phys. Rev. B 71, 153102 (2005).

**PI John Cooke**

R. F. Klie, J. P. Buban, M. Varela, A. Francescheti, C. Jooss, Y. Zhu, N. D. Browning, S. T. Pantelids, and S. J. Pennycook, "Enhanced Current Transport at Grain Boundaries in High-Tc Superconductors", Nature 435, 475-478 (2005).

S. A. Chambers, J. R. Williams, M. A. Henderson, A. G. Joly, M. Varela, and S. J. Pennycook, "Structure, Band Offsets and Photochemistry at Epitaxial &alpha-Cr2O3/ &alpha-Fe2O3 Heterojunctions", Surface Science Letters 587, L197-L207, (2005).

Y. Yan, M. M. Al-Jassim, M. F. Chisholm, L. A. Boatner, S. J. Pennycook, and M. Oxley, "[1100] / [1102] Twin Boundaries in Wurtzite ZnO and Group-III-Nitrides"(PDF 373), Phys. Rev. B 71, 041301-0413094, (2005).

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).

M. Califano, A. Zunger, A. Franceschetti, "Efficient inverse Auger recombination at threshold in CdSe nanocrystals", Nano Letters 4, 525-531 (2004).

**PI Michael Cross**

Cross, Michael K.-H.Chiam, M.C.Cross, H.S.Greenside, and P.F.Fischer, "Transport of passive tracers by spiral defect chaos in Rayleigh-Benard convection", Phys. Rev. E71, 036205 (2005)

**PI Peter Cummings**

V. Meunier and B. Sumpter, Journal of Chemical Physics in press (2005).

J. Shin, V. Meunier, A. P. Baddorf, and S. V. Kalinin, Applied Physics Letters 85, 4240 (2004).

V. Meunier, S. V. Kalinin, J. Shin, A. P. Baddorf, and R. J. Harrison, Physical Review Letters 93 (2004).

A. Calzolari, C. Cavazzoni, and M. B. Nardelli, Physical Review Letters 93 (2004).

Y.-S. Li, M. Buongiorno Nardelli, and N. Marzari, Phys. Rev. Lett. in press (2005).

A. Ferretti, A. Calzolari, R. Di Felice, F. Manghi, M. J. Caldas, M. B. Nardelli, and E. Molinari, Phys. Rev. Lett. 94 (2005).

L. Guo and E. Luijten, Reversible gel formation of triblock copolymers studied by molecular dynamics simulation, J. Polym. Sci. Part B: Polym. Phys. 43, 959� (2005).

C. Zhang, M.-H. Du, H.-P. Cheng, X.-G. Zhang, A. E. Roitberg, and J. L. Krause, ''Coherent Electron Transport through an Azobenzene Molecule: A Light-Driven Molecular Switch,'' Phys. Rev. Lett. 92, 158301 (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, 1(4), 265-279 (2004).

A. Striolo, C. McCabe and P. T. Cummings, Thermodynamic and Transport Properties of Polyhedral Oligomeric Silsesquioxanes in Poly(Dimethyl Siloxane), Journal of Physical Chemistry B, 109 14300 - 14307 (2005).

Rivera, J. L., McCabe, C., and Cummings, P. T., The oscillatory damped behavior of incommensurate double-walled carbon nanotubes, Nanotechnology 16 (2005) 186-198.

Leng, Y. and Cummings, P. T., Fluidity of hydration layers nanoconfined between mica surfaces, Phys. Rev. Letts., 94 art. no. 026101 (2005).

Striolo, A., Chialvo, A. A., Gubbins, K. E. and Cummings, P. T., Water in carbon nanotubes: Adsorption isotherms and thermodynamic properties from molecular simulation, Journal of Chemical Physics 122 Art. No. 234712. (2005).

Paricaud, P., Predota, M., Chialvo, A. A. and Cummings, P. T., "From dimer to condensed phases at extreme conditions: Accurate predictions of the properties of water by a Gaussian charge polarizable model," Journal of Chemical Physics 122 Art. No. 244511 (2005).

Naicker, P. K., Cummings, P. T., Zhang, H., and Banfield, J. F., Characterization of Titanium Dioxide Nanoparticles Using Molecular Dynamics Simulations. J. Phys. Chem. B 109 (2005) 15243-15249.

A. Striolo, C. McCabe and P. T. Cummings, Effective Interactions between Polyhedral Oligomeric Sislesquioxanes Dissolved in normal Hexadecane from Molecular Simulation, Macromolecules, in press (2005).

**PI Larry Curtiss**

Mechanisms of lithium transport in amorphous polyethylene oxide Y. H. Duan, J. W. Halley, L. A. Curtiss, P. C. Redfern JOURNAL OF CHEMICAL PHYSICS 122 (5): Art. No. 054702 FEB 1 2005

A. S. Barnard, P. Zapol, L.A. Curtiss, Anatase and Rutile Surfaces with Adsorbates Representative of Acidic and Basic Conditions, Surf. Sci., 582 172 (2005).

A.S. Barnard, P. Zapol, L. Curtiss, Modeling the Morphology and Phase Stability of TiO2 Nanocrystals in Water, J. Chem. Theory. Comput. 1, 107-116 (2005).

A. Barnard , P. Zapol, Predicting the Energetics, Phase Stability and Morphology Evolution of Faceted and Spherical Anatase Nanocrystals, J. Phys. Chem. B 108, 18435 (2004).

## D

**PI Daniel D'Ippolito**

D'Ippolito, Daniel "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, Phys. Rev. Lett. 93, 265001 (2004).

"Edge instability regimes with applications to blob transport and the quasi-coherent mode," J. R. Myra and D. A. D'Ippolito, accepted for publication in Phys. Plasmas (2005).

**PI Valerie Daggett**

The Scientist. 19(7) April 11, 2005. Unraveling Protein Folding. p42

**PI Ronald Davidson**

"Kinetic Description of Neutralized Drift Compression and Transverse Focusing of Intense Ion Charge Bunches", R. C. Davidson and H. Qin, Physical Review Special Topics on Accelerators and Beams 8, in press (2005).

"Darwin Model for Intense Charged Particle Beams", E. A. Startsev, W. W. Lee and R. C. Davidson, Proceedings of the 2005 Particle Accelerator Conference, in press (2005).

"Nonlinear Delta-f Particle Simulations of Collective Effects in High-Intensity 3D Bunched Beams", H. Qin, R. C. Davidson and E. A. Startsev, Proceedings of the 2005 Particle Accelerator Conference, in press (2005).

"Anisotropy-Driven Collective Instabilities in Intense Charged Particle Beams", E. A. Startsev, R. C. Davidson and H. Qin, Proceedings of the 2005 Particle Accelerator Conference, in press (2005).

"Three- Dimensional Simulation Studies of Temperature Anisotropy Instability in Intense Charged Particle Beams ", E. A. Startsev, R.C. Davidson and H. Qin, Nuclear Instruments and Methods in Physics Research A544, 125 (2005).

"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 A544, 255 (2005).

"Chaotic Particle Trajectories in High-Intensity Finite-Length Charge Bunches", S.R. Hudson, H. Qin and R.C. Davidson, Nuclear Instruments and Methods in Physics Research A544, 458 (2005).

"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 A544, 353 (2005).

E.V. Belova, et al., Advances in the numerical modeling of field-reversed configurations, invited talk, 47th APS DPP Meeting, Denver CO, October 2005 (to be published in Phys. Plasmas 13, 2005).

E.V. Belova, R. C. Davidson, H. Ji, M. Yamada, Kinetic effects on the stability properties of field-reversed configurations: II. Nonlinear evolution, Phys. Plasmas 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 11, 2586 (2004).

E.D. Fredrickson, W.W. Heidbrink, C.Z. Cheng, N.N. Gorelenkov, E. Belova, A.W. Hyatt, G.J. Kramer, J. Manickam, J. Menard, R. Nazikian, T.L. Rhodes, and E. Ruskov, Study of aspect ratio efects on kinetic MHD instabilities in NSTX and DIII-D, Proceedings of the 20th Int. Conf. Vilamoura, 2004, paper IAEA-EX5-3, (International Atomic Energy Agency, Vienna, 2004).

E.V.Belova, R.C. Davidson, H. Ji, M. Yamada, C.D. Cothran, M.R. Brown, M.J. Schafer, Numerical study of the formation, ion spin-up and nonlinear stability properties of field-reversed configurations, Proceedings of the 20th Int. Conf. Vilamoura, 2004, paper IAEA-IC/P6-34 (International Atomic Energy Agency, Vienna, 2004).

S.P. Gerhardt, M. Yamada, H. Ji, E. Belova et al., FRC Studies via spheromak merging in the Magnetic Reconnection Experiment, Bull. Am. Phys. Soc. 49, 192, 2004.

M.R. Brown et al., Doublet CT studies at SSX-FRC, Bull. Am. Phys. Soc. 49, 192, 2004.

E.V. Belova et al., Conducting shell and energetic beam ion stabilization of the MHD modes in the FRC, Bull. Am. Phys. Soc. 49, 192, 2004.

**PI Eric DeWeaver**

DeWeaver, E., and C. M. Bitz, 2004: Atmospheric circulation and Arctic sea ice in CCSM3 at medium and high resolution. J. Climate, submitted to the special edition on the NCAR CCSM3.

DeWeaver, E., and S. Nigam. 2004: On the Forcing of ENSO Teleconnections by Anomalous Heating and Cooling. Journal of Climate: Vol. 17, No. 16, pp. 3225-3235.

**PI David Dean**

Coupled-cluster approach to nuclear physics, Phys. Rev. C69, 054320 (2004), D.J. Dean and M. Hjorth-Jensen

Coupled-cluster calculations of ground and excited states of nuclei, Phys. Rev. Lett. 92, 132501 (2004), K. Kowalski, D.J. Dean, M. Hjorth-Jensen, T. Papenbrock, and P. Piecuch

Effective interactions and the nuclear shell model, Prog. Part. Nucl. Phys. 53, 419 (2004), D.J. Dean, T. Engeland, M. Hjorth-Jensen, M.P. Kartamyshev, and E. Osnes.

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, Nucl. Phys. A747, 87 (2005)

Gamow-Teller GT distributions in nuclei with mass 90<=A<=97, A. Juodagalvis and D.J. Dean, Phys. Rev. C72, 024306 (2005)

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

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

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

Nuclear electron capture in core-collapse supernovae, W.R. Hix, O.E.B. Messer, A. Mezzacappa, J. Sampaio, K. Langanke, G. Martinez-Pinedo, M. Liebendoerfer, and D.J. Dean, Nucl. Phys. A758, 31 (2005).

**PI James Demmel**

E. J. Riedy. "Parallel Combinatorial Computing and Sparse Matrices," SIAM Computational Science and Engineering. February 2005.

J. Demmel, R. Vuduc, and K. Yelick. "The BeBOP Interface for a Self-Adapting Sparse Matrix Kernel Library," SIAM Computational Science and Engineering. February 2005.

**PI Stephen Derenzo**

Derenzo SE, Bourret-Courchesne E, Weber MJ and Klintenberg. MK. Scintillation studies of CdS(In): effects of codoping strategies. Nucl Instr Meth 2005; A537:261-265. (LBNL 55516)

Shah KS, Glodo J, Klugerman M, Higgins W, Gupta T, Wong P, Moses WW, Derenzo SE, Weber MJ and Dorenbos P. LuI3:Ce - a new scintillator for gamma ray spectroscopy. IEEE Trans Nucl Sci 2004; NS-51:2303-2305.

Moses WW, Choong WS, Derenzo SE, Bross AD, Dysert R and al. e. Observation of fast scintillation of cryogenic PbI2 with VLPCs. IEEE Trans Nucl Sci 2004; NS-51:2533-2536.

Klassen NV, Shmurak SZ, Shmyto IM, Strukova GK, Derenzo SE and Weber MJ. Structure and luminescence spectra of lutetium and yttrium borates synthesized from ammonium nitrate melt. Nucl Instr Meth 2005; A537:144-148.

Kurlov VN, Klassen NV, Dodonov AM, Shmurak SZ, Strukova GK, Shmyto IM, Derenzo SE and Weber MJ. Growth of YAG:Re3+ (Re=Ce, Eu) shaped crystals by the EFG/Stepanov technique. Nucl Instr Meth 2005; A537:197-199.

Shiran N, Gektin A, Neicheva S, Weber M, Derenzo S, Kirm M, True M., Shpinkov I, Spassk D, Shimamura K and Ichinose N. Energy transfer in pure and Ce-doped LiCaAlF6 and LiSrAlF6 crystals. Nucl Instr Meth 2005; A537:266-270.

Shmurak SZ, Strukova GK, Shmyto IM, Klassen NV, Kobelev NP, Derenzo SE and Weber MJ. Studies of nanocrystalline rare earth gallate and aluminate scintillators prepared by a new method. Nucl Instr Meth 2005; A537:149-153.

Qi J, Huber JS, Huesman RH, Moses WW, Derenzo SE, et al. Septa design for a prostate specific PET camera. IEEE Trans Nucl Sci 2005; NS-52:107-113.

**PI Tomas Diaz de la Rubia**

"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, Nucl. Instr. and Meth. Phys. Res. B 228, 163 (2005).

"Shock-induced void collapse in fcc metals", L. Davila, P. Erhart, E.M. Bringa, M.A. Meyers, V.A. Lubarda, M. Schneider, R. Becker and M. Kumar, Applied Physics Letters 86, 161902 (2005).

"Atomistic simulation of shocks in porous metals", P. Erhart, E. Bringa and M. Kumar, Phys. Rev. B, Phys. Rev. B 72, 052104 (2005).

"Classical Many-Body Potential for Concentrated Alloys and the Inversion of Order in Iron-Chromium Alloys", A. Caro, D. A. Crowson, and M. Caro, Phys. Rev. Lett. 95, 075702 (2005).

"Simulations of carbon sputtering in fusion reactor divertor plates", J. Marian, L. A. Zepeda-Ruiz, G. H. Gilmer, E. M. Bringa, and T. Rognlien, Physica Scripta, in press.

"High-Energy Ion Tracks in Thin Films", D.M. Follstaedt, A.K. Norman, P. Rossi, B.L. Doyle, F.D. McDaniel and E.M. Bringa, Nucl. Instr. and Meth. in Phys. Res. B, in press.

"Thermodynamics of Fe-Cu Alloys as Described by a Classic Potentials", A. Caro, M. Caro, E. M. Lopasso, P. E. A. Turchi, and D. Farkas, accepted in J. Nucl. Mater.

"Atomistic simulation of grain boundary pinning in CuFe alloys", L.A. Zepeda-Ruiz, G.H. Gilmer, B. Sadigh, A. Caro, and T. Oppelstrup, accepted in Appl. Phys. Lett.

"Wave propagation in polycrystals", E.M. Bringa, A. Caro, M. Victoria and N. Park, Journal of Metals, September 2005, in press.

"Ultra-hard nanocrystalline metals by shock loading", E.M. Bringa et al., Science, 2005, in press.

"Shock deformation of fcc metals on sub-nanosecond time scales", E. M. Bringa et al., considered for publication in Nature.

**PI Dimitre Dimitrov**

D. A. Dimitrov, D. L. Bruhwiler, J. R. Cary, P. Messmer, P. Stoltz, Kevin L. Jensen, Donald W. Feldman, and Patrick G. O'Shea, Development of Advanced Models for 3D Photocathode PIC Simulations, to appear in the Proceedings of the 2005 Particle Accelerator Conference (2005).

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

**PI Chris Ding**

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

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

**PI Julie Ditri**

V. Y. Borovkov, S. P. Kolesnikov, V. I. Kovalchuk, J. L. d'Itri, "Probing Adsorption Sites of Silica-Supported Platinum with 13C16O 12C16O and 13C18O 12C16O Mixtures. A Comparative FTIR Investigation." Journal of Physical Chemistry B, in press.

V. I. Avdeev, V. I. Kovalchuk, G. M. Zhidomorov, J. L. d'Itri, "Ethylene Adsorption on the Pt-Cu Bimetallic Catalysts. Density Functional Theory Cluster Study." Surface Science, 583 (2005) 46-59.

W. D. Rhodes, J. L. Margitfalvi, I. Borbath, K. Lazar, V. I. Kovalchuk, J. L. d'Itri, "Hydrogen-Assisted 1,2-Dichloroethane Dechlorination Catalyzed by Pt-Sn/SiO2 Catalysts of Different Preparations." Journal of Catalysis, 230 (2005) 86-97.

**PI Sebastian Doniach**

W.J. Zheng, S. Doniach. A comparative study of motor-protein motions by using a simple elastic-network model. Proc. Nat. Acad. Sci. (U.S.A.) 100.23: 13253-13258 (November 11, 2003).

Y. Bai, R. Das, D. Herschlag, S. Doniach. Probing Counterion Modulated Repulsion and Attraction Between Nucleic Acid Duplexes in Solution. Proc. Nat. Acad. Sci. U.S.A. 102.4: 1035-1040 (January 25, 2005.

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

**PI William Dorland**

K. Hallatschek and W. Dorland, Giant Electron Tails and Passing Electron Pinch Effects in Tokamak-Core Turbulence, Phys. Rev. Lett. 95, 055002 (2005).

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

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

D. J. Applegate et al., Microstability in a ``MAST-like'' high confinement mode spherical tokamak equilibrium, Phys. Plasmas 11, 5085 (2004).

B. D. Jemella, J. F. Drake and M. A. Shay, Singular structure of magnetic islands resulting from reconnection, Phys. Plasmas 11, 5668, 2004.

J. F. Drake, M. Swisdak, W. Thongthai and M. A. Shay, Production of energetic electrons during magnetic reconnection, Phys. Rev. Lett. 94, 095001, 2005.

M. Swisdak, J. F. Drake, J. G. McIlhargey, and M. A. Shay, The transition from anti-parallel to component magnetic reconnection, J. Geophys. Res. 110, A05210, 2005.

P. Cassak, M. A. Shay and J. F. Drake, A catastrophe model for the onset of fast magnetic reconnection, Phys. Rev. Lett. submitted 2005.

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

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

R. G. Kleva and P. N. Guzdar, Ballooning mode stability in high beta tokamaks with a q=1 magnetic island, Phys. Plasmas 11, 4983 (2004).

R. G. Kleva, P. N. Guzdar and W. Dorland, Edge transport and the low-to-high transition in tokamaks with D-shaped magnetic flux surfaces, Phys. Plasmas 11, 4280 (2004).

**PI German Drazer**

Hysteresis, force oscillations and non-equilibrium effects in the adhesion of spherical nanoparticles to atomically smooth surfaces, G. Drazer, B. Khusid, J. Koplik and A. Acrivos, Phys. Rev. Lett. 95 016102 (2005)

Wetting and particle adsorption in nanoflows, G. Drazer, B. Khusid, J. Koplik and A. Acrivos, Phys. Fluids 17 017102 (2005)

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

Permeability anisotropy induced by the shear displacement of rough fracture walls, H. Auradou, G. Drazer, J. P. Hulin, and J. Koplik, Water Resources Research 41, W09423 (2005)

Self-Affine Fronts in Self-Affine Fractures: Large and Small-Scale Structure, G. Drazer, J. Koplik, H. Auradou and J.P. Hulin, Phys. Rev. Lett. 92, 014501 (2004).

**PI Philip Duffy**

J. Iorio, 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; Climate Dynamics, 23, 243-258, 2004.

**PI Thomas Duguet**

M. Bender, G. F. Bertsch, P.-H. Heenen, Phys. Rev. Lett. 94 (2005) 102503

M. Bender, P. Bonche, T. Duguet, and P.-H. Heenen, Phys. Rev. C 69 (2004) 064303

T. Duguet, Phys. Rev. C 69, 054317 (2004)

## E

**PI Charlotte Elster**

Three-Body Scattering without Partial Waves, H. Liu, Ch. Elster, W. Gloeckle, AIP Conference Proceedings, Vol. 768, p. 430, NY 2005 (invited contribution)

**PI Eric Esarey**

C.G.R. Geddes, Cs. Toth, J. van Tilborg, E. Esarey, C.B. Schroeder, J.R. Cary and W.P. Leemans, "Guiding of Relativistic Laser Pulses by Preformed Plasma Channels," Phys. Rev. Lett., accepted (2005).

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

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

C.G.R. Geddes, Cs. Toth, J. van Tilborg, E. Esarey, C.B. Schroeder, D.L. Bruhwiler, C. Nieter, J.R. Cary and W.P. Leemans, "High-quality electron beams from a laser wakefield accelerator using plasma-channel guiding," Nature 431 (2004), p. 538.

P. Messmer and D.L. Bruhwiler, "A parallel electrostatic solver for the VORPAL code," Comp. Phys. Comm. 164 (2004), p. 118.

## F

**PI Roland Faller**

Q. Sun, R. Faller J Phys Chem B 109,15714 (2005) Molecular Dynamics of a Polymer in Mixed Solvent: Atactic Polystyrene in a Mixture of Cyclohexane and N,N-Dimethylformamide

**PI William Fawley**

A.A. Zholents et al., "CURRENT-ENHANCED SASE USING AN OPTICAL LASER AND ITS APPLICATION TO THE LCLS", Proceedings of the 2004 FEL Conference, pp. 582-585.

A.H. Lumpkin, W.M. Fawley, and D.W. Rule, "A CONCEPT FOR Z-DEPENDENT MICROBUNCHING MEASUREMENTS WITH COHERENT X-RAY TRANSITION RADIATION IN A SASE FEL", Proceedings of the 2004 FEL Conference, pp. 515-518.

**PI Andrew Felmy**

E.J. Bylaska, M. Dupuis, and P.G. Tratnyek (2005) Ab Initio Electronic Structure Study of One-Electron Reduction of Polychlorinated Ethylenes, J. Phys. Chem. A, vol. 109, 5905-5916.

T.W. Swaddle, J. Rosenqvist, P. Yu, E. Bylaska, B.L. Phillips, W.H. Casey (2005) Kinetic Evidence for Five-Coordination in AlOH(aq)2+ Ion, Science, vol. 308, 1450-1453.

E.J. Bylaska, D.A. Dixon, A.R. Felmy, E. Apra, T.L. Windus, C.-G. Zhan, and P.G. Tratnyek (2004) The Energetics of the Hydrogenolysis, Dehydrohalogenation, and Hydrolysis of 4,4'-Dichloro-diphenyl-trichloroethane from ab initio Electronic Structure Theory, J. Phys. Chem A, vol 108, 5883-5893.

R. Miehr, P.G. Tratnyek, J.Z. Bandstra, M.M. Scherer, M.J. Alowitz, and E.J Bylaska (2004) Diversity of Contaminant Reduction Reactions by Zerovalent Iron: Role of the Reductate, Environ. Sci. Technol., vol. 38, 139-147.

**PI Graham Fleming**

Two-dimensional spectroscopy of electronic couplings in photosynthesis, T. Brixner, J. Stenger, H. M. Vaswani, M. Cho, R. E.Blankenship and G. R.Fleming, Nature, 434, 625 (2005).

Exciton Analysis in 2D Electronic Spectroscopy, M. Cho, H. M. Vaswani, T. Brixner, J. Stenger and G. R. Fleming, J. Phys. Chem. B, 109, 10542 (2005).

Carotenoid Cation Formation and the Regulation of Photosynthetic Light Harvesting, N.E. Holt, D. Zigmantas, L. Valkunas, X-P. Li, K. K. Niyogi and G. R. Fleming, Science, 307, 433-436 (2005).

Electronic Couplings and Energy Transfer Dynamics in the Oxidized Primary Electron Donor of the Bacterial Reaction Center, X. J. Jordanides, G. D. Scholes, W. A. Shapley, J. R. Reimers, and G. R. Fleming. J. Phys. Chem. B., 108, 1753-1765 (2004).

The Mechanism of Energy Transfer and Trapping in Photosystem I, H. M. Vaswani, M. Yang, A. Damjanovic, and G. R. Fleming. Femtochemistry and Femtobiology, Ultrafast Events in Molecular Science, eds. M.M. Martin and J. T. Hynes, Elsevier, 401-408 (2004).

Toward an Understanding of the Mechanism of Nonphotochemical Quenching in Green Plants, N. E. Holt, G. R. Fleming, and K. K. Niyogi. Biochem. 43, 8281-8289 (2004).

Quantum Mechanics for Plants, G. R. Fleming and G. D. Scholes. News and Views, Nature, 256-257 (2004).

Femtosecond Fluorescence Upconversion Studies of Light Harvesting by Beta Carotene in Oxygenic Photosynthetic Core Proteins, N.E. Holt, J.T.M. Kennis, and G.R. Fleming. J Phys Chem B. 108, 19029-19035 (2004).

The Design of Natural Photosynthetic Antenna Systems, H.M. Vaswani, N.E. Holt and G.R. Fleming. In Artificial Photosynthesis, Chapter 4. ed. A. Collings, Wiley VCH, 67-85 (2005).

Lord George Porter Medal Lecture: Carotenoid-Chlorophyll Complexes: Ready-to- Harvest, N.E Holt, H.M. Vaswani, and G.R. Fleming, Pure and Applied Chemistry (IUPAC), 77, 925-945 (2005).

**PI Ching-Yao Fong**

M. C. Qian, C. Y. Fong, L. H. Yang, J. E. Pask, and S. Dag, 'Spin-polarized ballistic transport channel in a thin superlattice composed of half-metallic compound with zinc-blende structure', Phys. Rev. B71, 12414 (2005).

S. Tongay, S. Dag, E. Durgun, R. T. Senger, C. Y. Fong, and S. Ciraci, 'Half-metallic propertie of linear chains composed og silicon- and corbon-transitional metel compounds', to appear in Phys. Rev. B.

C. Y. Fong, M. C. Qian, 'Digital ferromagnetic heterostructure composed of Mn in Si', Bull. Am. Phys. Soc. 50, 1055 (2005).

C. Y. Fong, M. C. Qian, W. Pickett, 'Spin-polarized ballistic transport in a thin superlattice of zincblende half metallic compounds', Bull. Am. Phys. Soc. 50, 1380 (2005).

**PI Michael Fox-Rabinovitz**

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

Park, R. J., K. E. Pickering, D. J. Allen, G. L. Stenchikov, M. S. Fox-Rabinovitz, 2004: Global simulation of tropospheric ozone using the University of Maryland Chemical Transport Model (UMD-CTM) 1. Model description and evaluation, J. Geophys. Res., 109, D09301, doi:10.1029/2003JD004266.

Park, R. J., K. E. Pickering, D. J. Allen, G. L. Stenchikov, and M.S. Fox-Rabinovitz, 2004: Global simulation of tropospheric ozone using the University of Maryland Chemical Transport Model (UMD-CTM): 2. Regional downscaling of transport and chemistry over the Central United States. J. Geophys. Res., v. 109, D09303.

Allen, D. J., K. E. Pickering, and M. Fox-Rabinovitz, 2004: Evaluation of pollutant outflow and CO sources during TRACE-P using model-calculated, aircraft-based, and MOPITT-derived CO concentrations, J. Geophys. Res., vol. 109, D15S03, doi:10.1029/2003JD2003004250.

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

**PI Alberto Franceschetti**

A. Franceschetti and M.C. Troparevsky, "Screening of point charges in Si quantum dots", Phys. Rev. B (in press).

R.F. Klie, J.P. Buban, M. Varela, A. Franceschetti, C. Jooss,Y. Zhu, N.D. Browning, S.T. Pantelides, and S.J. Pennycook, "Enhanced current transport at grain boundaries in high-Tc superconductors", Nature 435, 475 (2005).

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).

**PI Stuart Freedman**

"Measurement of Neutrino Oscillation with KamLAND: Evidence for Spectral Distortion", KamLAND Collaboration, Phys. Rev. Lett. 94, 081801 (2005).

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

"Results from KamLAND", A. Suzuki for the KamLAND collaboration, Nucl. Phys. Proc. Suppl. 137, 21 (2004).

"KamLAND: Updated results", K. Inoue for the KamLAND collaboration, Nucl. Phys. Proc. Suppl. 145, 11 (2005).

"The KamLAND anti-neutrino oscillation experiment", J. Maricic and J.G. Learned for the KamLAND collaboration, Contemp. Phys. 46, 1 (2005).

"Measurement of reactor anti-nu/e oscillation with KamLAND", A. Kozlov for the KamLAND collaboration, Nucl. Phys. Proc. Suppl. 149, 131 (2005).

**PI Arthur Freeman**

Pressure effects on the electronic properties and superconductivity of the ?-pyrochlore oxides: AOs2O6 (A=Na, K, Rb, Cs) (R. Saniz and A. J. Freeman) Phys. Rev. B 72, 024522 (2005).

Tunable Conductivity and Conduction Mechanism in a UV light activated electronic conductor (M. I. Bertoni, T. O. Mason, J. E. Medvedeva, A. J. Freeman, K. R. Poeppelmeier, and B. Delley), Journal of Applied Physics 97, 103713 (2005).

Combining high conductivity with complete optical transparency: A band-structure approach (J.E. Medvedeva, and A.J. Freeman), Europhysics Letters 69, 583 (2005).

Hopping versus bulk conductivity in transparent oxides: 12CaO.7Al2O3 (J.E. Medvedeva, and A.J. Freeman), Applied Physical Letters 85, 955 (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).

**PI Alex Friedman**

R. H. Cohen, A. Friedman, A. W. Molvik, A. Azevedo, M. A., Furman, J.-L. Vay, P. Stoltz, "Simulating Electron Cloud Effects in Heavy-Ion Accelerators," Nuclear Instruments and Methods in Physics Research A 544, 210 (2005).

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

A. Friedman, "Simulation of Intense Beams for Heavy Ion Fusion," Nuclear Instruments and Methods in Physics Research A 544, 160 (2005).

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

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

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

W. M. Sharp, D. A. Callahan, M. Tabak, S. S. Yu, P. F. Petersen, D. V. Rose, D. R. Welch, "Chamber-Transport Simulation Results for Heavy-Ion Fusion," Nucl. Fusion 44, S221-S227, (2004).

J.-L. Vay, P. Colella, P. McCorquodale, D. B. Serafini, B. Van Straalen, A. Friedman, D.P. Grote, J.-C., Adam, A. H. H'eron, "Application of Adaptive Mesh Refinement to Particle-In-Cell Simulations of Plasmas and Beams", Phys. Plasmas 11, 2928-2934, (2004).

J.-L. Vay, P. Colella, A. Friedman, D. P. Grote, P. McCorquodale, D. B. Serafini, "Implementations of Mesh Refinement schemes for Particle-In-Cell Plasma Simulations", Comput. Phys. Commun. (in press, 2005).

E. Sonnendrucker, F. Filbet, A. Friedman, E. Outdet, J.-L.Vay, "Vlasov simulations of beams with a moving grid," Comput. Phys. Commun. (in press, 2005).

**PI Charlotte Froese-Fischer**

Breit-Pauli energy levels, transition probabilities and lifetimes for 3d5 levels in Fe IV of astrophysical interest C. Froese Fischer and R. H. Rubin Mon. Not. Royal Astron. Soc. 355 461-474 (2004): erratum ibid 355 1400 (2004).

Angular integrations using symbolic state expansions C. Froese Fischer and D. Ellis Lithuanian J. Physics 44 121-134 (2004)

Breit-Pauli oscillator strengths, lifetimes and Einstein A-coefficients in singly ionized sulphur Physica Scripta 72 172-184 (2005)

Breit-Pauli lifetimes and transition probabilities for Si I C. Froese Fischer Physical Review A 71 042506 (2005)

Relativistic calculations for highly charged ions C. Froese Fischer Nucl. Inst. Meth. Phys. Res. B: 235 100-104 (2005)

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

**PI Inez Fung**

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

Bonfils, C., I. Fung, S.C. Doney and J. John (2004). "On the detection of summertime terrestrial photosynthetic variability from its atmospheric signature". Geophys. Res. Lett., 31 L09207, doi:10.1029/2004GL019453.

