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List of recent original publications

2008

Skvor J., Nezbeda I.
On universality of the wrapping percolation transition.
Coll. Czech. Chem. Commun. , submitted.

Rouha M., Moucka F., Nezbeda I.
The effect of cross interactions on mixing properties: Non-Lorentz-Berthelot Lennard-Jones mixtures.
Coll. Czech. Chem. Commun. , submitted.

Kolafa J., Moucka F., Nezbeda I.
Handling electrostatic interactions in molecular simulations: A systematic study.
Coll. Czech. Chem. Commun., submitted.

2007

Moucka F., Nezbeda I.
Efficient multi-particle sampling in Monte Carlo simulations on fluids: Application to polarizable models.
J. Chem. Phys. 126, 224106 (2007).

Jirsak J., Nezbeda I.
Molecular-based equation of state for TIP4P water.
J. Mol. Liq. 136, 310 (2007).

Melnyk R., Moucka F., Nezbeda I., Trokhymchuk A.
A novel perturbation theory for the structure factor of the attractive hard-core Yukawa fluid.
J. Chem. Phys. 107, 094510 (2007).

Jirsak J., Nezbeda I.
Towards a statistical mechanical theory of water: Analytical theory for a short-ranged reference system.
J. Chem. Phys. 127, 124508 (2007).

Figueroa-Gerstenmaiera S., Francova M., Kowalski M., Lisal M., Nezbeda I., Smith W. R.
Molecular-level computer simulation of a vapor-compression refrigeration cycle.
Fluid Phase Equil. 259, 195 (2007).

Rouha M., Nezbeda I.
Lower virial coefficients of primitive models of polar and associating fluids.
J. Mol. Liq. 131-132, 158 (2007).

Jirsak J., Nezbeda I.
Molecular mechanisms underlying the thermodynamic properties of water.
J. Mol. Liq. 134, 99 (2007).

Vlcek L., Nezbeda I.
Excess properties of aqueous mixtures of methanol: Simple models versus experiment.
J. Mol. Liq. 131-132, 158 (2007).

2006

Jedlovszky P., Predota M., Nezbeda I.
Hydration of apolar solutes of varying size: A systematic study.
Mol. Phys. 104, 2465 (2006).

Gonzales-Salgado D., Nezbeda I.
Excess properties of aqueous mixtures of methanol: Simulation versus experiment.
Fluid Phase Equil. 240, 161 (2006).(abstract)

Smith W. R., Lisal M., Nezbeda I.
Molecular-level Monte-Carlo simulation at fixed entropy..
Chem. Phys. Lett. 426, 436 (2006).

Vega C., Abascal J. L. F., Nezbeda I.
Vapor-liquid equilibria from the triple point up to the critical point for the new generation of TIP4P like models: TIP4P/Ew, TIP4P/2005, and TIP4P/Ice.
J. Chem. Phys. 125, 034503 (2006).

Lisal M., Brennan J.K., Smith W.R.
Chemical reaction equilibrium in nanoporous materials: No dimerization reaction in carbon slit nanopores.
J. Chem. Phys. 124, 064712 (2006).

Smith W.R., Lisal M., Brennan J.K.
Effects of confinement on chemical reaction equilibrium in nanoporous materials.
In Computational Science and its Applications - ICCSA 2006, Glasgow, UK. May 2006, M. Gavrilova et al. (Eds.),
Lecture Notes in Computer Science, 3984, 743-751, Springer-Verlag (Berlin-Heidelberg), 2006.

2005

Vlcek L., Nezbeda I.
From realistic to simple models of fluids. III. Primitive models of carbon dioxide, hydrogen sluphide, and acetone, and their properties.
Mol. Phys. 103, 1905 (2005).(abstract)

Chialvo A. A., Kettler M., Nezbeda I.
Effect of the range of interactions on the properties of fluids. Part II. Structure and phase behavior of acetonitrile, hydrogen fluoride, and formic acid.
J. Phys. Chem. B. 109, 9736 (2005).(abstract)

Vlcek L., Nezbeda I.
Potential of mean force between ions in infinitely diluted simple short-range models of aqueous electrolytes.
Cond. Matter Phys. 8, 261-270 (2005).(abstract)

Moucka F., Nezbeda I.
Detection and characterization of structural changes in the hard-disk fluid under freezing and melting conditions.
Phys. Rev. Lett. 94, 040601 (2005).(abstract)

Nezbeda I.
Towards a unified view of fluids.
Mol. Phys. 103, 59-76 (2005).(abstract)

Lisal M., Smith W.R., Kolafa J.
Molecular simulations of aqueous electrolyte solubility: 1. The expanded-ensemble osmotic molecular dynamics method for the solution phase.
J. Phys. Chem. B 109, 12956 (2005).

