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Publications

• "Gravity Currents Impinging on Bottom-Mounted Square Cylinders: Flow Fields and Associated Forces", E. Gonzalez-Juez, E. Meiburg and G. Constantinescu, in press, J. Fluid Mech. (2009).
• “CO oxidation by Ti- and Al-doped ZnO: oxygen activation by adsorption on the dopant”, R. G. S. Pala, W. Tang, M. M. Sushchikh, J-N. Park, A. J Forman, G. Wu, A. Kleiman-Shwarsctein, J. Zhang, E. W McFarland, and H. Metiu, J. Catalysis JCAT09-113R1,in press. (2009)
• "Shallow water analysis of gravity current flows past isolated obstacles.", E. Gonzalez-Juez,. and E. Meiburg, In press: J. Fluid Mech. (2009).
• “Overhauser dynamic nuclear polarization and molecular dynamics simulations using pyrroline and piperidine ring nitroxide radicals”, B. D. Armstrong, P. Soto, J.-E. Shea, S. Han J. Mag. Res. (2009) in press.
• ”TiReX: Replica-exchange molecular dynamics using Tinker”, E. S. Penev, S. Lampoudi, J.-E. Shea Comp. Phys. Comm. (2009) in press.
• “Diversity of kinetic pathways in amyloid fibril formation”, G. Bellesia, J.-E. Shea., The Journal of Chemical Physics, in press (2009).
• "Membrane-Protein interactions in a generic coarse-grained model for lipid bilayers", B. West, F. L. H. Brown and F. Schmid, Biophys. J., 96, 101-115 (2009).
• "A hybrid elastic/discrete-particle approach to biomembrane dynamics with application to the mobility of curved integral membrane proteins", A. Naji, P. J. Atzberger and F. L. H. Brown, Phys. Rev. Lett., 102, 138102 (2009).
• "Non-d0 Mn-driven ferroelectricity in antiferromagnetic BaMnO3", J.M. Rondinelli, A.S. Eidelson and N.A. Spaldin, Phys. Rev. B, 79 20,5119 (2009).
• " Structural effects on the spin-state transition in epitaxially strained LaCoO3 films", J.M. Rondinelli and N.A. Spaldin, Phys. Rev. B, 79, 054409 (2009).
• “Effect of beta-sheet propensity on peptide aggregation”, G. Bellesia, J.-E. Shea, The Journal of Chemical Physics 130, 145103 (2009).
• “What determines the structure and stability of KFFE monomers, dimers and protofibrils ?”, G. Bellesia, J.-E. Shea., Biophysical Journal 96(3), 875-886 (2009).
• “Hydrogen interactions with acceptor impurities in SnO2: First-principles calculations”, J. B. Varley, A. Janotti, A. K. Singh, and C. G. Van de Walle, Phys. Rev. B 79, 245206 (2009).
• "Gravity currents impinging on submerged cylinders: flow fields and associated forces.", E. D. Gonzalez-Juez, E. Meiburg, and S. G. Constantinescu, J. Fluid Mech. 631, 65-102 (2009).
• “Amyloid -beta-Protein: Experiment and Theory on the 21-30 Fragment”, M. M. Murray, M. Griffin-Krone, S. L. Bernstein, A. Baumketner, M. M. Condron, N. D. Lazo, D. B. Teplow, T. Wyttenbach, J.-E. Shea, and M. T. Bowers, J. Phys. Chem. B, 113, 6041, (2009).
• “The effect of surface tethering on the folding of the src-SH3 protein domain”, Z. Zhuang, A. I Jewett1, P. Soto and J.-E. Shea, Phys. Biol. 6, 015004, (2009) .
• "The interaction of a gravity current with a circular cylinder mounted above a wall: Effect of the gap size.", E. D. Gonzalez-Juez, E. Meiburg, E. and S. G. Constantinescu, J. Fluid Struct. 25, 629-640 (2009).
• "Superexchange-Driven Magnetoelectricity in Magnetic Vortices". K. T. Delaney, M. Mostovoy, and N. A. Spaldin. Phys. Rev. Lett, 102, 157203 (2009).
• "Stability of Si impurity in high-? oxides". N. Umezawa, K. Shiraishi, T. Chikyow, Microelectronic Engineering, 86, 1780, (2009).
• "Periodic density functional theory studies of Li-doped polythiophene: Dependence of electronic and structural properties on dopant concentration". A. Ramirez-Solis, B. Kirtman, R. Bernal-Jaquez, and C. M. Zicovich-Wilson, J. Chem. Phys. 130, 164904, (2009).
• "Effects of barium incorporation into HfO2 gate dielectrics on reduction in charged defects: First-principles study", N. Umezawa, Appl. Phys. Lett. 94, 022903 (2009).
• "Point defects in Al2O3 and their impact on gate stacks,", J.R. Weber, A. Janotti, C.G. Van de Walle. Microelectronic Engineering, 86, 1756 (2009).
• “Hydrogen interactions with acceptor impurities in SnO2: First-principles calculations”, J. B. Varley, A. Janotti, A. K. Singh, and C. G. Van de Walle, Phys. Rev. B 79, 245206 (2009).

