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portrait of faculty member Kofke
  

David A. Kofke

UB Distinguished Professor
Department Chair

306 Furnas Hall
(716) 645-2911 ext. 2215
Fax: (716) 645-3822
kofke@buffalo.edu
Short bio Research Publications Teaching

Chapters in Books

  • D.A. Kofke and D. Frenkel, “Perspective: Free energies and phase equilibria”, Handbook of Molecular Modeling, S. Yip, editor, Kluwer Academic Publishers, Dordrecht, (in press) (2005).
  • P.A. Monson and D.A. Kofke, “Solid-fluid equilibrium: Insights from simple molecular models”, Adv. Chem. Phys. 115, 113-179 (2000).
  • D.A. Kofke and J.A. Henning, “Thermodynamic integration along coexistence lines”, pages 99-127, Chapter 4 in Molecular Dynamics. From Classical to Quantum Methods, J. Seminario and P. Balbuena, eds., Volume 7 of Series in Theoretical and Computational Chemistry, Prof. P. Politzer, series editor. Elsevier Science Publishers, Amsterdam (1999).
  • D.A. Kofke, "Semigrand Canonical Monte Carlo Simulation; Integration Along Coexistence Lines", Adv. Chem. Phys., 105, 405-442 (1998).

Refereed Journal Publications

  • J.R. Errington and D.A. Kofke, "Calculation of surface tension through area sampling,"J. Chem. Phys., 127, 174709/1-12, (2007).
  • K.E. Benjamin, A.J. Schultz, and D.A. Kofke, "Virial coefficients of polarizable water: Applications to thermodynamic properties and molecular clustering,"J. Phys. Chem. C, 111, 16021-16027, (2007).
  • J.K. Singh, K.E. Benjamin, A.J. Schultz, and D.A. Kofke, "Higher-order virial coefficients of water models," J. Phys. Chem. B, 111, 11463-11473 (2007).
  • D.A. Kofke, "On the sampling requirements for exponential-work free-energy calculations," Mol. Phys., 104(22-24), 3701-3708, (2006).
  • K.M. Benjamin, A.J. Schultz, and D.A. Kofke, "Gas-Phase molecular clustering of TIP4P and SPC/E water models from higher-order virial coefficients," Ind. Eng. Chem. Res., 45(16), 5566-5573, (2006).
  • S. Wierzchowski, Z.H. Fang, D.A. Kofke, and J.L. Tilson, “Three-body effects in hydrogen fluoride: Survey of potential energy surfaces”, Mol. Phys., 104(4), 503-513, (2006).
  • D. Wu and D.A. Kofke, "Phase-space overlap measures. 2. Design and implementation of staging methods for free-energy calculations," J. Chem. Phys., 123, 084109/1-10, (2005).
  • D. Wu and D.A. Kofke, "Phase-space overlap measures. 1. Fail-safe bias detection in free energies calculated by molecular simulation," J. Chem. Phys., 123, 054103/1-10, (2005).
  • D. Wu and D.A. Kofke, “Rosenbluth sampled nonequilibrium work method for calculation of free energies in molecular simulation”, J. Chem. Phys., 122, 204104/1-13, (2005).
  • A. Kone and D.A. Kofke, "Selection of temperature intervals for parallel-tempering simulations," J. Chem. Phys., 122, 206101/1-2, (2005).
  • J.K. Singh and D.A. Kofke, “Molecular simulation study of the effect of pressure on the vapor-liquid interface of the square-well fluid”, Langmuir, 21, 4218-4226, (2005).
  • S.K. Kwak and D.A. Kofke, “Effect of monovacancies on the relative stability of fcc and hcp hard-sphere crystals”, J. Chem. Phys., 122, 176101/1-2, (2005).
  • S.K. Kwak and D.A. Kofke, “Evaluation of bridge-function diagrams via Mayer sampling Monte Carlo simulation”, J. Chem. Phys. 122, 104508/1-7, (2005).