Angert, A., S. Biraud, C. Bonfils, W. Buermann, and I. Fung (2004). "CO2 seasonality indicates origins of post-Pinatubo sink". Geophysical Res. Lett. 31, L11103, doi:10.1029/2004GL019760.

Lintner, B., A. Gilliland, I. Fung (2004). "Mechanisms of convection-induced modulation of passive tracer interhemispheric transport interannual variability". J. Geophys. Res., 109, doi:10.1029/2003JD004306.

Bonfils C, A. Angert, C.C. Henning, S. Biraud, S.C. Doney and I. Fung. "Extending the record of photosynthetic activity in the eastern United States into the presatellite period using surface diurnal temperature". Geophysical Research Letters 32 (8): Art. No. L08405 APR 26 2005

Angert, A., Sebastien Biraud , Celine Bonfils , Cara Henning , Wolfgang Buermann , Jorge Pinzon , Compton Tucker , Inez Fung (2005). "Drier summers cancel out the CO2 uptake enhancement induced by warmer springs". Proc. Nat. Acad. Sci. (USA), 102, 10823-10827.

## G

**PI Giulia Galli-Gygi**

Theoretical study of biotin adsorption on the clean and hydroxylated Si-SiC(001) surface, Y.Kanai, G.Cicero, A.Selloni, R.Car and G.Galli, J.Phys.Chem.B 109, 13656 (2005).

Growth of carbon nanotubes on iron nanoparticle : microscopic mechanism from a- initio molecular dynamics, J.-Y. Raty, F,Gygi and G.Galli , Phys.Rev.Lett. 95, 096103 2005 (in press). [Article featured on the cover].

Water at a hydrophilic solid surface probed by first principles molecular dynamics: inhomogeneous, thin layers of dense fluid, G.Cicero, J.Grossman, A.Catellani and G.Galli, J.Amer.Chem.Soc.127, 6830 (2005).

Theory of alkyl-terminated silicon quantum dots, F.Reboredo and G.Galli, J.Phys.ChemB. 109, 1072 (2005).

"Doping the undopable", G.Galli, Nature 436, 32 (2005).

"The electronic structure of water within Density Functional Theory", D.Prendergast, J.Grossman, and G.Galli, J.Chem.Phys. 123, 014501 (2005).

"First principles studies of nanodiamond opctical and electronic properties", J.-Y.Raty and G.Galli, Comp. Phys.Comm. 169, 14 (2005).

**PI Alan Garfinkel**

Fukumoto, G. H., S. T. Lamp, C. Motter, J. H. Bridge, A. Garfinkel and J. I. Goldhaber (2005). Metabolic inhibition alters subcellular calcium release patterns in rat ventricular myocytes: implications for defective excitation-contraction coupling during cardiac ischemia and failure. Circ Res 96(5): 551-7.

Weiss, J. N., Z. Qu, P. S. Chen, S. F. Lin, H. S. Karagueuzian, H. Hayashi, A. Garfinkel and A. Karma (2005). The dynamics of cardiac fibrillation. Circulation 112(8): 1232-40.

Wu, T. J., S. F. Lin, A. Baher, Z. Qu, A. Garfinkel, J. N. Weiss, C. T. Ting and P. S. Chen (2004). Mother rotors and the mechanisms of D600-induced type 2 ventricular fibrillation. Circulation 110(15): 2110-8.

Submitted to Circulation: Fagen Xie, Zhilin Qu, Carin Siegerman, Marta Vakulenko, Kalyanam Shivkumar, James N. Weiss and Alan Garfinkel: The Effects of Atrial Anatomy on Human Atrial Fibrillation: a Simulation Study.

**PI Bruce Garrett**

B.S. Thomas, N.A. Marks, L.R. Corrales and R. Devanathan, "Threshold displacement energies in rutile TiO2: A molecular dynamics simulation study", Nucl. Instr. and Meth. B (in press).

L.R. Corrales and R. Devanathan, 'Characterization of Energy Conservation in Primary

S. S. Xantheas, E. Apra, J. Chem. Phys. 120, 823 (2004).

G. S. Fanourgakis, E. Apra and S. S. Xantheas, J. Chem. Phys. 121, 2655 (2004).

**PI Steven Ghan**

Ghan, S. J., and T. Shippert, 2005: Load balancing and scalability of a subgrid orography scheme in a global climate model. Int. J. High Performance Comput. Appl., in press.

Ghan, S. J., T. Shippert, and J. Fox, 2005: Physically-based global downscaling: Regional evaluation. J. Climate, accepted.

**PI Ahmed Ghoniem**

Y. M. Marzouk, A. F. Ghoniem, and D. Wee. Simulations of high Reynolds number transverse jets and analysis of the underlying vortical structures. 43rd AIAA Aerospace Sciences Meeting Conference and Exhibit, Reno, Nevada, Jan 2005.

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

R. Speth, Y. M. Marzouk, and A. F. Ghoniem, Impact of hydrogen addition on flame response to stretch and curvature. 43rd AIAA Aerospace Sciences Meeting and Exhibit, Reno, NV, Jan 2005.

R. Speth, Y. M. Marzouk, and A. F. Ghoniem, A quasi-one-dimensional unsteady laminar flame formulation with independent strain rate and curvature. 3rd MIT Conference on Computational Fluid and Solid Mechanics, Cambridge, MA, Jun 2005.

Y. M. Marzouk and A. F. Ghoniem. K-means clustering for partition and dynamic load balance of parallel hierarchical N-body simulation. Journal of Computational Physics. 207:493-528 (2005)

Y. M. Marzouk and A. F. Ghoniem. Vorticity structure and evolution in a transverse jet. Submitted to Journal of Fluid Mechanics.

D. Wee and A. F. Ghoniem. Modified interpolation kernels for treating diffusion and remeshing in vortex methods. Journal of Computational Physics. (In print)

**PI James Glimm**

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

Shock Wave Interactions in Spherical and Perturbed Spherical Geometries, 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, Nonlinear Analysis, Elsevier, 2004, In press.

Jet Simulation in a Diesel Engine, James Glimm, M.-N. Kim, X.-L. Li, R. Samulyak and Z.-L. Xu, MIT Conference on Computational Fluid and Solid Mechanics, Elsevier Science, In press, 2004.

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

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

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

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

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

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

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

J. Glimm, S. Hou, Y. Lee, D. Sharp, and K. Ye, Sources of Uncertainty and Error in the Simulation of Flow in Porous Media, Comp., Applied Mathematics, 2004, 23, 109--120.

J. Glimm, H. Jin, and Y. Zhang, Front Tracking for Multiphase Fluid Mixing, Computational Methods in Multiphase Flow II, 2004, 13--22, A. A. Mammoli, C. A. Brebbia, WIT Press, Southampton, UK.

J. Glimm, X.-L. Li, and Z.-L. Xu, Front Tracking Algorithm Using Adaptively Refined Meshes, Proceedings of the 2003 Chicago Workshop on adaptive Mesh Refinement Methods, the Lecture Notes in Computational Science and Engineering, ISSN: 1439-7358, 2004. T. Lu, R. Samulyak, and J. Glimm, Direct Numerical Simulation of Bubbly Flows and its Applications, Phys. Fluids, 2004.

Z. L. Xu, M. Kim, W. Oh, J. Glimm, R. Samulyak, X. L. Li, and C. Tzanos, Atomization of a High Speed Jet, Physics of Fluids, in press, 2005

Y. Zhang, J. Glimm, and S. Dutta, Tracked Flame Simulation for Type Ia Supernova, bookProceeding of Third MIT Conference, 2005, Elsevier, accepted.

**PI Yousry Gohar**

Yousry Gohar, Blanket Design And Optimization Demonstrations Of The First Wall/Blanket/Shield Design And Optimization System (BSDOS), Fusion Technology Volume 48, May 2005

**PI Yadin Goldschmidt**

``Flux melting in BSCCO: Incorporating both electromagnetic and Josephson couplings'', S. Tyagi and Y. Y. Goldschmidt, Phys. Rev. B 70, 024501 (2004).

``String solutions to the 2D Sine-Gordon equation: Application to the Josephson interaction in high-temperature superconductors'', Y. Y. Goldschmidt and S. Tyagi, Phys. Rev. B 71, 014503 (2005).

``Molecular dynamics of pancake vortices with realistic interactions: Observing the vortex lattice melting transition'', Y. Y. Goldschmidt, Phys. Rev. B 72, 064518 (2005).

**PI Balasubraman Govindasamy**

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, 23, 243-258.

Govindasamy, B., S. Thompson, A. Mirin, M. Wickett, K. Caldeira, C. Delire, 2005: Increase of carbon-cycle feedback with climate sensitivity: Results from a coupled climate and carbon cycle model, Tellus, 57(B), 153-163.

G. Bala, A. Mirin, M. Wickett, K. Caldeira, C. Delire, 2005: Multi-century changes to global climate and carbon cycle: Results from a coupled climate and carbon cycle model, J. Climate (in press)

Oliker, L., J. Carter, M. Wehner, A. Canning, S. Ethier, B. Govindasamy, A. Mirin, D. Parks, 2005: Leading computational methods on scalar and vector platforms, SC 2005 High Performance computing, networking, and storage conference, Seatle, Washington, Nov., 2005.

Thompson, S.., B. Govindasamy and coauthors, 2004: Quantifying the effects of Co2-fertilized vegetation on future global climate and carbon dynamics, Geophys. Res. Lett., 31, L23211.

**PI Stephen Gray**

Controlled spatiotemporal excitation of metal nanoparticles with chirped optical pulses T.-W. Lee and S. K. Gray, Phys. Rev. B, 71, 035423 (1-9) (2005).

Near-field photochemical imaging of noble metal nanostructures C. Hubert, A. Rumyantsev, G. Lerondel, J. Grand, S. Kostcheev, L. Billot, A. Vial, R. Bachelot, P. Royer, S.-H. Chang, S. K. Gray, G. P. Wiederrecht, and G. C. Schatz, Nano Letters 5, 615-619 (2005).

An OpenMP/MPI approach to the parallelization of iterative four-atom quantum mechanics D. M. Medvedev, E. M. Goldfield, and S. K. Gray, Comp. Phys. Comm. 166, 94-108 (2005).

Regenerated surface plasmon polaritons T.-W. Lee and S. K. Gray, Appl. Phys. Lett., 86, 141105 (3 pages) (2005).

Surface plasmon generation and light transmission by isolated nanoholes and arrays of nanoholes in thin metal films S.-H. Chang and S. K. Gray, Optics. Express, 13, 3151 -3165 (2005).

Fourier spectral simulations and Gegenbauer reconstructions for electromagnetic waves in the presence of a metal nanoparticle M. S. Min, T.-W. Lee, P. F. Fischer, and S. K. Gray, J. Comp. Phys., in press (2005).

Methyl radical: ab initio global potential energy surface, vibrational levels, and partition function D. M. Medvedev, L. B. Harding, and S. K. Gray, Mol. Phys., in press (2005).

Surface plasmon waves in large-area subwavelength hole arrays E.-S. Kwak, J. Henzie, S.-H. Chang, S. K. Gray, G. C. Schatz, and T. W. Odom, Nano Letters, in press (2005).

**PI Chris Greene**

"Theoretical study of dissociative recombination of C_2v triatomic ions: application to H2D and D2H . V. Kokoouline and C.H. Greene accepted for publication in Phys. Rev. A

"Theoretical study of the H3 ion dissociative recombination process. Review." V. Kokoouline and C.H. Greene J. Phys.: Conf. Ser. 4: 74-82 (2005)

"Electron-molecule scattering calculations in a 3D finite element R-matrix approach" S. Tonzani and C. H. Greene J. Chem. Phys. 122, 014111 (2005)

"Low energy electron scattering from DNA and RNA bases: shape resonances and radiation damage" S. Tonzani and C. H. Greene J. Chem. Phys. submitted

**PI Keith Gubbins**

A. Striolo, K. E. Gubbins, T. D. Burchell, J. M. Simonson, D. R. Cole, M. S. Gruszkiewicz, A. A. Chialvo and P. T. Cummings, "Temperature Effect on Water Adsorption in Porous Carbons, Langmuir, accepted (2005)

A. Striolo, C. McCabe, and P. T. Cummings, "Effective Interactions between Polyhedral Oligomeric Silsesquioxanes in Hexadecane from Molecular Simulation", Macromolecules, accepted (2005)

B. Coasne, F. R. Hung, R. J.�M. Pellenq, F. R. Siperstein, and K. E. Gubbins, "Adsorption of simple gases in MCM-41 materials: the role of surface roughness", Langmuir, accepted (2005)

F. R. Hung, B. Coasne, K. E. Gubbins, F. R. Siperstein, and M. Sliwinska-Bartkowiak, "A Monte Carlo study of capillary condensation of krypton within realistic models of templated mesoporous silica materials", Stud. Surf. Sci. Catal., accepted (2005)

B. Coasne, J. Czwartos, K. E. Gubbins, F. R. Hung and M. Sliwinska-Bartkowiak, "Confinement effect on freezing of binary mixtures", Stud. Surf. Sci. Catal., accepted (2005)

J. Czwartos, B. Coasne, K. E. Gubbins, F. R. Hung and M. Sliwinska-Bartkowiak, "Freezing and melting of azeotrope mixtures confined in nanopores: experiment and molecular simulation", Mol. Phys. 103, 3103 (2005)

F. R. Hung, B. Coasne, E. E. Santiso, K. E. Gubbins, F. R. Siperstein and M. Sliwinska-Bartkowiak, "Molecular modeling of freezing of simple fluids confined within carbon nanotubes", J. Chem. Phys. 122, 144706 (2005)

M. Sliwinska-Bartkowiak, F. R. Hung, E. E. Santiso, B. Coasne, F. R. Siperstein and K. E. Gubbins, "Effect of confinement on freezing of CCl4 in cylindrical pores", Adsorption 11, 391 (2005)

A. Striolo, C. McCabe and P. T. Cummings, "Thermodynamic and transport properties of polyhedral oligomeric sislesquioxanes in poly(dimethylsiloxane)", J. Phys. Chem. B 109, 14300 (2005)

A. Striolo, A. A. Chialvo, K. E. Gubbins and P. T. Cummings, "Water in carbon nanotubes: Adsorption isotherms and thermodynamic properties from molecular simulation", J. Chem. Phys. 122, 234712 (2005)

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 11, 397 (2005)

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 11, 337 (2005)

**PI Maciej Gutowski**

I.N. Yakovkin, M. Gutowski, The SrTiO3/Si(001) Epitaxial Interface: A Density Functional Theory Study, Phys. Rev. B, 70, 165319, (2004).

A. Gutowska, L. Li, Y. Shin, Ch. Wang, S. Li, J. Linehan, R. Scott Smith, B. Kay, B. Schmid, W. Shaw, M. Gutowski, and T. Autrey, Nano-Scaffold Mediates Hydrogen Release and Reactivity of Ammonia Borane, Angew. Chem. Int. Ed., 44, 2, (2005).

D. A. Dixon, M. Gutowski, Thermodynamic Properties of Molecular Borane Amines, BH4-, and NH4+ for Chemical Hydrogen Storage Systems from Ab Initio Electronic Structure Theory, J. Phys. Chem. A., 109, 5129, (2005).

M. Gutowski, T. Autrey, J. Linehan, Favorable Energetics of Hydrogen Release and Uptake in the NHxBHx Compounds (x=4-1). A Density Functional Theory Study, J. Phys. Chem. B, accepted for publication.

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, 157, (2004).

M. Haranczyk, M Gutowski, Valance and Dipole-Bound Anions of the Most Stable Tautomers of Guanine, J. Am. Chem. Soc., 127, 699, (2005).

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., 127, 2238, (2005).

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, 157, (2004).

M. Haranczyk, M Gutowski, Valance and Dipole-Bound Anions of the Most Stable Tautomers of Guanine, J. Am. Chem. Soc., 127, 699, (2005).

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., 127, 2238, (2005).

D. Radisic, K.H. Bowen, Jr., I. Dabkowska, P. Storoniak, J. Rak, M. Gutowski, The AT Base Pair Anion vs. (9-methyl-A)(1-methyl-T) Base Pair Anion, J. Am. Chem. Soc., 127, 6443, (2005).

R. Bachorz, J. Rak, M. Gutowski, Stabilization of Very Rare Tautomers of Uracil by an Excess Electron, Phys. Chem. Chem. Phys., 7, 2116, (2005).

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 a pi* Excess Electron, J. Chem. Phys., 122, 204304, (2005).

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

B.C. Garrett, D.A. Dixon, D.M. Camaioni, D.M. Chipman, M.A. Johnson, C.D. Jonah, G.A. Kimmel, J.H. Miller, T. Rescigno, P.J. Rossky, S.S. Xantheas, S.D. Colson, A.H. Laufer, D. Ray, P.F. Barbara, K.H. Bowen, S.E. Bradforth, I. Carmichael, L. Corrales, J.P. Cowin, M. Dupuis, J.A. Franz, M. Gutowski, K.D Jordon, B.D Kay, C.W Mccurdy, D. Meisel, S. Mukamel, A.R. Nilsson, T.M. Orlando, N.G. Petrik, S.M. Pimblott, J.R. Rustad, G.K. Schenter, S.J. Singer, L Wang, D.M. Bartels, K.H. Becker, J.V. Coe, K.B. Eisenthal, J.A. La Verne, S.V. Lymar, T.E. Madey, A. Tokmakoff, C. Wittig, and T.S. Zwier, The Role of Water on Electron-Initiated Processes and Radical Chemistry: Issues and Scientific Advances, Chem. Rev., 105, 355, (2005).

M. Haranczyk, M. Gutowski, Finding Adiabatically Bound Anions of Guanine through Combinatorial-Computational Approach, Angew. Chem. Int. Ed., accepted for publication.

M. Haranczyk, J. Rak, M. Gutowski, Stabilization of Very Rare Tautomers of 1-methylcytosine by an Excess Electron, J. Phys. Chem. A. (Jack Simons Festschrift), 107, issue 097, xxxx, (2005).

**PI Parvez Guzdar**

Nusinovich GS, Sinitsyn EV, Velikovich L, et al. Startup-scenarios in high-power gyrotrons IEEE TRANSACTIONS ON PLASMA SCIENCE 32 (3): 841-852 Part 1 JUN 2004

Miao YY, Antonsen TM, Nusinovich GS, et al. Prebunching of electrons in harmonic-multiplying cluster-cavity gyro-amplifiers IEEE TRANSACTIONS ON PLASMA SCIENCE 32 (3): 970-980 Part 1 JUN 2004

Gillingham DR, Antonsen TM Linear theory of shot noise in harmonic gyroklystrons and Gyro-TWT amplifiers IEEE TRANSACTIONS ON PLASMA SCIENCE 32 (3): 987-993 Part 1 JUN 2004

## H

**PI Stephan Haas**

Phys. Rev. B 72, 024440 (2005)

Phys. Rev. Lett. 94, 197204 (2005)

Phys. Rev. Lett. 94, 147208 (2005)

Phys. Rev. Lett. 93, 167203 (2004)

J. Appl. Phys. 98, 044508 (2005)

Appl. Phys. Lett. 85, 121 (2004)

Phys. St. Sol. B 242, 363 (2005)

Europhysics Lett. 68, 720 (2004)

**PI Edward Hamilton**

Peronne E, Poulsen MD, Stapelfeldt H, et al. Nonadiabatic laser-induced alignment of iodobenzene molecules Phys. Rev. A 70 (6): Art. No. 063410 DEC 2004

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

**PI Bruce Harmon**

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

R. Biswas, Z.-Y.Li and K. M. Ho, Impedance of photonic crystals and photonic crystal waveguides, Applied Physics Letters.84, (8) 1254 (2004). Virtual Journal of Nanoscience and Technology 9, (March 1 2004).

Z. Y. Li and K. M. Ho, "Anomalous propagation loss in photonic crystal waveguides", Phys. Rev. Lett. 92, 063904 (2004).

"Finding the Reconstructions of Semiconductor Surfaces via a Genetic Algorithm", F. C. Chuang, C. V. Ciobanu, V. B. Shenoy, C. Z. Wang, and K. M. Ho, Surf. Sci. Lett., 573, L375 (2004).

"Structure of Si(114) determined by global optimization methods", F. C. Chuang, C. V. Ciobanu, C. Predescu, C. Z. Wang, and K. M. Ho, Surf. Sci. 578, 183 (2005).

"A first-principles studies of group IV dimmer chains on Si(100)", T. L. Chan, C. Z. Wang, Z. Y. Lu, K. M. Ho, Phys. Rev. B 72, 045405 (2005).

"Interface relaxation and electronic corrugation in the Pb/Si(111)-Pb-a-R3xR3", M. Hupalo, V. Yeh, T. L. Chan, C. Z. Wang, K. M. Ho, and M. C. Tringides, Phys. Rev. B 71, 193408 (2005).

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

"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, Phil. Mag. 85, 233 (2005).

"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).

"Physical trends in amorphous carbon: a tight-binding molecular dynamics study", C. Mathioudakis, G. Kopidakis, P. C. Kelires, C. Z. Wang, and K. M. Ho, Phys. Rev. B 70, 125202 (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 70, 104113 (2004).

"Representation of Electronic Structures in Crystals in Terms of Highly Localized Quansiatomic Minimal Basis Orbitals", W.C. Lu, C.Z. Wang, Z. L. Chan, K. Ruedenberg, and K. M. Ho, Phys. Rev. B (Rapid Communications) 70, 041101 (2004).

"Tight-binding molecular dynamics for carbon and applications to nanostructure formation", C. Z. Wang and K. M. Ho, J. Computational and Theoretical Nanoscience 1, 1 (2004).

**PI Charles Harris**

Kling, M. F.; Cahoon, J. F.; Glascoe, E. A.; Shanoski, J. E.; Harris, C. B. The Role of Odd-electron Intermediates and In-cage Electron Transfer in Ultrafast Photochemical Disproportionation Reactions in Lewis Bases. J. Am. Chem. Soc. 2004, 126, 11414-11415.

Shanoski, J.E.; Payne, C.K.; Kling, M.F.; Glascoe, E.A.; Harris, C.B. Ultrafast Infrared Mechanistic Studies of the Interaction of 1-Hexyne with Group 6 Hexacarbonyl Complexes. Organometallics 2005, 24, 1852-1859.

Snee, P.T.; Shanoski, J.; Harris, C.B. Mechanism of Ligand Exchange Studied using Transition Path Sampling. J. Am. Chem. Soc. 2005, 127, 1286-1290.

Cahoon, J.F.; Kling, M.F.; Schmatz, S.; Harris, C.B. 19-Electron Intermediates and Cage-Effects in the Photochemical Disproportionation of [CpW(CO)3]2 with Lewis Bases. J. Am. Chem. Soc. 2005, 127,

Garrett-Roe, S.; Shipman, S.T.; Szymanski, P.; Strader, M.L.; Yang, A.; Harris, C.B. "Ultrafast Electron Dynamics at Dielectric/Metal Interfaces: Intraband Relaxation of Image State Electrons as Friction." J. Phys. Chem. B (cover), 2005, in press.

**PI Robert Harrison**

Ryan Olson, Sergey Varganov, Mark S. Gordon and Horia Metiu. (2005): The binding of the noble metal cations Au+ and Ag+ to propene. Chemical Physics Letters, Volume 412, 416-419.

Olson R. M., Varganov S., Gordon M., Metiu H., Chretien S., Piecuch P., Kowalski K., Kucharski S. A., Musial M. (2005): Where does the planar-to-nonplanar turnover occur in small gold clusters? Journal of the American Chemical Society 127, 1049-1052.

Varganov S. A., Olson R. M., Gordon M. S., Metiu H. (2004): A study of the reaction of molecular hydrogen with small gold clusters. Journal of Chemical Physics 120, 5169-5175.

**PI Martin Head-Gordon**

Auxiliary basis expansions for large-scale electronic structure calculations, Y. Jung, A. Sodt, P.M.W. Gill and M. Head-Gordon, Proc. Nat. Acad. USA 102, 6692-6697 (2005).

Search for stratospheric bromine reservoir species: Theoretical study of the stability of mono-, tri-, and pentacoordinated bromine compounds, T. J. Lee, C. N. Mejia, G. J. O. Beran, and M. Head-Gordon, J. Phys. Chem. A 109, 8133 (2005).

A local correlation model that yields intrinsically smooth potential energy surfaces, J.E. Subotnik and M. Head-Gordon, J. Chem. Phys. 123, 064108 (2005).

Scaled opposite spin second order Moller-Plesset theory with improved physical description of long- range dispersion interactions, R.C. Lochan, Y. Jung, and M. Head-Gordon, J. Phys. Chem. A 109, 7598 -7605 (2005).

Intermolecular pi-to-pi bonding between stacked aromatic dyads. Experimental and theoretical binding energies and near-IR optical transitions for phenalenyl radical/ radical versus radical/cation dimerizations, D. Small, V. Zaitsev, Y. Jung, S. V. Rosokha, M. Head-Gordon, and J. K. Kochi, J. Am. Chem. Soc. 126, 13850 (2004).

Pan, A.C, J.P. Garrahan and D. Chandler. " Heterogeneity and growing lengthscales in the dynamics of kinetically constrained lattice gases in two dimensions," cond-mat /0410525; Phys. Rev. E., in press (2005).

Berthier, L. D. Chandler and J.P.Garrahan. "Length scale for the onset of Fickian diffusion in super- cooled liquids," Euro. Phys. Lett. 69, 320-326 (2005).

Merolle, M., J.P. Garrahan and D. Chandler. " Space-time thermodynamics of the glass transition," Proc. Nat. Acad. Sci. USA 102, 10837-10840, (2005).

Jung, Y.J., J.P. Garrahan and D. Chandler, " Dynamical exchanges in facilitated models of supercooled liquids, " cond-mat /0504535; J.Chem. Phys., in press (2005).

Pan, A.C., " Rotational correlation and dynamic heterogeneity in a kinetically constrained lattice gas," cond-mat/0506778; J. Chem. Phys., in press (2005).

Pan, A. and D. Chandler. "Dynamics of Nucleation in the Ising Model," J. Phys. Chem. B , 108, 19681-19686 (2004).

Pan, A.C, J.P. Garrahan and D. Chandler. " Decoupling of self-diffusion and structural relaxation during a fragile-to-strong cross-over in a kinetically constrained lattice gas," cond-mat/0501739; ChemPhysChem, in press (2005).

"An orbital-based definition of radical and multiradical character", A. D. Dutoi, Y. Jung, and M. Head-Gordon, J. Phys. Chem. A 108, 10270 (2004).

"Ultrafast photoinitiated long-range electron transfer in cyclophane-bridged zincporphyrin-quinone complexes via conical intersections", A. Dreuw, G. A. Worth, L. S. Cederbaum, and M. Head-Gordon, J. Phys. Chem. B 108, 19049 (2004).

"An orbital-based definition of radical and multiradical character", A. D. Dutoi, Y. Jung, and M. Head-Gordon, J. Phys. Chem. A 108, 10270 (2004).

"Ultrafast photoinitiated long-range electron transfer in cyclophane-bridged zincporphyrin-quinone complexes via conical intersections", A. Dreuw, G. A. Worth, L. S. Cederbaum, and M. Head-Gordon, J. Phys. Chem. B 108, 19049 (2004).

**PI Teresa Head-Gordon**

D. Russo, R. K. Murakra, J. R.D. Copley, T. Head-Gordon (2005). Hydration dynamics near a model protein backbone. J.Phys.Chem. B 109(26); 12966-12975

N. Marianayagam, N. Fawzi & T. Head-Gordon (2005). Protein folding by distributed computing and the denatured state ensemble, Protein Science 14, 993-1003.

N. Fawzi, V. Chubukov, L.A. Clark, S. Brown & T. Head-Gordon (2005). Influence of denatured and intermediate states of folding on protein aggregation. Protein Science 14, 993-1003.

D. Russo, R. K. Murarka, G. Hura, E. R. Verschell, J. R.D. Copley, & T. Head-Gordon (2004). Evidence for anomalous hydration dynamics as a function of temperature near a model hydrophobic peptide J.Phys.Chem. B (Stillinger Feitschrift) 108, 19885-19893.

E. Eskow, B. Bader, R. Byrd, S. Crivelli, T. Head-Gordon, V. Lamberti and R. Schnabel (2004). An optimization approach to the problem of protein structure prediction. Accepted to Math Programming Series A (published online Feb, 2004).

D. Russo, G. Hura, & T. Head-Gordon (2004). Hydration dynamics near a model protein surface. Biophys. J. 86, 1852-1862

H. W. Horn, W. C. Swope, J. W. Pitera, J. D. Madura, T. J. Dick, Greg Hura, T. Head-Gordon (2004). Development of an improved four-site water model for biomolecular simulations: TIP4P-Ew. J. Chem. Phys.120, 9665-9678.

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.

**PI Eric Held**

``Free-boundary simulations of DIII-D plasmas with the NIMROD code," S. E. Kruger, D. D. Schnack, C. R. Sovinec, and E. D. Held, to appear in Comp. Phys. Comm., 164 (34) 2004.

``Stationary Equilibria of Two Fluid Plasmas Having Significant, Internal, Static Electric Fields" W. F. Edwards and E. D. Held, Phys. Rev. Lett., 93, 255001 2004.

**PI Brian Hingerty**

Substrate discrimination by formamidopyrimidine-DNA glycosylase- A Mutational analysis. Zaika, E. I., Perlow, R. A., Matz, E., Broyde, S., Gilboa, R., Grollman, A. P. and Zharkov, D. O. J. Biol. Chem. 279, 4849-61 (2004).

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

Structural and stereosiomer 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 Wang, L., Hingerty, B. E., Shapiro R. and Broyde, S., Chemical Research in Toxicology 3, 311-324 (2004).

Altering DNA polymerase incorporation fidelity by distorting the dNTP binding pocket with a bulky carcinogen-damaged templated Yan, s., Wu, M., Geacintov, N. E. and Broyde, S. Biochemistry 43, 7750-7765 (2004).

Perlow-Poehnolt, Rebecca A., Likhterov, Ilya, Scicchitano, David. A., Geacintov, Nicholas E. and Broyde, Suse The spacious active site of a Y-Family DNA polymerase facilitates promiscuous nucleotide incorporation opposite a bulky carcinogen-DNA adduct: Elucidating the structure-function relationship through experimental and computational approaches, J. Biol. Chem., 279, 36951-61 (2004).

Accommodation of a 1S benzo[c]phenanthrenyl-N6-dA Adduct in a Y-family Dpo4 DNA polymerase active site: structural insights through molecular dynamics simulations. Wang, L., Wu, M., Yan, S. Frank, Patel, D. J., Geacintov< N. E. and Broyde, S. Chemical Research in Toxicology, 18, 441-56 (2005).

Methylation of cytosine at C5 in a CpG sequence context causes a conformational switch of a benzo[a]pyrene diol epoxide-N2-guanine adduct in DNA from a mionor groove alignment to intercalation with base displacement. Zhang, N., Huang, X., Kolbanovskiy, A., Hingerty, B. E., Amin, S., Broyde, S., Geacintov, N. E., Patel, D. J. J. Mol. Biol., 346, 951-65 (2005).

Spiroiminohydantoin lesions derived from guanine oxidation: structures, energetics and functional implications. Jia, L., Shafirovich, V., Shapiro, R., Geacintov, N. E. and Broyde, S., Biochemistry44, 6043-51 (2005).

