Skip to main content
SpringerLink
Log in

Science: Molecular Simulations and Mesoscale Methods

  • Chapter
Applying Molecular and Materials Modeling

Abstract

Molecular simulation of fluids is having an increasingly significant impact on the chemical, pharmaceutical, materials and related industries. This is because molecular simulation provides a set of tools for predicting entirely computationally many useful functional properties of systems of interest to these industries. These properties include thermodynamic properties (such as equations of state, phase equilibria, and critical constants), mechanical properties (such as stress-strain relationships and elastic moduli), transport properties (such as viscosity, diffusion and thermal conductivity), and morphological information (such as location and shape of binding sites on a biomolecule and crystal structure). Furthermore, this list is by no means exhaustive, and it continues to grow as algorithmic and computer hardware advances make it possible to access additional properties.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Log in via an institution
Chapter
USD 29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 169.00
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 219.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 219.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

References

  • Allen, M.P., and D.J. Tildesley. 1987. Computer Simulation of Liquids. Oxford: Oxford University Press.

    Google Scholar 

  • Andersen, H.C. 1980. Molecular-dynamics simulations at constant pressure and-or temperature. J. Chem. Phys. 72: 2384–2393.

    Article  CAS  Google Scholar 

  • Barton, T.J., L.M. Bull, W.G. Klemperer, D.A. Loy, B. McEnaney, M. Misono, P.A. Monson, G. Pez, G.W. Scherer, J.C. Vartuli, and O.M. Yaghi. 1999. Tailored porous materials. Chemistry of Materials 11 (10): 2633–2656.

    Article  CAS  Google Scholar 

  • Biggin, P.C., and M.S.P. Sansom. 1999. Interactions of alpha-helices with lipid bilayers: a review of simulation studies. Biophysical Chemistry 76 (3): 161–183.

    Article  CAS  Google Scholar 

  • Binder, K. 1997. Applications of Monte Carlo methods to statistical physics. Reports on Progress in Physics 60 (5): 487–559.

    Article  CAS  Google Scholar 

  • Binder, K., A. Baumgartner, A.N. Burkitt, D. Ceperley, A.M. Ferrenberg, D.W. Heermann, H.J. Herrmann, D.P. Landau, W. vonderLinden, H. DeRaedt, K.E. Schmidt, W. Selke, D. Stauffer, and A.P. Young. 1995. Recent developments in the Monte Carlo simulation of condensed matter. In Monte Carlo Method in Condensed Matter Physics, Second, Corrected and Updated Edition. ISBN 3–540–60174–0.

    Google Scholar 

  • Binder, K., and W. Paul. 1997. Monte Carlo simulations of polymer dynamics: Recent advances. Journal of Polymer Science Part B-Polymer Physics 35 (1): 1–31.

    Article  CAS  Google Scholar 

  • Bird, R.B., C.F. Curtiss, R.C. Armstrong, and O. Hassager. 1987. Dynamics of Polymeric Liquids: Kinetic Theory. Second ed. 2 vols. Vol. 2. New York: John Wiley and Sons.

    Google Scholar 

  • Blochl, P.E., P. Margl, and K. Schwarz. 1996. Ab initio molecular dynamics with the projector augmented wave method. In B.B. Laird, R.B. Ross, and T. Ziegler (Eds.).

    Google Scholar 

  • Chemical Applications of Density-Functional Theory. Washington, DC. American Chemical Society. ACS Symposium Series 692.See http://www.oupusa.org/toc/tc_0841234035.html and http://www.oup-usa.org/isbn/0841234035.html.

    Google Scholar 

  • Boero, M., K. Terakura, T. Ikeshoji, C.C. Liew, and M. Parrinello. 2000. Car-Parrinello simulation of water at supercritical conditions. Progress of Theoretical Physics Supplement (138):259–261.

    Google Scholar 

  • Bonet Avalos, J., and A.D. Mackie. 1999. Dynamic and transport properties of dissipative particle dynamics with energy conservation. Journal of Chemical Physics 111: 52675276.

    Google Scholar 

  • Bruge, F., M. Bernasconi, and M. Parrinello. 1999. Ab initio simulation of rotational dynamics of solvated ammonium ion in water. Journal of the American Chemical Society 121 (47): 10883–10888.