  • S. Wierzchowski and D.A. Kofke, “Trimer based polarization as a multibody molecular model. Application to hydrogen fluoride”, J. Amer. Chem. Soc., 127, 690-698, (2005).
  • D.A. Kofke, “Free energy methods in molecular simulation”, Fluid Phase Equil., 228-229C, 41-48, (2005).
  • S.K. Kwak and D.A. Kofke, “Elastic constants and effect of strain on monovacancy concentration in FCC hard-sphere crystals”, Phys. Rev. B70, 214113 1-6 (2004).
  • D. Wu and D.A. Kofke, “Asymmetric bias in free-energy perturbation measurements using two Hamiltonian-based models”, Phys. Rev. E70, 066702 1-11 (2004).
  • J.K. Singh and D.A. Kofke, “Molecular simulation study of the effect of molecular association on vapor-liquid interfacial properties”, J. Chem. Phys.121 (19) 9574-9580 (2004).
  • D. Wu and D.A. Kofke, “Model for small-sample bias of free-energy calculations applied to Gaussian-distributed nonequilibrium work measurements”, J. Chem. Phys.121(18) 8742-8747 (2004).
  • D.A. Kofke, “Comment on ‘The incomplete beta function law for parallel tempering sampling of classical canonical systems’”, J. Chem. Phys.121(2) 1167 (2004).
  • J.K. Singh and D.A. Kofke, “Mayer sampling: Calculation of cluster integrals using free-energy perturbation methods” Phys. Rev. Lett. 92(22) 220601 (2004).
  • N. Lu, D. Wu, T.B. Woolf and D.A. Kofke, “Using overlap and funnel sampling to obtain accurate free energies from non-equilibrium work measurements”, Phys. Rev. E 69 057702 (2004); selected also to appear in Virt. J. Biol. Phys. Res.7(11) (2004).
  • J. Adhikari and D.A. Kofke, “Molecular simulation study of miscibility of ternary and quaternary InGaAlN alloys”, J. Appl. Phys.95(11) 6129-6137 (2004).
  • D.A. Kofke, “Getting the most from molecular simulation”, Mol. Phys.102(4) 405-420 (2004).
  • J. Adhikari and D.A. Kofke, “Molecular simulation study of miscibility in In­ xGa 1-x N ternary alloys”, J. Appl. Phys.95(8) 4500-4502 (2004).
  • J.K. Singh and D.A. Kofke, “Molecular simulation study of the vapor-liquid interfacial behavior of a dimer-forming associating fluid”, Mol. Sim.30(6) 343-351 (2004).
  • S. Wierzchowski and D.A. Kofke, “Liquid-phase activity coefficients for saturated HF/H 2O mixtures with vapor-phase nonidealities described by molecular simulation”, Ind. Eng. Chem. Res., 43(1) 218-227 (2004).
  • N. Lu, D.A. Kofke and T.B. Woolf, “Improving the efficiency and reliability of free-energy perturbation calculations using overlap sampling methods”, J. Comp. Chem.25(1), 28-39 (2004).
  • S. Wierzchowski and D.A. Kofke, “Fugacity coefficients of saturated water from molecular simulation”, J. Phys. Chem. B, 107, 12808-12813 (2003).
  • S. Wierzchowski, D.A. Kofke, and J. Gao, “Hydrogen fluoride phase behavior and molecular structure: A QM/MM potential model approach”, J. Chem. Phys119(14), 7365-7371 (2003).
  • S. Wierzchowski and D.A. Kofke, “Hydrogen fluoride phase behavior and molecular structure: Ab initio derived potential models”, J. Chem. Phys119(12), 6092-6099 (2003).
  • N. Lu, J. Adhikari, and D.A. Kofke, “Variational formula for the free energy based on incomplete sampling in a molecular simulation”, Phys. Rev. E68(2), 026122 (2003).
  • J.K. Singh, D.A. Kofke, and J.R. Errington, “Surface tension and vapor-liquid phase coexistence for the square well fluid”, J. Chem. Phys. 119(6), 3405-3412 (2003).
