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Publications - 2006
Bennett, R. and D'Imperio, N. Performance evaluation of a 3D
electrodynamics simulation on massively parallel computers. Presented
at SIAM Conference on Parallel Processing for Scientific Computing, Feb.
22-24, 2006, San Francisco, CA.
Chang, Y.-C., Davenport, J.W., and James, R.B. Symmetrized-basis
LASTO calculations of defects in CdTe and ZnTe. Physical Review B 73:
035211 (2006). BNL-75696-2006-JA.
D'Imperio, N.L., et al. Parallel 3-D Space Charge Calculations in the
Unified Accelerator Library. EPAC 2006, July 2006.
Du, J., Fix, B., Glimm, J., Jia, X., Li, X., Li, Y., and Wu, L. A simple
package for front tracking. J. Comp. Phys. 213(2): 613-628 (2006). Stony
Brook University Preprint No. SUNYSB-AMS-05-02.
Du, J., Wang, S., Glimm, J., and Samulyak, R. A comparison study of two
methods for elliptic boundary value problems. SIAM J. Sci. Computing,
submitted, 2006.
Fischer, D.A., Moodenbaugh, A.R., Li, Q., Gu, G.D., Zhu, Y., Davenport, J.W.,
Welch, D.O., and Su, H. Soft X-ray absorption spectroscopy of
the MgB2 boron K edge in MgB2/Mg composite. Modern Physics Lett. B 20:
1207 (2006). BNL-77093-2006-JA.
George, E., Glimm, J., Li, X.L., Li, Y.H., and Liu, X.F. The influence
of scale-breaking phenomena on turbulent mixing rates. Phys. Rev. E
73: 016304-1 - 016304-5 (2006).
Grell, L., Parkin, C., Slatest, L., and Craig, P.A. EZ-Viz, a tool for
simplifying molecular viewing in PyMOL. Biochemistry and Molecular
Biology Education 34(6): 402-407 (2006). BNL-77236-2006-JA.
Hornak, V., Okur, A., Rizzo, R.C., and Simmerling, C. HIV-1 protease
flaps spontaneously open and reclose in molecular dynamics simulations.
PNAS 103(4): 915-920 (2006). BNL-75697-2006-JA.
Hornak, V, Okur, A., Rizzo, R.C., and Simmerling, C. Flap structure and
dynamics in HIV-1 protease simulations. Abstracts of Papers of the American
Chemical Society 231, Mtg. Abstract 379-MEDI (2006).
Hornak, V., Okur, A., Rizzo, R.C., and Simmerling, C. HIV-1 protease
flaps spontaneously close to the correct structure in simulations following
manual placement of an inhibitor into the open state. J. Am. Chem.
Soc. 128: 2812-2813 (2006). BNL-76788-2006-JA.
Hornak, V., Abel, R., Okur, A., Strockbine, B., Roitberg, A., and Simmerling,
C. Comparison of multiple Amber force fields and development of
improved protein backbone parameters. Proteins: Structure, Function
and Bioinformatics 65(3): 712-725 (2006). BNL-76845-2006-JA.
Jin, H., Glimm, J., and Sharp, D.H. Compressible two-pressure
two-phase flow models. Phys. Letters A 353(6): 469-474 (2006).
BNL-76785-2006-JA.
Jin, H., Glimm, J., and Sharp, D.H. Entropy of averaging for
compressible two-pressure two-phase flow models. Phys. Lett. A 360:
114-121 (2006). BNL-77599-2007-JA. Stony Brook University
Preprint No. SUNYSB-AMS-06-08.
Kocharian, A.N., Fernando, G.W., Palandage, K., and Davenport, J.W.
Exact study of charge-spin separation, pairing fluctuations, and pseudogaps
in four-site Hubbard clusters. Phys. Rev. B 74: 024511 (2006).
BNL-76855-2006-JA.
Layten, M., Hornak, V., and Simmerling, C. The open structure of a
multi-drug-resistant HIV-1 protease is stabilized by crystal packing
contacts. J. Am. Chem. Soc. 128: 13360-13361 (2006). BNL-76793-2006-JA.
Liu, X., George, E., Bo, W.G., and Glimm, J. Turbulent mixing with
physical mass diffusion. Phys. Rev. E 73(5): 056301-1 - 0556301-8 (2006). BNL-76786-2006-JA.
Liu, J.-J., Glimm, J., and Li, X.L. A conservative front tracking
method. In F. Asakura, H. Aiso, S. Kawashima, A. Matsumura, S.