Lisal M., Bendová M., Smith W.R.
Monte Carlo adiabatic simulation of equilibrium reacting systems: The ammonia synthesis reaction.
Fluid Phase Equil. 235, 50-57 (2005).

Nezbeda I., Kolafa J.
On the Role of the Range of Intermolecular Interactions in Fluids.
In "Ionic Soft Matter: Modern Trends in Theory and Applications", D. Henderson, M. Holovko, and A. Trokhymchuk, (Editors). Springer (Dordrecht), 2005.

2004

Nezbeda I.
Role of the range of intermolecular interactions in fluids.
Curr. Opinion in Colloid and Interface Sci. 9, 107-111 (2004).(abstract)

Lisal M., Nezbeda I.
Conformations of homopolymer chains and their phase behavior in a simple supercritical solvent.
Fluid Phase Equil. 222-223C, 247-254 (2004).(abstract)

Vlcek L., Nezbeda I.
Thermodynamics of simple models of associating fluids: Primitive models of ammonia, methanol, ethanol, and water.
Mol. Phys. 102, 771-781 (2004).(abstract)

Vlcek L., Nezbeda I.
From realistic to simple models of associating fluids. II. Primitive models of ammonia, ethanol, and models of water revisited.
Mol. Phys. 102, 385-497 (2004).(abstract)

Lisal M., Nezbeda I., Smith W. R.
Vapor-liquid equilibria in five-site (TIP5P) models of water.
J. Phys. Chem. B 108, 7412-7414 (2004).(abstract)

Nezbeda I., Smith W. R.
On the calculation of the critical temperature from the second virial coefficient.
Fluid Phase Equil. 216, 183-186 (2004).(abstract)

Lisal M., Aim K., Mecke M., Fischer J.
Revised equation of state for two-center Lennard-Jones fluids.
Int. J. Thermophys. 25, 159-173 (2004).

Lisal M., Brennan J. K., Smith W. R., Siperstein F. R.
Dual control cell reaction ensemble molecular dynamics: A method for simulations of reactions and adsorption in porous materials.
J. Chem. Phys. 121, 4901-4912 (2004).

Budinsky R., Vacek V., Lisal M.
Vapor-liquid equilibria of alternative refrigerants and their binaries by molecular simulations employing the reaction Gibbs ensemble Monte Carlo method.
Fluid Phase Equil. 222-223, 213-223 (2004).

Lisal M., Smith W. R., Aim K.
Analysis of Henry’s constant for carbon dioxide in water via Monte Carlo simulation.
Fluid Phase Equil. 226, 161-172 (2004).

Brennan J. K., Lisal M., Gubbins K. E., Rice B. M.
Reaction ensemble molecular dynamics: Direct simulation of the dynamic equilibrium properties of chemically reacting mixtures.
Phys. Rev. E 70, 061103-1 - 061103-4 (2004).

2003

Vlcek L., Slovak J., Nezbeda I.
Thermodynamic perturbation theory of the second-order: Implementation for models with double-bonded sites.
Mol. Phys. 101, 2921-2927 (2003). (abstract)

Lisal M., Nezbeda I.
Conformations of Attractive, Repulsive, and Amphiphilic Polymer Chains in a Simple Supercritical Solvent: Molecular Simulation Study.
J. Chem. Phys. 119, 4026-4034 (2003). (abstract)

Nezbeda I.
Modeling of aqueous electrolytes at a molecular level Simple short-range models and structure breaking and structure enhancement phenomena.
J. Mol. Liquids 103-104C, 309-317 (2003). (abstract)

Slovak J., Nezbeda I.
On accuracy of Wertheim's thermodynamic perturbation theory for primitive models of water.
Mol. Phys. 101, 789-798 (2003). (abstract)

Predota M., Ben-Naim A., Nezbeda I.
On independence of the solvation of interaction sites of a water molecule.
J. Chem. Phys. 118, 6446-6454 (2003). (abstract)

Lisal M., Hall C. K., Gubbins K. E., Panagiotopoulos A. Z.
Formation of spherical micelles in a supercritical solvent: Lattice Monte Carlo simulation and multicomponent solution model.
Molec. Simul. 29, 139-157 (2003).