  • N. Lu, D.A. Kofke and T.B. Woolf, “Staging is more important than perturbation method for computation of enthalpy and entropy changes in complex systems”, J. Phys. Chem. B107, 5598-5611 (2003).
  • N. Lu, J. Singh, and D.A. Kofke, “Appropriate methods to combine forward and reverse free-energy perturbation averages,” J. Chem. Phys.118(7), 2977-2984 (2003).
  • C.D. Barnes and D.A. Kofke, “A comparison of some variational formulas for the free energy as applied to hard-sphere crystals”, J. Chem. Phys. 117(20), 9111-9115 (2002).
  • D.A. Kofke, “On the acceptance probability of replica-exchange Monte Carlo trials”, J. Chem. Phys.117(15) 6911-6914 (2002). Erratum: 120(22) 10852 (2004).
  • A. Galindo, S.J. Grice, G. Jackson, D.P. Visco, Jr., and D.A. Kofke, “Improved models for the phase behavior of hydrogen fluoride: Chain and ring aggregates in the SAFT approach and the AEOS model”, Molec. Phys.100(14), 2241-2259 (2002).
  • J. Adhikari and D.A. Kofke “ Monte Carlo and cell-model calculations for the solid-fluid Phase behavior of the triangle-well model”, Molec. Phys.100(10) 1543-1550 (2002).
  • C.D. Barnes and D.A. Kofke “ A self-referential method for calculation of the free energy of crystals by Monte Carlo simulation”, Phys. Rev. E, 65 036709-(1-9) (2002).
  • D.A. Kofke and B.C. Mihalick, “Web-based technologies for teaching and using molecular simulation”, Fluid Phase Equil.194-197, 327-335 (2002).
  • N. Lu, C.D. Barnes and D.A. Kofke, “Free-energy calculations for fluid and solid phases by molecular simulation”, Fluid Phase Equil.194-197, 219-226 (2002).
  • S. Wierzchowski and D.A. Kofke, “UB association-bias algorithm applied to the Monte Carlo simulation of hydrogen fluoride”, Fluid Phase Equil.194-197, 249-256 (2002).
  • N. Lu and D.A. Kofke, “Accuracy of free-energy perturbation calculations in molecular simulation. II. Heuristics”, J. Chem. Phys.115(15), 6866-6875 (2001).
  • S. Wierzchowski and D.A. Kofke, “A general-purpose biasing scheme for Monte Carlo simulation of associating fluids”, J. Chem. Phys.114(20), 8752-8762 (2001).
  • N. Lu and D.A. Kofke, “Accuracy of free-energy perturbation calculations in molecular simulation. I. Modeling”, J. Chem. Phys.114(17), 7303-7310 (2001).
  • Lu and D.A. Kofke, “Simple model for insertion/deletion asymmetry of free-energy calculations”, in “Foundations of Molecular Modeling and Simulation”, AIChE Symp. Ser., 97 , 146-149 (2001).
  • D.P. Visco, Jr. and D.A. Kofke, “An improved thermodynamic equation of state for hydrogen fluoride”, Ind. Eng. Chem. Res.38(10), 4125-4129 (1999); Erratum, 39, 242 (2000).
  • D.P. Visco, Jr. and D.A. Kofke, “A comparison of molecular-based models to determine vapor-liquid phase coexistence in hydrogen fluoride”, Fluid Phase Equil.158-160, 37-47 (1999).
  • N. Lu and D.A. Kofke, “Optimal intermediates in staged free-energy calculations”, J. Chem. Phys.111(10), 4414-4423 (1999).
  • S.P. Pandit and D.A. Kofke, “Evaluation of a locus of azeotropes by molecular simulation”, AIChE J.45(10), 2237-2244 (1999).
  • C.D. Barnes and D.A. Kofke, “Exact solution for the singlet density distributions and second-order correlations of normal-mode coordinates for hard rods in one dimension”, J. Chem. Phys.110(23), 11390-11398 (1999).
  • D.P. Visco, Jr. and D.A. Kofke, “Modeling the Monte Carlo simulation of associating fluids”, J. Chem. Phys., 110(12), 5493-5502 (1999).