    Article  CAS  Google Scholar 

  • Car, R., and M. Parrinello. 1985. Unified approach for molecular dynamics and density-functional theory. Phys. Rev. Letts. 55: 2471.

    Article  CAS  Google Scholar 

  • Chan, H.S., and K.A. Dill. 1993. The protein folding problem. Physics Today 46 (2): 24–32.

    Article  CAS  Google Scholar 

  • Chen, B., and J.I. Siepmann. 1999. Transferable potentials for phase equilibria. 3. Explicit-hydrogen description of normal alkanes. Journal of Physical Chemistry B 103 (25): 53705379.

    Google Scholar 

  • Chialvo, A.A., and P.T. Cummings. 1999. Molecular-based modeling of water and aqueous solutions at supercritical conditions. In Advances in Chemical Physics, Vol. 109.

    Google Scholar 

  • Cochran, H.D., P.T. Cummings, S.T. Cui, S.A. Gupta, R.K. Bhupathiraju, and P.F. LoCascio. 1998. Classical molecular simulations of complex, industrially-important systems on the Intel Paragon. Computers and Mathematics with Applications 35: 73–84.

    Article  Google Scholar 

  • Cracknell, R.F., K.E. Gubbins, M. Maddox, and D. Nicholson. 1995. Modeling fluid behavior in well-characterized porous materials. Accounts of Chemical Research 28 (7): 281–288.

    Article  CAS  Google Scholar 

  • Cui, S.T., P.T. Cummings, and H.D. Cochran. 1996. Multiple time step nonequilibrium molecular dynamics simulation of n-decane. Journal of Chemical Physics 104: 255–262.

    Article  CAS  Google Scholar 

  • Cui, S.T., P.T. Cummings, H.D. Cochran, J.D. Moore, and S.A. Gupta. 1998. Nonequilibrium molecular dynamics simulation of the rheology of linear and branched alkanes. International Journal of Thermophysics 19 (2): 449–459.

    Article  CAS  Google Scholar 

  • Cummings, P.T., and D.J. Evans. 1992. Molecular approaches to transport properties and non-Newtonian rheology. Ind. Eng. Chem. Research 31:1237–1252.

    Google Scholar 

  • de Pablo, J., M. Laso, and U.W. Suter. 1992. Estimation of the chemical potential of chain molecules by simulation. J. Chem. Phys. 96: 6157–6162.

    Article  Google Scholar 

  • de Pablo, J.J., and F.A. Escobedo. 1999. Monte Carlo methods for polymeric systems. In Monte Carlo Methods in Chemical Physics. eds. D.M. Ferguson, J.I. Siepman and D.G. Truhlar. Wiley.

    Google Scholar 

  • de Pablo, J.J., M. Laso, J.I. Siepmann, and U.W. Suter. 1993. Continuum-configurational-bias Monte-Carlo simulations of long-chain alkanes. Molecular Physics 80 (1): 55–63.

    Article  Google Scholar 

  • de Pablo, J.J., Q.L. Yan, and F.A. Escobedo. 1999. Simulation of phase transitions in fluids. Annual Review of Physical Chemistry 50: 377–411.

    Article  Google Scholar 

  • Duan, Y., and P.A. Kollman. 1998. Pathways to a protein folding intermediate observed in a 1-microsecond simulation in aqueous solution. Science 282 (5389): 740–744.

    Article  CAS  Google Scholar 

  • Ermak, D.L., and J.A. McCammon. 1978. Brownian dynamics with hydrodynamic interactions. J. Chem. Phys. 64: 1352.

    Article  Google Scholar 

  • Errington, J.R., and A.Z. Panagiotopoulos. 1998. Phase equilibria of the modified Buckingham exponential-6 potential from Hamiltonian scaling grand canonical Monte Carlo. J. Chem. Phys. 109: 1093–1100.

    Article  CAS  Google Scholar 

  • Escobedo, F.A., and J.J. de Pablo. 1999. Molecular simulation of polymeric networks and gels: Phase behavior and swelling. Physics Reports-Review Section of Physics Letters 318 (3): 86–112.

    Google Scholar 

  • Espanol, P. 1995. Hydrodynamics from dissipative particle dynamics. Physical Review E 52 (2): 1734–1742.

    Article  CAS  Google Scholar 

  • Evans, D.J., W.G. Hoover, B.H. Failor, B. Moran, and A.J.C. Ladd. 1983. Nonequilibrium molecular dynamics via Gauss’s principle of least constraint. Phys. Rev. A 28: 1016.