Structural aspects of polycyclic aromatic carcinogen-damaged DNA and its recognition by NER proteins. Geacintov, N. E., Naegli, H., Patel, D. J. and Broyde, S. in DNA Damage Recognition, Chapter 13. Stuructural aspects of polycyclic aromatic carcinogen-damaged DNA and its recognition by NER proteins, edited by W. Siede, Y. W. Kow, and P. W. Doetsch Marcel Dekker Inc. In Press

Molecular dynamics of a food carcinogen-dna adduct in a dna polymerase: elucidating mutagenic nucleotide incorporation and extension Zhang, L., Shapiro, R. and Broyde, S., Chemical Research in Toxicology In Press.

Structural Characterization of Covalently Modified DNA by Using a Combined NMR/Molecular Mechanics Approach. Cosman, M. and Hingerty, B.E. (2005) in Nanotechnology in Biology and Medicine (Tuan Vo Dinh, editor) CRC Press, in press.

Perlow, R. A., Zharkov, D. O., Grollman, A. and Broyde, S. Substrate discrimination by formamidopyrimidine-DNA glycosylast: molecular dynamics simulations show distinguishing interactions within the active site, Biochemistry, In Press.

Structural and thermodynamic features of spiroiminohydantoin damaged DNA duplexes. Jia, L., Shafirovich, V., Shapiro, R., Geacintov, N. E. and Broyde, S., Biochemistry, In Press

## I

**PI Hong Im**

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

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., 30:893-900.

Yoo, C. S. and Im, H. G. (2004), "Transient dynamics of edge flames in a laminar nonpremixed hydrogen-air counterflow," Proc. Combust. Inst., 30:349-356.

Sankaran, R., Im, H. G., Hawkes, E. R. and Chen, J. H. (2004), "The effects of nonuniform temperature distribution on the ignition of a lean homogeneous hydrogen-air mixture," Proc. Combust. Inst., 30:875-882.

Yoo, C. S., Wang, Y., Trouve A. and Im, H. G. (2005), "Characteristic boundary conditions for direct simulations of turbulent counterflow flames", Combust. Theory Modelling, in press.

Wang, Y. and Trouve A. (2005), "Direct numerical simulation of non-premixed flame-wall interactions", Combustion and Flame, in press.

## J

**PI Bing Jap**

P. Walian, T.A. Cross. and B.K. Jap (2004) "Structural genomics of membrane proteins" Genome Biol. 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, 233-245.

S. Zhou, H. Zhou, P.J. Walian and B.K. Jap (2005) "CD147 is a regulatory subunit of the gamma-secretase complex in Alzheimer's disease amyloid beta-peptide production" Proc. Natl. Acad. Sci. USA, 102, 7499-7504.

**PI Stephen Jardin**

P. Garabedian, L. P. Ku, et al., "Reactors with stellarator stability and tokamak transport," Fusion Science and Technology, 47(3) 400, 2005.

J. Lyon, L. P. Ku, et al., "Optimization of stellarator reactor parameters," Fusion Science and Technology, 47(3) 414, 2005.

L. P. Ku and the Aries Team, "Reactor configuration development for ARIES-CS," 21th Symposium on Fusion Engineering, Knoxville, Tennessee, September 26-29, 2005.

L. P. Ku and the Aries Team, "Modular coil design for the ultra-low aspect ratio quasi-axially symmetric stellarator MHH2," 21th Symposium on Fusion Engineering, Knoxville, Tennessee, September 26-29, 2005.

J. Lyon, L. P. Ku, et al., "Optimization of the ARIES-CS Compact Stellarator Reactor Parameters," 21th Symposium on Fusion Engineering, Knoxville, Tennessee, September 26-29, 2005.

L. P. Ku and P. R. Garabedian, "New classes of quasi-axisymmetric configurations," Proc. of the 15th International Stelarator Workshop, Madrid, Spain, October 3-7, 2005.

L. P. Ku and P. R. Garabedian, "New classes of qusi-axially symmetric stellarator configurations," to be submitted to Fusion Science and Technology. 8. T. K. Mau and the Aries Team, "Divertor Heat Load Studies for Compact Stellarator Reactors," 21th Symposium on Fusion Engineering, Knoxville, Tennessee, September 26-29, 2005.

Jardin, Stephen Strauss, HR; Pletzer, A; Park, W; Jardin, S; Breslau, J; Sugiyama, L. 2004. MHD simulations with resistive wall and magnetic separatrix. COMPUTER PHYSICS COMMUNICATIONS 164 (1-3): 40-45.

Strauss, HR; Sugiyama, LE; Fu, GY; Park, W; Breslau, J. 2004. Simulation of two fluid and energetic particle effects in stellarators. NUCLEAR FUSION 44 (9): 1008-1014.

Chen, J; Breslau, J; Fu, G; Jardin, S; Park, W. 2004. Symmetric solution in M3D. COMPUTER PHYSICS COMMUNICATIONS 164 (1-3): 468-471.

Samtaney, RS; Jardin, SC; Colella, P; Martin, DF. 2004. 3D Adaptive Mesh Refinement simulations of pellet injection in tokamaks. COMPUTER PHYSICS COMMUNICATIONS 164 (1-3): 220-228.

Jardin, SC. 2004. A triangular finite element with first-derivative continuity applied to fusion MHD applications. JOURNAL OF COMPUTATIONAL PHYSICS 200 (1): 133-152.

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

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

V. Wheatley, D. I. Pullin and R. Samtaney, "RegRegular shock refraction at an oblique planar density interface in magnetohydrodynamics", J. Fluid Mech., vol. 522, 2005.

R. Samtaney, S. C. Jardin, P. Colella and D. F. Martin, "3D Adaptive mesh refinement simulations of pellet injection in tokamaks", Computer Physics Comm., Vol 164, 2004.

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

**PI Julius Jellinek**

Structural And Electronic Properties Of Small Beryllium Clusters: A Theoretical Study S. Srinivas and J. Jellinek J. Chem. Phys. 121, 7243-7252 (2004)

Structure And Magnetism Of VnBzn 1 Sandwich Clusters J. Wang, P. H. Acioli, and J. Jellinek J. Am. Chem. Soc. 127, 2812-2813 (2005)

Reaction Dynamics Of Nin (n=19 AND 20) With D2: Dependence On Cluster Size, Temperature, And Initial Rovibrational State Of The Molecule M. Boyukata, Z. B. Guvenc, S. Ozcelik, P. Durmus, and J. Jellinek Int. J. Mod. Phys. C 16, 295-308 (2005)

Stuffed Fullerene Structures For Medium-Sized Silicon Clusters J. Zhao, J. Wang, J. Jellinek, S. Yoo, and X. C. Zeng Eur. Phys. J D 34, 35-37 (2005)

The Size Dependence Of Static Polarizabilities And Adsorption Spectra Of Ag Clusters J. C. Idrobo, S. Ogut, and J. Jellinek Phys Rev B (in press)

Computational Electron Spectroscopy - Application To Magnesium Clusters J. Jellinek and P. H. Acioli Lecture Series in Computer and Computational Sciences (in press)

**PI Chueng-Ryong Ji**

Light-Front Zero-Mode Contribution to the Good Current in Weak Transition,H.-M. Choi and C.-R. Ji, Phys. Rev. D72, 013004 (2005)

Manifestations of the Vector Anomaly in Covariant and Light-Front Calculations of the Anomalous Magnetic Moment of W - Bosons, B.L.G. Bakker and C.-R. Ji, Phys. Rev. D71, 053005 (2005)

Time to Space Conversion in Quantum Field Theory of Flavor Mixing, C.-R. Ji and Y. Mishchenko, Annals of Physics 315, 488 (2005)

Vector Anomaly and Practicality of Light-Front Dynamics, C.-R. Ji and B.L.G. Bakker, Few Body Systems 36, 137 (2005)

Scalar Mesons in the Light-Front Quark Model, M. DeWitt, C.-R. Ji, and H.-M. Choi, Few Body Systems 36, 83 (2005)

Light-Front Quark Model Analysis of the Rho-Meson Electromagnetic Form Factors, H.-M. Choi and C.-R.Ji, Few Body Systems 36, 61 (2005)

Nucleon Compton Scattering in the Perturbative Limit, R.Thomson and C.-R.Ji, Few Body Systems 36, 237 (2005)

Exploring Properties of Dark and Visible Mass Distribution on Different Scales in the Universe, Y. Mishchenko and C.-R. Ji, Int. J. Mod. Phys. A20, 3124 (2005)

Elecreomagnetic Structure of the Rho Meson in the Light-Front Quark Model,H.-M. Choi and C.-R. Ji, Phys. Rev. D70, 053015 (2004)

Investigating the Parity of the Exotic $\Theta^ $ Baryon from the Kaon Photoproduction, B.-G. Yu, T.-K. Choi, and C.-R. Ji, Phys. Rev. C70, 045205 (2004)

Distribution of Masses in Galaxy Cluster CL0024 and Particle Mass of Dark Matter, Y.Mishchenko and C.-R.Ji, Progress in Dark Matter Research, pp. 217-239, Nova Science Publishers, Inc. , 2005.

Genral Formulation of Flavor Mixing in Quantum Field Theory, Y. Mishchenko and C.-R.Ji, Focus on Quantum Field Theory, pp. 115-149, Nova Science Publishers, Inc. 2005.

Duality and Canonical Transformation in the Scalar Field Theory, C.-R.Ji, Y.Mishchenko and A.Shalaby, Recent Research Development in Physics Vol.5, pp. 1489-1510 (2004).

A Novel Variational Approach for Quantum Field Theory: Example of Study of the Ground State and Phase Transition in Nonlinear Sigma Model, Y. Mishchenko and C.-R.Ji, submitted to Int. J. Mod. Proc.Suppl.A; quant-ph/0410197.

## K

**PI Martin Karplus**

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

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

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

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

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

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

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

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

Protein Structural Transitions and their Functional Role, Phil. Trans. R. Soc. A 363, 331-355 (2005), by M. Karplus, Y. Q. Gao, J. Ma, A. van der Vaart, and W. Yang.

Molecular Dynamics and Protein Function, Proc. Natl. Acad. Sci. USA 102, 6679-6685 (2005), by M. Karplus and J. Kuriyan.

**PI Thomas Katsouleas**

T. Katsouleas, Progress on plasma accelerators: from the energy frontier to tabletops, Plasma Phys. Control. Fusion 46 (2004) B575-B582.

M.J. Hogan, C.D. Barnes, C.E. Clayton, F.J. Decker, S. Deng, P. Emma, C. Huang, R.H. Iverson, D.K. Johnson, C. Joshi, T. Katsouleas, P. Krejcik, W. Lu, K.A. Marsh, W.B. Mori, P. Muggli, C.L. Oonnell, E. Oz, R.H. Siemann, D. Walz, Multi-GeV Energy Gain in a Plasma-Wakefield Accelerator, Phys. Rev. Lett. 95, 054802 (2005).

**PI Ricky Kendall**

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," Lecture Notes in Computer Science. 3349, 1-11, 2005.

M.-S. Wu, R. A. Kendall, K. Wright, "Optimizing Collective Communications on SMP Clusters," in the Proceedings of the 2005 International Conference on Parallel Processing (ICPP-05), Georg Sverdrups House, University of Oslo, Norway, June 14-17, 2005.

M.-S. Wu, R. A. Kendall, Z. Zhang, K. Wright, "Performance Modeling and Tuning Strategies of Mixed Mode Collective Communications, accepted in Supercomputing 2005.

**PI Davd Keyes**

Parallel algorithms for PDE-constrained optimization, V. Akcelik, G. Biros, O. Ghattas, J. Hill, D. Keyes, and B. van Bloemen Waanders, Frontiers of Parallel Computing, M. Heroux, P. Raghaven, H. Simon, eds, SIAM, accepted (2005).

Dynamic data-driven inversion for terascale simulations: Real-time identification of airborne contaminants, V. Akcelik, G. Biros, A. Dragenescu, J. Hill, O. Ghattas, and B. van Bloemen Waanders, Proceedings of SC2005, accepted (2005).

Adaptive smoothed aggregation (aSA) multigrid, M. Brezina, R. Falgout, S. MacLachlan, T. Manteuffel, S. McCormick, and J. Ruge, SIAM Review 47 (2005), pp. 317-346.

An element agglomeration nonlinear additive Schwarz preconditioned Newton method for unstructured finite element problems, X.-C. Cai, L. Marcinkowski, and P. Vassilevski, Applications of Mathematics, 50 (2005), pp. 247-275.

Self-Adapting Linear Algebra Algorithms and Software, J. Demmel, J. Dongarra, V. Eijkhout, E. Fuentes, A. Petitet, R. Vuduc, R. C. Whaley, K. Yelick. Proceedings of the IEEE, Special Issue on Program Generation, Optimization, and Adaptation, 93 (2005).

Performance Models for Evaluation and Automatic Tuning of Symmetric Sparse Matrix-Vector Multiply B. C. Lee, R. Vuduc, J. Demmel, K. Yelick, International Conference on Parallel Processing, Montreal (2004) [Winner, Best Paper Award].

Parallel performance of some two-level ASPIN algorithms, L. Marcinkowski and X.-C. Cai, Lecture Notes in Computational Science and Engineering, Springer, 40 (2004), pp. 641-648.

Domain Decomposed Fully Coupled Implicit Methods for a Magnetohydrodynamics Problem", S. Ovtchinnikov, F. Dobrian, X.-C. Cai and D. Keyes, Proceedings of the 16th International Conference on Domain Decomposition Methods, Springer, accepted (2005).

Domain Decomposition Methods, Algorithms and Theory, A. Toselli and O. Widlund, Computational Mathematics, Vol. 34, Springer (2004).

**PI Kwiseon Kim**

K. Kim, P. Graf, W. Jones, "A genetic algorithm based inverse band structure method for semiconductor alloys," Journal of Computational Physics, 208:735-760 (2005).

**PI Sung-Hou Kim**

Sims GE, Choi IG, Kim SH Protein conformational space in higher order phi-psi maps Proceedings Of The National Academy Of Sciences Of The United States Of America 102 (3): 618-621 JAN 18 2005

Hou JT, Jun SR, Zhang C, et al. Global mapping of the protein structure space and application in structure-based inference of protein function Proceedings Of The National Academy Of Sciences Of The United States Of America 102 (10): 3651-3656 MAR 8 2005

**PI Richard Klein**

"How Protostellar Outflows Help Massive Stars Form" Krumholz, M. R., McKee, C. F., & Klein, R. I., 2005a, ApJ, 618, L33.

"Bondi Accretion in the Presence of Vorticity" Krumholz, M. R., McKee, C. F., & Klein, R. I., 2005b, ApJ, 618, 757.

"A General Theory of Turbulence-Regulated Star Formation, from Spirals to Ultraluminous Infrared Galaxies" Krumholz, M. R. & McKee, C. F. 2005, ApJ, 630, 250.

Krumholz, M.R., Klein, R.I. & McKee, C.F. 2005, in "IAU Symposium 227: Massive Star Birth: A Crossroads of Astrophysics", eds. R. Cesaroni, E. Churchwell, M. Felli & C.M. Walmsley, in press.

**PI John Klepeis**

N. Drummond, A.J. Williamson, R.J. Needs and Giulia Galli, Electron emission from diamondoids: A diffusion quantum Monte Carlo study, Physical Review Letters 95, 096801 (2005).

F. Reboredo and A.J. Williamson, Optimized nonorthogonal localized orbitals for linear scaling quantum Monte Carlo calculations, Physical Review B 71, 121105(R) (2005).

A. Puzder, A.J. Williamson, N. Zaitseva, G. Galli, L. Manna and A.P. Alivisatos The Effect of Organic Ligand Binding on the Growth CdSe Nanoparticles Probed by Ab-Initio Calculations, Nano Letters 4, 2361 (2004).

A. J. Williamson, F. Reboredo and G. Galli, Chemisorption at the Nanoscale: An alternative mechanism for hydrogen storage, Applied Physics Letters, 85, 2917 (2004).

**PI Kwok Ko**

A. Kabel, Applications of Parallel Computational Methods to Charged-Particle Beam Dynamics, to be published in Nucl. Instr. Methods A

Chao Yang, Weiguo Gao, Zhaojun Bai, Xiaoye Li, Lie-Quan Lee, Parry Husbands, and Esmond G. Ng, An Algebraic Sub-structuring for Large-scale Eigenvalue Calculation, SIAM Journal On Scientific Computing, 2005, accepted

**PI Boris Kogan**

Huffaker R, Lamp ST, Weiss JN, Kogan B. Intracellular calcium cycling, early afterdepolarizations, and reentry in simulated long QT syndrome. Heart Rhythm. 2004 Oct; 1(4):449-50.

**PI Joel Koplik**

Self-affine fronts in self-affine fractures, Phys. Rev. Lett. 92, 014501 (2004), G. Drazer, H. Auradou, J. Koplik and J.-P. Hulin.

Permeability anisotropy induced by the shear displacement of the walls of a single fracture, Water Resources Res. in press (2005), H. Auradou, G. Drazer, J.-P. Hulin and J. Koplik.

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

Wetting and particle absorption in nanoflows, Phys. Fluids 17, 017102 (2004), G. Drazer, B. Khusid, J. Koplik and A. Acrivos.

Hysteresis, force oscillations, and non-equilibrium effects in the adhesion of nanoparticles to atomically smooth surfaces, Phys. Rev. Lett. 95, 016102 (2005), G. Drazer, B. Khusid, J. Koplik and A. Acrivos.

**PI Veerabhadra Kotamarthi**

Harris, L and V. R. Kotamarthi, The characteristics of the Chicago Lake Breeze and its Effects on Trace Particle Transport: Results from and Episodic Event Simulation. Accepted Journal of Applied Meteorology, 2005.

Gaffney, J. S., N. A. Marley, M. M. Cunningham and V. R. Kotamarthi, Beryllium-7 Measurements in the Houston and Phoenix Urban Areas: Estimation of upper atmospheric ozone contributions. J. Air and Waste Manage. Assoc., 55, 1228-1235, 2005.

Im, H. K., M. L. Stein and V. R. Kotamarthi, Predicting CMAQ ammonia wet deposition and a novel approach to inverse modeling. Accepted Journal of Geophysical Research, 2005

**PI Steven Krueger**

Luo, Y., S. K. Krueger, and S. Moorthi, 2005: Cloud properties simulated by a single-column model. Part I: Comparison to cloud radar observations of cirrus clouds. J. Atmos. Sci., 62, 1428-1445.

Luo, Y., S. K. Krueger, and K.-M. Xu, 2005: Cloud Properties Simulated by a Single-Column Model. Part II: Evaluation of Cumulus Detrainment and Ice-phase Microphysics Using a Cloud Resolving Model. Submitted to J. Atmos. Sci., April 2005.

Xie, S., M. H. Zhang, M. Branson, R. T. Cederwall, A. D. Del Genio, Z. A. Eitzen, S. J. Ghan, S. F. Iacobellis, M. Khairoutdinov, S. A. Klein, S. K. Krueger, W. Lin, U. Lohmann, D. A. Randall, R. C. J. Somerville, Y. C. Sud, G. K. Walker, A. Wolf, X. Wu, K.-M. Xu, J. J. Yio, G. Zhang, and J. Zhang, 2005: Simulations of Midlatitude Frontal Clouds by SCMs and CRMs during the ARM March 2000 Cloud IOP. J.~Geophys. Res., 110, D15S03, doi:10.1029/2004JD005119.

**PI John Kuriyan**

Kazmirski, S. L, Podobnik, M., Weitze, T. F., O'Donnell, M., & Kuriyan, J. (2004). Structural analysis of the inactive state of the Escherichia coli DNA polymerase clamp-loader complex. Proc. Natl. Acad. Sci. USA 101, 16750-16755.

Karplus, M. & Kuriyan, J. (2005). Molecular dynamics and protein function. Proc. Natl. Acad. Sci. USA 102, 6679-6685.

Kazmirski, S. L., Zhao, Y., Bowman, G. D., O'Donnell, M., & Kuriyan, J. (2005). Out-of-plane motions in open sliding clamps: Molecular dynamics simulations of eukaryotic and archaeal proliferating cell nuclear antigen. Proc. Natl. Acad. Sci. USA 102, In Press.

## L

**PI Andrew Lacis**

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

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

**PI Jean-Francois Lamarque**

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

**PI Uzi Landman**

U. Landman, "Materials by Numbers: Computations as Tools of Discovery", perspective article in Proc. Nat. Acad. Sci. (USA), 102, 6671 (2005).

B. Yoon, H. Hakkinen, U. Landman, A. Wvrz, S. Abbet, K. Judai, U. Heiz, "Charging Effects on Bonding and catalyzed oxidation of CO on Au8 Clusters Supported on MgO", Science, 307, 403 (2005).

A. Bongiorno and U. Landman, "Water Enhanced Catalysis of CO oxidation on Supported Gold Nanoclusters", Phys. Rev. Lett. September 6, 2005.

C. Yannouleas and Uzi Landman, "Electron Localization and Entaglement in a Two-Electron Quantum Dot", Phys. Rev. Lett. (2005). ArXiv: cond-mat/ 0501612

I. Romanovsky, C. Yannouleas, U. Landman, "Crystalline Boson Phases in Harmonic Traps: Beyond Gross-Pitaevskii Mean Field", Phys. Rev. Lett. 93, 230405 (2004).

**PI Jean-Noel Leboeuf**

William Nevins, Greg Hammett, Andris Dimits, William Dorland, Dan E. Shumaker, "Discrete particle noise in particle-in-cell simulations of plasma microturbulence" , Submitted to Phys.Plasmas, August 2005.

Waltz RE, Candy J, Hinton FL, Estrada-Mila C, Kinsey JE. Advances in comprehensive gyrokinetic simulations of transport in tokamaks. [Journal Paper] Nuclear Fusion, vol.45, no.7, July 2005, pp.741 -50. Publisher: IAEA;IOP, Austria.

Kinsey JE, Waltz RE, Candy J. Nonlinear gyrokinetic turbulence simulations of E*B shear quenching of transport. [Journal Paper] Physics of Plasmas, vol.12, no.6, June 2005, pp.62302-1-9. Publisher: AIP, USA.

Zimmerman DS, Triana SA, Sisan DR, Tillotson WA, Dorland W, Lathrop DP. Characterization of the magnetorotational instability from a turbulent background state. [Conference Paper] AIP. American Institute of Physics Conference Proceedings, no.733, 2004, pp.13-20. USA.

Rogers BN, Dorland W. Noncurvature-driven modes in a transport barrier. [Journal Paper] Physics of Plasmas, vol.12, no.6, June 2005, pp.62511-1-12. Publisher: AIP, USA.

Drake JF, Shay MA, Thongthai W, Swisdak M. Production of energetic electrons during magnetic reconnection. [Journal Paper] Physical Review Letters, vol.94, no.9, 11 March 2005, pp.095001/1-4. Publisher: APS, USA.

Armaou A, Kevrekidis IG, Theodoropoulos C. Equation-free gaptooth-based controller design for distributed complex/multiscale processes. [Journal Paper] Computers & Chemical Engineering, vol.29, no.4, 15 March 2005, pp.731-40. Publisher: Elsevier, UK.

Estrada-Mila C, Candy J, Waltz RE. Gyrokinetic simulations of ion and impurity transport. [Journal Paper] Physics of Plasmas, vol.12, no.2, Feb. 2005, pp.22305-1-14. Publisher: AIP, USA.

Applegate DJ, Roach CM, Cowley SC, Dorland WD, Joiner N, Akers RJ, Conway NJ, Field AR, Patel A, Valovic M, Walsh MJ. Microstability in a "MAST-like" high confinement mode spherical tokamak equilibrium. [Journal Paper] Physics of Plasmas, vol.11, no.11, Nov. 2004, pp.5085-94. Publisher: AIP, USA.

Leboeuf, Jean-Noel James C. Kniep, Jean-Noel G. Leboeuf, and Viktor K. Decyk,"Gyrokinetic Particle-In-Cell Calculations of Ion Temperature Gradient Driven Turbulence with Parallel Nonlinearity and Strong Flow Corrections", Comp. Phys. Comm. 164/1-3, 98-102 (2004).

M. Yagi, S. Yoshida, S.-I. Itoh, H. Naitou, H. Nagahara, J.-N. Leboeuf, K. Itoh, T. Matsumoto, S. Tokuda, and M. Azumi, " Nonlinear simulation of tearing mode based on 4-field RMHD model", Nucl. Fusion 45, 900-906 (2005).

V. I. Sotnikov, J. N. Leboeuf, C. Deeney, and C.A. Coverdale, P. Hellinger, P. Travnicek, and V. Fiala, "Hybrid simulation of the Z-pinch instabilities for profiles generated in the process of wire array implosion in the Saturn pulsed power generator", Accepted for Publication, Phys. Plasmas, July 17, 2004.

P.-A. Gourdain and J. N. Leboeuf, "High resolution magnetohydrodynamic equilibrium code for unity beta plasmas", Submitted for Publication, Journal of Computational Physics, October 13, 2004.

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

P.L. Pritchett, "Externally Driven Magnetic Reconnection in the Presence of a Normal Magnetic Field", J. Geophys. Res., 110, A05209, doi:10.1029/2004JA010948, 2005.

P.L. Pritchett, "Onset of Magnetic Reconnection", in Reconnection of Magnetic Fields, edited by J. Birn and E. Priest, in press, Cambridge Univ. Press, Cambridge, 2005.

B. Lembege, P.L. Pritchett, M.V. Goldman, and D.L. Newman, "Kinetic and Nonlinear Processes in Space Plasma", Rev. Radio Sci., in press, 2005.

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

P.L. Pritchett, "The "Newton Challenge": Kinetic Aspects of Forced Magnetic Reconnection", J. Geophys. Res., in press, 2005.

A Numerical Instability in an ADI Algorithm for Gyrokinetics, by E. Belli & G. Hammett. Comput. Phys. Comm., accepted for publication, June 2005.

Dongbin Xiu, Kevrekidis IG, Ghanem R. An equation-free, multiscale approach to uncertainty quantification. Computing in Science & Engineering, vol.7, no.3, May-June 2005, pp.16 -23. Publisher: IEEE Comput. Soc, USA.

Cattell C, Dombeck J, Wygant J, Drake JF, Swisdak M, Goldstein ML, Keith W, Fazakerley A, Andre M, Lucek E, Balogh A. Cluster observations of electron holes in association with magnetotail reconnection and comparison to simulations. Journal of Geophysical Research, vol.110, no.A1, 1 Jan. 2005, pp.16 pp.. Publisher: American Geophys. Union, USA.

**PI Frank Lee**

"Baryon magnetic moments in the background field method", F.X. Lee, R. Kelly, L. Zhou, W. Wilcox. Phys. Lett. B 627, 71 (2005), hep-lat/0509067.

"Electric Polarizability of Neutral Hadrons from Lattice QCD", J. Christensen, W. Wilcox, F.X. Lee, L. Zhou, Phys. Rev. D 72, 034503 (2005).

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

"Baryon Resonances And Pentaquarks On The Lattice", F.X. Lee, C. Bennhold, Nucl.Phys.A754:248-260,2005.

"Excited Baryons And Pentaquarks On The Lattice", F.X. Lee, Int.J.Mod.Phys.A20:250-262,2005.

"Roper Resonance and S11(1535) in Lattice QCD", S.J. Dong, T. Draper, I. Horvath, F.X. Lee, K.F. Liu, N. Mathur, J.B. Zhang, Phys. Lett. B605, 137 (2005). hep-ph/0306199.

"A study of pentaquarks on the lattice with overlap fermions", N. Mathur, F.X. Lee, A. Alexandru, C. Bennhold, Y. Chen, S.J. Dong, T. Draper, I. Horvath, K.F. Liu, S. Tamhankar, J.B. Zhang, Phys. Rev. D 70, 074508 (2004), hep-ph/0406196.

"Inherently Global Nature of Topological Charge Fluctuations in QCD", I. Horvath, A. Alexandru, J.B. Zhang, Y. Chen, S.J. Dong, T. Draper, F.X. Lee, K.F. Liu, N. Mathur, S. Tamhankar, H.B. Thacker, Phys. Lett. B 612, 21 (2005), hep-lat/0501025.

"Topological Charge Barrier in the Markov-Chain of QCD", D.B. Leinweber, A.G. Williams, J.B. Zhang, F.X. Lee, Phys. Lett. B 585, 187 (2004). hep-lat/0312035.

"Inherently Global Nature of Topological Charge Fluctuations in QCD", I. Horvath, A. Alexandru, J.B. Zhang, Y. Chen, S.J. Dong, T. Draper, F.X. Lee, K.F. Liu, N. Mathur, S. Tamhankar, H.B. Thacker, Phys. Lett. B 612, 21 (2005), hep-lat/0501025.

"Topological Charge Barrier in the Markov-Chain of QCD", D.B. Leinweber, A.G. Williams, J.B. Zhang, F.X. Lee, Phys. Lett. B 585, 187 (2004). hep-lat/0312035.

**PI Patrick Lee**

K.S.D.Beach, P.A.Lee and P. Monthoux, "Field induced antiferromagnetism and the Kondo Insulator-to-Metal Transition", Phys. Rev. Lett. 92,026401 (2004)

**PI Wei-li Lee**

"Theoretical and Numerical Properties of a Gyrokinetic Plasma: issues related to transport time scale simulation," W. W. Lee, Comp. Phys. Comm. 164, 244 (2004).

"Electron Thermal Transport in Tokamaks: ETG or TEM Turbulence?," Z. Lin Y. Nishimura, H. Qu, T. S. Hahm, J. L. V. Lewandowski, G. Rewoldt, W. X. Wang, P. H. Diamond, C. Holland, F. Zonca, and Y. Li, IAEA-CN/TH/8-4 (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. Control. Fusion 46, A323 (2004)

"Turbulence spreading and transport scaling in global gyrokinetic particle simulations", Z. Lin and T. S. Hahm, Phys. Plasmas 11, 1099 (2004).

"Global delta f Particle Simulation of Neoclassical Transport and Ambipolar Electric Field in General Geometry," W.X. Wang, W.M. Tang, F.L. Hinton et al., Comp. Phys. Communications 164, 178 (2004)

"On the Dynamics of Edge-Core Coupling," T.S. Hahm, P.H. Diamond, Z. Lin, G. Rewoldt, et al., to appear in Phys. Plasmas (2005), Paper TH/1-4 IAEA (2004)

"Physics behind Transport Barrier Theory and Simulations," T.S. Hahm, Plasma Phys. Control. Fusion 44, A87 (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, Comp. Phys. Comm. 164, 456 (2004).

"Role of nonlinear toroidal coupling in electron temperature gradient turbulence," Z. Lin, L. Chen and F. Zonca, 12, 056125 (2005).

"Gyrokinetic delta f simulation of the collisionless and collisonal tearing mode instability," Phys. Plasmas 12, Art. No. 012311 (2005).

"Global particle-in-cell simulations of microturbulence with kinetic electrons," J. L. V. Lewandowski, invited talk, APS/DPP (2005).

**PI William Lester**

A. Aspuru-Guzik, R. Salomon-Ferrer, B. Austin, and W. A. Lester, Jr.,"A Sparse Algorithm for the Evaluation of the Local Energy in Quantum Monte Carlo", J. Comput. Chem. 26, 708 (2005).

A. Aspuru-Guzik, R. Salomon-Ferrer, B. Austin, R. Perusquia-Flores, M. A. Griffin, R. A. Oliva, D. Skinner, D. Domin, and W. A. Lester, Jr.," Zori 1.0: A Parallel Quantum Monte Carlo Electronic Package", J. Comput. Chem. 26, 856 (2005).

