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Publications - 2007
Allen, P.B. Nanocrystalline Nanowires: I. Structure Nano
Letters 7(1): 6-10 (2007). BNL-77232-2006-JA.
Allen, P.B. Nanocrystalline Nanowires: II. Photons. Nano
Letters, 7(1): 11-14 (2007). BNL-77233-2006-JA.
Allen, P.B. Nanocrystalline Nanowires: III. Electrons.
Nano Letters 7(5): 1220-1223 (2007). BNL-77234-2006-JA.
Bo, W., Cheng, B., Du, J., Fix, B., George, E., Glimm, J., Grove, J.,
Jia, X., Jin, H., Lee, Y., Li, X., Li, Y., Liu X., Sharp, D.H., Wu, L., and
Yu, Y. Recent progress in the stochastic analysis of turbulent mixing.
Contemporary Mathematics 429: 33-44 (2007). Stony Brook University
Preprint No. SUNYSB-AMS-05-18.
Bo, W., Cheng, B., Du, J., Fix, B., George, E., Glimm, J., Grove, J.,
Jia, X., Jin, H., Lee, Y., Li, X., Li, Y., Liu X., Sharp, D.H., Wu, L., and
Yu, Y. FronTier and applications to scientific and engineering
problems. Proc. in Applied Mathematics and Mechanics 7(1):
1024507-1024508 (2007).
Chen, X. and Deng, Y. Long-term molecular dynamics simulations of botulinum biotoxin type-A at different pH values and temperatures. J.
Molecular Modeling 13(5): 559-572 (2007). BNL-77463-2007-JA.
Chen, Y.-R., Zhang, L., and Hybertsen, M.S. Theoretical study of trends in conductance for
molecular junctions formed with armchair carbon nanotube electrodes. Phys. Rev. B
76: 115408 (2007). BNL-77870-2007-JA.
Cheng, Y., Cheng, X., and Deng, Y. Simulating botulinum neurotoxin
with constant pH molecular dynamics in generalized Born implicit solvent.
Computer Physics Communications 177(1-2): 210-213 (2007). BNL-77464-2007-JA.
Fang, B. and Deng, Y. Performance of 3D FFT on 6D QCDOC Torus parallel
supercomputer. Computer Physics Communications 176: 531-538, 2007.
BNL-77465-2007-JA.
Fang, B., Deng, Y., and Martyna, G. A fine grained parallel smooth particle mesh Ewald
algorithm for biophysical simulation studies: Application to the 6-D
torus QCDOC supercomputer. Computer Physics Communications 177(4):
362-377 (2007).
Fernando, G.W., Kocharian, A.N., Palandage, P., Wang, T., and Davenport, J.W.
Phase separation and electron pairing in repulsive Hubbard clusters.
Phys. Rev. B 75: 085109-1 - 085109-5 (2007). BNL-77703-2007-JA.
Glimm, J., Fix, B., Li, X., Liu, J., Liu, X., Lu, T., Samulyak, R., and Xu,
Z. Front tracking under TSTT. Proceedings of the IGPP-CalSpace
Conference, Astronomical Society of the
Pacific 359: 15 (2007).
Han, G., Deng, Y., Glimm, J., and Martyna, G. Error and timing
analysis of multiple time-step integration methods for molecular dynamics.
Computer Physics Communications 176: 271-291 (2007). BNL-77462-2007-JA.
Kim, J., Zhu, W., Chang, L., Benter, P., and Ernst, T. Unified structural
equation modeling approach for the analysis of multisubject, multivariate
functional MRI data. Human Brain Mapping 28: 85-93 (2007).
Kocharian, A.N., Fernando, G.W., Wang, A.T., Palandage, K., and Davenport,
J.W. Exact thermodynamics of pairing and charge-spin separation
crossovers in small Hubbard nanoclusters. Phys. Lett. A. 364: 57-65
(2007). BNL-77675-2007-JA.
Liu, J., Lim, H.-K., Glimm, J., and Li, X. A conservative front
tracking method in N-dimensions. J. Sci. Comp. 31(1/2): 213-236 (2007).
BNL-79187-2007-JA. Stony Brook
University Preprint No. SUNYSB-AMS-06-04.
Liu, X., Li, Y., Glimm, J., and Li, X.L. A front tracking algorithm
for limited mass diffusion. J. Computational Physics 222: 644-653
(2007). BNL-78119-2007-JA. Stony Brook University Preprint No.
SUNYSB-AMS-06-01.