    Article  CAS  Google Scholar 

  • Evans, D.J., and G.P. Morriss. 1990. Statistical Mechanics of Nonequilibrium Liquids. New York: Academic Press.

    Google Scholar 

  • Evans, G.T. 1999. Dissipative particle dynamics: Transport coefficients. Journal of Chemical Physics 110: 1338–1342.

    Article  CAS  Google Scholar 

  • Ferrenberg, A.M., and R.H. Swendsen. 1988. New Monte-Carlo technique for studying phase-transitions. Physical Review Letters 61 (23): 2635–2638.

    Article  CAS  Google Scholar 

  • Ferrenberg, A.M., and R.H. Swendsen. 1989. Optimized Monte-Carlo data-analysis. Physical Review Letters 63 (12): 1195–1198.

    Article  CAS  Google Scholar 

  • Flekkey, E.G., and P.V. Coveney. 1999. From molecular dynamics to dissipative particle dynamics. Physical Review Letters 83: 1775–1778.

    Article  Google Scholar 

  • Freire, J.J. 1999. Conformational properties of branched polymers: Theory and simulations. In Branched Polymers

    Google Scholar 

  • Frenkel, D., and B. Smit. 1996. Understanding Molecular Simulation: From Algorithms to Applications. San Diego: Academic Press.

    Google Scholar 

  • Geissler, P.L., C. Dellago, D. Chandler, J. Hutter, and M. Parrinello. 2000. Ab initio analysis of proton transfer dynamics in (H2O)3H+ Chemical Physics Letters 321 (3–4): 225–230.

    Article  CAS  Google Scholar 

  • Gelb, L.D., K.E. Gubbins, R. Radhakrishnan, and M. Sliwinska-Bartkowiak. 1999. Phase separation in confined systems. Reports on Progress in Physics 62 (12): 1573–1659.

    Article  CAS  Google Scholar 

  • Gillespie, D.T. 1968. Ph.D. dissertation. Johns Hopkins University.

    Google Scholar 

  • Gillespie, D.T. 1976. General method for numerically simulating stochastic time evolution of coupled chemical-reactions. Journal of Computational Physics 22 (4): 403–434.

    Article  CAS  Google Scholar 

  • Glotzer, S.C. 1995. Computer simulations of spinodal decomposition in polymer blends. In Annual Reviews of Computational Physics, edited by D. Stauffer. Singapore: World Scientific.

    Google Scholar 

  • Groot, R.D., T.J. Madden, and D.J. Tildesley. 1999. On the role of hydrodynamic interactions in block copolymer microphase separation. Journal of Chemical Physics 110: 9739–9749.

    Article  CAS  Google Scholar 

  • Groot, R.D., and P.B. Warren. 1997. Dissipative particle dynamics: Bridging the gap between atomistic and mesoscopic simulation. Journal of Chemical Physics 107: 4423–4435.

    Article  CAS  Google Scholar 

  • Haliloglu, T., I. Bahar, B. Erman, E.G. Kim, and W.L. Mattice. 1996. A dynamic rotational isomeric state approach for extension of the time scale of the local dynamics observed in fully atomistic molecular dynamics simulations: Application to polybutadiene. Journal of Chemical Physics 104 (12): 4828–4834.

    Article  CAS  Google Scholar 

  • Haliloglu, T., and W.L. Mattice. 1998. Mapping of rotational isomeric state chains with asymmetric torsional potential energy functions on a high coordination lattice: Application to polypropylene. J. Chem. Phys. 108: 6989–6995.

    Article  CAS  Google Scholar 

  • Hofmann, D., L. Fritz, J. Ulbrich, C. Schepers, and M. Bohning. 2000. Detailed-atomistic molecular modeling of small molecule diffusion and solution processes in polymeric membrane materials. Macromolecular Theory and Simulations 9 (6): 293–327.

    Article  CAS  Google Scholar 

  • Johnson, J.K., A.Z. Panagiotopoulos, and K.E. Gubbins. 1994. Reactive canonical MonteCarlo-A new simulation technique for reacting or associating fluids. Molecular Physics 81 (3): 717–733.

