研究领域

Physical Chemistry

Research activities in Dr. Stuart's laboratory involve computer simulations of complex systems. The group is interested in modeling problems such as the reactivity in condensed-phase hydrocarbons and liquid water, or the chemical effects that contribute to friction. These systems often involve chemical reaction and polarization dynamics that are beyond the capabilities of traditional molecular modeling potentials, but are too complex to treat with traditional quantum mechanical methods. Consequently, much of this work involves developing improved classical simulation methods for treating electrostatic interactions and chemical bonding effects. Research efforts also involve the development of novel computer algorithms for molecular simulations, including algorithms for parallel computers, as well as efficient sampling and dynamics techniques. Chemical systems of interest include carbon nanotubes; polymerization and energetic processes in polymers; liquid water; and aqueous solvation.

近期论文

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Uberuaga BP, Stuart SJ, Windl W, Masquelier MP, & Voter AF (2012) Fullerene and graphene formation from carbon nanotube fragments. Computational and Theoretical Chemistry 987:115-121. Kucukkal TG & Stuart SJ (2012) Polarizable Molecular Dynamics Simulations of Aqueous Dipeptides. Journal of Physical Chemistry B 116(30):8733-8740. Knippenberg MT, Mikulski PT, Ryan KE, Stuart SJ, Gao GT, & Harrison JA (2012) Bond-order potentials with split-charge equilibration: Application to C-, H-, and O-containing systems. Journal of Chemical Physics 136(16). Hur J & Stuart SJ (2012) Modified reactive empirical bond-order potential for heterogeneous bonding environments. Journal of Chemical Physics 137(5). Collier G, Vellore NA, Yancey JA, Stuart SJ, & Latour RA (2012) Comparison Between Empirical Protein Force Fields for the Simulation of the Adsorption Behavior of Structured LK Peptides on Functionalized Surfaces. Biointerphases 7(1-4). Biswas PK, Vellore NA, Yancey JA, Kucukkal TG, Collier G, Brooks BR, Stuart SJ, & Latour RA (2012) Simulation of Multiphase Systems Utilizing Independent Force Fields to Control Intraphase and Interphase Behavior. Journal of Computational Chemistry 33(16):1458-1466. Podila, R.; Reppert, J.; Li, N.; Loebick, C. Z.; Stuart, S. J.; Pfefferle, L. D.; Rao, A. M., Curvature-induced symmetry lowering and anomalous dispersion of the G-band in carbon nanotubes. Carbon 2011, 49 (3), 869-876. Fallet, M.; Stuart, S. J., Evolution of carbon based surfaces under bombardment: Examining the steady-state surface properties and the effect of potential. Nuclear Instruments & Methods in Physics Research Section B-Beam Interactions with Materials and Atoms 2011, 269 (11), 1271-1275. Reinhold, C. O.; Krstic, P. S.; Stuart, S. J.; Zhang, H.; Harris, P. R.; Meyer, F. W., Isotope dependence of chemical erosion of carbon. Journal of Nuclear Materials 2010, 401 (1-3), 1-12. .Vellore, N. A.; Yancey, J. A.; Collier, G.; Latour, R. A.; Stuart, S. J., Assessment of the Transferability of a Protein Force Field for the Simulation of Peptide-Surface Interactions. Langmuir 2010, 26 (10), 7396-7404. Yancey, J. A.; Vellore, N. A.; Collier, G.; Stuart, S. J.; Latour, R. A., Development of molecular simulation methods to accurately represent protein-surface interactions: The effect of pressure and its determination for a system with constrained atoms. Biointerphases 2010, 5 (3), 85-95. Collier, G.; Vellore, N. A.; Latour, R. A.; Stuart, S. J., Development of molecular simulation methods to accurately represent protein-surface interactions: Method assessment for the calculation of electrostatic effects. Biointerphases 2009, 4 (4), 57-64. Krstic, P. S.; Hollmann, E. M.; Reinhold, C. O.; Stuart, S. J.; Doerner, R. P.; Nishijima, D.; Pigarov, A. Y., Transfer of rovibrational energies in hydrogen plasma-carbon surface interactions. Journal of Nuclear Materials 2009, 390-91, 88-91. Krstic, P. S.; Reinhold, C. O.; Stuart, S. J., Plasma-surface