Lu, T., Miao, X., and Metcalf, H. Nonadiabatic transitions in
finite-time adiabatic rapid passage. Phys. Rev. A 75: 063422-1 -
063422-5 (2007).
Lu, T., Samulyak, R., and Glimm, J. Direct numerical simulation of bubbly
flows and application to cavitation mitigation. J. Fluids Engineering -
Trans. ASME 129(5):
595-604 (2007). BNL-73502-2007-JA-R1.
Okur, A., Roe, D., Cui, G., Hornak, V., and Simmerling, C. Improving
convergence of replica exchange simulations through coupling to a high
temperature structure reservoir. J. Chem. Theory and Computation
3(2): 557-568 (2007). BNL-76951-2006-JA.
Palandage, K., Fernando, G., Kocharian, A., and Davenport, J. An exact
study of pairing fluctuations and phase diagrams in four-site Hubbard
nanoclusters. J. Computer-Aided Mater. Des. 14: 103-108 (2007).
BNL-78005-2007-JA.
Quek, S.Y., Venkataraman, L., Choi, H.J., Louie, S.G., Hybertsen, M.S., and
Neaton, J.B. Amine-gold linked single-molecule circuits: Experiment and
theory. Nano Letters 7(11): 3477-3482 (2007). BNL-78033-2007-JA.
Quinn, J.R., Foss, Jr., F.W., Venkataraman, L., Hybertsen, M.S., and Breslow,
R. Single-molecule junction conductance through diaminoacenes.
J. Am. Chem. Soc. 129(21): 6714 (2007). BNL-77704-2007-JA.
Rissland, P. and Deng, Y. Electrostatic force computation for biomolecules
on supercomputers with torus networks. Parallel Computing 33(2): 116-123
(2007).
Roe, D.R., Okur, A., Wickstrom, L., Hornak, V., and Simmerling, C.
Secondary structure bias in generalized Born solvent models:
Comparison of conformational ensembles and free energy of solvent
polarization from explicit and implicit solvation. J. Chem. Phys. B
111: 1846-1857 (2007). BNL-77921-2007-JA.
Samulyak, R., Lu, T., and Parks, P. A magnetohydrodynamic simulation of
pellet ablation in the electrostatic approximation. Nuclear Fusion 47:
103-118 (2007). BNL-75843-2006-JA.
Samulyak, R., Du, J., Glimm, J., and Xu, Z. A numerical algorithm for
MHD of free surface flows at low magnetic Reynolds numbers. J. Computational
Phys. 226(2): 1532-1549 (2007).
Shen, X., Allen, P.B., Muckerman, J.T., Davenport, J.W., and Zheng, J.-C.
Wire versus tube: Stability of small one-dimensional ZnO
nanostructures. Nano Letters 7: 2267 (2007). BNL-78124-2007-JA.
Stolyarova (Polyakova), E., Rim, K.T., Ryu, S., Maultzsch, J., Kim, P., Brus,
L.E., Heinz, T.F., Hybertsen, M.S., and Flynn, G.W. High-resolution
scanning tunneling microscopy imaging of mesoscopic graphene sheets on an
insulating surface. Proc. Nat. Acad. Sci. 104(22): 9209-9212 (2007).
BNL-77779-2007-JA.
Strockbine, B. and Rizzo, R.C. Binding of anti-fusion peptides with HIVgp41
from molecular dynamics simulations: Quantitative correlation with
experiment. Proteins: Struct., Funct., Bioinf. 67(3): 630-642 (2007).
Wickstrom, L. Bi, Y., Hornak, V., Raleigh, D., and Simmerling, C.
Reconciling the solution and X-ray structures of the villin headpiece
helical subdomain: molecular dynamics simulations and double mutant
cycles reveal a stabilizing cation-Pi interaction. Biochemistry
46(12): 3624-3634 (2007). BNL-76950-2006-JA.
Xu, Z., Kim, M., Lu, T., Oh, W., Glimm, J., Samulyak, R., Li, X., and Tzanos,
C. Discrete bubble modeling of unsteady cavitating flow. Int. J.
for Multiscale Computational Engrg. 4(5/6): 601-616 (2007).
BNL-78120-2007-JA.
Xu, Z., Glimm, J., Zhang, Y., and Liu, X. A multiscale front tracking
method for compressible free surface flows. Chem. Engineering Science
62(13): 3538-3548 (2007). BNL-79256-2007-JA.
Zhang, Y., Drake, R.P., and Glimm, J. Numerical evaluation of the
impact of laser preheat on interface structure and instability.
Physics of Plasmas 14: 062703 (2007).
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Last Modified: August 20, 2009
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