    Article  CAS  Google Scholar 

  • Karim, A., J.F. Douglas, B.P. Lee, S.C. Glotzer, J.A. Rogers, R.J. Jackman, E.J. Amis, and G.M. Whitesides. 1998. Phase separation of ultrathin polymer-blend films on patterned substrates. Phys. Rev. E 57: R6273.

    Article  CAS  Google Scholar 

  • Kofke, D.A. 1993. Gibbs-Duhem Integration: A new method for direct evaluation of phase coexistence by molecular simulation (preliminary communication). Molec. Phys. 78: 1331–1336.

    Article  CAS  Google Scholar 

  • Kremer, K., and G.S. Grest. 1990. Dynamics of entangled linear polymer melts: A molecular-dynamics simulation. J. Chem. Phys. 92: 5057–5086.

    Article  CAS  Google Scholar 

  • Ladd, A.J.C. 1984. Equations of motion for non-equilibrium molecular dynamics simulations of viscous flow in molecular fluids. Molecular Physics 53 (2): 459–463.

    Article  CAS  Google Scholar 

  • Langer, S.A., and S.C. Glotzer. 1997. Morphogenesis in polymer/nematic liquid crystal blends. Physica A 239: 358.

    Article  CAS  Google Scholar 

  • Laso, M., J.J. de Pablo, and U.W. Suter. 1992. Simulation of phase-equilibria for chain molecules. J. Chem. Phys. 97: 2817–2819.

    Article  CAS  Google Scholar 

  • Lees, A.W., and S.F. Edwards. 1972. The computer study of transport processes under extreme conditions. J. Phys. C: Solid State 5: 1921.

    Article  Google Scholar 

  • Levi, A.C., and M. Kotrla. 1997. Theory and simulation of crystal growth. Journal of Physics-Condensed Matter 9 (2): 299–344.

    Article  CAS  Google Scholar 

  • MacKerell, A.D., D. Bashford, M. Bellott, R.L. Dunbrack, J.D. Evanseck, M.J. Field, S. Fischer, J. Gao, H. Guo, S. Ha, D. Joseph-McCarthy, L. Kuchnir, K. Kuczera, F.T.K. Lau, C. Mattos, S. Michnick, T. Ngo, D.T. Nguyen, B. Prodhom, W.E. Reiher, B. Roux, M. Schlenkrich, J.C. Smith, R. Stote, J. Straub, M. Watanabe, J. Wiorkiewicz-Kuczera, D. Yin, and M. Karplus. 1998. All-atom empirical potential for molecular modeling and dynamics studies of proteins. Journal of Physical Chemistry B 102 (I 8): 3586–3616.

    Article  CAS  Google Scholar 

  • Marsh, C.A., and P.V. Coveney. 1998. Detailed balance and H-theorems for dissipative particle dynamics. Journal of Physics A 31: 6561–8.

    Article  CAS  Google Scholar 

  • Martin, G. 1998. Modelling materials driven far from equilibrium. Current Opinion in Solid State & Materials Science 3 (6): 552–557.

    Article  CAS  Google Scholar 

  • Martin, M.G., and J.I. Siepmann. 1998. Transferable potentials for phase equilibria. 1. United-atom description of n-alkanes. J. Phys. Chem. 102: 2569–77.

    CAS  Google Scholar 

  • Marx, D., M. Sprik, and M. Parrinello. 1997. Ab initio molecular dynamics of ion solvation. The case of Be2+ in water. Chemical Physics Letters 273 (5–6): 360–366.

    Article  CAS  Google Scholar 

  • Marx, D., M.E. Tuckerman, J. Hutter, and M. Parrinello. 1999. The nature of the hydrated excess proton in water. Nature 397 (6720): 601–604.

    Article  CAS  Google Scholar 

  • Marx, D., M.E. Tuckerman, and M. Parrinello. 2000. Solvated excess protons in water: quantum effects on the hydration structure. Journal of Physics-Condensed Matter 12 (8A): A153 - A159.

    Article  CAS  Google Scholar 

  • McCabe, C., S.T. Cui, P.T. Cummings, P.A. Gordon, and R.B. Saeger. 2001. Examining the rheology of 9-octylheptadecane to giga-pascal pressures. J. Chem. Phys. 114. 18871891.

    Google Scholar 

  • McCabe, C., P.T. Cummings, and S.T. Cui. 2000. Characterizing the viscosity-temperature dependence of lubricants by molecular simulation. Fluid Phase Equil. submitted for publication.