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

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

A. Aspuru-Guzik and W. A. Lester, Jr., "Quantum Monte Carlo: Theory and Application to Molecular Systems," accepted by Adv. Quant. Chem.

A. C. Kollias, D. Domin, G. Hill, M. Frenklach, and W. A. Lester, Jr., "Quantum Monte Carlo Study of Small Hydrocarbon Atomization Energies," accepted by Mol. Phys.

**PI Lai-Yung Ruby Leung**

Liang, X., L.R. Leung, M. Huang, Y. Qian, M.S. Wigmosta, G.B. Matanga, and D. Mathews. 2005. "PUB Working Group on Orographic Precipitation, Surface and Groundwater Interactions, and Their Impacts on Water Resources." IAHS Redbook, submitted.

Qian, Y., D.P. Kaiser, L.R. Leung, and M. Xu, 2005. "More Frequent Cloud Free Sky and Less Surface Solar Radiation in China From 1955-2000." Geophys. Res. Lett., submitted.

Leung, L.R., Y.-H. Kuo, and J. Tribbia. 2005. "Research Needs and Directions of Regional Climate Modeling Using WRF and CCSM." Bull. Amer. Meteorol. Soc., submitted.

Duffy, P. B., W. Arritt, J. Coquard, W. Gutowski, J. Han, J. Iorio, J. Kim, L. R. Leung, J. Roads, E. Zeledon. 2005. "Simulations of Present and Future Climates in the Western U.S. with Four Nested Regional Climate Models." J. Clim., accepted.

Qian, Y., Q. Song, S. Menon, S. Yu, S. Liu, G. Shi, L.R. Leung, and Y. Luo. 2005. "Climate Impacts of Atmospheric Sulfate and Black Carbon Aerosols." In A Review of Global Change Research in East Asia, SCOPE/ START Rapid Assessment Book for East Asia, in press.

Zhao, Z.-C., L.R. Leung, and Y. Qian. 2005. "Characteristics of Diurnal Variations of Rainfall in China for the Recent Years." CLIVAR Exchanges, Vol 10(3), 24-26.

Leung, L.R., and Y. Qian. 2005. "Hydrologic Response to Climate Variability, Climate Change, and Climate Extreme in the U.S.: Climate Model Evaluation and Projections." In Regional Hydrological Impacts of Climatic Change Impact Assessment and Decision Making, Wagener, T. et al. (Eds). IAHS Publication 295, pp37-44.

Leung, L.R. 2005. "Effects of Climate Variability and Change on Mountain Water Resources in the Western U.S." In Global Change and Mountain Regions: A State of Knowledge Overview, U.M. Huber, H.K.M. Bugmann, and M.A. Reasoner, (eds.), Springer, Dordrecht, pp355-366.

Wang, Y.-Q, L.R. Leung, J.L. McGregor, D.-K. Lee, W.-C. Wang, Y. Ding, and F. Kimura. 2004. "Regional Climate Modeling: Progress, Challenges, and Prospects." Journal of the Meteorological Society of Japan, Vol 82(6), 1599-1628.

Leung, L.R., S. Zhong, Y. Qian, and Y. Liu. 2004. "Evaluation of Regional Climate Simulations of the 1998 and 1999 East Asian Summer Monsoon Using the GAME/HUBEX Observational Data." Journal of the Meteorological Society of Japan, Vol 82(6), 1695-1713.

Guo, J., X. Liang, and L.R. Leung. 2004. "A New Multi-scale Flow Network Generation Scheme for Land Surface Models." Geophys. Res. Lett., Vol 31, doi:10.1029/2004GL021381.

Guo, J., X. Liang, and L.R. Leung. 2004. "Impact of Different Precipitation Data Sources on Water Budgets." J. Hydrology, 298(1-4):311-334.

Liang, X., J. Guo, and L.R. Leung. 2004. "Assessment of the Effects of Spatial Resolutions on Daily Water Flux Simulations." J. Hydrology, 298(1-4):287-310.

**PI Yu Lin**

Lin, Y., X. Y. Wang, Z. Lin, and L. Chen, A Gyrokinetic Electron and Fully Kinetic Ion Plasma Simulation Model, Plasma Physics and Controlled Fusion, 47, 657, 2005.

Sun, X., Y. Lin, and X. Wang, Structure of Reconnection Layer With a Shear Flow Perpendicular to the Anti-Parallel Magnetic Field Component, Physics of Plasmas, 12, 012305, 2005.

Lin, Y. and X. Y. Wang, Three-Dimensional Global Hybrid Simulation of Dayside Dynamics Associated with the Quasi-Parallel Bow Shock, Journal of Geophysical Research, in press, 2005.

**PI Feng Liu**

Guang-Hong Lu and Feng Liu, Towards quantitative understanding of formation and stability of Ge hut island on Si(001), Physical Review Letters 94, 176103 (2005).

Guang-Hong Lu, Martin Cuma, and Feng Liu, First-principles study of strain stabilization of Ge(105) facet on Si(001), Physical Review B, in press.

Guang-Hong Lu, Minghuang Huang, Martin Cuma and Feng Liu, Relative stability of Si surfaces: a first-principles study, Surface Science 588, 61 (2005).

Bin Yan, Feng Liu, and M.G. Lagally, Local strain-mediated chemical potential control of quantum dot self-organization in heteroepitaxy, Physical Review Letters 92, 025502 (2004).

M. Huang, M. Cuma, and Feng Liu, Seeing the Atomic Orbital: first-principles study of effect of tip termination on atomic force microscopy, Physical Review Letters 90, 256101 (2003).

Minghuang Huang, P. Rugheimer, M. G. Lagally, and Feng Liu, Bending of nanoscale ultrathin substrates by growth of strained thin films and islands, Physical Review B, in press.

**PI Keh-Fei Liu**

`The Negativity of the Overlap-Based Topological Charge Density Correlator in Pure-Glue QCD and the Non-Integrable Nature of its Contact Part', I. Horvath, A. Alexandru, J.B. Zhang, Y. Chen, S.J. Dong, T. Draper, K.F. Liu, N. Mathur, S. Tamhankar, and H.B. Thacker, Phys. Lett. B617 (2005) 49-59, [hep-lat/0504005].

`Inherently Global Nature of Topological Charge Fluctuations in QCD', I. Horvath, A. Alexandru, J.B. Zhang, Y. Chen, S.J. Dong, T. Draper, F.X. Lee, K.F. Liu, N. Mathur, S. Tamhankar, and H.B. Thacker, Phys. Lett. B612 (2005) 21-28 [hep-lat/0501025].

`A Finite Baryon Density Algorithm', Keh-Fei Liu, QCD and Numerical Analysis III, p. 101, Springer, 2005

`A study of pentaquarks on the lattice with overlap fermions', N. Mathur, F.X. Lee, A. Alexandru, C. Bennhold, Y. Chen, S.J. Dong, T. Draper, I. Horvath, K.F. Liu, S. Tamhankar, and J.B. Zhang, Phys. Rev. D70 (2004) 074508 [hep-ph/0406196].

`Roper Resonance and S_{11}(1535) from Lattice QCD', N. Mathur, Y. Chen, S.J. Dong, T. Draper, I. Horvath, F.X. Lee, K.F. Liu, J.B. Zhang, Phys. Lett. B605 (2005) 137-143 [hep-ph/0306199].

`Chiral Logs in Quenched QCD', Y. Chen, S.J. Dong, T. Draper, I. Horvath, F.X. Lee, K.F. Liu, N. Mathur, J.B. Zhang, Phys. Rev. D70 (2004) 034502 [hep-lat/0304005].

`Heavy and Light and Quarks with Lattice Chiral Fermions', K.F. Liu and S.J. Dong, To appear in Int. Jou. Mod. Phys. (2005)

`Progress on a canonical finite density algorithm' Andrei Alexandru, Manfried Faber, Ivan Horvath, and Keh-Fei Liu, Nucl. Phys. Proc. Suppl. 140 (2005) 517 [hep-lat/0410002].

`Charmonium Spectrum from Quenched QCD with Overlap Fermions' S. Tamhankar, A. Alexandru, Y. Chen, S. J. Dong, T. Draper, I. Horvath, F. X. Lee, K. F. Liu, N. Mathur, and J. B. Zhang, Nucl. Phys. Proc. Suppl. 140 (2005) 434 [hep-lat/0409128].

`Nonperturbative renormalisation of composite operators with overlap quarks', J. B. Zhang, D. B. Leinweber, K. F. Liu, and A. G. Williams, Nucl. Phys. Proc. Suppl. 128 (2004) 240-247 [hep-lat/0311030].

`Improved Measure of Local Chirality', Terrence Draper, Andrei Alexandru, Ying Chen, Shao-Jing Dong, Ivan Horvath, Frank Lee, Nilmani Mathur, Harry B. Thacker, Sonali Tamhankar, and Jianbo Zhang, Nucl. Phys. Proc. Suppl. 140 (2005) 434 hep-lat/0408006].

`Low-dimensional long-range topological structure in the QCD vacuum', I. Horvath, S.J. Dong, T. Draper, F.X. Lee, K.F. Liu, N. Mathur, J.B. Zhang, and H.B. Thacker, Nucl. Phys. Proc. Suppl.129 (2004) 677.

**PI Zhengyu Liu**

Liu, Z., Q. Zhang, and L. Wu (2004). Remote Impact on Tropical Atlantic Climate Variability: Statistical Assessment and Dynamic Assessment. Journal of Climate 17(7), p. 1529-1549, DOI: 10.1175/1520-0442. CCR #820.

Liu, Z., W. Lewis, A Ganopolski (2004) A Coordinated Acceleration Scheme to the Simulation of Long Term Climate Evolution. Climate Dynamics 22: 771-781, DOI: 10.1007/s00382-004-0416-y. CCR #843

Liu, Z. and L. Wu. (2004): Atmospheric Response to North Pacific SST: The Role of Ocean-Atmosphere Coupling. J. Clim., 17,1859-1882.

Notaro, M., Z. Liu, R. Gallimore, S. Vavrus, J. Kutzbach, I.C. Prentice, and R. Jacob. Simulated and Observed Pre-Industrial to Modern Vegetation and Climate Changes. Accepted by Journal of Climate. CCR #854

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

Vavrus S., M. Notaro and Z. Liu, (2005) "A mechanism for abrupt climate change associated with tropical Pacific SSTs". J. Clim., in press.

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

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

Yang, H., Z. Liu and Q. Zhang, (2004): Tropical Ocean Decadal Variability and the Resonance of Planetary Wave Basin Modes: II: Numerical Study. J. Clim., 17, 1711-1721.

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

**PI Steven Louie**

A. Trave, F.J. Ribeiro, S.G. Louie and M.L. Cohen, "Energetics and structural characterization of C60 polymerization in BN and carbon Nanopeapods", Phys. Rev. B 70, 205418 (2004).

V. Brouet, W.L. Yang, X.J. Zhou, H.J. Choi, S.G. Louie, M.L. Cohen, A. Goldoni, F. Parmigiani, Z. Hussain and Z.X. Shen, "Orientation- dependent C60 electronic structures revealed by photoemission spectroscopy", Phys. Rev. Lett. 93, 197601 (2004).

M.L. Tiago, S. Ismail-Beigi, and S.G. Louie, "Effect of Semicore Orbitals on the Electronic Band Gaps of Si, Ge, and GaAs Within the GW Approximation", Phys. Rev. B 69, 125212 (2004).

K.H. Khoo, M.S.C. Mazzoni, and S.G. Louie, "Tuning the Electronic Properties of Boron Nitride Nanotbues with Transverse Electric Field s: A Giant DC Stark Effect", Phys. Rev. B 69, 201401 (2004).

M.L. Tiago, S. Ismail-Beigi, and S.G. Louie, "Photoisomerization of Azobenzene from First-Principles Constrained Density-Functional Calculations", J. Chem. Phys. 122, 094311 (2005).

M. Grobis, K.H. Khoo, R. Yamachika, X Lu, K. Nagaoka, S.G. Louie, M.F. Crommie, H. Kato and H. Shinohara, "Spatially Dependent Inelastic Tunneling in a Single Metallofullerene", Phys. Rev. Lett 94, 136802 (2005).

J.L. Li, G.M. Rignanese, and S.G. Louie, "Quasiparticle Energy Bands of NiO in the GW Approximation," Phys. Rev B 71, 193102 (2005).

M.L. Tiago, M. Rohlfing and S.G. Louie, "Bound Excitons and Optical Properties of Bulk Trans-Polyacetylene", Phys. Rev. B 70, 193204 (2004).

J.B. Neaton, K.H. Khoo, C.D. Spataru, and S.G. Louie, "Electronic Transport and Optical Properties of Carbon Nanostructures from First Principles", Comp. Phys. Comm. 169, 1 (2005).

**PI Walter Loveland**

R. Arratia-Perez, L. Hernadez-Acevedo and G. L. Malli," Calculated optical and magnetic properties of hexafluorouranate(V)anion:UF6-",J.Chem.Phys.121,7743 (2004).

G. L. Malli," Relativistic Quantum Chemistry of Heavy and Superheavy Elements:Fully Relativistic Coupled-Cluster Calculations for Molecules of Heavy and Transactinide Superheavy Elements", Fundamental World of Quantum Chemistry, Vol III,323-363(2004)..

G. L. Malli, M. Siegert and D. P. Turner, " Relativistic and Electron Correlation Effects for Molecules of Heavy Elements: Ab initio Fully Relativistic Coupled-Cluster Calculations for PbH4",Int .J. Quantum. Chem 99, 940-949(2004).

K. E. Gregorich and W. Loveland et al. " Attempts to confirm superheavy element production in the 48Ca+ 238U reaction", Phys .Rev. C 72, 014605(2005).

W. Loveland, A. Gallant and C. Joiner, J. Radioanal. Nucl. Chem. 263,1 51(2005).

W. Loveland," Synthesis of heavy nucleiusing radioactive beams",Nucl.Phys. A746,108c(2004).

P. R. Watson, W. Loveland, P. M. Zelinski, K .E. Gregorich and H. Nitsche, Nucl. Instru. Meth. Phys. Res.B 226,543(2004).

J. F. Liang, D. Shapira, C. J. Gross, J. R. Beene, J. D. Bierman, A. Galindo-Uribarri, J. Gomez del Compo, P. A. Hausladen, Y. Larochelle, W. Loveland et. al " Sub-barrier fusion enhancement in neutron-rich 132 Sn on 64 Ni", Prog. Theoret. Physics Supplement, 154,106 (2004).

## M

**PI Chung-Pei Ma**

M. Boylan--Kolchin, C.-P. Ma, and E. Quataert (2005), Monthly Notices of Royal Astronomical Society, 362, 184. [astro-ph/0502495] ``Dissipationless Mergers of Elliptical Galaxies and the Evolution of the Fundamental Plane''

B. Hagan, C.-P. Ma, and A. Kravtsov (2005), Astrophysical Journal, 633. ``Impact of Dark Matter Substructure on the Matter and Weak Lensing Power Spectra''

M. Boylan-Kolchin, C.-P. Ma, and E. Quataert (2004), Astrophysical Journal Letters, 613, L37. ``Core Formation in Galactic Nuclei due to Recoiling Black Holes''

**PI Evan Ma**

Atomic packing and short-to-medium range order in metallic glasses, H.W. Sheng, W.K. Luo, F.M. Alamgir, J.M. Bai, and E. Ma Nature, (accepted, 2005)

**PI Kyoko Makino**

D.A. Ovsyannikov, K. Makino, and M. Berz (Eds.), Proceedings, Eighth International Computational Accelerator Physics Conference, St. Petersburg, Russia, 2004. To appear as special Volumes of Nuclear Instruments and Methods.

M. Berz and K. Makino (Eds.), Proceedings, Seventh International Computational Accelerator Physics Conference, East Lansing, IOP Publishing Conference Series 175, 2004

M. Berz, K. Makino and Y.-K. Kim, Long-term Stability of the Tevatron by Validated Global Optimization, Nuclear Instruments and Methods, in print, 2005

C. J. Johnstone, M. Berz and K. Makino, Staging Accelerations in a Neutrino Factory, Nuclear Instruments and Methods, in print, 2005

P. Snopok, M. Berz, K. Makino, and C. Johnstone, Simulation and Optimization of the Tevatron Accelerator, Lecture Notes in Computer Science, Marcel Dekker, 2005

J. Grote, M. Berz and K. Makino, High-Order Representation of Poincare Maps, Lecture Notes in Computer Science, Marcel Dekker, 2005

M. Berz and K. Makino, Performance of Taylor Model Methods for Validated Integration of ODEs, PARA04 State of the Art in Scientific Computing, in print, 2005

P. V. Snopok, C. J. Johnstone, M. Berz, D.A. Ovsyannikov and A.D. Ovsyannikov, Study and Optimal Correction of a Systematic Skew Quadrupole Field in the Tevatron, Nuclear Instru-ments and Methods, in print, 2005

S. Manikonda and M. Berz, A Highly Accurate High-Order Method to Solve the Helmholtz Boundary Value Problem for the 3D Laplace Equation, International Journal of Pure and Applied Mathematics, in print, 2005

S.L. Manikonda and M. Berz, Multipole Expansion Solution of the Laplace Equation using Surface Data, Nuclear Instruments and Methods, 2004

K. Makino and M. Berz, Tetra Cooler Ring Simulations in COSY INFINITY, Neutrino Factories and Superbeams, AIP Conference Proceedings 721, 418, 2004

J. Grote, M. Berz and K. Makino, High-Order DA Methods for the Determination of Poincare Sections, Nuclear Instruments and Methods, 2004

M. Berz, K. Makino and C. J. Johnstone, Propagation of a Large-Emittance Muon Beam through a Straight, Quadrupole-based Precooling Channels, in: Neutrino Factories and Super-beams, AIP Conference Proceedings 721, 413, 2004

A. A. Poklonskiy, D. Neuffer, C.J. Johnstone, M. Berz and K. Makino, Optimizing the Adia-batic Buncher and Phase Rotator, Nuclear Instruments and Methods, 2004

K. Makino and M. Berz, COSY INFINITY Version 9, Nuclear Instruments and Methods, in print, 2004

D. Errede, M Berz, C. J. Johnstone, K. Makino, and A. van Ginneken. Stochastic processes in muon ionization cooling. Nuclear Instruments and Methods A519, 466-471, 2004

B. Erdelyi and M. Berz, Local Theory and Applications of Extended Generating Functions, International Journal of Pure and Applied Mathematics, 11,3, 241-282, 2004

C. J. Johnstone, M. Berz, D. Errede, and K. Makino. Muon beam ionization cooling in a linear quadrupole channel. Nuclear Instruments and Methods A519, 472-482, 2004

C. O. Maidana, M. Berz, and K. Makino. Muon beam ring cooler simulations using COSY INFINITY. IOP Conference Proceedings 175, 211-218, 2004

M. L. Shashikant, M. Berz, and B. Erdelyi. COSY Infinity EXPO symplectic tracking for LHC. IOP Conference Proceedings 175, 299-305, 2004

K. Makino, M. Berz, D. Errede, and C. J. Johnstone. High order map treatment of superimposed cavities, absorbers, and magnetic multipole and solenoid fields. Nuclear Instruments and Methods A519, 162-174, 2004

M. Berz and K. Makino. New approaches for the validation of transfer maps using remain-der-enhanced differential algebra. Nuclear Instruments and Methods A519, 53-62, 2004

**PI Osni Marques**

A Survey of High Quality Computational Libraries and Their Impact in Science and Engineering Applications, T. Drummond, O. Marques, J. Roman and V. Vidal. High Performance Computing for Computational Science - VECPAR 2004, Lecture Notes in Computer Science 3402, Springer Verlag.

Building A Software Infrastructure for Computational Science Applications: Lessons and Solutions, O. Marques and T. Drummond, Second International Workshop on Software Engineering for High Performance Computing System Applications, St. Louis, MO - May 15, 2005.

**PI Angelo Mascarenhas**

Y. Zhang, A. Mascarenhas, and L.W. Wang, III-V-Bi versus III-V-N: similar and dissimilar aspects, Phys. Rev. B 71, 155201 (2005).

B. S. Ma, F. H. Su, K. Ding, G. H. Li, Y. Zhang, A. Mascarenhas, H. P. Xin, and C. W. Tu, Pressure behavior of the alloy band-edge and nitrogen related centers in GaAs0.999N0,001, Phys. Rev. B 71, 45213 (2005).

Y. Zhang and A. Mascarenhas, Total and negative refraction of electromagnetic waves, Modern Physics Letters B 19, 21 (2005) (An invited review paper).

B. Fluegel, Y. Zhang, J. F. Geisz, and A. Mascarenhas, Confirmation of the impurity-band model for GaP(1-x)Nx, Phys. Rev. B (in press).

B. Fluegel, Y. Zhang, J. F. Geisz, and A. Mascarenhas, Comment on Experimental evidence for N-induced strong coupling of host conduction band states in GaP(1-x)Nx: Insight into the dominant mechanism for giant band-gap bowing, Phys. Rev. B (accepted)

**PI Manos Mavrikakis**

"Why Au and Cu are more selective than Pt for Preferential Oxidation of CO at low temperature", S. Kandoi, A. A. Gokhale, L. C. Grabow, J. A. Dumesic, M. Mavrikakis, Catalysis Letters 93, 93 (2004).

"Competitive Paths for Methanol Decomposition on Pt(111)", J. Greeley, M. Mavrikakis, Journal of the American Chemical Society 126, 3910 (2004).

"Adsorption and dissociation of O2 on Pt-Co and Pt-Fe alloys", Y. Xu, A. Ruban, M. Mavrikakis, Journal of the American Chemical Society 126, 4717 (2004).

"Strain-Induced Formation of Subsurface Species in Transition Metals", J. Greeley, W. P. Krekelberg, M. Mavrikakis, Angewandte Chemie International Edition 43, 4296 (2004).

"Effect of Sn on the reactivity of Cu surfaces", A. A. Gokhale, G. Huber, J. A. Dumesic, M. Mavrikakis, Journal of Physical Chemistry B 108, 14062 (2004).

"Molecular-level Descriptions of Surface Chemistry in Kinetic Models using Density Functional Theory", with A. Gokhale, S. Kandoi, J. Greeley, M. Mavrikakis, J. A. Dumesic, Chemical Engineering Science 59, 4679 (2004).

"A New Class of Alloy Catalysts Designed from First-Principles", J. Greeley, M. Mavrikakis, Nature Materials 3, 810 (2004).

"Trends of Low Temperature Water Gas Shift Reactivity on Transition Metals", N. Schumacher, A. Boisen, S. Dahl, A. A. Gokhale, S. Kandoi, L. C. Grabow, J. A. Dumesic, M. Mavrikakis, I. Chorkendorff, Journal of Catalysis 229, 265 (2005).

"Surface and Subsurface Hydrogen: Adsorption Properties on Transition Metals and Near-Surface Alloys", J. Greeley, M. Mavrikakis, Journal of Physical Chemistry B 109, 3460 (2005).

"Controlling the Catalytic Activity of Platinum Monolayer Electrocatalysts for Oxygen Reduction with Different Substrates", J. Zhang, M.B. Vukmirovic, Y. Xu, M. Mavrikakis, R. R. Adzic, Angewandte Chemie International Edition 44, 2132 (2005).

"On the origin of the catalytic activity of nanometer gold particles for low temperature CO oxidation", N. Lopez, T. V. W. Janssens, B. S. Clausen, Y. Xu, M. Mavrikakis, T. Bligaard, J. K. N�rskov, Journal of Catalysis - Priority Communication, 223, 232 (2004).

"Effect of Subsurface Oxygen on the Reactivity of the Ag(111) Surface", Y. Xu, J. Greeley, M. Mavrikakis, Journal of the American Chemical Society, 127, 12823 (2005).

"Mixed-Metal Pt Monolayer Electrocatalysts for Enhanced Oxygen Reduction Kinetics", J. Zhang, M.B. Vukmirovic, K. Sasaki, A.U. Nilekar, M. Mavrikakis, R.R. Adzic, Journal of the American Chemical Society (Communication), 127, 12480 (2005).

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

"Near Surface Alloys for Hydrogen Fuel Cell Applications", J. Greeley, M. Mavrikakis, Catalysis Today (in press).

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

"Near Surface Alloys for Hydrogen Fuel Cell Applications", J. Greeley, M. Mavrikakis, Catalysis Today (in press).

"Effect of Subsurface Oxygen on the Reactivity of the Ag(111) Surface", Y. Xu, J. Greeley, M. Mavrikakis, Journal of the American Chemical Society (in press).

"Mixed-Metal Pt Monolayer Electrocatalysts for Enhanced Oxygen Reduction Kinetics", J. Zhang, M.B. Vukmirovic, K. Sasaki. A.U. Nilekar, M. Mavrikakis, R.R. Adzic, Journal of the American Chemical Society (in press).

**PI William McCurdy**

D. A. Horner, J. Colgan, F. Martin, C. W. McCurdy and M. S. Pindzola and T. N. Rescigno, "Symmetrized Complex Amplitudes for He Double Photoionization from the Time-Dependent Close Coupling and Exterior Complex Scaling Methods", Phys. Rev. A 70, 064701 (2004).

D. A. Horner, C. W. McCurdy and T. N. Rescigno, "Electron-Helium Scattering in the S-wave Model Using Exterior Complex Scaling", Phys. Rev. A 71, 012701 (2005).

W. Vanroose, F. Martin, T. N. Rescigno and C. W. McCurdy,"Nonperturbative Theory of Double Photoionization of the Hydrogen Molecule", Phys. Rev. A 70, 050703 (2004).

D. A. Horner, C. W. McCurdy and T. N. Rescigno, "Electron Impact Excitation-Ionization of Helium in the S-Wave Limit", Phys. Rev. A 71, 010701 (2005).

C. S. Trevisan, K. Houfek, Zh. Zhang, A. E. Orel, C. W. McCurdy and T. N. Rescigno, "A Nonlocal Model of Dissociative Electron Attachment and Vibrational Excitation of NO", Phys. Rev. A 71, 052714 (2005).

D.J. Haxton, C. W. McCurdy and T. N. Rescigno, "Topology of the Adiabatic Potential Energy Surfaces for the Resonance States of the Water Anion", Phys. Rev. A 72, 022705 (2005).

**PI William McMahon**

"Step structures on MOVCD grown III-V phosphide (001) surfaces: How do steps and Sb affect CuPt ordering of GaInP?"; I.G. Batyrev, W.E. McMahon, S.B Zhang, J.M. Olson, and S.-H. Wei; Phys. Rev. Lett. 94, 096101 (2005).

"Borderline Magic Clustering: The Fabrication of Tetravalent Pb Cluster Arrays on Si(111) - (7 x 7) Surfaces"; Shao-Chun Li, Jin-Feng Jia, Rui-Fen Dou, Qi-Kun Xue, Iskander G. Batyrev, and S. B. Zhang; Phys. Rev. Lett. 93, 116103 (2004).

"An STM and LEED Study of MOCVD-Prepared P/Ge (100) to (111) Surfaces"; W.E. McMahon, A.E. Kibbler and J.M. Olson; Surf. Sci. 571 (1-3), 146-156 (2004).

"Tip size effect on the appearance of a STM image for complex surfaces: Theory versus experiment for Si(111)-7x7"; Y. L. Wang, H.-J. Gao, H. M. Guo, H. W. Liu, I. G. Batyrev, W. E. McMahon, and S. B. Zhang; Phys. Rev. B 70, 073312 (2004).

"An RDS, LEED, and STM Study of MOCVD-Prepared Si(100) Surfaces"; T. Hannappel, W.E. McMahon and J.M. Olson; J. Cryst. Growth 272 (1-4), 24-29 (2004).

**PI Anthony Mezzacappa**

"A Comparison of Algorithms for the Efficient Solution of the Linear Systems Arising from Multi-Group Flux-Limited Diffusion Problems", F.D. Swesty, D. C. Smolarski, and P. Saylor, The Astrophysical Journal Supplement ser., vol. 153, 369 (2004), July (2004)

"Self-consistent Hartree-Fock mass formulae: a review", J.Rikovska Stone, J.Phys.G: Nucl.Part.Phys. 31, R1-R20 (2005)

"The Double Pulsar J0737-3039: Testing the neutron star equation of state" Ph.Podsiadlowski, J.D.M.Dewi, P.Lesaffre, J.C.Miller, W.Newton and J.R.Stone, Mon.Not.R.Astron.Soc, 361, 1243 (2005)

"Dipole giant resonance in heavy deformed nuclei" J.A.Maruhn, P.-G.Reinhard, P.D.Stevenson, J.Rikovska Stone, M.R.Strayer, Phys.Rev. C71, 064328 (2005)

"Magnetic moments of 2 1 states around 132Sn" B.A.Brown, N.J.Stone, J.R.Stone, I.Towner and M.Hjorth-Jensen, Phys.Rev.C71, 044327 (2005)

"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, Nucl. Phys. A747, 87 (2005)

"Gamow-Teller GT distributions in nuclei with mass 90<=A<=97", A. Juodagalvis and D.J. Dean, in press, Phys. Rev. C (2005)

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

"Advances in Multi-dimensional Simulation of Core-Collapse Supernovae", F. D. Swesty and E. S. Myra, To appear in Open Issues in Core Collapse Supernovae, June (2005)

"Issues with Core-Collapse Supernova Progenitor Models", S. W. Bruenn, To appear in Open Issues in Core Collapse Supernovae, June (2005)

Equation of state for baryonic matter: J.R.Stone, To appear in Open Issues in Understanding of Core-Collapse Supernovae (June 2005)

**PI David Mikkelsen**

"Studies of Improved Electron Confinement on NSTX," D. Stutman, K. W. Hill, S. M. Kaye, M. H. Redi, E. J. Synakowski, M. G. Bell, R. E. Bell, C. Bourdelle, W. Dorland, M. Finkenthal, S. Kubota, B. P. LeBlanc, F. Levinton, J. E. Menard, D. R. Mikkelsen, K. Tritz, and the NSTX Team, submitted to Nuclear Fusion, early version is available as paper EX/P2-8, IAEA Fusion Energy Conference, 1-6 November 2004, Vilamoura, Portugal.

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

"Impact of the alpha parameter on the microstability of internal transport barriers", C. Bourdelle, G.T. Hoang, X. Litaudon, C.M. Roach and T. Tala for the ITPA Topical Group on Transport and ITB Physics, and the International ITB Database Working Group, Nucl. Fusion 45 (2005) 110-130

"Transport modelling and gyrokinetic analysis of advanced high performance discharges", J.E. Kinsey, F. Imbeaux, G.M. Staebler, R. Budny, C. Bourdelle, A. Fukuyama, X. Garbet, T. Tala, V. Parail, for the ITPA Topical Group on Transport Physics and the ITB Database Working Group Nucl. Fusion 45 (2005) 450-458

**PI Norman Miller**

Miller, N.L., A.W. King, M.A. Miller, E.P. Springer, M.L. Wesely and others. 2005: The Doe Water Cycle Pilot Study, Bull. Amer. Meteorological Soc., 359-374.

Maxwell, R.M. and N.L. Miller, 2005: On the development of a coupled land surface and groundwater model for use in watershed management. J. Hydrometeorology. 6, 233-247.

Brekke, L.D., N.W.T. Quinn, N.L. Miller, and J.A. Dracup, 2004: Climate Change Impacts Uncertainty for San Joaquin River Basin, J. Amer. Water Resources Assoc., 40, 149-164.