2008

• “Electrical activity of hydrogen impurities in GaSb: First-principles calculations”, A. Peles, A. Janotti, and C. G. Van de Walle, Phys. Rev. B 78, 035204 (2008).
• “Sources of unintentional n-type conductivity in InN”, A. Janotti and C. G. Van de Walle, Appl. Phys. Lett. 92, 032104 (2008).
• “Energetics of infinite homopolypeptide chains: a new look at commonly used force fields”, E. Penev, J. Ireta, & J.E-. Shea, J Phys Chem B, 112, 6872 (2008).
• "Variable density and viscosity, miscible displacements in capillary tubes", S.H. Vanaparthy, E. Meiburg, European Journal of Mechanics - B/Fluids, 27, 268-289 (2008).
• "Carbon-nitrogen molecules in GaAs and GaP" S. Limpijumnong, P. Reunchan, A. Janotti, and C. G. Van de Walle, Phys. Rev. B 77, 195209 (2008).
• "CO Oxidation by Rutile TiO2(110) Doped with V, W, Cr, Mo, and Mn" by Hyun You Kim, Hyuck Mo Lee, R. G. S. Pala, V. Shapovalov and H. Metiu, J. Phys. Chem. C 112, 12398 (2008).
• "Elastic Modeling of Biomembranes and Lipid Bilayers". F. L. H. Brown, Annual Review of Physical Chemistry. 59, 685-712 (2008).
• “Structure and stability of amyloid fibrils formed from synthetic beta-peptides”, G. Bellesia, J.-E. Shea, Frontiers in Bioscience 13(9), 6957-6965 (2008).
• "Cytoskeleton mediated effective elastic properties of model red blood cell membranes", R. Zhang and F. L. H. Brown, J. Chem. Phys. 129, 065101 (2008).
• "A numerical study of the electrostatic properties of two finite-width charged dielectric slabs in water", Y. S. Jho, M. W. Kim, P. A. Pincus and F. L. H. Brown, J. Chem. Phys., 129, 134511 (2008).
• "Generating Functions for Single-Molecule Statistics", F. L. H. Brown in “Theory and Evaluation of Single Molecule Signals” E. Barkai, F. Brown, M. Orrit and H. Yang editors, World Scientific Publishing Co. Singapore (2008).
• "A Model for Lipid Bilayers in Implicit Solvent", G. Brannigan and F. L. H. Brown in “Coarse-graining of condensed phase and biomolecular systems”, G. A. Voth editor, CRC Press, Boca Raton (2008).
• “CO oxidation by rutile TiO2(110) doped with V, W, Cr, Mo and Mn”, Hyun You Kim, Hyuck Mo Lee, R. G. S. Pala, V. Shapovalov, and H. Metiu, J. Phys. Chem. C 112, 12398-12408 (2008).
• ”Vacancy formation and CO adsorption on gold-doped ceria surfaces”, M. Nolan, V. Soto Verdugo, and H. Metiu, Surface Science 602, 2734-2742 (2008).
• ”Catalysis by very small Au clusters”, S. Chrétien, S. K. Buratto, and H. Metiu, Current Opinion in Solid State and Materials Science 11(5-6), 62-75 (2008).
• "Electronic properties of bulk and thin film SrRuO3: a search for the metal-insulator transition" J. M. Rondinelli, N. M. Caffrey, S. Sanvito and N. A. Spaldin, Phys. Rev. B, 78 155107 (2008).
• "Comparative study of Higgs transition in one-component and two-component lattice superconductor models" O. I. Motrunich. A Vishwanath. arXiv:0805.1494v1 [cond-mat.stat-mech].
• "Competition between polar distortions and octahedral rotations in epitaxially strained LaAlO3" A. J. Hatt and N. A. Spaldin. arXiv:0808.3792v1 (2008).
• “Selective promotion of different modes of methanol adsorption via the cation substitutional doping of a ZnO (101bar0) surface”, R. G. S. Pala and H. Metiu, J. Catalysis 254(2), 325-331 (2008).
• ”Preface to special topic: A survey of some new developments in heterogeneous catalysis”, H. Metiu, J. Chem. Phys. 128 (18), art. no. 182501 (2008).
• "O2 evolution on a clean partially reduced rutile TiO2(110) surface and on the same surface precovered with Au1 and Au2: The importance of spin conservation" S. Chretien and H. Metiu, J. Chem. Phys. 129, 074705 (2008).
• "Enhanced adsorption energy of Au1 and O2 on the stoichiometric TiO2(110) surface by coadsorption with other molecules", S. Chretien and H. Metiu, J. Chem. Phys. 128, 044714 (2008).
• "Role of hydrogen at germanium/dielectric interfaces", C.G. Van de Walle, J.R. Weber, A. Janotti, Thin Solid Films, Volume 517, Issue 1, Fifth International Conference on Silicon Epitaxy and Heterostructures (ICSI-5), 144-147 (2008).
• "Sources of Electrical Conductivity in SnO2" A. K. Singh, A. Janotti, M. Scheffler, and C. G. Van de Walle. Phys. Rev. Lett. 101, 055502 (2008).
• "Computational studies of conductivity in wide-band-gap semiconductors and oxides", C G Van deWalle. J. Phys.: Condens. Matter 20 (2008) .
• "Atomic and electronic structure of hydrogen-related centers in hydrogen storage materials". C. G. Van de Walle, A. Pelesa, A. Janottia and G.B. Wilson-Shorta. Physica B: Physics of Condensed Matter, (2008).
• "Mutual Passivation of Electrically Active and Isovalent Impurities in Dilute Nitrides". A. Janotti, P. Reunchan, S. Limpijumnong, and C. G. Van de Walle, Phys. Rev. Lett. 100, 045505 (2008).
• “Reduction in charged defects associated with oxygen vacancies in hafnia by magnesium incorporation: First-principles study”, N. Umezawa, M. Sato, and K. Shiraishi. Appl. Phys. Lett.. 93, 223104 (2008).
• “Computational Methods in Nanostructure Design: Replica Exchange Simulations of Self-Assembling Peptides”. G.Bellesia, S. Lampoudi, S. & J.-E. Shea, Methods in Molecular Biology, Humana Press 474, 9, (2008).
• “Optimizing optical absorption of TiO2 by alloying with TiS2”, N. Umezawa, A. Janotti, P. Rinke, T. Chikyow, and C. G. Van de Walle, Appl. Phys. Lett. 92, 041104 (2008).