    Google Scholar 

  • McQuarrie, D.A. 1976. Statistical Mechanics: Harper and Row, New York.

    Google Scholar 

  • Mehta, M., and D.A. Kofke. 1993. Implementation of the Gibbs ensemble using a thermodynamic model for one of the coexisting phases. Molec. Phys. 79: 39–52.

    Article  CAS  Google Scholar 

  • Mooij, G.C.A.M., D. Frenkel, and B. Smit. 1992. Direct simulation of phase-equilibria of chain molecules. J. Phys. Condens. Matter 4: L255–L259.

    Article  Google Scholar 

  • Moore, J.D., S. Cui, H.D. Cochran, and P.T. Cummings. 2000a. Molecular dynamics study of a short-chain polyethylene melt. I. Steady-state shear. Journal of Non-Newtonian Fluid Mechanics 93: 83–99.

    Article  CAS  Google Scholar 

  • Moore, J.D., S. Cui, H.D. Cochran, and P.T. Cummings. 2000b. Molecular dynamics study of a short-chain polyethylene melt. Il. Transient response upon onset of shear. Journal of Non-Newtonian Fluid Mechanics 93: 101–116.

    Article  CAS  Google Scholar 

  • Moore, J.D., S.T. Cui, H.D. Cochran, and P.T. Cummings. 2000c. Rheology of lubricant basestocks: A molecular dynamics study of C30 isomers. J. Chem. Phys. 113 (19): 8833–8840.

    Article  CAS  Google Scholar 

  • Moore, J.D., S.T. Cui, H.D. Cochran, and P.T. Cummings. 1999. The transient rheology of a polyethylene melt under shear. Physical Review E 60: 6956–6959.

    Article  CAS  Google Scholar 

  • Moore, J.D., S.T. Cui, P.T. Cummings, and H.D. Cochran. 1997. Lubricant characterization by molecular simulation. A.I.Ch.E. Journal 43: 3260–3263.

    Article  CAS  Google Scholar 

  • Mundy, C.J., J. Hutter, and M. Parrinello. 2000. Microsolvation and chemical reactivity of sodium and water clusters. Journal of the American Chemical Society 122 (19):48374838.

    Google Scholar 

  • Nakano, A., R.K. Kalia, and P. Vashishta. 1999. Scalable molecular-dynamics, visualization, and data-management algorithms for materials simulations. Computing in Science & Engineering 1 (5): 39–47.

    Article  CAS  Google Scholar 

  • Nath, S.K., F.A. Escobedo, and J.J. de Pablo. 1998. On the simulation of vapor-liquid equilibria for alkanes. Journal of Chemical Physics 108 (23): 9905–9911.

    Article  CAS  Google Scholar 

  • Neumaier, A. 1997. Molecular modeling of proteins and mathematical prediction of protein structure. Siam Review 39 (3): 407–460.

    Article  Google Scholar 

  • Norman, G.E., and V.S. Filinov. 1969. Investigations of phase transitions by a Monte Carlo method. High Temp. (USSR) 7: 216–22.

    Google Scholar 

  • Onuchic, J.N., H. Nymeyer, A.E. Garcia, J. Chahine, and N.D. Socci. 2000. The energy landscape theory of protein folding: Insights into folding mechanisms and scenarios. In

    Google Scholar 

  • Advances in Protein Chemistry. Vol 53. F.M. Richards, D. Eisenberg, P.S. Kim, C.R. Matthews (eds.). Academic Press. 88–153.

    Google Scholar 

  • Orkoulas, G., and A.Z. Panagiotopoulos. 1999. Phase behavior of the restricted primitive model and square-well fluids from Monte Carlo simulations in the grand canonical ensemble. J. Chem. Phys. 110:1581–1590.

    Google Scholar 

  • Panagiotopoulos, A.Z. 1987a. Adsorption and capillary condensation of fluids in cylindrical pores by Monte Carlo simulation in the Gibbs ensemble. Molec. Phys. 62: 701.

    Article  CAS  Google Scholar 

  • Panagiotopoulos, A.Z. 1987b. Direct determination of phase coexistence properties of fluids by Monte Carlo simulation in a new ensemble. Molec. Phys. 61: 813.

    Article  CAS  Google Scholar 

  • Panagiotopoulos, A.Z. 1992. Direct determination of fluid-phase equilibria by simulation in the Gibbs ensemble-A review. Molecular Simulation 9 (1): 1–23.