Hayhoe, K., D. Cayan, C.B. Field, P.C. Frumhoff, E.P. Maurer, N.L. Miller, S.C. Moser, S.H. Schneider, and Others, 2004: Emissions Pathways, Climate Change, and Impacts on California. Proc. National Academy of Science, 101, 12422-12427. Maxwell, R.M. and N.L. Miller, 2005: On the development of a coupled land surface and groundwater model for use in watershed management.

Quinn, N.W.T., L.D. Brekke, N.L. Miller, T. Hienzer, H. Hildalgo, and J.A. Dracup, 2004: Model integration for assessing future hydroclimate impacts on water resources, agricultural production, and environmental quality in the San Joaquin Basin, California. Envir. Modeling and Software, 19, 305-316.

**PI William Miller**

Yamamoto T, Miller WH, "Path integral evaluation of the quantum instanton rate constant for proton transfer in a polar solvent", Journal of Chemical Physics 122 (4): Art. No. 044106 Jan 22 2005

Vanicek J, Miller WH, Castillo JF, et al., "Quantum-instanton evaluation of the kinetic isotope effects", Journal of Chemical Physics ,123 (5): Art. No. 054108 Aug 1 2005

Predescu C, Miller WH, "Optimal choice of dividing surface for the computation of quantum reaction rates", Journal of Physical Chemistry B 109 (14): 6491-6499 Apr 14 2005

Ceotto M, Yang S, Miller WH, "Quantum reaction rate from higher derivatives of the thermal flux-flux autocorrelation function at time zero". Journal of Chemical Physics, 122 (4): Art. No. 044109 Jan 22 2005

Li YM, Miller WH, "Different time slices for different degrees of freedom in Feynman path integration", Molecular Physics 103 (2-3): 203-208 Jan-Feb 2005

**PI Warren Mori**

C. Ren, M. Tzoufras, F. S. Tsung, W. B. Mori, S. Amorini, R. A. Fonseca, L. O. Silva, J. C. Adam, and A. Heron, "Global Simulation for Laser-Driven MeV Electrons in Fast Ignition", Phys. Rev. Lett., 93, 185004 (2004).

M. S. Wei, S. P. D. Mangles, Z. Najmudin, B. Walton, A. Gopal, M. Tatarakis, A. E. Dangor, E. L. Clark, R. G. Evans, S. Fritzler, R. J. Clarke, C. Hernandez-Gomez, D. Neely, W. Mori, M. Tzoufras, and K. Krushelnick, "Ion Acceleration by Collisionless Shocks in High-Intensity Laser-Underdense Plasma Interaction", Phys. Rev. Lett., 93, 155003 (2004).

M. J. Hogan, C. D. Barnes, C. E. Clayton, F. J. Decker, S. Deng, P. Emma, C. Huang, R. H. Iverson, D. K. Johnson, C. Joshi, T. Katsouleas, P. Krejcik, W. Lu, K. A. Marsh, W. B. Mori, P. Muggli, C. L. O’ ???END Connell, E. Oz, R. H. Siemann, and D. Walz, "Multi-GeV Energy Gain in a Plasma-Wakefield Accelerator", Phys. Rev. Lett., 95, 054802 (2005).

S. P. D. Mangles, B. R. Walton, M. Tzoufras, Z. Najmudin, R. J. Clarke, A. E. Dangor, R. G. Evans, S. Fritzler, A. Gopal, C. Hernandez-Gomez, W. B. Mori, W. Rozmus, M. Tatarakis, A. G. R. Thomas, F. S. Tsung, M. S. Wei, and K. Krushelnick, "Electron Acceleration in Cavitated Channels Formed by a Petawatt Laser in Low-Density Plasma", Phys. Rev. Lett., 94, 245001 (2005).

S. P. D. Mangles et al, "Monoenergetic beams of relativistic electrons from intense laser-plasma interactions", Nature, 431, p. 535 (2004).

F. S. Tsung, R. Narang, W. B. Mori, C. Joshi, R. A. Fonseca, and L. O. Silva, "Near-GeV-Energy Laser- Wakefield Acceleration of Self-Injected Electrons in a Centimeter-Scale Plasma Channel", Phys. Rev. Lett., 93, 185002 (2004).

C. Ren, M. Tzoufras, F. S. Tsung, W. B. Mori, S. Amorini, R. A. Fonseca, L. O. Silva, J. C. Adam, and A. Heron, "Global Simulation for Laser-Driven MeV Electrons in Fast Ignition", Phys. Rev. Lett., 93, 185004 (2004).

M. S. Wei, S. P. D. Mangles, Z. Najmudin, B. Walton, A. Gopal, M. Tatarakis, A. E. Dangor, E. L. Clark, R. G. Evans, S. Fritzler, R. J. Clarke, C. Hernandez-Gomez, D. Neely, W. Mori, M. Tzoufras, and K. Krushelnick, "Ion Acceleration by Collisionless Shocks in High-Intensity Laser-Underdense Plasma Interaction", Phys. Rev. Lett., 93, 155003 (2004).

**PI James Morris**

M. Krcmar, C. L. Fu and J. R. Morris, 'First-principles Study of Structural and Defect Properties in FeCo Intermetallics," Integrative and Interdisciplinary Aspects of Intermetallics, edited by M. Mills, 842, S1.4.1 (2004).

Rachel S. Aga, James R. Morris and Mikhail I. Mendelev, "Homogeneous Crystal Nucleation in Undercooled Aluminum," to appear in TMS Letters.

## N

**PI Farrokh Najmabadi**

A. Grossman, T.Kaiser, P.K.Mioduszeski, "Magnetic Structure at the Edge of a Compact Stellarator (NCSX) Journal of Nuclear Materials 337-339 (2005) 400-404.

P.Mioduszewski, A. Grossman, et al. Journal of Nuclear Materials 313 (2003) 1304.

A.E. Koniges, A. Grossman, et al. Nuclear Fusion 43 (2003) 107.

A.Grossman, "Magnetic Fields at the Scrape-Off Layer of a Compact Stellarator (NCSX)" presented at 16th International Conference on Plasma Surface Interactions in Controlled Fusion Devices, Portland, USA May 24-28 2004

T.K. Mau, H.McGuiness, A.Grossman, R.Raffray, D. Steiner, "Divertor Heat Load Studies for Compact Stellarator Reactors" to be presented at the 21th Symposium on Fusion Engineering, Knoxville Tenessee (2005). Paper to be published thereafter.

**PI Rick Nebel**

"The SEL macroscopic modeling code," A.H. Glasser and X.Z. Tang, Computer Physics Communications; Dec 1 2004; v.164, no.1-3, p.237-243.

"A nonstaggered, conservative, Del .B=0, finite-volume scheme for 3D implicit extended magnetohydrodynamics in curvilinear geometries," L. Chacon, Computer Physics Communications; 15 Nov. 2004; vol.163, no.3, p.143-71.

"Volume preserving integrators for solenoidal fields on a grid," J.M. Finn and L. Chacon, Physics of Plasmas; May 2005; vol.12, no.5, p.54503-1-4.

"New role of the lower-hybrid drift instability in the magnetic reconnection," Ricci, Paolo; Brackbill, JU; Daughton, W.; Lapenta, Giovanni, Physics of Plasmas; May 2005; v.12, no.5, p.1-7.

"Nonlinear evolution of the lower-hybrid drift instability in a current sheet," Daughton, W; Lapenta, G; Ricci, P, Physical Review Letters; 3 Sept. 2004; vol.93, no.10, p.105004/1-4.

"Force-free magnetic relaxation in driven plasmas," X.Z. Tang and A.H.Boozer, Physical Review Letters 94, 225004 (2005).

"Constrained resonance in magnetic self-organization," X.Z. Tang and A.H. Boozer, Physical Review Letters (in press, 2005).

"Flux amplification in helicity injected spherical tori," X.Z.Tang and A.H.Boozer, Phys. Plasmas 12, 042113 (2005).

"Chandrasekhar-Kendall modes and Taylor relaxation in an axisymmetric torus," X.Z. Tang and A.H. Boozer, Phys. Plasma (in press, 2005).

**PI John Negele**

The N to Delta electromagnetic transition form-factors from lattice QCD. C. Alexandrou, Ph. de Forcrand, H. Neff, J. W. Negele, W. Schroers, A. Tsapalis Phys.Rev.Lett.94:021601,2005. [hep-lat/0409122]

N to Delta electromagnetic transition form-factors from lattice QCD. C. Alexandrou, Ph. de Forcrand, Th. Lippert, H. Neff, J. W. Negele, K. Schilling, W. Schroers, A. Tsapalis Phys.Rev.D69:114506,2004. [hep-lat/0307018]

Transverse structure of nucleon parton distributions from lattice QCD. Ph. Haegler, J. W. Negele, D. B Renner, W. Schroers, Th. Lippert, and K. Schilling Phys.Rev.Lett.93:112001,2004. [hep-lat/0312014]

Confinement from merons. By F. Lenz, J.W. Negele, M. Thies. Phys.Rev.D69:074009,2004. [hep-th/0306105]

Helicity dependent and independent generalized parton distributions of the nucleon in lattice QCD. Ph. Haegler, J. W. Negele, D. B Renner, W. Schroers, Th. Lippert, and K. Schilling Eur.Phys.J.A24s1:29-33,2005. [hep-ph/0410017]

Hadronic physics with domain-wall valence and improved staggered sea quarks. D. B Renner, W. Schroers, R. Edwards, G. T. Fleming, Ph. Haegler, J. W. Negele, K. Orginos, A.V. Pochinsky, D. Richards Nucl.Phys.Proc.Suppl.140:255-260,2005. [hep-lat/0409130]

Momentum dependence of the N to Delta transition form-factors. C. Alexandrou, Ph. de Forcrand, H. Neff, J. W. Negele, W. Schroers, A. Tsapalis Nucl.Phys.Proc.Suppl.140:293-295,2005. [hep-lat/0408017]

Insight into nucleon structure from lattice calculations of moments of parton and generalized parton distributions. J.W. Negele, R.C. Brower, P. Dreher, R. Edwards, G. Fleming Ph. Haegler, Th. Lippert, A.V. Pochinsky, D. B. Renner, D. Richards, K. Schilling, W. Schroers Nucl.Phys.Proc.Suppl.128:170-178,2004. [hep-lat/ 0404005]

A Partially quenched analysis of the eta - eta-prime system in N(f) = 2 QCD. By H. Neff, Th. Lippert, J. Negele, K. Schilling. Nucl.Phys.Proc.Suppl.129:218-220,2004. [hep-lat/0401004]

**PI Brian Nelson**

Aps Invited Talk Paper: Three-dimensional magnetohydrodynamic simulations of the Helicity Injected Torus with Steady Inductive drive Izzo, V.A. (Univ. of Washington, Seattle, WA, USA); Jarboe, T.R. Source: Physics of Plasmas, v 12, n 5, May 2005, p 56109-1-8

Initial studies of steady inductive helicity injection on the HIT-SI experiment Sieck, P.E. (Univ. of Washington, Seattle, WA, USA); Hamp, W.T.; Izzo, V.A.; Jarboe, T.R.; Nelson, B.A.; O'Neill, R.G.; Redd, A.J.; Smith, R.J. Source: IEEE Transactions on Plasma Science, v 33, n 2, pt.2, April 2005, p 723-8

Recent results from the HIT-SI spheromak Sieck, P.E. (Washington Univ., St. Louis, MO, USA); Hamp, W.T.; Izzo, V.A.; Jarboe, T.R.; Nelson, B.A.; O'Neill, R.G.; Redd, A.J.; Smith, R.J. Source: IEEE Conference Record - Abstracts. 31st IEEE International Conference On Plasma Science (IEEE Cat. No.04CH37537), 2004, p 160

**PI Gregory Newman**

Commer, M., and Newman, G., 2004, A parallel finite-difference approach for three-dimensional transient electromagnetic modeling with galvanic sources: Geophysics, Soc. of Expl. Geophys., 69, 1192-1202.

Newman, G. A., and Boggs, P. T., 2004, Solution accelerators for large-scale three-dimensional electromagnetic inverse problems: Inverse Problems, 20, S151-S170.

Newman, G. A., and Commer, M., 2005, New advances in transient electromagnetic inversion: Geophysical Journal International, 160, 5-32.

Newman, G. A., Hoversten, M., Gasperikova, E., and Wannamaker, P.E., 2005, 3D Magnetotelluric Characterization of the Coso Geothermal Field: Proc. 30th Workshop on Geothermal Reservoir Engineering, Stanford University, Stanford California, January 31-February 2, SGP- TR-176.

**PI Cheuk-Yiu Ng**

P. Wang, H. K. Woo, K.-C. Lau, X. Xing, C. Y. Ng, A. Zyubin and A. Mebel J. Chem. Phys. 2005 (submitted). "Infrared vibrational spectroscopy of cis-dichloroethene in Rydberg states."

K.-C. Lau and C. Y. Ng, J. Chem. Phys. 122, 224310 (2005). "Accurate ab initio predictions of ionization energies of hydrocarbon radicals: CH2, CH3, C2H, C2H3, C2H5, C3H3, and C3H5."

J. Yang, Y. Mo, K. C. Lau, Y. Song, X. M. Qian, and C. Y. Ng, Phys. Chem. Chem. Phys. 7, 1518 (2005). "A combined vacuum ultraviolet laser and synchrotron pulsed field ionization study of BCl3."

C. Y. Ng, Journal of Electron Spectroscopy and Related Phenomena (Invited review) 142, 179 (2005). "Two-color photoionization and photoelectron studies by combining infrared and vacuum ultraviolet."

P. Wang, X. Xing, S. J. Baek, and C. Y. Ng, J. Phys. Chem. A (Letter) 108, 10035, (2004). "Rovibrationally selected and resolved pulsed field ionization-photoelectron study of ethylene."

A. Brooks, K.-C. Lau, C. Y. Ng, and T. Baer, Eur. J. Mass. Spectro. 10, 819 (2004). "The C3H7 appearance energy from 2-iodopropane and 2-chloropropane studied by threshold photoelectron photoion coincidence."

P. Wang, X. Xing, K.-C. Lau, H. K. Woo, C. Y. Ng, J. Chem. Phys.(communications) 121, 7049 (2004). "Rovibrational-state-selected pulsed field ionization-photoelectron study of methyl iodide using two-color infrared-vacuum ultraviolet lasers."

M. Hochlaf, T. Baer, X. M. Qian, and C. Y. Ng, J. Chem. Phys. 123, in press (2005). "A Photoionization and Pulsed Field Ionization-Photoelectron Study of Cyanogen."

M.-K. Bahng, X. Xing, S. J. Baek, and C. Y. Ng, J. Chem. Phys. 123, 084133 (2005). "A two-color infrared-vacuum ultraviolet laser pulsed field ionization photoelectron study of NH3."

X. N. Tang, Y. Hou, C. Y. Ng, and B. Ruscic, J. Chem. Phys. 123, 074330(2005). "Pulsed field ionization photoelectron-photoion coincidence study of the process N2 plus hv -> 2N and e-: Bond Dissociation Energies of N2 and N2 cation."

T.-S. Chu, R.-F. Lu, K.-L. Han, X.-N. Tang, H.-F. Xu, and C. Y. Ng, J. Chem. Phys. 122, 244322 (2005). "A time-dependent wave-packet quantum scattering study of the reaction H2 (v=0-2,4,6;j=1) and He -> HeH and H."

X. N. Tang, H. F. Xu, T. Zhang, Y. Hou, C. Chang, C. Y. Ng, Y. Chiu, R. A. Dressler, and D. J. Levandier, J. Chem. Phys. 122, 164301 (2005). "A pulsed-field ionization photoelectron secondary ion coincidence study of the H2(X,v=0--15,N=1) plus He proton transfer reaction."

**PI Esmond Ng**

Timothy A. Davis, John R. Gilbert, Stefan I. Larimore, and Esmond G. Ng, "A column approximate minimum degree ordering algorithm". ACM Trans. Math. Software 30 (2004), pp. 353-376.

Timothy A. Davis, John R. Gilbert, Stefan Larimore, and Esmond G. Ng. "Algorithm 836: COLAMD, a column approximate minimum degree ordering algorithm". ACM Trans. Math. Software 30 (2004), pp. 377-380.

L. Grigori and X. S. Li. "Performance Analysis of Parallel Right-looking Sparse LU Factorization on Two-dimensional Grids of Processors". To appear in Proceedings of the PARA04 Workshop on State-of-the art in Scientific Computing, Springer Lecture Notes in Computer Science.

Xiaoye S. Li. "An Overview of SuperLU: Algorithms, Implementation, and User Interface". ACM Trans. on Math. Software, Vol. 31, No. 3, 2005.

Chao Yang, Esmond G. Ng, and Pawel A. Penczek. "Matrix-free Constructions of Circulant and Block Circulant Preconditioners". Numerical Linear Algebra and Applications 11 (2004), pp. 773-793.

Chao Yang, Esmond G. Ng, and Pawel A. Penczek, "Unified 3-D Structural and Projection Orientation Refinement Using Quasi-Newton Algorithm". J. Structural Biology 149 (2005), pp. 53-64.

Chao Yang, Weiguo Gao, Zhaojun Bai, Xiaoye S. Li, Lie-Quan Lee, Parry Husbands, and Esmond G. Ng, "An Algebraic Sub-structuring Algorithm for Large-scale Eigenvalue Calculation". To appear in SIAM J. Sci. Comput., 2005.

Chao Yang, Weiguo Gao, Zhaojun Bai, Xiaoye Li, Lie-Quan Lee, Parry Husbands, and Esmond G. Ng. "Algebraic Sub-structuring for Electromagnetic Applications". To appear in Proceedings of the PARA04 Workshop on State-of-the-art in Scientific Computing (as Lecture Notes in Computer Science), Springer, 2005.

Padma Raghavan, Ingyu Lee, and Esmond G. Ng. "Effective Preconditioning Through Ordering Interleaved With Incomplete Factorization". Submitted to SIAM J. Matrix Anal. Appls. (LBNL-58671)

Weiguo Gao, Xiaoye S. Li, Chao Yang, and Zhaojun Bai. "Performance Evaluation of a Multilevel Sub-structuring Method for Sparse Eigenvalue Problems". To appear in Proceedings of the 16th International Conference on Domain Decomposition Methods, Springer Lectures Notes in Computational Science and Engineering.

**PI Arthur Nozik**

C. Engtrakul, J.M. Nedeljkovic, Yong-Hyun Kim, S.P. Ahrenkiel, K.E.H. Gilbert, J.L. Alleman, S.B. Zhang, O.I. Micic, A.J. Nozik, and M.J. Heben, Self-Organization of Semiconductor Quantum Nanocrystals on Carbon Single-Wall Nanotubes into Close-Packed Linear Arrays, in Functional Carbon Nanotubes, edited by D.L. Carroll, B. Weisman, S. Roth, and A. Rubio (Mater. Res. Soc. Symp. Proc. 858E, Warrendale, PA , 2005), HH12.6.

Yong-Hyun Kim, M. J. Heben, and S. B. Zhang, First-Principles Band Offsets of Carbon Nanotubes with III-V Semiconductors, Proceedings of the 27th International Conference on the Physics of Semiconductors (Flagstaff, 2004), AIP Conference Proceedings 772, 1031 (2005).

Yufeng Zhao, Yong-Hyun Kim, Mao-Hua Du, and S. B. Zhang, Icosahedral Quantum Dots and 2D Quasicrystals for Group IV Semiconductors, Proceedings of the 27th International Conference on the Physics of Semiconductors (Flagstaff, 2004), AIP Conference Proceedings 772, 625 (2005).

Jun Feng, Shi-You Ding, Melvin P. Tucker, Michael E. Himmel, Yong-Hyun Kim, S. B. Zhang, Brian M. Keyes, and Garry Rumbles, Cyclodextrin driven hydrophobic/hydrophilic transformation of semiconductor nanoparticles, Appl. Phys. Lett. 86, 033108 (2005).

Yufeng Zhao, Yong-Hyun Kim, A.C. Dillon, M.J. Heben, and S.B. Zhang, Hydrogen storage in novel organometallic buckyballs, Phys. Rev. Lett. 94, 155504 (2005).

**PI Peter Nugent**

"Could There Be a Hole in Type Ia Supernovae?; " Kasen, D., P. Nugent, R. C. Thomas, & L. Wang Astrophysical Journal, vol:610, 2004.

"Type IIP Supernovae as Cosmological Probes: A Spectral-fitting Expanding Atmosphere Model Distance to SN 1999em; " Baron, E., P. E. Nugent, D. Branch, & P. H. Hauschildt Astrophysical Journal, vol:616, 2004.

"Discovery of a Transient U-Band Dropout in a Lyman Break Survey: A Tidally Disrupted Star at z=3.3?; " Stern, D., P. G. van Dokkum, P. Nugent, D. J. Sand, R. S. Ellis, M. Sullivan, J. S. Bloom, D. A. Frail, J.-P. Kneib, L. V. E. Koopmans, & T. Treu Astrophysical Journal, vol:612, 2004.

"A Definitive Measurement of Time Dilation in the Spectral Evolution of the Moderate-Redshift Type Ia Supernova 1997ex; " Foley, R. J., A. V. Filippenko, D. C. Leonard, A. G. Riess, P. Nugent, & S. Perlmutter Astrophysical Journal, vol:626, 2005.

"GRB 020410: A Gamma-Ray Burst Afterglow Discovered by Its Supernova Light; " Levan, A., P. Nugent, A. Fruchter, I. Burud, D. Branch, J. Rhoads, A. Castro-Tirado, J. Gorosabel, J. M. C. Cer�n, S. E. Thorsett, C. Kouveliotou, S. Golenetskii, J. Fynbo, P. Garnavich, S. Holland, J. Hjorth, P. M�ller, E. Pian, N. Tanvir, M. Ulanov, R. Wijers, & S. Woosley Astrophysical Journal, vol:624, 2005.

"Restframe I-band Hubble diagram for type Ia supernovae up to redshift z ~ 0.5;" Nobili, S., R. Amanullah, G. Garavini, A. Goobar, C. Lidman, V. Stanishev, G. Aldering, P. Antilogus, P. Astier, M. S. Burns, A. Conley, S. E. Deustua, R. Ellis, S. Fabbro, V. Fadeyev, G. Folatelli, R. Gibbons, G. Goldhaber, D. E. Groom, I. Hook, D. A. Howell, A. G. Kim, R. A. Knop, P. E. Nugent, R. Pain, S. Perlmutter, R. Quimby, J. Raux, N. Regnault, P. Ruiz-Lapuente, G. Sainton, K. Schahmaneche, E. Smith, A. L. Spadafora, R. C. Thomas, L. Wang, & The Supernova Cosmology Project Astronomy and Astrophysics, vol:437, 2005.

"Spectroscopic confirmation of high-redshift supernovae with the ESO VLT.;" Lidman, C., D. A. Howell, G. Folatelli, G. Garavini, S. Nobili, G. Aldering, R. Amanullah, P. Antilogus, P. Astier, G. Blanc, M. S. Burns, A. Conley, S. E. Deustua, M. Doi, R. Ellis, S. Fabbro, V. Fadeyev, R. Gibbons, G. Goldhaber, A. Goobar, D. E. Groom, I. Hook, N. Kashikawa, A. G. Kim, R. A. Knop, B. C. Lee, J. Mendez, T. Morokuma, K. Motohara, P. E. Nugent, R. Pain, S. Perlmutter, V. Prasad, R. Quimby, J. Raux, N. Regnault, P. Ruiz-Lapuente, G. Sainton, B. E. Schaefer, K. Schahmaneche, E. Smith, A. L. Spadafora, V. Stanishev, N. A. Walton, L. Wang, W. M. Wood-Vasey, & N. Yasuda (The Supernova Cosmology Project) Astronomy and Astrophysics, vol:430, 2005.

"A possible bright blue supernova in the afterglow of GRB 020305;" Gorosabel, J., J. P. U. Fynbo, A. Fruchter, A. Levan, J. Hjorth, P. Nugent, A. J. Castro-Tirado, J. M. Castro Cer�n, J. Rhoads, D. Bersier, & I. Burud Astronomy and Astrophysics, vol:437, 2005.

"Spectroscopic Observations and Analysis of the Peculiar SN 1999aa;" Garavini, G., G. Folatelli, A. Goobar, S. Nobili, G. Aldering, A. Amadon, R. Amanullah, P. Astier, C. Balland, G. Blanc, M. S. Burns, A. Conley, T. Dahl�n, S. E. Deustua, R. Ellis, S. Fabbro, X. Fan, B. Frye, E. L. Gates, R. Gibbons, G. Goldhaber, B. Goldman, D. E. Groom, J. Haissinski, D. Hardin, I. M. Hook, D. A. Howell, D. Kasen, S. Kent, A. G. Kim, R. A. Knop, B. C. Lee, C. Lidman, J. Mendez, G. J. Miller, M. Moniez, A. Mour�o, H. Newberg, P. E. Nugent, R. Pain, O. Perdereau, S. Perlmutter, V. Prasad, R. Quimby, J. Raux, N. Regnault, J. Rich, G. T. Richards, P. Ruiz-Lapuente, G. Sainton, B. E. Schaefer, K. Schahmaneche, E. Smith, A. L. Spadafora, V. Stanishev, N. A. Walton, L. Wang, & W. M. Wood-Vasey Astronomical Journal, vol:128, 2004.

LBNL-58336 "UV Spectroscopy of Type Ia Supernovae at Low- and High-Redshift;" Nugent, P., in 1604-2004: Supernova as Cosmological Lighthouses, Padua, Italy, ASP Conference Series, 2005.

## O

**PI Volker Oberacker**

"Time-dependent response calculations of nuclear resonances," A.S. Umar and V.E. Oberacker, Phys. Rev. C71, 034314 (2005)

"Coordinate space Hartree-Fock-Bogoliubov calculations for the zirconium isotope chain up to the two-neutron dripline", A. Blazkiewicz, V.E. Oberacker, A.S. Umar, and M. Stoitsov, Phys. Rev. C71, 054321 (2005)

"TDHF studies with Modern Skyrme forces", A.S. Umar and V.E. Oberacker, Eur. Phys. J. A24, May 2005

"2-D Lattice HFB Calculations for Neutron-Rich Zirconium Isotopes", A. Blazkiewicz, V.E. Oberacker, and A.S. Umar, Eur. Phys. J. A24, May 2005

"HFB Calculations for Nuclei far from Stability", A.S. Umar, V.E. Oberacker, E. Teran, and A. Blazkiewicz, book chapter in ``Structure and Dynamics of Elementary Matter", ed. W. Greiner et al.; Kluwer Academic Publishers (2004), p. 561-567

"Solution of the HFB continuum problem on a 2-D lattice: neutron-rich and dripline nuclei", V.E. Oberacker, A.S. Umar, A. Blazkiewicz and E. Teran, book chapter in ``A New Era of Nuclear Structure Physics", ed. Y. Suzuki, S. Ohya, M. Matsuo & T. Ohtsubo, World Scientific (2004), pp.179-183

**PI Joseph Oefelein**

J. C. Oefelein. Mixing and Combustion of Cryogenic LOX-H2 Shear-Coaxial Jet Flames at Supercritical Pressure (Invited). Combustion Science and Technology, accepted May 2005.

J. C. Oefelein, R. W. Schefer and R. S. Barlow. Toward Validation of LES for Turbulent Combustion (Invited). AIAA J, accepted May 2005.

J. C. Oefelein. Thermophysical Characteristics of Shear-Coaxial LOXH2 Flames at Supercritical Pressure. Proc. Combust. Inst., 30, 2929�7, 2005.

S. V. Apte, K. Mahesh, P. Moin, and J. C. Oefelein. Large eddy simulation of swirling particle-laden flows in a coaxial-jet combustor. International Journal of Multiphase Flow, 29 (8): 1311�1, 2003.

**PI Doug Olson**

"Experimental and Theoretical Challenges in the Search for the Quark Gluon Plasma: The STAR Collaboration's Critical Assessment of the Evidence from RHIC Collisions", STAR Collaboration (J. Adams et al.), Nucl. Phys. A 757, 102 (2005). e-Print Archives (nucl-ex/0501009)

"Cross Sections and transverse single-spin asymmetries in forward neutral pion asymmetries from proton collisions at sqrt(s) = 200 GeV", STAR: J. Adams et al. Phys. Rev. Lett. 92: 171801 (2004)

"Measurements of transverse energy distributions in Au Au collisions at sqrt(sNN) = 200 GeV", STAR Collaboration, Phys. Rev. C 70, 054907 (2004). e-Print Archives (nucl-ex/0407003)

"Pseudorapidity Asymmetry and Centrality Dependence of Charged Hadron Spectra in d Au Collisions at sqrt(sNN) = 200 GeV", STAR Collaboration (J. Adams et al.), Phys. Rev. C 70, 064907 (2004). e-Print Archives (nucl-ex/0408016)

"Azimuthal anisotropy and correlations at large transverse momenta in p p and Au Au collisions at sqrt(sNN)= 200 GeV", STAR Collaboration (J. Adams et al.), Phys. Rev. Lett. 93 (2004) 252301. e-Print Archives (nucl-ex/0407007)

"Transverse Momentum Correlations and Minijet Dissipation in Au-Au Collisions at sqrt(sNN) = 130 GeV" (2004), e-Print Archives (nucl-ex/0408012)

"Pion, Kaon, Proton, and Anti-Proton Transverse Momentum Distributions from p p and d Au Collisions at S(NN)**1/2 = 200-GeV", STAR Collaboration (J. Adams et al.), Phys. Lett. B 616, 8 (2005) . e-Print Archive: nucl-ex/0309012

"Phi meson production in Au Au and p p collisions at sqrt(s)=200 GeV", STAR Collaboration (J. Adams et al.), Phys. Lett. B 612, 181 (2005). e-Print Archives (nucl-ex/0406003)

"Transverse-momentum dependent modification of dynamic texture in central Au Au collisions at sqrt(sNN) = 200 GeV", STAR Collaboration (J. Adams et al.) , Phys. Rev. C 71, 031901(R) (2005). e-Print Archives (nucl-ex/0407001)

"Pion interferometry in Au Au collisions at sqrt(sNN) = 200 GeV", STAR Collaboration (J. Adams et al.), Phys. Rev. C 71, 044906 (2005). e-Print Archives (nucl-ex/0411036)

"Open charm yields in d+Au collisions at sqrt(sNN) = 200 GeV", STAR Collaboration ( J. Adams et al.), Phys. Rev. Lett. 94, 062301 (2005). e-Print Archives (nucl-ex/0407006).

"K(892)* Resonance Production in Au+Au and p+p Collisions at sqrt(sNN) = 200 GeV at STAR", STAR Collaboration (J. Adams et al.), Phys. Rev. C 71, 064902 (2005). e-Print Archives (nucl-ex/0412019), LBNL-56878.

"Experimental and Theoretical Challenges in the Search for the Quark Gluon Plasma: The STAR Collaboration's Critical Assessment of the Evidence from RHIC Collisions", STAR Collaboration (J. Adams et al.), Nucl. Phys. A 757, 102 (2005). e-Print Archives (nucl-ex/0501009).

"Multiplicity and Pseudorapidity Distributions of Photons in Au + Au Collisions at sqrt(sNN) = 62.4 GeV" (2005).

## P

**PI Ian Parrish**

Ian J. Parrish and James M. Stone, "Nonlinear Evolution of the Magnetothermal Instability in Two Dimensions." Accepted to Astrophysical Journal. Preprint on the web as astro-ph/0507212.

**PI Joyce Penner**

Liu, X., J.E.Penner, J.E., and M. Herzog, 2005: Global modeling of aerosol dynamics: Model description, evaluation and interactions between sulfate and non-sulfate aerosols, J. Geophys. Res., in press.