  • D.A. Kofke and P.G. Bolhuis, “Freezing of polydisperse hard spheres” Phys. Rev. E59(1), 618-622 (1999).
  • D.A. Kofke and P.T. Cummings, “Precision and accuracy of staged free-energy perturbation methods for computing the chemical potential by molecular simulation”, Fluid Phase Equil.150-151, 41-49 (1998).
  • D.P. Visco and D.A. Kofke “Vapor-Liquid Equilibria and Heat Effects of Hydrogen Fluoride from Molecular Simulation”, J. Chem. Phys.109(10), 4015-4027 (1998).
  • D.P. Visco, Jr., E. Juwono, and D.A. Kofke, "Heat Effects of Hydrogen Fluoride from Two Thermodynamic Models", Int. J. of Thermophys., 19, 1111 (1998).
  • D.A. Kofke and P.T. Cummings, “Quantitative Comparison and Optimization of Methods for Evaluating the Chemical Potential by Molecular Simulation”, Molec. Phys.92(6), 973-996 (1997).
  • A.A. Khare, D.A. Kofke and G.T. Evans, “Tracer Diffusion in Perfectly Aligned Liquid Crystalline Phases”, Molec. Phys.91(6), 993-1003 (1997).
  • D.P. Visco, Jr., D.A. Kofke, and R.R. Singh, “Thermal properties of Hydrogen Fluoride from an EOS + Association Model”, AIChE J.43(9), 2381-2384 (1997).
  • D.S. Vaidya, J.M. Nitsche, S.L. Diamond, and D.A. Kofke, “Potential for Use of Liquid Crystals as Dynamically Tunable Electrophoretic Media”, AIChE J.43, 1366 (1997).
  • D.S. Vaidya, J.M. Nitsche, S.L. Diamond, and D.A. Kofke, “Perturbation Solution to the Convection-Diffusion Equation with Moving Fronts”, AIChE J.43(3), 631-644 (1997).
  • G.T. Evans, D.S. Vaidya, and D.A. Kofke, “Evidence for Harmonic Behavior in Hard Particle Smectic A Phases”, Molec. Phys.90, 683 (1997).
  • P.G. Bolhuis and D.A. Kofke, “Numerical Study of Freezing in Polydisperse Colloidal Suspensions”, J. Phys.: Condens. Matter8, 9627-9631 (1996).
  • P.J. Camp, C.P. Mason, M.P. Allen, A.A. Khare, and D.A. Kofke, “The Isotropic-Nematic Phase Transition in Uniaxial Hard Ellipsoid Fluids: Coexistence Data and the Approach to the Onsager Limit”, J. Chem. Phys.105(7), 2837-2849 (1996).
  • P.G. Bolhuis and D.A. Kofke, “A Monte Carlo Study of Freezing of Polydisperse Hard Spheres”, Phys. Rev. E54(1), 634-643 (1996).
  • D.S. Vaidya, J.M. Nitsche, S.L. Diamond, and D.A. Kofke, “Convection-Diffusion of Solutes in Dynamic Media”, Adsorption3, 41-54 (1996).
  • D.A. Kofke, M.R. Grosso, S. Gollapudi, and C.R.F. Lund, “CESL: The Chemical Engineering Simulation Laboratory”, Chem. Eng. Educ. 30(2), 114-119 (Spring 1996).
  • D.S. Vaidya, J.M. Nitsche, S.L. Diamond, and D.A. Kofke, “Convection-Diffusion of Solutes in Media with Piecewise Constant Transport Properties”, Chem. Eng. Sci. 51(24) 5299-5312 (1996).
  • J.A. Dunne, A.L. Myers, and D.A. Kofke, “Simulation of Adsorption of Liquid Mixtures of N 2 and O 2 in a Model Faujasite Cavity at 77.5 K”, Adsorption2, 41-50 (1996).
  • M. Mehta and D.A. Kofke, “Molecular Simulation in a Pseudo Grand-Canonical Ensemble”, Molec. Phys. 86(1), 139-147 (1995).
  • H.-C. Chiu and D.A. Kofke, “A Theory for the 1-1/2 Fluid”, J. Chem. Phys.103(4), 1599-1606 (1995).
  • R. Agrawal and D.A. Kofke, “Thermodynamic and Structural Properties of Model Systems at Solid-Fluid Coexistence. II. Melting and Sublimation of Lennard-Jonesium”, Molec. Phys.85(1), 43-59 (1995).
  • R. Agrawal and D.A. Kofke, “Thermodynamic and Structural Properties of Model Systems at Solid-Fluid Coexistence. I. fcc and bcc Soft Spheres”, Molec. Phys. 85(1), 23-42 (1995).
