UB - University at Buffalo, The State University of New York Chemical and Biological Engineering
portrait of faculty member Kofke

David A. Kofke

UB Distinguished Professor
Department Chair

306 Furnas Hall
(716) 645-1173
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