2007

• “Native Point Defects in ZnO”, A. Janotti and C. G. Van de Walle, Phys. Rev. B 76, 165202 (2007).
• “Absolute deformation potentials and band alignment of wurtzite ZnO, MgO, and CdO”, A. Janotti and C. G. Van de Walle, Phys. Rev. B 75, 121201 (2007).
• “Self-consistent band-gap corrections in density functional theory using modified pseudopotentials”, D. Segev, A. Janotti, and C. G. Van de Walle, Phys. Rev. B 75, 035201 (2007).
• "Contributions of Gaussian curvature and non-constant lipid volume to protein deformation of lipid bilayers", G. Brannigan and F. L. H. Brown, Biophys. J. 92, 864-876 (2007).
• "Simple Models for Biomembrane Structure and Dynamics", F. L. H. Brown, Comp. Phys. Comm., 177, 172-175 (2007).
• "Single-molecule photon emission statistics of driven three-level systems", Y. Peng, Y. Zheng and F. L. H. Brown, J. Chem. Phys. 126, 104303 (2007).
• "Diffusion on ruffled membrane surfaces", A. Naji and F. L. H. Brown, J. Chem. Phys., 126, 104303 (2007).
• "Microdomain ordering in laterally confined block copolymer thin films" August W. Bosse, Carlos J. Garcia-Cervera, Glenn H. Fredrickson. Macromolecules, 40 9570-9581 (2007) .
• "Density functional study of the interaction between small Au clusters, Aun (n = 1--7) and the rutile TiO2 surface. II. Adsorption on a partially reduced surface", S. Chretien and Horia Metiu, J. Chem. Phys. 127, 244708 (2007).
• “Self assembly of beta-sheet forming peptides into chiral fibrillar aggregates”, G. Bellesia, J.-E. Shea. The Journal of Chemical Physics 126, 245104 (2007).
• "Role of charged defects and impurities in kinetics of hydrogen storage materials: A first-principles study" A. Peles and C. G. Van de Walle, Phys. Rev. B 76, 214101 (2007).
• "An Electroweak Oscillon". N. Graham. PhysRevLett. 98, 189904 (2007).
• "Surface reconstructions on InN and GaN polar and nonpolar surfaces", D. Segev, C. G. Van de Walle, Surface Science, 601, (2007).
• “Catalysis by doped oxides: CO oxidation by AuxCe1-xO2”, V. Shapovalov, H. Metiu, Journal of Catalysis, 245, 205-214, (2007).
• “Probing the structural hierarchy and energy landscape of an RNA T-loop hairpin”, Z. Zhuang, L. Jaeger, & J.-E. Shea, Nucleic Acids Res 35, 6995-7002 (2007).
• "Microscopic origins of surface states on nitride surfaces". C. G. Van de Walle and D. Segev, J. Appl. Phys. 101, 081704 (2007).
• "Dangling-bond defects and hydrogen passivation in germanium" J. R. Weber, A. Janotti, P. Rinke, and C. G. Van de Walle, Appl. Phys. Lett. 91, 142101 (2007).
• "Numerical Simulation of an Electroweak Oscillon". N. Graham. Physical Review D, 76, 085017, (2007)
• “Hydrogen multicenter bonds”, A. Janotti and C. G. Van de Walle. Nature Materials 6, 44 - 47 (2007)
• “An Efficient Real Space Method for Orbital-Free Density-Functional Theory”, C.J. García-Cervera, Comm. Comp. Phys., 2 (2), 334-357 (2007).
• "Convergence of third order correlation energy in atoms and molecules", K. Kahn, A. A. Granovsky, J. Noga, Journal of Computational Chemistry, 28 547-554 (2007).
• "Hydrogen-related defects in sodium alanate", A. Peles, C.G. Van de Walle, Journal of Alloys and Compounds, Proceedings of the International Symposium on Metal-Hydrogen Systems, Fundamentals and Applications (MH2006), 446-447, 459-461, (2007).