    Article  Google Scholar 

  • Panagiotopoulos, A.Z. 1996. Current advances in Monte Carlo methods. Fluid Phase Equilibria 116 (1–2):257–266.

    Google Scholar 

  • Panagiotopoulos, A.Z. 2000. Monte Carlo methods for phase equilibria of fluids. Journal of Physics-Condensed Matter 12 (3):R25–R52.

    Google Scholar 

  • Panagiotopoulos, A.Z., N. Quirke, M. Stapleton, and D.J. Tildesley. 1988. Phase equilibria by simulation in the Gibbs ensemble. Alternative derivation, generation, and application to mixture and membrane equilibria. Mol. Phys. 63: 527.

    Article  CAS  Google Scholar 

  • Pande, V.S., A.Y. Grosberg, and T. Tanaka. 2000. Heteropolymer freezing and design: Towards physical models of protein folding. Reviews of Modern Physics 72 (1): 259–314.

    Article  CAS  Google Scholar 

  • Parrinello, M. 1997. From silicon to RNA: The coming of age of ab initio molecular dynamics. Solid State Communications 102 (2–3): 107–120.

    Article  Google Scholar 

  • Phung, T.N., J.F. Brady, and G. Bossis. 1996. Stokesian dynamics simulation of Brownian suspensions. Journal of Fluid Mechanics 313: 181–207.

    Article  CAS  Google Scholar 

  • Pinches, M.R.S., D.J. Tildesley, and W. Smith. 1991. Large scale molecular dynamics on parallel computers using the link-cell algorithm. Molecular Simulation 6: 51–87.

    Article  Google Scholar 

  • Plimpton, S. 1995. Fast parallel algorithms for short-range molecular-dynamics. Journal of Computational Physics 117 (1):1–19.

    Google Scholar 

  • Plimpton, S., and B. Hendrickson. 1995. Parallel molecular-dynamics algorithms for simulation of molecular-systems. In Parallel Computing in Computational Chemistry. T.G. Mattson (ed.). ACS Symposium Series 592. 114–132.

    Chapter  Google Scholar 

  • Plimpton, S., and B. Hendrickson. 1996. A new parallel method for molecular dynamics simulation of macromolecular systems. Journal of Computational Chemistry 17 (3):326337.

    Google Scholar 

  • Radeke, M.R., and E.A. Carter. 1997. Ab initio dynamics of surface chemistry. Annual Review of Physical Chemistry 48:243–270.

    Google Scholar 

  • Ramaniah, L.M., M. Bernasconi, and M. Parrinello. 1998. Density-functional study of hydration of sodium in water clusters. Journal of Chemical Physics 109 (16): 6839–6843.

    Article  CAS  Google Scholar 

  • Rognan, D. 1998. Molecular dynamics simulations: A tool for drug design. Perspectives in Drug Discovery and Design 9–11:181–209.

    Google Scholar 

  • Rudisill, J.W., and P.T. Cummings. 1991. The contribution of internal degrees of freedom to the non-Newtonian rheology of model polymer fluids. Rheologica Acta 30: 33–43.

    Article  CAS  Google Scholar 

  • Sarman, S., D.J. Evans, and P.T. Cummings. 1998. Recent developments in non-equilibrium molecular dynamics. Physics Reports 305: 1–92.

    Article  CAS  Google Scholar 

  • Schlijper, A.G., P.J. Hoogerbrugge, and C.W. Manke. 1995. Computer simulation of dilute polymer solutions with the dissipative particle dynamics method. Journal of Rheology 39 (3): 567–579.

    Article  CAS  Google Scholar 

  • Silvestrelli, P.L., and M. Parrinello. 1999. Structural, electronic, and bonding properties of liquid water from first principles. Journal of Chemical Physics 111 (8): 3572–3580.

    Article  CAS  Google Scholar 

  • Smith, W.R., and B. Triska. 1994. The reaction ensemble method for the computer-simulation of chemical and phase-equilibria.1. Theory and basic examples. Journal of Chemical Physics 100 (4): 3019–3027.

    Article  CAS  Google Scholar 

  • Sorensen, M.R., and A.F. Voter. 2000. Temperature-accelerated dynamics for simulation of infrequent events. Journal of Chemical Physics 112 (21): 9599–9606.