Nishibata, and K. Nishihara (eds.) Hyperbolic Problems: Theory,
Numerics, and Applications, pp. 57-62. Yokohama Publishers, Osaka,
Japan, 2006.
Mokhov, N.V., Czarapata, P.C. Drozhdin, A.I., Still, D.A., and Samulyak,
R.V. Beam-induced damage to the Tevatron components and what has been
done about it. Fermilab Preprint: FERMILAB-Conf-06/415-AD, November
2006.
Moustakas, D.T., Lang, P.T., Pegg, S., Pettersen, E., Kuntz, I.D.,
Brooijmans, N., and Rizzo, R.C. Development and validation of a
modular, extensible docking program: DOCK 5. J. Comput. Aided
Mol. Des. 20: 601-619 (2006).
Okur, A., Wickstrom, L., Layten, M., Geney, R., Song, K., Hornak, V., and
Simmerling, C. Improved efficiency of replica exchange simulations
through use of a hybrid explicit/implicit solvation model. J. Chemical
Theory and Computation 2: 420-433 (2006). BNL-76787-2006-JA.
Rafi, S.B., Cui, G., Song, K., Cheng, X., Tonge, P.J., and Simmerling, C.
Insight through molecular mechanics Poisson-Boltzmann surface area
calculations into the binding affinity of triclosan and three analogues for
FabI, the E. coli enoyl reductase. J. Med. Chem. 49(15):
4574-4580 (2006). BNL-76844-2006-JA.
Rissland, P. and Deng, Y. Structure and performance of molecular dynamics
package MDoC on QCDOC. Parallel Computing, submitted, 2006.
Rizzo, R.C., Aynechi, T., Case, D.A., and Kuntz, I.D. Estimation of
absolute free energies of hydration using continuum methods: Accuracy
of partial charge models and optimization of nonpolar contributions.
J. Chem. Theory and Computation 2: 128-139 (2006).
Samulyak, R., Lu, T., Prykarpatskyy, Y., Glimm, J., Xu, Z., and Kim, M.-N.
Comparison of heterogeneous and homogenized numerical models of cavitation. Int. J. Multiscale Comp. Eng. 4(3):
377-389
(2006).
BNL-73185-2004-JA.
Shen, X., Peterson, M.R., Zheng, Z.-C., Davenport, J.W., Muckerman, J.T.,
and Allen, P.B. Electronic structure of ZnO nanowire. Phys. Rev.
B, submitted, 2006. BNL-77172-2006-JA.
Song, K., Hornak, v., de los Santos, C., Grollman, A.P., and Simmerling, C.L.
Computational analysis of the binding mode of 8-oxo-guanine to
formamidopyrimidine-DNA glycosylase. Biochemistry 45(36): 10886-10894
(2006).
BNL-76846-2006-JA.
Wang, X., Zhu, W., Pradhan, K., Ji, C., Ma, Y., Semmes, O.J., Glimm, J., and
Mitchell, J. Feature extraction in the analysis of proteomic mass
spectra. Proteomics 6: 2095-2100 (2006).
Wickstrom, L., Okur, A., Song, K., Hornak, V., Raleigh, D.P., and Simmerling,
C.L. The unfolded state of the villin headpiece helical subdomain:
Computational studies of the role of locally stabilized structure. J.
Mol. Biol. 360(5): 1094-1107 (2006). BNL-76792-2006-JA.
Xu, Z.L., Kim, M., Oh, W., Glimm, J., Samulyak, R., Li, X.L., and Tzanos, C.
Comparison of heterogeneous and homogenized numerical models of cavitation. Int. J. Multiscale Comp. Eng. 4: 377-389 (2006). Stony Brook University
Preprint No. SUNYSB-AMS-05-08.
Xu, Z., Kim, M.-N., Oh, W., Glimm, J., Samulyak, R., Li, X., Lu, T., and Tzanos,
C. Discrete bubble modeling of unsteady cavitating flow. Int. J. Multiscale Comp. Eng.
4: 601-616 (2006). Stony Brook University Preprint No. SUNYSB-AMS-05-08.
Yu, Y., Zhao, M., Lee, T., Pestieau, N., Bo, W., Glimm, J., and Grove, J.W.
Uncertainty quantification for chaotic computational fluid dynamics.
J. Comp. Phys. 217: 200-216 (2006). Stony Brook University Preprint No.
SUNYSB-AMS-05-16 and LANL Preprint No. LA-UR-05-6212.
BNL-77166-2006-JA.
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Last Modified: January 15, 2009
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Claire Lamberti
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