2006 and earlier

• “Defects and their removal in block copolymer thin film simulations". A. W. Bosse, S. W. Sides, K. Katsov‡, C. J. Garcia-Cervera, and G. H. Fredrickson. Journal of polymer science. Part B, Polymer physics (44), 2495 (2006).
• “Electronic structure of nitride surfaces”, D. Segev, C. G. Van de Walle, Journal of Crystal Growth, First International Symposium on Growth of Nitrides - ISGN-1, 300, 199-203 (2006) .
• “Effects of solvent on the structure of the Alzheimer amyloid-b(25-35) peptide”, G. Wei & J.-E Shea. Biophys. J. 91, 1638, (2006).
• "Origins of Fermi-level pinning on GaN and InN polar and nonpolar surfaces", D. Segev and C. G. Van de Walle. Europhys. Lett. 76, 305 (2006).
• “Folding landscapes of the Alzheimer A\beta12-28 peptide from all-atom replica exchange molecular dynamics simulations in explicit solvent”A. Baumketner and J.-E. Shea, J. Mol. Biol., 362, 567-579, (2006).
• "Density functional study of the CO oxydation on a doped rutile TiO2(110): effects of ionic Au in catalysis", S. Chrétien and H. Metiu, Catal. Lett. 107, 143 (2006).
• “Stability of the Gyroid Phase in Diblock Copolymers at Strong Segregation. Macromolecules”, E. W. Cochran, C. J. Garcia-Cervera, and G. H. Fredrickson. 39(7), 2449–2451 (2006).
• “Aggregation of polyalanine in a hydrophobic environment”, P. Soto, A. Baumketner, J.E. Shea. J Chem Phys. 124(13),134904 (2006).
• “Effects of surface tethering on protein folding mechanisms”, M. Friedel, A. Baumketner and J.-E. Shea, Proc. Nat. Acad. Sci. USA, 103: 8396-8401 (2006)
• "Orbital magnetic field effects in spin liquid with spinon Fermi sea: Possible application to kappa-(ET)2 Cu2 (CN)3", O. I. Motrunich, Phys. Rev. B 73, 155115 (2006).
• “Prediction of Broadband Ground-Motion Time Histories: Hybrid Low/High- Frequency Method with Correlated Random Source Parameters”, P. Liu, R. J. Archuleta, S. H. Hartzell, Bulletin of the Seismological Society of America 96, 2118-2130 (2006).
• “Structure of the 21-30 fragment of amyloid Beta protein”, A. Baumketner, S. L. Bernstein, T. Wyttenbach, N. D. Lazo, D. B. Teplow, M. T. Bowers and J.-E. Shea, Protein Science, 15, 1239, (2006).
• A. Baumketner and J.-E. Shea ' The thermodynamics of folding of a beta hairpin peptide probed through replica exchange molecular dynamics simulations ', Theor. Chem. Acc. 116, 262, (2006)
• “Controlling the near surface orientation of block copolymer lamellae and cylinders using chain architecture and surface energy.”, V. Khanna, E. W. Cochran, A. Hexemer, G. E. Stein, G. H. Fredrickson, E. J. Kramer, S. F. Hahn, X. Li, and J. Wang. PMSE Preprints, 95, 41–42 (2006).
• The QCD Equation of State with Asqtad Staggered fermions, The MILC Collaboration: C. Bernard, T. Burch, C. DeTar, S. Gottlieb, U.M. Heller, J. Hetrick, L. Levkova, F. Maresca, D. Renner, R. Sugar and Doug Toussaint, Proceedings of Science (Lattice 2006).