**PI Saul Perlmutter**

"New Spectra of High Redshift Type Ia Supernovae and a Comparison with their Low Redshift Counterparts" I. Hook, et al., Accepted for publication in the Astronomical Journal.

"Measurement of Omega_M, Omega_Lambda from an analysis of Type Ia SNe with CMAGIC", A. Conley, et al., Submitted for publication in the Astrophysical Journal.

"Search for spectral evolution in high-redshift Type Ia supernovae: evidence for SN 1991T/SN 1999aa- like object at z=0.279", G. Garavini, et al., Submitted for publication in the Astronomical Journal.

"Spectral Signatures of Gravitationally Confined Thermonuclear Supernova Explosions" Kasen, Daniel; Plewa, Tomasz. The Astrophysical Journal, Volume 622, Issue 1, pp. L41-L44.

"Theoretical uncertainty in baryon oscillations," Eisenstein, Daniel; White, Martin. Physical Review D, vol. 70, Issue 10, id. 103523

"Baryons and weak lensing power spectra," White, Martin. Astroparticle Physics, Volume 22, Issue 2, p. 211-217.

"Is dark energy dynamical? Prospects for an answer" Linder, Eric V.; Miquel, Ramon Physical Review D, vol. 70, Issue 12, id. 123516

"Observing Dark Energy with SNAP" Linder, E. V.; For The Snap Collaboration Observing Dark Energy, ASP Conference Series, Vol. 339, Edited by Sidney C. Wolff and Tod R. Lauer. San Francisco: Astronomical Society of the Pacific, 2005., p.87

**PI Peter Petreczky**

T. Blum, P. Petreczky, Nucl. Phys. B (Proc. Suppl.) 140 (2005) 553.

**PI Franz-Josef Pfreundt**

"Integrated Performance Analysis of Computer Systems (IPACS)", G. Falcone et al, Praxis der Informationsverarbeitung und Kommunikation, PIK3-05 154-163

**PI Steven Pieper**

Quantum Monte Carlo calculations of excited states in A=6-8 nuclei, Steven C. Pieper, R. B. Wiringa, and J. Carlson, Phys. Rev. C 70, 054325-1:11 (2004).

Quantum Monte Carlo Calculations of Light Nuclei, S. C. Pieper, Nucl. Phys. 751, 516c-532c (2005).

Neutron Spectroscopic Factors in ^{9}Li from ^{2}H(^{8}Li,$p$)^{9}Li, A. H. Wuosmaa, K. E. Rehm, J. P. Greene, D. J. Henderson, R. V. F. Janssens, C. L. Jiang, L. Jisonna, E. F. Moore, R. C. Pardo, M. Paul, D. Peterson, Steven C. Pieper, G. Savard, J. P. Schiffer, R. E. Segel, S. Sinha, X. Tang, and R. B. Wiringa, Phys. Rev. Lett. 94, 082502-1:4 (2005).

**PI Ali Pinar**

Vaibhav Donde, Vanessa Lspez, Bernard Lesieutre, Ali Pinar, Chao Yang, and Juan Meza, "Identification of Severe Multiple Contingencies in Electric Power Networks," Proceedings of the North American Power Symposium, Ames Iowa, 2005.

**PI Michael Pindzola**

Lattice calculations of the photoionization of lithium, J P Colgan, F J Robicheaux, and M S Pindzola, Phys. Rev. Letts. 93, 053201 (July 2004).

Time-dependent close-coupling theory for e H elastic and inelastic scattering, M C Witthoeft, S D Loch, and M S Pindzola, Phys. Rev. A 70, 022711 (August 2004).

Electron-impact single and double ionization of helium, M S Pindzola, F J Robicheaux, J P Colgan, M C Witthoeft, and J A Ludlow, Phys. Rev. A 70, 032705 (Sept 2004).

Simulation of coherent interactions between Rydberg atoms, F J Robicheaux, J V Hernandez, T Topcu, and L D Noordam, Phys. Rev. A 70, 042703 (Oct 2004).

Time-dependent close-coupling calculations for the double photoionization of He and H2, J P Colgan, M S Pindzola, and F J Robicheaux, J. Phys. B 37, L377 (Dec 2004).

Electron-impact excitation of Xe 26 and its resultant spectral signature, N R Badnell, K A Berrington, H P Summers, M G O'Mullane, A D Whiteford, and C P Ballance, J. Phys. B 37, 4589 (Dec 2004).

Electron-impact ionization of metastable neon, C P Ballance, D C Griffin, J A Ludlow, and M S Pindzola, J. Phys. B 37, 4779 (Dec 2004).

The validity of classical and perturbative quantal methods for electron-impact ionization from excited states in H-like ions, D C Griffin, C P Ballance, M S Pindzola, F J Robicheaux, S D Loch, J A Ludlow, M C Witthoeft, J P Colgan, C J Fontes, and D R Schultz, J. Phys. B 38, L199 (June 2005).

The agreement of Breit-Pauli and Dirac R-matrix collision strengths for iron peak elements: an Fe 14 case study, K A Berrington, C P Ballance, D C Griffin, and N R Badnell, J. Phys. B 38, 1667 (June 2005).

Continuum-coupling in electron-atom scattering, C P Ballance, D C Griffin, N R Badnell, S D Loch, and M S Pindzola, in "Atomic Processes in Plasmas", eds. J S Cohen, S Mazevet, D P Kilcrease, (AIP, New York, 2004).

Multiple photoionization of atoms and ions using the time-dependent close-coupling method, U Kleiman, J P Colgan, M S Pindzola, and F J Robicheaux, in "Electron and Photon Impact Ionization and Related Topics", ed. B Piraux, (IOP, Bristol, 2005).

**PI Tomasz Plewa**

Kasen, D. & Plewa, T. 2005, ApJ, 622, 41

Kasen, D., Nugent, P., Thomas, R.C., & Wang, L. 2004, ApJ, 610, 876

Kasen, D., Nugent, P., Wang, L. et al. 2003, ApJ, 593, 788

**PI Wilfred Post**

Johnston, C.A., P. Groffman, D.D. Breshears, Z.G. Cardon, W. Currie, W. Emanuel, J. Gaudinski, R.B. Jackson, K. Lajtha, K. Nadelhoffer, D. Nelson Jr., W.M. Post, G. Retallack, L. Wielopolski 2004. Carbon cycling in soil. Frontiers in Ecology and the Environment 2:522-528.

Post, W.M. and A.W. King (in press). Climate Change and Terrestrial Ecosystem Production. IN R. Lal, ed. Global Climate Change and Food Security, CRC Press.

Post, W. M., E. M.Hanlon, and C. T. Garten Jr. (submitted). Elevated CO2 Effects on Soil C Dynamics in a Sweetgum Plantation. Global Change Biology.

Gu, L., W. M. Post, and A. W. King 2004. Fast labile carbon turnover obscures sensitivity of heterotrophic respiration from soil to temperature: A model analysis, Global Biogeochem. Cycles, 18, GB1022, doi:10.1029/2003GB002119.

Kittel, T. G. F., N. A. Rosenbloom, J. A. Royle, C. Daly, W. P. Gibson, H. H. Fisher, P. Thornton, D. N. Yates, S. Alenbach, C. Kaufman, R. McKeown, D. Batchelet, D. S. Schimel, and VEMAP2 Participants. 2004. The VEMAP Phase 2 bioclimatic database I: A gridded historical (20th Century) climate dataset for modeling ecosystem dynamics across the conterminous United States. Climate Research 27:151-170.

Paustian, K., B. Babcock, L. Chimenti, W. Post, N. Rosenberg, W. Schlesinger, P. Robertson, J. Hatfield, C. Rosenzweig, C. Rice, B. McCarl, R. Lal, C. Kling, A. Mosier, S. McLaughlin, D. Zilberman 2004. Agriculture's Response to Global Climate Change. Report No. 138, Council for Agricultural Science and Technology, Ames, IA.

Ranatunga K., S. D. Wullschleger, W. M. Post, R. Keenan and M. L. Tharp (submitted). Aboveground biomass and soil carbon stocks as influenced by harvest management practices in New South Wales, Australia: Simulations with the forest succession model LINKAGES. Australian Journal of Forestry.

Luxmoore, R. J., M. L. Tharp, and W. M. Post (submitted). Simulated nitrogen fertilization and temperature effects on biomass and soil carbon of loblolly pine and cottonwood plantations in the Southeastern United States. Forest Ecology and Management.

Blasing, T. J., C. T. Broniak, and G. Marland. The annual cycle of fossil-fuel carbon dioxide emissions in the USA, Tellus, in press.

Blasing, T.J., C. T. Broniak and G. Marland. State-by-state carbon dioxide emissions from fossil fuel use in the United States 1960-2000, Environmental Science and Policy, in press.

**PI Gerald Potter**

Evaluating parameterizations in general circulation models: Climate simulation meets weather prediction by Phillips et al., 2004: Bulletin of the American Meteorological Society, 85, 1903 -1915.

Impact of a revised convective triggering mechanism on Community Atmosphere Model, Version 2, simulations: Results from short-range weather forecasts by Xie et al. : Journal of Geophysical Research, 109, D14102, doi:10.1029/2004JD004692, 2004.

Simulations of midlatitude frontal clouds by single-column and cloud-resolving models during the Atmospheric Radiation Measurement March 2000 cloud intensive operational period by Xie et al. : Journal of Geophysical Research, 110, D15503, doi: 10.1029/2004JD005119, 2005.

Diagnosis of Community Atmospheric Model 2 (CAM2) in numerical weather forecast configuration at Atmospheric Radiation Measurement sites by Boyle et al.: Journal of Geophysical Research, 110, D15516, doi: 10.1029/2004JD005109, 2005.

Moisture and temperature balances at the Atmospheric Radiation Measurement Southern Great Plains Site in forecasts with the Community Atmosphere Model (CAM2) by Williamson et al. : Journal of Geophysical Research, 110, D15516, doi: 10.1029/2004JD005109, 2005.

**PI Joel Primack**

"The Dark Side of the Halo Occupation Distribution", Andrey V. Kravtsov, Andreas A. Berlind, Risa H. Wechsler, Anatoly A. Klypin, Stefan Gottloeber, Brandon Allgood, and Joel R. Primack 2004, Astrophys.J., 609, 35-45

"Modeling Galaxy-Mass Correlations in Dissipationless Simulations", Tasitsiomi, A., Kravtsov, A., Wechsler, R. H. & Primack, J., 2004, Astrophys.J., 614, 533-546

"The Physics of Galaxy Clustering I: A Model for Subhalo Populations", Andrew R. Zentner, Andreas A. Berlind, James S. Bullock, Andrey V. Kravtsov & Risa H. Wechsler 2005, Astrophys.J., 624, 505-525

"Simulations of Dust in Interacting Galaxies. I. Dust Attenuation", Jonsson, Patrik Jonsson, T. J. Cox, Joel R. Primack & Rachel S. Somerville 2005, Astrophys.J., in press [astro-ph/0503135]

"The Effects of Feedback in Simulations of Disk-Galaxy Major Mergers", T.J. Cox, Patrik Jonsson, Joel R. Primack & Rachel S. Somerville, 2005, Astrophys.J., submitted [astro-ph/0503201]

"Phase-Space Structure of Dark-Matter Haloes: Scale-Invariant PDF Driven by Substructure", I. Arad, A. Dekel, A. Klypin 2004, Mon.Not.Roy.Astron.Soc. 353, 15-29

"Impact of Dark Matter Substructure on the Matter and Weak Lensing Power Spectra" Bradley Hagan, Chung-Pei Ma, Andrey V. Kravtsov 2005, Astrophys.J., in press [astro-ph/0504557]

## Q

## R

**PI Bala Radhakrishnan**

Jaramillo RA, Babu SS, Ludtka GM, Kisner RA, Wilgen JB, Mackiewicz-Ludtka G, Nicholson DM, Kelly SM, Muruaananth M, Bhadeshia HKDH "Effect of 30 T magnetic field on transfomations in a novel bainitic steel," Scripta Materialia 52 (6): 461-466 MAR 2005

Nicholson DMC, Fuentes-Cabrera M, Widom M, Wang Y, Mihalkovic M, "Electronic Structure Based Approaches to Metallic Glass Stability," The Science of Complex Phases 183 (2005) Ed. Massalski and Turchi (TMS Warrendale PA).

Radhakrishnan B, Sarma GB, "Simulating the interaction between a straight boundary and a particle," Materials Science Forum 467-470: 1105-1110 Part 1-2 2004

Sarma GB, Radhakrishnan B, "Modeling microstructural effects on the evolution of cube texture during hot deformation of aluminum," Materials Science And Engineering A-Structural Materials Properties Microstructure And Processing 385 (1-2): 91-104, 2004

Radhakrishnan B, Sarma G, "The effect of coarse non-deformable particles on the deformation and static recrystallization of aluminium alloys," Philosophical Magazine 84 (22): 2341-2366, 2004

Radhakrishnan B, Sarma G, "Simulating the deformation and recrystallization of aluminum bicrystals," JOM 56 (4): 55-62 APR 2004

**PI Abhay Ram**

D. R. Ernst, "Role of Trapped Electron Mode Turbulence in Internal Transport Barrier Control in Alcator C-Mod," Phys. Plasmas 11(5) 2637 (2004). APS 2003 Invited Paper UI1.5.

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

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

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

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

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

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

**PI David Randall**

Cole, J. N., H. W. Barker, D. A. Randall, M. F. Khairoutdinov, and E. Clothiaux, 2005: Interactions between Clouds and Radiation at Scales Unresolved by Global Climate Models. Geophys. Res. Lett., 32, L06703, doi: 10.1029/2004GL020945.

Cole, J. N. S., H. W. Barker, W. Oirok, E. E. Clothiaux, M. F. Khairoutdinov, and D. A. Randall, 2005: Atmopsheric radiative transfer through global arrays of 2D clouds. Submitted to Geophys. Res. Lett. (in press).

Khairoutdinov, M., D. A. Randall, and C. DeMott, 2005: Simulation of the atmospheric general circulation using a cloud-resolving model as a super-parameteriztion of physical processes. J. Atmos. Sci. , 62, 2136-2154.

**PI Lawrence Rauchwerger**

N. Thomas, G. Tanase, O. Tkachyshyn, J. Perdue, N.M. Amato, L. Rauchwerger, ``A Framework for Adaptive Algorithm Selection in STAPL'', in Proc. of ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming (PPOPP), Chicago, IL, June, 2005.

Shawna Thomas, Gabriel Tanase, Lucia K. Dale, Jose E. Moreira, Lawrence Rauchwerger, Nancy M. Amato, ``Parallel Protein Folding with STAPL,'' special issue of extended papers from the Third IEEE International Workshop On High Performance Computational Biology (HiCOMB 2004), Concurrency and Computation: Practice and Experience, accepted December 2004, to appear.

**PI John Rehr**

"Combined BSE/TDDFT approach for x-ray absorption calculations," A. L. Ankudinov, Y. Takimoto, and J.J. Rehr, Phys. Rev. B 71, 165110 (2005).

"Final-state rule vs the Bethe-Salpeter equation for deep-core x-ray absorption spectra," J.J. Rehr, J. A. Soininen, and E. L. Shirley, Physica Scripta T115, 207 (2005).

"Modeling Core-Hole Screening in Core-Execitation Spectroscopies," E. L. Shirley, J. A. Soininen, and J. J. Rehr, Physica Scripta, T115, 31 (2005).

"First-principles ultraviolet and x-ray spectra over broad ranges," E. L. Shirley, J. A. Soininen, and J. J. Rehr, in Optical Constants of Materials for UV to X-Ray Wavelengths, edited by R. Soufli and J.F. Seely, SPIE Proceedings, Vol. 5538, pp. 125-127 (SPIE, Bellingham, WA, 2004).

"Multi-pole Representation of the Dielectric Matrix," J. A. Soininen, J. J. Rehr and E. L. Shirley, Physica Scripta T115, 243 (2005).

"Nonspherical potential, vibronic, and local field effects in x-ray absorption," A. L. Ankudinov and J. J. Rehr, Physica Scripta T115, 24 (2005).

"Inelastic Scattering from Core-electrons: a Multiple Scattering Approach," J.A. Soininen, A.L. Ankudinov, and J.J. Rehr, Phys. Rev. B 72, 045136 (2005).

**PI Edward Rezayi**

Universality of the Edge-Tunneling Exponent of Fractional Quantum Hall Liquids, X. Wan, F. Evers, and E.H. Rezayi, Physical Review Letters 94, 16684 (2005).

Mobility gap in fractional quantum Hall liquids: Effects of disorder and layer thickness, X. Wan, D.N Sheng, E.H. Rezayi, Kun Yang, R.N. Bhatt, and F.D.M. Haldane, Physical Review B 72, 075325 (12 pages), (2005).

Incompressible state of rapidly-rotating bosons at filling factor 3/2, E. H. Rezayi, N. Read, and N. R. Cooper, Physical Review Letters, in production.

**PI Tony Rollett**

J. J. Hoyt, M. Asta and D. Y. Sun, "Molecular Dynamics Simulations of the Crystal-Melt Interfacial Free Energy of and Mobility in Mo and V," Phil. Mag. (in press).

E. A. Marquis, M. Asta, D. N. Seidman and C. Woodward, "Composition Evolution of Nanoscale Al3Sc Precpitates in an Al-Mg-Sc Alloy," Acta Materialia (in press).

J. J. Hoyt, M. Asta, T. Haxhimali, A. Karma, R. E. Napolitano, R. Trivedi, B. B. Laird and J. R. Morris, "Crystal-Melt Interfaces and Solidification Morphologies in Metals and Alloys," MRS Bulletin 29, 935 (2005).

Rachel S. Aga, James R. Morris and Mikhail I. Mendelev, "Homogeneous Crystal Nucleation in Undercooled Aluminum," to appear in TMS Letters.

S. Wang, C. Z. Wang, F.-C. Chuang, J. R. Morris and K. M. Ho, "Ab initio molecular dynamics simulation of liquid AlxGe1-x Alloys," Phys. Rev. B. 70, 224205 (2004).

S. Wang, C. Z. Wang, F.-C. Chuang, J. R. Morris and K. M. Ho, "Ab initio molecular dynamics Simulation of liquid Al88Si12 Alloys," J.Chem. Phys 122, 034508 (2005).

**PI William Rowan**

"A System for Direct Comparisons of Nonlinear Simulations of Turbulence with Measurements," R. V. Bravenec and W. M. Nevins, to be published in Rev. Sci. Instrum. (2005).

"Gyrokinetic Simulations of ETG-Free Dis,charges on DIII-D," R.V. Bravenec, T. L. Rhodes, J. Candy, G. M. Staebler, and G. R. McKee, Bull. Am. Phys. Soc. 49, 158 (2004).

"Comparisons of Measurements and Gyrokinetic Simulations of Turbulence and Transport in Alcator C- Mod EDA H-Mode Discharges," M. B. Sampsell, R. V. Bravenec, J. Candy, D. R. Ernst, and W. M. Nevins, Bull. Am. Phys. Soc. 49, 217 (2004).

**PI Robert Ryne**

J. Amundson, P. Spentzouris, J. Qiang, R. Ryne, " Synergia: A 3-D PIC Code with Space Charge," accepted by J. Comp. Phys. (2005).

K. Ohmi, M. Tawada, Y. Cai, S. Kamada, K. Oide, J. Qiang, "Study of the beam-beam limit in e e- circular colliders," Phys. Rev. Lett. vol. 92, 214801 (2004)

K. Ohmi, M. Tawada, Y. Cai, S. Kamada, K. Oide, and J. Qiang, "Luminosity limit due to the beam-beam interactions with or without crossing angle," Phys. Rev. ST Accel. Beams, vol 7, 104401 (2004).

Dave Higdon, Marc Kennedy, James C. Cavendish, John A. Cafeo, Robert D. Ryne, "Combining Field Data and Computer Simulations for Calibration and Prediction," SIAM Journal on Scientific Computing, Volume 26, Number 2, pp. 448-466 (2004).

J. Qiang, M.A. Furman, R.D. Ryne, "A Parallel Particle-In-Cell Model for Beam-Beam Interactions in High Energy Ring Colliders," J.Comp.Phys.198:278-294 (2004).

## S

**PI Roman Samulyak**

R. Samulyak, Y. Prykarpatskyy, Richtmyer-Meshkov instability in liquid metal flows: influence of cavitation and magnetic fields, Mathematics and Computers in Simulations, 65 (2004), 431 - 446.

R. Samulyak, T. Lu, Y. Prykarpatskyy, Direct and homogeneous numerical approaches to multiphase flows, Lecture Notes in Comp. Sci., 3039 (2004), 653 - 660. Springer-Verlag, Berlin - Heidelberg, 2004.

**PI Henry Schaefer**

N. J. DeYonker, S. Li, Y. Yamaguchi, and H. F. Schaefer, "Applications of Equation-of-motion Coupled Cluster Methods to Low-Lying Singlet and Triplet Electronic States of HBO and BOH", J. Chem. Phys. (in press)

R. K. Sreeruttun, P. Ramasami, A. Paul, C. S. Wannere, and H. F. Schaefer, "Effects of Fluorine on the Structures and Energetics of the Propynal and Propargyl Radicals and they Anions", J. Or. Chem. (in press)

W. D. Allen, M. S. Schuurman, and H. F. Schaefer, "On G0 anharmonicity in Polyatomic Zero Point Vibrational Energies", J. Chem. Phys. (in press)

M. S. Schuurman, W. D. Allen, and H. F. Schaefer, "The Highly Anharmonuc BH5 Potential Energy Surface Characterized in the Ab Initio Limit", J. Chem. Phys. (in press)

M. S. Schuurman, W. D. Allen, and H. F. Schaefer, "The Ab Initio Limit Quartic Force Field of BH3", J. Comput. Chem. (in press)

R. K. Sreeruttun, P. Ramasami, G. Yan, C. S. Wannere, P. R. Schleyer, and H. F. Schaefer, "The alkylethynyl radicals, C-center dot equivalent to C-CnH2n 1 (n=1-4), and their anions", Int. J. Mass. Spec. 241 (2-3): 295 (2005)

M. Schuurman, S. Muir, W. D. Allen, and H. F. Schaefer, "Toward Subchemical Accuracy in Computational Thermochemistry: Focal Point Analysis of the Heat of Formation of NCO and [H,N,C,O] Isomers", J. Chem. Phys. 120, 11586 (2004).

Y. Yamaguchi and H. F. Schaefer, "The Diazocarbene (CNN) Molecule: Characterization of the Triplet Sigma Minus and Triplet Pi Electronic States", J. Chem. Phys. 120, 9536 (2004).

S. E. Wheeler, W. D. Allen, and H. F. Schaefer, "Thermodynamics of Disputed Soot Formation Intermediates C4H3 and C4H5", J. Chem. Phys. 121, 8800 (2004).

**PI Rocco Schiavilla**

"Polarization transfer in 4He(e,e'p)3H:Is the ratio GEp/GMp modified in medium?",R. Schiavilla, O. Benhar, A. Kievsky, L.E. Marcucci, and M. Viviani, Phys. Rev. Lett. 94, 072303 (2005)

"Induced polarization in the 2H(gamma,n)p reaction at low energy", R. Schiavilla, Phys. Rev. C in press.

"Electromagnetic structure of A=2 and 3 nuclei and the nuclear current operator", L.E. Marcucci, M. Viviani, R. Schiavilla, A. Kievsky, and S. Rosati, Phys. Rev. C 72, 014001 (2005)

"Electromagnetic structure of few-body nuclear systems",L.E. Marcucci, M. Viviani, A. Kievsky, S. Rosati, and R. Schiavilla, "Italian Nuclear Physics Conference", in press

"Electrodisintegration of 3He below and above deuteron breakup threshold", L.E.Marcucci, M. Viviani, R. Schiavilla, A. Kievsky, and S. Rosati, Eur. Phys. J.A24, 95 (2005)

**PI Dalton Schnack**

S.E. Kruger, D.D. Schnack, and C. R. Sovinec "Dynamics of a Major Disruption of a DIII-D Plasma" Physics of Plasmas 12, 056113 2005.

S.E. Kruger, C. R. Sovinec, D.D. Schnack, and E. D. Held "Free-boundary Simulations of DIII-D Plasmas with the NIMROD Code" Computer Physics Communications, 164 (34) 2004.

A. Y. Pankin, G. Bateman, D. P. Brennan, D. D. Schnack and et al. "Theory-based model for the pedestal, edge stability and ELMs in tokamaks" (Submitted for publication in Nuclear Fusion) 2005.

**PI David Schultz**

Helium atom in a box: doubly excited levels within the s-wave model, D M Mitnik, Phys. Rev. A 70, 022703 (Aug 2004).

Coherence parameters for charge transfer in collisions of protons with helium calculated using a hybrid numerical approach, T Minami, C O Reinhold, D R Schultz, and M S Pindzola, J. Phys. B 37, 4025 (Oct 2004).

Strong contributions of indirect processes to the electron-impact ionization cross section of Sc ions, J Jacobi, H Knopp, S Schippers, A Muller, S D Loch, M C Witthoeft, M S Pindzola, and C P Ballance, Phys. Rev. A 70, 042717 (Oct 2004).

Electron-impact ionization of Bi q for q=1-10, S D Loch, M S Pindzola, N R Badnell, F Scheuermann, K Kramer, K Huber, and E Salzborn, Phys. Rev. A 70, 052714 (Nov 2004).

Dielectronic recombination of Pb 79 via high angular momenta, N R Badnell, D M Mitnik, M S Pindzola, S D Loch, and S A Abdel-Naby, Phys. Rev. A 70, 054701 (Nov 2004).

Dielectronic recombination data for dynamic finite-density plasmas: VII. The neon isoelectronic sequence, O Zatsarinny, T W Gorczyca, K Korista, N R Badnell, and D W Savin, Astronomy and Astrophysics 426, 699 (2004).

Dielectronic recombination data for dynamic finite-density plasmas: D M Mitnik and N R Badnell, VIII. The nitrogen isoelectronic sequence, Astronomy and Astrophysics 425, 1153 (2004).

Helium line intensity ratio in microwave generated plasmas, N K Podder, J A Johnson, C T Raynor, S D Loch, C P Ballance, and M S Pindzola, Physics of Plasmas 11, 5436 (Dec 2004)

The influence of metastable levels on the electron-impact single ionization of C 2, S D Loch, M C Witthoeft, M S Pindzola, I Bray, D V Fursa, M Fogel, R Schuch, P Glans, C P Ballance, and D C Griffin, Phys. Rev. A 71, 012716 (Jan 2005).

Atomic data from the IRON project: LVI. Electron excitation of Be-like Fe XXIII for n=2,3,4 configurations, M C Chidichimo, G Del Zanna, H E Mason, N R Badnell, J A Tully, and K A Berrington, Astron. Astrophys. 430, 331 (2005).

Electron-impact excitation and ionization of H2+ using a configuration-average distorted-wave method, M S Pindzola, F J Robicheaux, J A Ludlow, J P Colgan, and D C Griffin, Phys. Rev. A 72, 012716 (July 2005).

Electron-ion recombination of Be-like C, N, and O, M Fogle, N R Badnell, P Glans, S D Loch, S Madzunkov, S A Abdel-Naby, M S Pindzola, and R Schuch, Astronomy and Astrophysics 442, 757 (2005).

**PI Edward Seidel**

Miguel Alcubierre, Bernd Bruegmann, Peter Diener, Francisco Siddhartha Guzman, Ian Hawke, Scott Hawley, Frank Herrmann, Michael Koppitz, Denis Pollney, Edward Seidel, and Jonathan Thornburg, 2005, Physical Review D, 72:044004, Dynamical evolution of quasi-circular binary black hole data.

**PI Marjorie Shapiro**

"Measurement of the Moments of the Hadronic Invariant Mass Distribution in Semileptonic B Decays" D. Acosta et al., The CDF Collaboration, Phys. Rev. D71, 051103 (2005)

Measurement of Partial Widths and Search for Direct CP Violation in D0 Meson Decays D. Acosta et al., The CDF Collaboration, Phys. Rev. Lett. 94, 122001 (2005)

"Measurement of the tt-bar Production Cross Section in p anti-p Collisions at s**(1/2) = 1.96 TeV using Lepton Jets Events with Secondary Vertex b-tagging" D. Acosta et al., The CDF Collaboration, Phys. Rev. D71, 052003 (2005)

**PI Junko Shigemitsu**

``High-Precision Lattice QCD Confronts Experiment'', C.T.H. Davies,..., A. Gray,......, J. Shigemitsu, M. Wingate et al.; Phys. Rev. Lett. 92: 022001 (2004).

``The Bs and Ds Decay Constants in 3 Flavor Lattice QCD'', M. Wingate, C.T.H. Davies, A. Gray, P. Lepage, J. Shigemitsu; Phys. Rev. Lett. 92: 162001 (2004).

"One-loop matching of the heavy-light A0 and V0 currents with NRQCD heavy and improved naive light quarks", E.Gulez, J. Shigemitsu, M. Wingate; Phys. Rev. D 69: 074501 (2004).

`First Determination of the Strange and Light Quark Masses from Full Lattice QCD'', C.Aubin, A. Gray, J. Shigemitsu, M. Wingate et al.; Phys. Rev. D 70: 031504 (2004).

``Accurate Determination of $\alpha_s$ from Realistic Lattice QCD'', Q.Mason, A. Gray, J. Shigemitsu et al.; hep-lat/0503005, Phys. Rev. Lett. 95: 052002, (2005).

``The B Meson �Decay Constant from Unquenched Lattice QCD'', A.Gray, M.Wingate, E.Gulez, J.Shigemitsu et al.; hep-lat/0507015, submitted to Physical Review Letters.

``Progress Calculating Decay Constants with NRQCD and AsqTad Actions'', M. Wingate, C. Davies, A. Gray, E. Gulez, P. Lepage, J. Shigemitsu; Nucl. Phys. B (Proc Suppl.) 129\&130, 325 (2004).

``Heavy Light Meson Semileptonic Decays with Staggered Light Quarks'', J. Shigemitsu, C. Davies, A. Gray, E. Gulez, P. Lepage, M. Wingate; Nucl. Phys. B (Proc Suppl.) 129\&130, 331 (2004).

`` Semileptonic B decays with Nf = 2+1 dynamical quarks'', J. Shigemitsu, C. Davies, A. Dougall, K. Foley, E. Gamiz, A. Gray, E. Gulez, P. Lepage, M. Wingate; Nucl. Phys. B (Proc Suppl.) 140, 464 (2005).

`` B leptonic Decays and B0 −B0 mixing with 2+1 flavors of dynamical quarks '', A. Gray, C. Davies, E. Gulez, P. Lepage, J. Shigemitsu, M. Wingate; Nucl. Phys. B (Proc Suppl.) 140, 446 (2005).

``BK from Improved Staggered Quarks'', E. Gamiz, S. Collins, C. Davies, J. Shigemitsu, M. Wingate; Nucl. Phys. B (Proc Suppl.) 140, 353 (2005).

**PI Donald Sinclair**

G.T.Bodwin, J.Lee and D.K.Sinclair, ``Spin correlations and velocity-scaling in color-octet NRQCD matrix elements,'' Phys. Rev. D72, 014009 (2005) [arXiv:hep-lat/0503032].

J.B.Kogut and C.G.Strouthos, ``The logarithmic triviality of compact QED coupled to a four-fermi interaction,'' Phys. Rev. D71 094012 (2005) [arXiv:hep-lat/0501003].

D.Toublan and J.B.Kogut, ``The QCD phase diagram at nonzero baryon, isospin and strangeness chemical potentials: Results from a hadron resonance gas model,'' Phys. Lett. B605, 129 (2005) [arXiv:hep-ph/0409310].