    Article  CAS  Google Scholar 

  • Sprik, M., J. Hutter, and M. Parrinello. 1996. Ab initio molecular dynamics simulation of liquid water: Comparison three gradient-corrected density functionals. Journal of Chemical Physics 105 (3): 1142–1152.

    Article  CAS  Google Scholar 

  • Stoltze, P. 2000. Microkinetic simulation of catalytic reactions. Progress in Surface Science 65 (3–4): 65–150.

    Article  CAS  Google Scholar 

  • Swendsen, R.H., J.S. Wang, and A.M. Ferrenberg. 1995. New Monte Carlo methods for improved efficiency of computer simulations in statistical mechanics. In Monte Carlo Method in Condensed Matter Physics, Second, Corrected and Updated Edition. Topics in Applied Physics. vol 71. Springer-Verlag.

    Google Scholar 

  • Trout, B.L., and M. Parrinello. 1998. The dissociation mechanism of H2O in water studied by first-principles molecular dynamics. Chemical Physics Letters 288 (2–4): 343–347.

    Article  CAS  Google Scholar 

  • Trout, B.L., and M. Parrinello. 1999. Analysis of the dissociation of Hp in water using first- principles molecular dynamics. Journal of Physical Chemistry B 103 (34): 7340–7345.

    Article  CAS  Google Scholar 

  • Tuckerman, M.E., B.J. Berne, and G.J. Martyna. 1992. Reversible multiple time step molecular dynamics. J. Chem. Phys. 97: 1990.

    Article  CAS  Google Scholar 

  • Tuckerman, M.E., and G.J. Martyna. 2000. Understanding modern molecular dynamics: Techniques and applications. Journal of Physical Chemistry B 104 (2): 159–178.

    Article  CAS  Google Scholar 

  • Uhlherr, A., and D.N. Theodorou. 1998. Hierarchical simulation approach to structure and dynamics of polymers. Current Opinion in Solid State & Materials Science 3 (6):544551.

    Google Scholar 

  • Voter, A.F. 1997a. Accelerating the dynamics of infrequent events. Abstracts of Papers of the American Chemical Society 213:284-PHYS.

    Google Scholar 

  • Voter, A.F. 1997b. Hyperdynamics: Accelerated molecular dynamics of infrequent events. Physical Review Letters 78 (20): 3908–3911.

    Article  CAS  Google Scholar 

  • Voter, A.F. 1997c. A method for accelerating the molecular dynamics simulation of infrequent events. Journal of Chemical Physics 106 (11): 4665–4677.

    Article  CAS  Google Scholar 

  • Voter, A.F. 1998. Parallel replica method for dynamics of infrequent events. Physical Review B-Condensed Matter 57 (22):R13985–RI3988.

    Google Scholar 

  • Wick, C.D., M.G. Martin, and J.I. Siepmann. 2000. Transferable potentials for phase equilibria. 4. United-atom description of linear and branched alkenes and alkylbenzenes. Journal of Physical Chemistry B 104 (33): 8008–8016.

    Article  CAS  Google Scholar 

  • Zachariah, M.R., and M.J. Carrier. 1999. Molecular dynamics computation of gas-phase nanoparticle sintering: A comparison with phenomenological models. Journal of Aerosol Science 30 (9):1139–1151.

    Google Scholar 

  • Zwanzig, R. 1965. Time correlation functions and transport coefficients in statistical mechanics. Ann. Rev. Phys. Chem. 16: 67.

    Article  CAS  Google Scholar 

Download references

Authors
  1. Peter T. Cummings
    View author publications

    You can also search for this author in PubMed Google Scholar

Rights and permissions

Reprints and permissions

Copyright information

© 2002 Springer Science+Business Media Dordrecht

About this chapter

Cite this chapter

Cummings, P.T. (2002). Science: Molecular Simulations and Mesoscale Methods. In: Applying Molecular and Materials Modeling. Springer, Dordrecht. https://doi.org/10.1007/978-94-017-0765-7_3

Download citation

  • DOI: https://doi.org/10.1007/978-94-017-0765-7_3

  • Publisher Name: Springer, Dordrecht

  • Print ISBN: 978-90-481-6134-8

  • Online ISBN: 978-94-017-0765-7

  • eBook Packages: Springer Book Archive

Publish with us

Policies and ethics

Search

Navigation