• "Kinematic Inversion of the 2004 Mw 6.0 Parkfield Earthquake", P. Liu, S. Custodio and R. J. Archuleta, , Bulletin of the Seismological Society of America., 96, 1-37 (2006).
• “Effects of cation d states on III-nitride and II-oxide wide-band-gap semiconductors”, A. Janotti, D. Segev, and C. G. Van de Walle. Physical Review B, 74, 045202 (2006)
• “New insights into the role of native point defects in ZnO”. A. Janotti and C. G. Van de Walle. Journal of Crystal Growth 287, 58-65 (2006)
• "Free Energy Landscapes for Amyloidogenic Tetrapeptides Dimerization", A. Baumketner, J.-E. Shea, Biophysical Journal, 89, 1493-1503 (2005).
• "2004 Mw 6.0 Parkfield, California, earthquake: Inversion of Near-Source Ground Motion Using Different Datasets" S. Custodio, , P. Liu and R. J. Archuleta, , Geophysical Research Letters. 32, L23312 (2005).
• "Effects of frustration, confinement, and surface interactions on the dimerization of an off-lattice beta-barrel protein.", M. Griffin, M. Friedel and J.E. Shea, J. Chem. Phys, 123, 174707 (2005).
• "Oxygen vacancies in ZnO". A. Janotti and C. G. Van de Walle . Applied Physics Letters 87, 122102 (2005).
• “The influence of different treatments of electrostatic interactions on the thermodynamics of folding of peptides”, A. Baumketner and J.-E. Shea, J. Phys. Chem. B 109, 21322 , (2005)
• “The Equation of State for QCD with 2+1 Flavors of Quarks, The MILC Collaboration:” C. Bernard, T. Burch, C. DeTar, S. Gottlieb, U.M. Heller, J. Hetrick, L. Levkova, F. Maresca, D. Renner, R. Sugar and Doug Toussaint, Proceedings of Science (Lattice 2005) 156 (2005).
• “Temperature Dependence of Order, Disorder, and Defects in Laterally Con?ned Diblock Copolymer Cylinder Monolayers”, M. R. Hammond, E. W. Cochran, G. H. Fredrickson, and E. J. Kramer. Macromolecules, 38(15), 6575–6585 (2005).
• “Thermal equilibrium defects in laterally confined monolayers of block copolymer cylinders.”, M. R. Hammond, E. W. Cochran, G. H. Fredrickson, and E. J. Kramer. Polymer Preprints (American Chemical Society, Division of Polymer Chemistry), 46(2), 576–577 (2005)
• “Variational study of triangular lattice spin-1/2 model with ring exchanges and spin liquid state in kappa-(ET)2 Cu2 (CN)3”, O. I. Motrunich Phys. Rev. B 72, 045105 (2005)
• M.E. O'Sullivan, J. Brevik, R. Wolski "The Performance of LDPC codes with Large Girth". Proc. 43rd Allerton Conference on Communication, Control and Computing}, Univ. Illinois, Aug., 2005.

Acknowledgements

In talks and publications, please acknowlege the CNSI Computer Facilities as well as:

• Dell and SGI users: NSF grant no. CHE-0321368
• HP (nano, QSR, Lattice) users: Hewlett-Packard

Please also send us the reference for your paper as we will need to collect a list for progress reports.