interactions of hydrogenated carbon. Nuclear Instruments & Methods in Physics Research Section B-Beam Interactions with Materials and Atoms 2009, 267 (4), 704-710. Li, X. F.; Latour, R. A.; Stuart, S. J., TIGER2: An improved algorithm for temperature intervals with global exchange of replicas. Journal of Chemical Physics 2009, 130 (17). Reinhold, C. O.; Krstic, P. S.; Stuart, S. J., Hydrogen reflection in low-energy collisions with amorphous carbon. Nuclear Instruments & Methods in Physics Research Section B-Beam Interactions with Materials and Atoms 2009, 267 (4), 691-694. Wang, Z.; Devel, M.; Dulmet, B.; Stuart, S., Geometry-Dependent Nonlinear Decrease of the Effective Young's Modulus of Single-walled Carbon Nanotubes Submitted to Large Tensile Loadings. Fullerenes Nanotubes and Carbon Nanostructures 2009, 17 (1), 1-10. Hollmann, E. M.; Krstic, P. S.; Doerner, R. P.; Nishijima, D.; Pigarov, A. Y.; Reinhold, C. O.; Stuart, S. J., Measurement and modeling of hydrogen molecule ro-vibrational accommodation on E-294 polycrystalline graphite. Plasma Physics and Controlled Fusion 2008, 50 (10). Knippenberg, M. T.; Stuart, S. J.; Cheng, H., Molecular dynamics simulations on hydrogen adsorption in finite single walled carbon nanotube bundles. Journal of Molecular Modeling 2008, 14 (5), 343-351 Krstic, P. S.; Reinhold, C. O.; Stuart, S. J., Energy and angle spectra of sputtered particles for low-energy deuterium impact of deuterated amorphous carbon. Journal of Applied Physics 2008, 104 (10). Liu, A.; Stuart, S. J., Empirical bond-order potential for hydrocarbons: Adaptive treatment of van der Waals interactions. Journal of Computational Chemistry 2008, 29 (4), 601-611. O'Brien, C. P.; Stuart, S. J.; Bruce, D. A.; Latour, R. A., Modeling of Peptide Adsorption Interactions with a Poly(lactic acid) Surface. Langmuir 2008, 24 (24), 14115-14124. Wang, F.; Stuart, S. J.; Latour, R. A., Calculation of adsorption free energy for solute-surface interactions using biased replica-exchange molecular dynamics. Biointerphases 2008, 3 (1), 9-18. H.Cheng, A.C.Cooper, G.P.Pez, M.K.Kostov, P.Piotrowski and S.J.Stuart, "Molecular Dynamics Simulations on the Effects of Diameter and Chirality on Hydrogen Adsorption in Single Walled Carbon Nanotubes", J.Phys Chem B 109 3780-3786 (2005) V. Raut, M. Agashe, S.J. Stuart, R.A. Latour, "Molecular Dynamics Simulations Of Peptide-Surface Interactions", Langmuir 21 1629-1639 (2005) M. Agashe, V. Raut, S.J. Stuart, R. A. Latour, "Molecular Simulation To Characterize The Adsorption Behavior Of A Fibrinogen gamma-Chain Fragment", Langmuir 21 1103 - 1117 (2005) O. Kum, B.Dickson, S.J. Stuart, B.P. Uberuaga and A.F. Voter, "n-Hexadecane Pyrolysis via Parallel Replica Dynamics", J. Chem. Phys. 121 9808-9819 (2004) M. Huhtala, A. Krasheninnikov, J. Aittoniemi, S.J. Stuart, K. NOrdlund and K. Kaski, "Improved mechanical load transfer between shells of multi-walled carbon nanotubes", Phys. Rev. B, 70 045404 (2004) Stuart, S.J., Hicks, J.M> and Mury, M.T., An Iterative Variable-Timestep Algorithm for Molecular Dynamics Simulations, Mol. Sim., 29, 177-186 (2003). Rick, S.W., and Stuart, S.J., Potentials and Algorithms for Incorporating Polarizability in Computer Simulations, in Rev. Comp. Chem., v. 18, Lipkowitz, K.B. and Boyd, D.B., eds., VCH Publishers, New York, (2002), pp. 89-146. Brenner, D.W., Shenderova, O.A., Harrison, J.A., Stuart, S.J., Ni, B., Sinnott, S.A, A Second-Generation Reactive Empirical Bond Order (REBO) Potential Energy Expression for Hydrocarbons, J. Phys.: Cond. Matt., 14, 783-802 (2002). Stuart, S.J., Li, Y., Gowda, S.B., Sanghavi, H., and Mintmire, J.W., An Object-Oriented Framework for Parallel, Reactive Molecular Dynamics, Parallel Dist. Comp. Sys., 476-482 (2002). . Krantzman, K.D., Z. Postawa, B.J. Garrison, N. Winograd, S.J. Stuart, and J.A. Harrison, Understanding collision cascades in molecular solids. Nuclear Instruments & Methods in Physics Research Section B- Beam Interactions with Materials and Atoms, 2001. 180: p. 159-163.