J.B.Kogut and D.K.Sinclair, ``The finite temperature transition for 2-flavor lattice QCD at finite isospin density,'' Phys. Rev. D70, 094501 (2004) [arXiv:hep-lat/0407027].

S.J.Hands, J.B.Kogut, L.Scorzato and C.G.Strouthos, ``Non-compact QED(3) with N(f) = 1 and N(f) = 4,'' Phys. Rev. B70, 104501 (2004)[arXiv:hep-lat/0404013].

J.B.Kogut and D.K.Sinclair, ``Finite dt dependence of the Binder cumulants for 3-flavor QCD at finite temperature and isospin density,'' [arXiv:hep-lat/0504003].

J.B.Kogut, C.G.Strouthos and I.N.Tziligakis, ``Non-compact QED(3) coupled to a four-fermi interaction,'' Nucl. Phys. Proc. Suppl. 140, 701 (2005) [arXiv:hep-lat/0409038].

J.B.Kogut and D.K.Sinclair, ``The finite temperature transition for 3-flavour lattice QCD at finite isospin density,'' Nucl. Phys. Proc. Suppl. 140, 526 (2005) [arXiv:hep-lat/0407041].

**PI George Smoot**

"Cosmic Background Radiation Mini-Review" by Douglas Scott, George Smoot "The Review of Particle Physics", S. Eidelman et al., Physics Letters B592, 1 (2004)

"Search for Cosmic Strings in CMB Anisotropies" E. Jeong, G.F. Smoot Astrophys.J. 624 (2005) 21-27

**PI Randall Snurr**

S.A. McMillan, R.Q. Snurr, L.J. Broadbelt, "Interaction of divalent metal cations with ferrierite: Insights from density functional theory," Micropor. Mesopor. Materials 68, 45-53 (2004).

T. D|ren, L. Sarkisov, O.M. Yaghi, R.Q. Snurr, "Design of new materials for methane storage," Langmuir 20, 2683-2689 (2004).

R.Q. Snurr, J.T. Hupp, S.T. Nguyen, "Prospects for nanoporous metal-organic materials in advanced separation processes," AIChE J. 50, 1090-1095 (2004).

T. D|ren, R.Q. Snurr, "Assessment of isoreticular metal-organic frameworks for adsorption separations: a molecular simulation study of methane/n-butane mixtures," J. Phys. Chem. B 108, 15703-15708 (2004).

**PI Philip Snyder**

D.P. Brennan, S.E. Kruger, T.A.Gianakon and D.D.Schnack, "A Categorization of Tearing Mode Onset in Tokamaks via Nonlinear Simulation," Nuclear Fusion 45 (2005) 1178.

J. Candy, "Beta scaling of transport in microturbulence simulations", Phys. Plasmas 12 (2005) 072307.

M. Choi, V.S. Chan, R.I. Pinsker, S.C. Chiu, and W.W. Heidbrink, "Monte Carlo Orbit/Full Wave Simulation of Ion Cyclotron Resonance Frequency Wave Damping on Resonant Ions in Tokamaks," Phys. Plasmas 12 1 (2005).

C. Estrada-Mila, J. Candy, and R.E. Waltz, "Gyrokinetic Simulations of Ion and Impurity Transport," Phys. Plasmas 12 (2005) 22305.

J.E. Kinsey, R.E. Waltz, and J. Candy, "Nonlinear Gyrokinetic Turbulence Simulations of ExB Shear Quenching of Transport," Phys. Plasmas 12 (2005) 062302.

J.E. Kinsey et al., "Transport Modelling and Gyrokinetic Analysis of Advanced High Performance Discharges," Nucl. Fusion 45 450 (2005).

P.B. Snyder, H.R. Wilson, and X.Q. Xu, "Progress in the Peeling-Ballooning Model of ELMs: Numerical Studies of Nonlinear Dynamics," Phys. Plasmas 12 056115 (2005).

R.E. Waltz, J. Candy, F.L. Hinton, C. Estrada-Mila, and J.E. Kinsey, "Advances in Comprehensive GyroKinetic Simulations of Transport in Tokamaks," Nucl. Fusion 45 (2005) 741.

R.E. Waltz and J. Candy, "Heuristic Theory of Nonlocally Broken Gyro-Bohm Scaling," Phys. Plasmas 12 (2005) 072303.

R. E. Waltz, "Rho-star Scaling and Physically Realistic Gyrokinetic Simulations of Transpiort in DIII-D," Fusion Science and Technology 48 (2005) 1051.

A.D. Turnbull, D.P. Brennan, M.S. Chu, L.L. Lao, P.B. Snyder, "Theory and Simulation Basis for Magnetohydrodynamic Stability in DIII-D", Fusion Sci. and Technol 48 (2005) 875.

J.E. Kinsey, G.M. Staebler and R.E. Waltz, "Predicting Core and Edge Transport Barriers in Tokamaks Using the GLF23 Drift-Wave Transport Model," Phys. Plasmas 12 052503 (2005).

A.D. Turnbull, D.P. Brennan, M.S. Chu, L.L. Lao, P.B. Snyder, "Theory and Simulation Basis for Magnetohydrodynamic Stability in DIII-D", to be published in Fusion Sci. and Technol 48 (2005)

**PI Carl Sovinec**

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

S. E. Kruger, C. R. Sovinec, D. D. Schnack, and E. D. Held, "Free-Boundary Simulations of DIII-D Plasmas with the NIMROD Code," Computer Physics Communications 164, 34 (2004).

C. C. Kim, C. R. Sovinec, S. E. Parker, and the NIMROD Team, "Hybrid Kinetic-MHD Simulations in General Geometry," Computer Physics Communications 164, 448 (2004).

S. Woodruff, B. I. Cohen, E. B. Hooper, H. S. McLean, B. W. Stallard, D. N. Hill, C. T. Holcomb, C. Romero-Talamaras, R. D. Wood, G. Cone, and C. R. Sovinec, "Controlled and Spontaneous Magnetic Field Generation in a Gun-Driven Spheromak," Physics of Plasmas 12, 52505 (2005).

S. E. Kruger, D. D. Schnack, and C. R. Sovinec, "Dynamics of the Major Disruption of a DIII-D Plasma," Physics of Plasmas 12, 56113 (2005).

E. B. Hooper, T. A. Kopriva, B. I. Cohen, D. N. Hill, H. S. McLean, R. D. Wood, S. Woodruff, and C. R. Sovinec, "Magnetic Reconnection during Flux Conversion in a Driven Spheromak," accepted for publication in Physics of Plasmas.

**PI Frank Spera**

Tradeoffs in Chemical and Thermal Variations in the Post-perovskite Phase Transition: Mixed phase Regions in the Lower Mantle?, Subm. Earth and Planetary Science Letters, april 15, 2005 (Spera, Giles and Yuen)

**PI Don Spong**

"Generation and damping of neoclassical plasma flows in stellarators," D. A. Spong, Phys. of Plasmas, Vol. 12, 056114 (2005).

"Topological instability along invariant surfaces and pseudochaotic transport," G. M. Zaslavsky, B. A. Carreras, V. E. Lynch, L. Garcia, and M. Edelman, to be published Phys. Rev. E.

"Non-diffusive transport in pressure-driven plasma turbulence: a fractional diffusion approach," D. del-Castillo-Negrete, B.A. Carreras, and V.E. Lynch, Phys. Rev. Letters 94, 065003 (2005).

"Recent advances in quasi-poloidal stellarator physics issues," D. A. Spong, S. P. Hirshman, J. F. Lyon, L. A. Berry and D. J. Strickler, Nuclear Fusion, Vol. 45, 918 (2005).

"Fluid limit of nonintegrable continuous-time random walks in terms of fractional differential Equations," R. Sanchez, B.A. Carreras, and B.Ph. van Milligen, Phys. Rev. E, 71, 011111 (2005).

"Probabilistic transport models for plasma transport in the presence of critical thresholds: beyond the diffusive paradigm," R. Sanchez, B.Ph. van Milligen, and B.A. Carreras, Phys. Plasmas 12, 056105 (2005).

"The foundations of diffusion revisited, B.Ph. van Milligen, B.A. Carreras, and R. Sanchez," to be published in Plasma Phys. Contrl. Fusion.

**PI Garrison Sposito**

O'Connor M.V., Sposito G. (2004) Investigation of biogenic manganese oxide by density functional theory. Abstracts of Papers of the American Chemical Society 228, U548-U549

**PI Phillip Sprangle**

D. F. Gordon, R. F. Hubbard, J. M. Cooley, B. Hafizi, A. Ting and P. Sprangle, Quasi-monoenergetic electrons from unphased injection into channel guided laser wakefield accelerators, Phys. Rev. E 71, 026404 (2005).

R. F. Hubbard, D. F. Gordon, J. H. Cooley, B. Hafizi, T. G. Jones, D. Kaganovich, P. Sprangle, A. Ting, A. Zigler, and J. Dexter, Trapping and Acceleration of Nonideal Injected Electron Bunches in Laser Wakefield Accelerators, IEEE Trans. Plasma Sci. 33, 712 (2005).

A. Ting, D. Kaganovich, D. F. Gordon, R.F. Hubbard and P. Sprangle, Generation and measurements of high energy injection electrons from the high density laser ionization and ponderomotive acceleration, Phys. Plasmas 12, 010701 (2005).

D. Kaganovich, A. Ting, D. Gordon, T. G. Jones, R. Hubbard, and P. Sprangle, Generation of high energy electrons in a double gas jet and laser wakefield acceleration, IEEE Trans. Plasma Sci. 33, 735 (2005).

**PI Ashok Srinivasan**

A. Srinivasan, Y. Yu, and N. Chandra. Application of reduced order modeling to time parallelization, 2005. To appear in Proceedings of HiPC. 2005

B. Radhakrishnan and G. Sarma, "Simulating the Effect of Coarse, Non-Deformable Particles on the Recrystallization Kinetics and Texture of Hot Deformed Aluminum", Philosophical Magazine A (22), pp. 2341-2366, 2004.

**PI Malcolm Stocks**

"Spin waves in paramagnetic BCC iron: spin dynamics simulations," Xiuping Tao, D. P. Landau, T. C. Schulthess, G. Malcolm Stocks, Phys. Rev. Lett. 95, 087207 (2005)

"Magnetic Interactions Influence the Properties of Helium Defects in Iron," Tatiana Seletskaia, Yuri Osetsky, R. E. Stoller and G. M. Stocks, Phys. Rev. Lett. 94, 046403 (2005)

"Magnetic structure of Ni?rich NiTa and permalloy?Ta alloys," Nassrin Y. Moghadam, G. Malcolm Stocks, Phys. Rev. B 71, 134421 (2005)

"Ab initio spin dynamics applied to nanoparticles: canted magnetism of a finite Co chain along a Pt(111) surface step edge," B. Ujfalussy, B. Lazarovits, L. Szunyogh, G. M. Stocks and P. Weinberger, Phys. Rev. (Rapid Communications) B 70, 100404 (2004)

"Ab initio study of canted magnetism of finite metallic chains at surfaces," B. Lazarovits, B. Ujfalussy, L. Szunyogh, G. M. Stocks and P. Weinberger, J. Phys.: Condens. Matter 16 No 48 S5833-S5840, (8 December 2004)

"Magnetic properties of quantum corrals from first-principles calculations," B. Lazarovits, B. Zjfalussy, L. Szunyogh, B. L. Gyvrffy, and P. Weinberger; J. Phys.: Condens. Matter 17 No 13 S1037-S1048 (6 April 2005)

"Polymorphous Coherent?Potential Approximation," S. Pella, J. S. Faulkner, G. Malcolm Stocks and B. Ujfalussy, Phys. Rev. B 70, 064203 (2004)

"Magnetic Structure of iron inclusions in copper," M. Eisenbach, G. M. Stocks, B. Zjfalussy, J. Appl. Phys. 95, 6684 (2004)

**PI Robert Street**

Chen, Y., R. L. Street, and F. L. Ludwig (2004) Stably stratified flows near a notched transverse ridge across the Salt Lake Valley. J. Appl. Meteor., 43, pp. 1308�28.

Chen, Y., R. L. Street, and F. L. Ludwig (2004) Mountain waves in Salt Lake Valley. Bulletin of the American Meteorological Society, 85, 943 � 43.

Chen, Y., Street, R. L., and Ludwig, F. L. (2004) On rotors, internal waves and hydraulic jumps in simulated stably-stratified flows in Utah's Salt Lake Valley. 11th Conf. on Mountain Meteorology and the Annual MAP, AMS, P1.2, 5 pages.

**PI Alberto Striolo**

A. Striolo, K.E. Gubbins, T.D. Burchell, J.M. Simonson, D.R. Cole, M.S. Gruszkiewicz, A.A. Chialvo, and P.T. Cummings, Temperature Effect on Water Adsorption in Porous Carbons, Langmuir, in press (2005).

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, (2005) in press.

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, (2005) in press.

A. Striolo, C. McCabe, and P.T. Cummings, Thermodynamic and Transport Properties of Polyhedral Oligomeric Silsesquioxanes in Poly(Dymethyl Siloxane), Journal of Physical Chemistry B, 109 (2005) 14300-14307.

A. Striolo, A.A. Chialvo, K.E. Gubbins, and P.T. Cummings, Water in Carbon Nanotubes: Adsorption Isotherms and Thermodynamic Properties from Molecular Simulation, Journal of Chemical Physics, 122 (2005) 234712; Virtual Journal of Nanoscale Science & Technology, Vol. 12, Issue 1, July 4th, 2005; Virtual Journal of Biological Physics Research, Vol. 10, Issue 1, July 1st, 2005

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

**PI Erich Strohmaier**

CUG2005: MPI, SHMEM, and UPC Performance on the Cray A Case Study using APEX-Map

EuroPar 2005: Apex-Map: A Synthetic Scalable Benchmark Probe to Explore Data Access Performance on Highly Parallel Systems

SC2005: Apex-Map: A Global Data Access Benchmark to Analyze HPC Systems and Parallel Programming Paradigms

SC2005: Measurement of Spatial and Temporal Locality in Memory Access Patterns, J. Weinberg, A. Snavely, M.O. McCracken, E. Strohmaier

**PI Maxim Sukharev**

"Optimal Control Approach to Suppression of Radiationless Transitions", M. Sukharev, T. Seideman, Phys. Rev. Lett. 93, 093004 (2004);

"Optical control of nonradiative decay in polyatomic molecules", M. Sukharev, T. Seideman, Phys. Rev. A, Vol. 71, 012509 (2005);

## T

**PI Xianzhu Tang**

"Force-free magnetic relaxation in driven plasmas," X.Z. Tang and A.H.Boozer, Physical Review Letters 94, 225004 (2005).

"Constrained resonance in magnetic self-organization," X.Z. Tang and A.H. Boozer, Physical Review Letters (in press, 2005).

"Flux amplification in helicity injected spherical tori," X.Z.Tang and A.H.Boozer, Phys. Plasmas 12, 042113 (2005).

"Chandrasekhar-Kendall modes and Taylor relaxation in an axisymmetric torus," X.Z. Tang and A.H. Boozer, Phys. Plasma (in press, 2005).

"The SEL spectral element code," A.H.Glasser and X.Z.Tang, Computer Physics Communications, 164: 237-243 (2004).

"Progress towards high performance plasmas in the National Spherical Torus Experiment (NSTX)," S.M.Kaye, et al, Nuclear Fusion (in press, 2005).

**PI Uwe Thumm**

On the effect of image states on resonant neutralization of hydrogen anions near metal surfaces, H. Chakraborty, T. Niederhausen, and U. Thumm, Nucl. Instr. Meth. B (to be published)

Resonant neutralization of H- near Cu surfaces: Effects of the surface symmetry and ion trajectory, H. Chakraborty, T. Niederhausen, and U. Thumm Phys. Rev. A 70, 052903 (2004)

Circular dichroism in laser-assisted proton-hydrogen collisions T. Niederhausen, B. Feuerstein, and U. Thumm Phys. Rev. A 70, 023408 (2004)

Effects of the surface Miller index on the resonant neutralization of hydrogen anions near Ag surfaces H. Chakraborty, T. Niederhausen, and U. Thumm Phys. Rev. A 69, 052901 (2004)

**PI Owen Toon**

A. S. Ackerman, M. P. Kirkpatrick, D. E. Stevens, O. B. Toon, 2004. The impact of humidity above stratiform clouds on indirect aerosol climate forcing, Nature, 432, 1014-1017.

Stevens, B., C.-H. Moeng, A. S. Ackerman, C. S. Bretherton, A. Chlond, S. de Roode, J. Edwards, J.-C. Golaz, H. Jiang, M. Khairoutdinov, M. P. Kirkpatrick, D. C. Lewellen, A. Lock, F. Mueller, D. E. Stevens, E. Whelan, and P. Zhu, Evaluation of large-eddy simulations via observations of nocturnal marine stratocumulus, Mon. Wea. Rev. 133, 1443-1462, 2005.

Kirkpatrick, M. P., A. S. Ackerman, D. E. Stevens, and N. N. Mansour, On the application of the dynamic Smagorinsky model to large-eddy simulations of the cloud-topped atmospheric boundary layer, In press at J. Atmos. Sci., 2005.

Xueref, I., C. Gerbig, A. Fridlind, A., J. C. Lin, S. C. Wofsy, B. C. Daube, A. S. Ackerman, J. E. Smith, D. Sayres, J. Vellovic, D. G. Baumgardner, D. Wang, E. Weinstock, A. E. Andrews, E. W. Gottlieb, and J. G. Anderson, Combining a receptor-oriented framework for tracer distributions with a cloud-resolving model to study transport in deep convective clouds: Application to the NASA CRYSTAL-FACE campaign, Geophys. Res. Lett. 31 (14), L14106, 2004.

**PI Doug Toussaint**

Light pseudoscalar decay constants, quark masses, and low energy constants from three-flavor lattice QCD, The 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, Phys. Rev. D 70, 114501 (2004) [arXiv:hep-lat/0407028].

First determination of the strange and light quark masses from full lattice QCD, HPQCD collaboration: MILC collaboration: UKQCD collaboration: C. Aubin, C. Bernard, C. Davies, C. DeTar, S. Gottlieb, A. Gray, E. Gregory, J. Hein, U.M. Heller, J. Hetrick, G. Lepage, Q. Mason, J. Osborn, R. Sugar, D. Toussaint), Phys. Rev. D 70 031504(R) (2004) [arXiv:hep-lat/0405022].

Semileptonic decays of D mesons in three-flavor lattice QCD, The Fermilab Lattice, MILC, and HPQCD Collaborations: C. Aubin, C. Bernard, C. DeTar, M. Di Pierro, A. El-Khadra, Steven Gottlieb, E. B. Gregory, U. M. Heller, J. Hetrick, A. S. Kronfeld, P. B. Mackenzie, D. Menscher, M. Nobes, M. Okamoto, M. B. Oktay, J. Osborn, J. Simone, R. Sugar, D. Toussaint, H. D. Trottier, Phys. Rev. Lett. 94, 011601 (2005) [arXiv:hep-lat/0408306].

Light hadrons with improved staggered quarks: approaching the continuum limit, The MILC Collaboration: C. Aubin, C. Bernard, T. Burch, C. DeTar, Steven Gottlieb, E.B. Gregory, U.M. Heller, J. Osborn, R. Sugar, D. Toussaint, Phys. Rev. D 70, 094505 (2004) [arXiv:hep-lat/0402030].

Topological susceptibility with three flavors of staggered quarks, The MILC Collaboration: C. Aubin, C. Bernard, Brian Billeter, C. DeTar, Steven Gottlieb, E. Gregory, U.M. Heller, J.E. Hetrick, J. Osborn (2), R.L. Sugar, D. Toussaint, Nucl. Phys. B (Proc. Suppl.) 140, 600 (2005) [arXiv:hep-lat/0409051].

The scaling dimension of low lying Dirac eigenmodes and of the topological charge density, The MILC Collaboration: C. Aubin, C. Bernard, Steven Gottlieb, E.B. Gregory, Urs M. Heller, J.E. Hetrick, J. Osborn, R. Sugar, D. Toussaint, Ph. de Forcrand, and O. Jahn, Nucl. Phys. B (Proc. Suppl.) 140, 626 (2005) [arXiv:hep-lat/0410024].

Leptonic decay constants f_Ds and f_D in three flavor lattice QCD, The Fermilab Lattice, HPQCD and MILC Collaborations: J.N. Simone, C. Aubin, C. Bernard, C. DeTar, M. di Pierro, A.X. El-Khadra, Steven Gottlieb, E.B. Gregory, U.M. Heller, J.E. Hetrick, A.S. Kronfeld, P.B. Mackenzie, D.P. Menscher, M. Nobes, M. Okamoto, M.B. Oktay, J. Osborn, R. Sugar, D. Toussaint, H.D. Trottier, Nucl. Phys. B (Proc. Suppl.) 140, 443 (2005) [arXiv:hep-lat/0410030].

The Omega- and the strange quark mass, D. Toussaint and C. Davies (MILC and UKQCD Collaborations), Nucl. Phys. B (Proc. Suppl.) 140, 234 (2005) [arXiv:hep-lat/0409129].

## U

## V

**PI George Vahala**

A. Macnab, G. Vahala and L. Vahala, "Non-uniform grid Lattice Boltzmann Simulations of 1D Dissipative MHD", Prog. Comput. Fluid Dynamics, 5, 37-49 (2005)

J. Carter, M. Soe, L. Oliker, Y. Tsuda, G. Vahala, L. Vahala and A. Macnab, "MHD Turbulence SImulations on the Earth Simulator Using the Lattice Boltzmann Method" , finalist for Gordon Bell Prize 2005 ; to be published in Proc. of SC|05 (Nov. 2005)

A. Macnab, G. Vhala, L. Vahala, J. Carter, M. Soe and W. Dorland, "The Lattice Boltzmann Representation for Plasma Physics", to be published in Physica A (2005)

G. Vahala, L. Vahala and J. Yepez, "Quantum Lattice Representation for Vector Solitons in an External Potential", to be published in Physica A (2005)

**PI Michel Van Hove**

"Atomistic Simulations of fcc Pt75Ni25 and Pt75Re25 Cubo-octahedral Nanoparticles", G. Wang, M.A. Van Hove, P.N. Ross and M.I. Baskes, Mat. Res. Soc. Symp. Proc. 818, 89-94 (2004).

"Monte Carlo Simulations of Segregation in Pt-Ni Catalyst Nanoparticles", G. Wang, M.A. Van Hove, P.N. Ross and M.I. Baskes, J. Chem. Phys. 122, 024706: 1-12 (2005).

"Surface Structures of Cubo-octahedral Pt-Mo Catalyst Nanoparticles from Monte Carlo Simulations", G. Wang, M.A. Van Hove, P.N. Ross and M.I. Baskes, J. Phys. Chem. 109, 11683-11692 (2005

"Quantitative Prediction of Surface Segregation in Bimetallic Pt-M Alloy Nanoparticles (M=Ni, Re, Mo)", G. Wang, M.A. Van Hove, P.N. Ross and M.I. Baskes, to be publ. in Prog. Surf. Sci.

**PI James Vary**

Richard J. Lloyd and James P. Vary, "All-charm Tetraquarks," Phys. Rev. D 70, 014009 (2004); hep-ph/0311179.

B.R. Barrett, P. Navratil, A. Nogga, W.E. Ormand, I. Stetcu, J.P. Vary and H. Zhan, "The Ab-Initio Large-Basis No-Core Shell Model," Proceedings of the 8th International Spring Seminar On Nuclear Physics, Paestum, Italy, World Scientific (Singapore) to appear.

A.M. Shirokov, A.I. Mazur, S.A. Zaytsev, J.P. Vary and T.A. Weber, "Nucleon-Nucleon Interaction in the J-Matrix Inverse Scattering Approach and Few-Nucleon Systems," Phys. Rev. C 70, 044005 (2004); nucl-th/0312029.

J.P. Vary, "How Effective are Strong Interactions," in Blueprints for the Nucleus, C. Johnson, Editor, International Journal of Modern Physics E 14, 1 (2005).

A. Abd El-Hady, J.P.Vary and J.R. Spence, "Radiative Decays of Bc Mesons in a Bethe- Salpeter Model," Phys. Rev. D 71, 034006 (2005).

Ionel Stetcu, Bruce R. Barrett, Petr Navratil, and James P. Vary, "Effective operators within the ab initio no-core shell model," Phys. Rev. C 71,044325 (2005); nucl-th/ 0412004,.

D. Chakrabarti, A. Harindranath, L. Martinovic, G. Pivovarov and J.P. Vary, "Ab initio results for the broken phase of scalar light front field theory," Phys. Letts. B 617, 92 (2005) hep-th/0310290.

D. Chakrabarti, A. Harindranath and J.P. Vary, "A Transition in the Spectrum of the Topological Sector of Phi4(2) Theory at Strong Coupling," Phys. Rev. D 71, 125012(2005); hep-th/05104094.

B. R. Barrett, D. J. Dean, M. Hjorth-Jensen and J. P. Vary, Editors, "Nuclear Forces and the Quantum Many-Body Problem," Journal of Physics G 31, S1235 (2005).

## W

**PI Haobin Wang**

H. Wang and M. Thoss, ``Self-consistent hybrid method: theory and applications to ultrafast electron transfer reactions in condensed phases'', Encyclopedia of Computational Chemistry, 2004.

M. Thoss and H. Wang, "Quantum Dynamical Simulation of Ultrafast Molecular Processes in the Condensed Phase", Chem. Phys., 315, xxx (2005).

I. Kondov, H. Wang, and M. Thoss, "Computational study of titanium (IV) complexes with organic chromophores", Int. J. Quan. Chem., in press.

**PI Lin-Wang Wang**

L.W. Wang, "Quantum transport calculations using auxiliary periodic boundary conditions", Phys. Rev. B 72, 45417 (2005)

L. Manna, L.W. Wang, R. Cingolani, A.P. Alivisatos, "First principle modeling of unpassivated and surfactant-passivated bulk facets of wurtzite CdSe", J. Phys. Chem. B 109, 6183 (2005)

X. Cartoixa, L.W. Wang, "Microscopic dieletric response functions in semiconductor quantum dots", Phys. Rev. Lett. 94, 236804 (2005)

J. Li, S.-H. Wei, L.W. Wang, "Stability of the DX center in GaAs quantum dots", Phys. Rev. Lett. 94, 185501 (2005).

J. Li, L.W. Wang, "Ab initio study of semiconductor quantum dots and wires", Phys. Rev. B (in press)�

Y. Zhang, A. Mascarenhas, L.W. Wang, "Similar and dissimilar aspects of III-V semiconductors containing Bi versus N", Phys. Rev. B 71, 155201 (2005).

J.W. Luo, S.S. Li, J.B. Xia, L.W. Wang, "Photoluminescence pressure coefficients of InAs/GaAs quantum dots", Phys. Rev. B 71, 245315 (2005)

J. Li, L.W. Wang, "Electronic structure of InP quantum rods: differences between wurtzite, zince blende, and different orientations", Nano Lett. 4, 29 (2004).

L.W. Wang, "Effects of stacking faults on the electronic structures of quantum rods", J. Comp. Theor. Nano. 1, 298 (2004).

J. Li, L.W. Wang, "Comparison between quantum confinement effects of quantum wires and quantum dots", Chem. Mater. 16, 4012 (2004).

J. Li, L.W. Wang, "Comparison between quantum confinement effects of quantum wires and quantum dots", Chem. Mater. 16, 4012 (2004)�

**PI Warren Washington**

Arblaster, J.M. and G.A. Meehl, 2005: Contributions of external forcings to Southern Annular Mode trends, Journal of Climate, accepted.

Barnett, T., R. Malone, W. Pennell, D. Stammer, A. Semtner, and W. Washington, 2004: The effects of climate change on water resources in the west: Introduction and Overview. Climatic Change, 62, 1-11.

Barnett, T.P., D. Pierce, K. AchutaRao, P. Gleckler, B. Santer, J. Gregory and W. Washington, 2005: Penetration of Human-Induced Warming into the World's Oceans. Science, 309, 284-287.

Dai, A., A. Hu, G.A. Meehl, W.M. Washington and W.G. Strand, 2005: Atlantic thermohaline circulation in a coupled general circulation model: Unforced variations vs. forced changes. J. Climate, in press.

Hu, A., G.A. Meehl, W.M. Washington, and A. Dai, 2004: Response of the Atlantic thermohaline circulation to increased atmospheric CO2 in a coupled model, Journal of Climate, 17, 4267-4279.

Lamarque, J.-F., P. Hess, L. Emmons, L. Buja, W.M. Washington and C. Granier, 2005: Tropospheric ozone evolution between 1890 and 1990, Journal of Geophysical Research, 110, D08304, doi: 10.1029/2004JD005537.

Meehl, G.A., C.Covey, B. McAvaney, M. Latif, and R.J. Stouffer, 2005: Overview of the Coupled Model Intercomparison Project. Bulletin of the American Meteorological Society, 86, 89-93.

Meehl, G. A., W. M. Washington, W. D. Collins, J.M. Arblaster, A. Hu, L. E. Buja, W. G. Strand, H. Teng, 2005: How much more global warming and sea level rise. Science, 307, 1769-1772.

Meehl, G.A., and C. Tebaldi, 2004: More intense, more frequent and longer lasting heat waves in the 21st century. Science, 305, 994-997.

van Loon, H., G.A. Meehl, and J.M. Arblaster, 2004: A decadal solar effect in the tropics in July-August. Journal of Atmospheric and Solar-Terrestrial Physics, 66, 1767-1778 (doi: 10.1016/j.jastp.2004.06.003)

Dai, A., W.M. Washington, G.A. Meehl, T.W. Bettge, and W.G. Strand, 2004: The ACPI climate change simulations. Climatic Change, 62, 29-43.

Hu, A. and G. A. Meehl, 2005: Reasons for a fresher northern North Atlantic in the late 20th Century. Geophysical Research Letters, 32, L11701,doi:1029/2005GL022900. Meehl G.A., J.M. Arblaster and C. Tebaldi, 2005: Understanding future patterns of precipitation extremes in climate model simulations, Geophysical Research Letters, in pres.

Meehl, G.A., W.M. Washington, J.M. Arblaster, and A. Hu, 2004: Factors affecting climate sensitivity in global coupled models. Journal of Climate, 17, 1584-1596.

Meehl, G.A., W.M. Washington, C. Ammann, J.M. Arblaster, T.M.L. Wigley, and C. Tebaldi, 2004: Combinations of natural and anthropogenic forcings and 20th century climate. Journal of Climate, 17, 3721-3727.

**PI William Weber**

R. Devanathan, L. R. Corrales, W. J. Weber, A. Chartier, and C. Meis, Molecular Dynamics Simulation of Defect Production in Collision Cascades in Zircon, Nucl. Instrum. and Methods in Physics Res. B 228 [1-4]: 299-303 (2005).

F. Gao, R. Devanathan, Y. Zhang, and W. J. Weber, Annealing Simulations of Nano-Sized Amorphous Structures in SiC, Nucl. Instrum. and Methods in Physics Res. B 228 [1-4]: 282-287 (2005).

F. Gao and W. J. Weber, Atomic-Level Computer Simulation of SiC: Defect Accumulation, Mechanical Properties and Defect Recovery, Philosophical Magazine 85 [4-7]: 509-518 (2005).

L. R. Corrales, A. Chartier, and R. Devanathan, Excess Kinetic Energy Dissipation in Materials, Nucl. Instrum. and Methods in Physics Res. B 228 [1-4]: 274-281 (2005).