  • R. Agrawal and D.A. Kofke, “Solid-Fluid Coexistence for Inverse-Power Potentials”, Phys. Rev. Lett.74(1), 122-125 (1995).
  • H.-C. Chiu and D.A. Kofke, “Transformation and Topological Reduction of Cluster Expansions using m-bonds”, J. Stat. Phys.78, 877-892 (1995).
  • R. Agrawal, M. Mehta, and D.A. Kofke, “Efficient Evaluation of Three-Phase Coexistence Lines”, Int. J. Thermophys.15(6), 1073-1083 (1994).
  • D. Vaidya, D.A. Kofke, S. Tang, and G. Evans, “Self Diffusion in the Nematic and Smectic A Phases of an Aligned Fluid of Hard Spherocylinders”, Molec. Phys, 83(1), 101-112 (1994).
  • M. Mehta and D.A. Kofke, “Coexistence Diagrams of Mixtures by Molecular Simulation”, Chem. Eng. Sci. 49(16), 2633-2645 (1994).
  • D.A. Kofke and A.J. Post, “Hard Particles in Narrow Pores. Transfer-Matrix Solution and the Periodic Narrow Box”, J. Chem. Phys. 98(6) 4853-4861 (1993).
  • D.A. Kofke, “Direct Evaluation of Phase Coexistence by Molecular Simulation via Integration Along the Saturation Line”, J. Chem. Phys. 98(5), 4149-4162 (1993).
  • D.A. Kofke, “Gibbs-Duhem Integration: A New Method for Direct Evaluation of Phase Coexistence by Molecular Simulation” (Preliminary Communication), Molec. Phys.78(6), 1331-1336 (1993).
  • M. Mehta and D.A. Kofke, “Implementation of the Gibbs Ensemble Using a Thermodynamic Model for One of the Coexisting Phases”, Molec. Phys. 79(1) 39-52 (1993).
  • A.J. Post and D.A. Kofke, “Fluids Confined to Narrow Pores: A Low-dimensional Approach”, Phys. Rev.A45(2), 939-952 (1992).
  • D. A. Kofke, “1-1/2 Fluid Theory: A New Approach to Conformal Solutions”, J. Chem. Phys.95(10), 7518-7525 (1991).
  • D. A. Kofke, “Solid-fluid Coexistence in Binary Hard Sphere Mixtures by Semigrand Monte Carlo Simulation”, Molec. Sim, 7, 285-302 (1991).
  • D.B. Kitchen, F. Hirata, J.D. Westbrook, R. Levy, D. Kofke, and M. Yarmush, “Conserving Energy During Molecular Dynamics Simulations of Water, Proteins, and Proteins in Water”, J. Comp. Chem.11(10), 1169-1180 (1990).
  • D.A. Kofke and E.D. Glandt, “A Composition Density Functional Theory for Mixtures Based upon an Infinitely Polydisperse Reference. 2. Freezing in Hard Sphere Mixtures”, J. Chem. Phys.92(7), 4417-4425 (1990).
  • D.A. Kofke and E.D. Glandt, “A Composition Density Functional Theory for Mixtures Based upon an Infinitely Polydisperse Reference. 1. Formalism and Theory”, J. Chem. Phys.92(1), 658-666 (1990).
  • D.A. Kofke and E.D. Glandt, “Infinitely Polydisperse Fluids”, J. Chem. Phys.90(1), 439-447 (1989).
  • D.A. Kofke and E.D. Glandt, “ Monte Carlo Simulation of Multicomponent Equilibria in a Semigrand Canonical Ensemble”, Molec. Phys.64(6), 1105-1131 (1988).
  • E.D. Glandt and D.A. Kofke, “An Efficient Algorithm for the Computation of Pair Correlation Functions for Hard Spheres in the Percus-Yevick Theory”, Molec. Phys. 64(1), 125-128 (1988)
  • D.A. Kofke and E.D. Glandt, “Nearly Monodisperse Fluids. I. Monte Carlo Simulations of Lennard-Jones Particles in a Semigrand Ensemble” J. Chem. Phys.87(8), 4881-4890, (1987).
  • D.A. Kofke and E.D. Glandt, “ Monte Carlo Simulation of Continuous Lennard-Jones Mixtures”, Fluid Phase Equil., 29, 327-35, (1986).

Last Updated: October 2007

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