A. Chartier, C. Meis, J.-P. Crocombette, W. J. Weber, and L. R. Corrales, Molecular Dynamic Simulation of Disorder Induced Amorphization in Pyrochlores, Physical Review Letters 94 [2]: 025505, 1-3 (2005).

R. Devanathan, F. Gao, and W. J. Weber, Amorphization of Silicon Carbide by Carbon Displacement, Applied Physics Letters 84 [19]: 3909-3911 (2004).

F. Gao, E. J. Bylaska, A. El-Azab, and W. J. Weber, Wannier Orbitals and Bonding Properties of Interstitial and Antisite Defects in GaN, Applied Physics Letters 85 [23]: 5565-5567 (2004).

F. Gao and W. J. Weber, Mechanical Properties and Elastic Constants Due to Damage Accumulation and Amorphization in SiC, Physical Review B 69 [22]: 224108, 1-10 (2004).

F. Gao, W. J. Weber, M. Posselt, and V. Belko, Atomistic Study of Intrinsic Defect Migration in 3C-SiC, Physical Review B 69 [24]: 245205, 1-5 (2004).

F. Gao, E. J. Bylaska, and W. J. Weber, Intrinsic Defect Properties in GaN Calculated by Ab Initio and Empirical Potential Methods, Physical Review B 70 [24]: 245208, 1-8 (2004).

H. L. Heinisch and W. J. Weber, Computational Model of Alpha-Decay Damage Accumulation in Zircon, Nucl. Instrum. and Methods in Physics Res. B 228 [1-4]: 293-298 (2005).

F. Gao, W. J. Weber, M. Posselt, and V. Belko, Atomic Computer Simulations of Defect Migration in 3C and 4H-SiC, Materials Science Forum 457-460: 457-460 (2004).

R. Devanathan, L. R. Corrales, W. J. Weber, A. Chartier, and C. Meis, Molecular Dynamics Simulation of Disordered Zircon, Physical Review B 69 [6]: 064115, 1-9 (2004).

H. L. Heinisch, L. R. Greenwood, W. J. Weber, and R. E. Williford, Displacement Damage in Silicon Carbide Irradiated in Fission Reactors, J. Nuclear Materials 327 [2-3]: 175-181 (2004).

W. J. Weber, F. Gao, R. Devanathan, W. Jiang, and Y. Zhang, Defects and Ion-Solid Interactions in Silicon Carbide, Materials Science Forum 475-479: 1345-1350 (2005).

**PI Michael Weinert**

Magnetism on the Surface of the Bulk Paramagnetic Intermetallic Compound YCo_2. S. Khmelevskyi, P. Mohn, J. Redinger, and M. Weinert, Phys. Rev. Lett. 94, 146403 (2005).

Selected growth of cubic and hexagonal GaN epitaxial films on polar MgO(111). V.K. Lararov, J. Zimmerman, S.H. Cheung, L. Li, M. Weinert, and M. Gajdardziska-Josifovska, Phys. Rev. Lett. 94, 216101 (2005).

Structure determination of disordered organic molecules on surfaces from the Bragg spots of low-energy diffraction and total-energy calculations. T. Zheng, W. T.Tysoe, H. C. Poon, M. Weinert, and D. K. Saldin, Phys. Rev. B 69, 035401 (2004).

X-ray absorption near-edge structure analysis of the chemical environment of zinc in the tribological film formed by zinc dialkyl dithiophosphate decompisiton on steel. M. D. Pauli, T. S. Rufasel, J. K. Mowlen, M. Weinert, D. K. Saldin, and W. T. Tysoe, Tribology International 38, 195 (2005).

Ultrahigh vacuum study of the requirements for formation of a chiral template. D. Stacchiola, L. Burkholder, T. Zheng, M. Weinert, and W. T. Tysoe, J. Phys.Chem.B 109, 851 (2005).

Structure of the hydrogen stabilized MgO(111)-(1x1) polar surface: Integrated experimental and theoretical studies. V. K. Lazarov, R. A. Plass, H-C. Poon, D.K.Saldin, M. Weinert, S. A. Chambers, and M.Gajdardziska-Josifovska, Phys. Rev. B 71, 115434 (2005).

**PI Harold Weitzner**

P. Garabedian, Computational mathematics and physics of fusion reactors, Proc. Natl. Acad. Sci. USA { 100} (2003) 13741-13745.

P. Garabedian and M. Meurer, Cavitational flow and magnetohydrodynamics, International Journal of Computational Fluid Dynamics {18} (2004) 413-420.

P. Garabedian and L.-P. Ku, Reactors with stellarator stability and tokamak transport, Fusion Sci. Technol. { 47} (2005) 400-405.

Harold H.R. Strauss, Linjin Zheng, M. Kotschenreuther, W. Park, S. Jardin, J. Breslau, A. Pletzer, Roberto Paccagnella, L. Sugiyama, M. Chu, M. Chance, A. Turnbull, Halo Current and Resistive Wall Simulations of ITER, Twentieth IAEA Fusion Energy Conference, Villamora, Portugal IAEA-CN-116/TH/2-2 (2004)

G.M. Zaslavsky and M. Edelman, Fractional kinetics: From pseudochaotic dynamics to Maxwell's Demon, Physica D 193, Iss.1-4, p. 128 (2004).

G.M. Zaslavsky and M. Edelman, Fractional dynamics of pseudochaotic systems First Workshop on Fractional Differentiation and its Applications of the International Federation of Automatic Control, July 19-21, 2004, Bordeaux, France (2004).

G.M. Zaslavsky, B.A. Carreras, V.E. Lynch, L. Garcia, M. Edelman, Topological Instability Along Invariant Surfaces and Pseudochaotic I.P. Smirnov, A.L. Virovlyansky, M. Edelman, G.M. Zaslavsky, Chaos- induced intensification of wave scattering, Phys. Rev. E, accepted (2005).

G.M. Zaslavsky and M. Edelman, Polynomial Dispersion of Trajectories in Sticky Dynamics, Phys. Rev. E, accepted (2005).

C. S. Chang, S. Ku, H. Weitzner, Numerical Study of neoclassical plasma pedestal in a tokamak geometry, Phys. Plasma 11, 2649 (2004)

H. Weitzner and C. S. Chang, Phys. Plasma 11, 3060 (2004).

R. Maingi, C. S. Chang et al., Effect of gas fueling location on H mode access in NSTX, Plas. Phys. Cont. Fusion (2005)

**PI Jack Wells**

"Multiscale Simulations of Carbon Nanotube Nucleation and Growth: Electronic Structure Calculations," J. C. Wells, D.W. Noid, B. G. Sumpter, and R. F. Wood, and Q. Zhang, J. Nanosci Nanotech. 4, 414 (2004).

"Adsorption of a Carbon Atom on the Ni38 Magic Cluster and Three Low-index Nickel Surfaces: a First- Principles, Comparative Study," Q.-M. Zhang, J.C. Wells, X.-G. Gong, and Z. Zhang, Phys. Rev. B 69, 205413 (2004).

"Far-field Modulation of Fluorescence Decay Rates in Pairs of Oriented Semiconducting Polymer Nanostructures," M.D. Barnes, P.S. Krstic, P. Kumar, J.C. Wells, Phys. Rev. B 71, 241303(R) (2005).

"Interaction between benzenedithiolate and gold: classical force field for chemical bonding," D.J. Keffer, P.S. Krstic, Y.-S. Leng, D.J. Dean, P.T. Cummings, and J.C. Wells, J. Chem. Phys. 122, 244721 (2005).

"Two Growth Models of Graphitic Carbon Nanofibers with Herring-bone Structure," I. A. Merkulov, A.V. Meleshko, J.C. Wells, H. Cui, V.I. Merkulov, M.L. Simpson, and D. H. Lowndes, Phys. Rev. B 72, 045409 (2005).

"GMG - A Guaranteed Global Optimization Algorithm: Application to Remote Sensing," C. Delon, V. Protopopescu, J.C. Wells, J. Barhen, Comp. Opt. App. (under review, 2005).

**PI Martin White**

de Putter R., White M., Using weak lensing to find halo masses, New Astronomy, 10, 676 (2005)

Amblard A., White M., Sunyaev Zeldovich polarization simulation, New Astronomy, 10, 423 (2005)

White M., Reducing the shear, Astroparticle Physics, 23, 354 (2005) Eisenstein D., White M., Theoretical uncertainty in baryon oscillations, Physical Review D, 70, (2004)

Vale C., Amblard A., White M., Cluster lensing of the CMB, New Astronomy, 10, 15 (2004)

White M., Baryons and weak lensing power spectra, Astroparticle Physics, 22, 217 (2004)

Amblard A., Vale C., White M., Weak lensing of the CMB by large-scale structure, New Astronomy, 9, 704 (2004)

White M., Vale C., Simulations of weak gravitational lensing, Astroparticle Physics, 22, 27 (2004)

Vale C., Hoekstra H., van Waerbeke L., White M., Large-Scale Systematic Signals in Weak Lensing Surveys, Astrophysical Journal, 613, L4 (2004)

Vale C., White M., Finding clusters in SZ surveys, to appear in New Astronomy.

Cohn J., White M., The formation histories of galaxy clusters, to appear in Astroparticle Physics.

White M., Baryon oscillations, to appear in Astroparticle Physics.

Linder E., White M., Going nonlinear with dark energy cosmologies, submitted to Phys. Rev. D.

**PI James Wiley**

L.J. Zheng and M. Kotschenreuther, "AEGIS: An adaptive ideal magnetohydrodynamics shooting code for axisymmetric plasmas", J. Computational Physics, in press (2005).

E. Spencer, W. Horton and I. Doxas, "The Dynamics of Storms and Substorms with the WINDMI Model," Advances in Space Research, in press (2005).

E.G. Evstatiev, W. Horton and P.J. Morrison, "Relativistic multi-wave model for plasma-wave interaction," to appear in Physics of Plasmas, July, 2005.

E.G. Evstatiev, P.J. Morrison, and W. Horton, "A relativistic beam-plasma system with electromagnetic waves," Phys. Plasmas 12, 072108 (2005).

W. Horton, M.J. Mithaiwala, E.A. Spencer, and I. Doxas, "WINDMI, a family of Physics network models for storms and substorms," a chapter in the book Multiscale Coupling of Sun-Earth Processes, ed. by A.T.Y. Lui, Y. Kamide, and G. Consolini, Elsevier Publ. Co., Amsterdam, The Netherlands, 2005) pp. 431-446.

R. Presura, V.V. Ivanov, Y. Sentoku, V.I. Sotnikov, P.J. Laca, N. Le Galloudec, A. Kemp, R. Mancini, H. Ruhl, A.L. Astanovitskiy, T.E. Cowan, T. Ditmire, C. Chiu, W. Horton, P. Valanju and S. Keely, "Laboratory Simulation of Magnetospheric Plasma Shocks," Astrophysics and Space Science 298: 299-303 (2005).

W. Horton, C. Chiu, and T. Ditmire, "Laboratory Simulations of Bow Shocks and Magnetospheres," Astrophysics and Space Science 298: 395-401 (2005).

W. Horton, J. C. Perez, T. Carter and R. Bengtson, "Vorticity probes and the characterization of vortices in the Kelvin-Helmholtz instability in the large plasma device experiment," Physics of Plasmas 12, No. 2, 022303 (2005).

W. Horton, H.V. Wong, P.J. Morrison, A. Wurm, J.H. Kim, J.C. Perez, J. Pratt, G.T. Hoang, B.P. LeBlanc and R. Ball, "Temperature gradient driven electron transport in NSTX and Tore Supra," Nuclear Fusion 45, 1-10 (2005).

H. Vernon Wong, B.-Y. Xu, W. Horton, J. Pratt, and J.W. Van Dam, "Nonlinear evolution of the firehouse instability in a magnetic dipole geotail geometry," Phys. Plasmas 12, 056502 (2005).

L.J. Zheng and M. Kotschenreuther, "Wall thickness effect on the resistive wall modes in toroidal plasmas", Phys. Plasmas 12, 072504 (2005).

M.J. Mithaiwala and W. Horton, Substorm injections produce sufficient electron energization to account for MeV flux enhancements following some storms, Journal of Geophysical Research, Vol. 110, A07224, doi: 10.1029/2004JA010511 (2005).

W. Horton, C. Chiu, T. Ditmire, P. Valanju, R. Presura, V.V. Ivanov, Y. Sentoku, V. I. Sotnikov, A. Esaulov, N. Le Galloudec, T. E. Cowan, I. Doxas, Laboratory simulation of magnetospheric plasma shocks, Adv. in Space Res. doi:10.1016/j.asr.2005.01.087

W. Horton, B-Y. Xu, and H. Vernon Wong, Firehose driven magnetic fluctuations in the magnetosphere, Geophys. Res. Lett., 31, L06807, doi:10.1029/2003GLO18309 (2004).

**PI John Wilkins**

Impurities block the alpha to omega martensitic transformation in titanium. R.G. Hennig, D.R. Trinkle, J. Bouchet, S.G. Srinivasan, R.C. Albers, and J.W. Wilkins. Nature Materials 4, 129 (2005).

Systematic pathway generation and sorting in martensitic transformations: Titanium alpha to omega. D.R. Trinkle, D.M. Hatch, H.T. Stokes, R.G. Hennig and R.C. Albers. Physical Review B 72, 014105 (2005).

A new mechanism for the alpha to omega martensitic transformation in pure titanium. D.R. Trinkle, R.G. Hennig, S.G. Srinivasan, D.M. Hatch, M.D. Jones, H.T. Stokes, R.C. Albers, and J.W. Wilkins. Physical Review Letters 91, 025701 (2003).

Complexity of Small Silicon Self-Interstitial Defects. D.A. Richie, J. Kim, S.A. Barr, K.R. A. Hazzard, R.G. Hennig, and J.W. Wilkins. Physical Review Letters 92, 45501 (2004).

Fast Diffusion Mechanism of Silicon Tri-interstitial Defects. Y. A. Du, S. A. Barr, K. R. A. Hazzard, T. J. Lenosky, R. G. Hennig, and J. W. Wilkins. cond-mat/0503479.

**PI Andrew Williamson**

F. Reboredo and A.J. Williamson, Optimized nonorthogonal localized orbitals for linear scaling quantum Monte Carlo calculations, Physical Review B 71, 121105(R) (2005).

N. Drummond, A.J. Williamson, R.J. Needs and Giulia Galli, Electron emission from diamondoids: A diffusion quantum Monte Carlo study, Physical Review Letters 95, 096801 (2005).

**PI Stan Woosley**

``One-Armed Spiral Instability in a Slowly Rotating, Post-Bounce Supernova Core," Christian Ott, Shangli Ou, Joel E. Tohline & Adam Burrows, Astrophys. J., 625, L119, 2005.

``Two-dimensional, Time-dependent, Multi-group, Multi-angle Radiation Hydrodynamics Test Simulation in the Core-Collapse Supernova Context," Livne, E. Burrows, A., Walder, R., Thompson, T.A., & Lichtenstadt, I., Astrophys. J., 609, 277, 2004.

``Viscosity and Rotation in Core-Collapse Supernovae," Thompson, T.A., Quataert, E. & Burrows, A., Astrophys. J., 620, 861, 2005

``Anisotropies in the Neutrino Fluxes and Heating Profiles in Two-dimensional, Time-dependent, Multi-group Radiation Hydrodynamics Simulations of Rotating Core-Collapse Supernovae," R. Walder, A. Burrows, C.D. Ott, E. Livne, I. Lichtenstadt, & M. Jarrah, Astrophys. J., 626, 317, 2005.

``Three-dimensional Numerical Simulations of Rayleigh-Taylor Unstable Flames in Type Ia Supernovae," M. Zingale, S.E. Woosley, C.A. Rendleman, M.S. Day, & J. B. Bell, 2005, ApJ, in press.

"Probing the geodynamo," Glatzmaier, G.A. & Olson, P. 2005 Scientific American, 292, 50-57.

"Binary Merger Progenitors for Gamma-Ray Bursts and Hypernovae" Fryer, C. L. and Heger, A., 2005, ApJ, 623, 302

"Diffuse X-rays from the Arches and Quintuplet Clusters" (2005), Rockefeller, G., Fryer, C. L. Melia, F., Wang, Q. D., ApJ, 623, 171

"Binary Merger Progenitors for Gamma-Ray Bursts and Hypernovae" (2005) Fryer, C. L. and Heger, A., ApJ, 623, 302

"Spin-Induced Disk Precession in Sagittarius A*", Rockefeller, G., Fryer, C.L., and Melia, F., accepted by ApJ

"Gravitational Waves from Axisymmetric, Rotating Stellar Core Collapse," Ott, C.D., Burrows, A., Livne, E., & Walder, R. 2004, Astrophys. J., 600, 834, 2004

"Planetary and Stellar Dynamos: Challenges for next generation models," Glatzmaier, G.A. (2005) in "Fluid Dynamics and Dynamos in Astrophysics and Geophysics" eds. A.M. Soward, C.A. Jones, D.W. Hughes, N.O. Weiss, Chp 11, 331-357 (2005, CRC Press).

**PI Ruqian Wu**

Ruqian Wu "Electronic and chemical properties of Au nano-particles on oxide substrates with O vacancies", APS bullitin, 2005

Ruqian Wu, "Atomic structures and chemical properties of PdAu bimetallic surfaces and clusters", DOE contractor meeting.

J.X. Cao, X.G. Gong, and Ruqian Wu, "Simulation for the growth of TiO2 on Mo(112) and Au clusters", in final preparation.

J.S. Hong and R.Q Wu, "The Mechanism of Magnetic Ordering and X-ray Magnetic Circular Dichroism of Co-doped ZnO", J. Appl. Phys. 97, 063911 (2005).

D. Wu, D.J. Keavney, Ruqian Wu, E. Johnston-Halperin, D.D. Awschalom, and Jing Shi, "Nearly concentration-independent local Mn configuration in ferromagnetic Ga1-xMnxAs", Phys. Rev. B 71, 153310 (2005).

J.S. Hong, D.S. Wang and R.Q. Wu, "Carrier induced magnetic ordering control in a digital (Ga,Mn)As structure", Phys. Rev. Lett. 94, 137206 (2005).

J.X. Cao, X.G. Gong and R.Q. Wu, "Adsorption and Segregation of Mn on GaAs(110) from First Principle Studies", Phys. Rev. B, in press.

R.Q. Wu "Nature of Mn Induced Spin Polarization and Magnetic Circular Dichroism of Ga1-xMnxAs", Phys. Rev. Lett. 94, 207201 (2005).

R.Q. Wu, "Perspective of Fundamental Research for Nanomagnetism", edited by J.A.C. Bland and D.L. Mills, (Elsevier, 2005).

R.Q. Wu, "Theory of Magnetocrystalline Anisotropy and Magneto-elasticity and Related Phenomena- Transition Metals", edited by H. Kronmller and S. Parkin, (John Wiley & Sons, 2005).

**PI Donald Wuebbles**

Forster, P. M., J. B. Burkholder, C. Clerbaux, P. F. Coheur, M. Dutta, L. K. Gohar, M. D. Hurley, G. Myhre, R. W. Portmann, A. Ravishankara, K. P Shine, T. J. Wallington, and D. Wuebbles, 2004: Resolving uncertainties in the radiative forcing of HFC-134a, J. Quant. Spec. Rad. Trans., DOI:10.1016/j.jqsrt.2004.08.038.

Naik, V., C. Delire, D. J. Wuebbles, 2004: The sensitivity of global isoprenoid emissions to climate variability and atmospheric CO2. J. Geophys. Res., 109, doi: 10.1029/2003JD004236.

Tao, Z., S. M. Larson, D. J. Wuebbles, A. Williams, and M. Caughey, 2004: Sensitivity of regional ozone to temporal distributions of emissions. Atmos. Environ., 38/37, 6279-6285, doi: 10.1016/j.atmosenv.2004.08.042.

Wuebbles, D. J., and K. Hayhoe, 2004: Climate change in the Midwest: informing regional policy decisions. Mitigation and Adaptation Strategies for Global Change, 9, 335-363.

Guillas, S., M. L. Stein, D. J. Wuebbles and J. Xia, 2005: Using chemical-transport modeling in statistical analysis of stratospheric ozone trends from observations. J. Geophys. Res., in press.

Reinsel, G. R., A. J. Miller, L.E. Flynn, R. M. Nagatani, G. C. Tiao, E. C. Weatherhead, and D. J. Wuebbles 2005: Trend analysis of total ozone data for turnaround and dynamical contributions. J. Geophys. Res., in press.

Tao, Z., S. M. Larson, A. Williams, M. Caughey and D. J. Wuebbles, 2005: Area, mobile, and point source contributions to ground level ozone: a summer simulation across the continental USA. Atmos. Environ., 39, 1869-1877.

Wei, C.-F., V. R. Kotamarthi, and D. J. Wuebbles, 2005: Episodic events of long-range transport of biomass into the Southern tropical Pacific Ocean during PEM-Tropics A period. J. Geophys. Res., in press.

## X

## Y

**PI Wei Yang**

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).

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).

Bitetti-Putzer, R., Dinner, A. R., Yang W., and Karplus, M. submitted. Conformational sampling via a self-regulating effective energy surface. J. Chem. Phys.

Banerjee, A.*, Yang, W.*, Karplus, M., and Verdine, G. L. 2005. Structure of hOGG1 interrogating undamaged DNA elucidates recognition of damaged DNA, Nature 434:612-618.

Gao, Y. Q.*, Yang, W.*, and Karplus, M. in press. A structure-based model for synthesis and hydrolysis of ATP by F1-ATPase, Cell

Yang, W., Gao, Y. Q., Cui, Q., Ma, J., and Karplus, M. 2003. The missing link between thermodynamics and structure in F1-ATPase. Proc. Natl. Acad. Sci. USA 100, 874-879.

**PI David Yarkony**

"Beyond two-state conical intersections. Three-state conical intersections in low symmetry molecules: the allyl radical." Matsika,S.,Yarkony,D.R. Journal of the American Chemical Society. vol 125, pg. 10672-10676.

" Accidental conical intersections of three states of the same symmetry. I. Location and relevance." Matsika,S., Yarkony, D.R. Journal of Chemical Physics. vol. 117. pg. 6907-6910.

**PI Katherine Yelick**

Amir Kamil, Jimmy Su, and Katherine Yelick, "Making Sequential Consistency Practical in Titanium." Supercomputing 2005 (SC|05), Seattle, Washington, November 2005. To appear.

Amir Kamil and Katherine Yelick, "Concurrency Analysis for Parallel Programs with Textually Aligned Barriers." 18th International Workshop on Languages and Compilers for Parallel Computing, Hawthorne, New York, October 2005.

Kaushik Datta, Dan Bonachea and Katherine Yelick. "Titanium Performance and Potential: an NPB Experimental Study." Languages and Compilers for Parallel Computing (LCPC), Hawthorne, New York, October 2005.

W.-Y. Chen, C. Iancu, and K. Yelick, "Communication Optimizations for Fine-grained UPC Applications," 14th International Conferences on Parallel Architectures and Compilation Techniques (PACT '05), St. Louis, MO, Sept. 17-21, 2005.

S. Kamil, P. Husbands, J. Shalf, L. Oliker, K. Yelick, "Impact of Modern Memory Subsystems on Cache Optimizations for Stencil Computations," 3rd Annual ACM SIGPLAN Workshop on Memory Systems Performance, June 2005.

J. Su and K. Yelick, "Automatic Support for Irregular Computations in a High-Level Language," 19th International Parallel and Distributed Processing Symposium (IPDPS), Denver, Colarado, April 2005.

Tong Wen and Phillip Colella. "Adaptive Mesh Refinement in Titanium," 19th International Parallel and Distributed Processing Symposium (IPDPS), December 2005.

**PI Pui-kuen Yeung**

Donzis, D.A., Sreenivasan, K.R. and Yeung, P.K. (2005) Scalar dissipation rate and Dissipative anomaly in isotropic turbulence. Journal of Fluid Mechanics Vol. 532, 199-216.

Yeung, P.K., Donzis, D.A. and Sreenivasan, K.R. (2005) High-Reynolds-number simulation of inertial-convective range in turbulent mixing. Physics of Fluids Vol. 17, 081703.

Donzis, D.A., Yeung, P.K. and Sreenivasan, K.R. (2004) Scaling and domain size effects in numerical simulations of rotating turbulence. Bulletin of the American Physical Society, Vol 49, No. 9, 193.

Yeung, P.K., Donzis, D.A. and Sreenivasan, K.R. (2004) Turbulence and scalar transport in numerical simulations of $2048^3$ resolution. Bulletin of the American Physical Society, Vol 49, No. 9, 22.

## Z

**PI Peter Zapol**

M. Sternberg, D. A. Horner, P. C. Redfern, P. Zapol, L. A. Curtiss Theoretical Studies of CN and C2 Addition to a (100)-(2x1) Diamond Surface: Nanocrystalline Diamond Growth Mechanisms (Invited) J. Theor. Comp. Nanosci. 2 (2005, in press).

M. Sternberg, P. Zapol, and L. A. Curtiss "C2 Adsorption on the (100) diamond surface: Cluster and periodic calculations", Molecular Physics, 103, 1017-1025 (2005).

**PI Shengbai Zhang**

"Hydrogen passivation effect in nitrogen-doped ZnO thin film", X. Li et al., Appl. Phys. Lett. 86, 122107 (2005).

"Resolving hydrogen binding sites by pressure - A first-principles prediction for ZnO", S. Limpijumnong and S. B. Zhang, Appl. Phys. Lett. 86, 151910 (2005).

"Substitutional diatomic molecule NO, NC, CO, N2, and O2, their vibrational frequencies, and the effects on p-doping of ZnO", S. Limpijumnong, X. Li, S.-H. Wei, and S. B. Zhang, Appl. Phys. Lett. 86, 211910 (2005).

"Structure-derived electronic and optical properties of transparent conducting oxides", D. Segev and S.-H. Wei, Phys. Rev. B 71, 125129 (2005).

"Properties of Ga-interstitial defects in (Al)GaNP", N.Q. Thinh et al., Phys. Rev. B 71, 125209 (2005).

"Evolution of structural properties and formation of N-N split interstitials in GaAsN alloys", P. Carrier, S.-H. Wei, S. B. Zhang, and S. Kurtz, Phys. Rev. B 71, 165212 (2005).

"Hydrogen pairs and local vibrational modes in H-irradiated GaAs:N", M.-H. Du, S. Limpijumnong, S. B. Zhang, Phys. Rev. B 72, 073202 (2005).

"Stability of the DX- center in GaAs Quantum Dots", J. Li and S.-H. Wei, Phys. Rev. Lett. 94, 185501 (2005).

"Local moments of Mn-doped magnetic semiconductors", S.-H. Wei, X. G. Gong, G. M. Dalpian, and S.-H. Wei, Phys. Rev. B 71, 144409 (2005).

"Step structures on III-V phosphide (001) surfaces: How do steps and Sb affect CuPt ordering of GaInP2?", I. G. Batyrev, W. E. McMahon, S. B. Zhang, J. M. Olson, and S.-H. Wei, Phys. Rev. Lett. 94, 096101 (2005).

**PI Zhenyu Zhang**

Persistent Step-Flow Growth of Strained Films on Vicinal Substrates, Wei Hong, Ho Nyung Lee, Mina Yoon, Hans M. Christen, Douglas H. Lowndes, Zhigang Suo, and Zhenyu Zhang, Phys. Rev. Lett. 95, 095501 (2005).

Kinetic pathway for the formation of Fe nanowires on stepped Cu(111) surfaces, Yina Mo, Kalman Varga, Efthimios Kaxiras, Zhenyu Zhang, Phys. Rev. Lett. 94, 155503 (2005).

Initial stages of Ti growth on diamond (100) surfaces: From single adatom diffusion to quantum wire formation, Jia Y, Zhu WG, Wang EG, Huo YP, Zhang ZY, Phys. Rev. Lett. 94, 086101 (2005).

"Lagrange functions": A family of powerful basis sets for real-space order-N electronic structure calculations, Varga K, Zhang ZY, Pantelides ST, Phys. Rev. Lett. 93, 176403 (2004).

Contrasting growth modes of Mn on Ge(100) and Ge(111) surfaces: Subsurface segregation versus intermixing, Zhu WG, Weitering HH, Wang EG, Kaxiras E, Zhang ZY, Phys. Rev. Lett. 93, 126102 (2004).

**PI Oleg Zikanov**

O. Zikanov and A. Vorobev, 2005, "LES modeling of anisotropic MHD turbulence"in proc. of Riga- Pamir conference on fundamental and applied MHD, Riga, June 2005, pp. 167-170

A. Vorobev and O. Zikanov, 2005, "Anisotropic MHD turbulence at low magnetic Reynolds number," in proc. TSFP-4, Williamsburg, VA, June 2005, pp. 524.

**PI Alex Zunger**

G. Bester, J. Shumway and A. Zunger, Broken-Symmetry and Quantum Entanglement of an exciton in InGaAs/GaAs Quantum Dot Molecules, Phys. Rev. B 71, 075325 (2005).

G. Bester and A. Zunger, Electric field control and optical signature of entanglement in quantum dot molecules. Physical Review B (In press).

G. Bester and A. Zunger, Cylindrically shaped zinc-blende semiconductor quantum dots do not have cylindrical symmetry: Atomistic symmetry, atomic relaxation, and piezoelectric effects, Phys. Rev. B 71, 045318 (2005).

L. He, G. Bester and A. Zunger, Electronic asymmetry in self-assembled quantum dot-molecules made of identical InAs/GaAs quantum dot, Physical Review B, Rapid Communication, 72, 081311(R) (2005).

G. A. Narvaez, G. Bester, A. Zunger, ``Pressure effects on neutral and charged excitons in self-assembled (In,Ga)As/GaAs quantum dots", Phys. Rev. B, Rapid Communication, 72, 041307 (2005).

G. A. Narvaez, G. Bester, A. Zunger, ``Dependence of the electronic structure of self-assembled InGaAs/GaAs quantum dots on height and composition," J. Appl. Phys. (In Press).

S.V. Dudiy, P. Kent and A. Zunger, "Penetration of electronic perturbations in dilute nitrogen impurities deep into the conduction band of GaPN", Phys. Rev. B, Rapid Communication, 70, 161304 (2004)

V. Blum and A. Zunger "Prediction of ordered structures in bcc binary systems" Phys. Rev. B, Rapid Communications, 72, 020104 (2005)

G. Hart, V. Blum, M. Walorski and A. Zunger, "Genetic determination of first-principles Hamiltonians", Nature Materials 4, 391 (2005)

V. Blum, G. Hart, M. J. Walorski and A. Zunger, "Using genetic algorithm to map first-principles results to model hamiltonians", Phys. Rev. B (In Press).

A. Zunger, S. Dudiy, K. Kim and W.B. Jones, "The Inverse Band Structure approach: find the atomic configuration that has desired electronic properties", ICPS proceedings, AIP Conf. Series Vol. 772, p. 1121 (2005).

**PI Piotr Zyla**

"Observation of Parity Violation in the Omega-minus -> Lambda K-minus Decay", HyperCP Collab., Phys. Lett. B617, 11 (2005);

"HyperCP: A high-rate spectrometer for the study of charged hyperon and kaon decays", HyperCP Collab., Nucl. Instrum. Methods A 541, 516 (2005);

"Search for Delta-S = 2 Nonleptonic Hyperon Decays", HyperCP Collab., Phys. Rev. Lett. 94 101804 (2005);

"Search for CP Violation in Xi and Lambda Hyperon Decays", HyperCP Collab., Phys. Rev. Lett. 93, 262001 (2004)