Colina C. M., Olivera-Fuentes C. G., Siperstein F. R., Lisal M., Gubbins K. E.
Thermal properties of supercritical carbon dioxide by Monte Carlo simulations.
Molec. Simul. 29, 405-412 (2003).

Lisal M., Smith W. R., Aim K.
Direct molecular-level Monte Carlo simulation of Joule-Thomson processes.
Molec. Phys. 101, 2875-2884 (2003).

2002

Lisal M., Kolafa J., Nezbeda I.
An examination of the five-site potential (TIP5P) for water.
J. Chem. Phys. 117, 8892-8897 (2002). (abstract)

Predota M., Nezbeda I., Cummings P. T.
Hydrophobic hydration at the level of primitive models. II. Large solutes and water restructuring.
Mol. Phys. 100, 2189-2200 (2002). (abstract)

Kettler M., Nezbeda I., Chialvo A. A. , Cummings P. T.
Effect of the range of interactions on the properties of fluids. Phase equilibria in pure carbon dioxide, acetone, methanol, and water.
J. Phys. Chem. B 106, 7537-7546 (2002). (abstract)

Kolafa J., Labik S., Malijevsky A.
The bridge function of hard spheres by direct inversion of computer simulation data.
Mol. Phys. 100, 2629-2640 (2002). (abstract)

Lisal M., Hall C. K., Gubbins K. E., Panagiotopoulos A. Z.
Micellar behavior in supercritical solvent-surfactant systems from lattice Monte Carlo simulations.
Fluid Phase Equil. 194-197, 233-247 (2002).

Lisal M., Hall C. K., Gubbins K. E., Panagiotopoulos A. Z.
Self-assembly of surfactants in a supercritical solvent from lattice Monte Carlo simulations.
J. Chem. Phys. 116, 1171-1184 (2002).

Lisal M., Smith W. R., Bures M., Vacek V., Navratil J.
REMC computer simulation of the thermodynamic properties of argon and air plasmas.
Molec. Phys. 100, 2487-2497 (2002).

Smith W. R., Lisal M.
Direct Monte Carlo simulation methods for nonreacting and reacting systems at fixed total internal energy or enthalpy.
Phys. Rev. E 66, 01114-1 - 01114-3 (2002).

Colina C. M., Lisal M., Siperstein F. R., Gubbins K. E.
Accurate CO2 Joule-Thomson inversion curve by molecular simulations.
Fluid Phase Equil. 202, 253-262 (2002).

2001

Nezbeda I.
On dispersion force correction terms in perturbed equations of state.
Fluid Phase Equil. 180, 165-171 (2001). (abstract)

Nezbeda I., Lisal M.
Effect of short and long range forces on the thermodynamic properties of water. A simple short range reference system.
Mol. Phys. 99, 291-300 (2001). (abstract)

Kolafa J., Nezbeda I., Lisal M.
Effect of short- and long-range forces on the properties of fluids. III. Dipolar and quadrupolar fluids.
Mol. Phys. 99, 1751-1764 (2001). (abstract)

Kettler M., Voertler H. L., Nezbeda I., Strnad M.
Coexistence properties of higher n-alkanes modelled as Kihara fluids: Gibbs ensemble simulations.
Fluid Phase Equil. 181, 83-94 (2001). (abstract)

Nezbeda I.
On molecular-based equations of state. Rigor versus speculations.
Fluid Phase Equil. 182, 3-15 (2001). (abstract)

Nezbeda I., Weingerl U.
A molecular-based theory for the thermodynamic properties of water.
Mol. Phys. 99, 1595-1606 (2001). (abstract)

Lisal M., Smith W. R., Nezbeda I.
Accurate vapor-liquid equilibrium calculations for complex systems using the reaction Gibbs ensemble Monte Carlo simulation method.
Fluid Phase Equil. 181, 127-146 (2001). (abstract)

Lee Y.-C., Kolafa J., Curtiss L.A., Ratner M., Shriver D.F.
Molten salt electrolytes. I. Experimental and theoretical studies of LiI/AlCl₃
J. Chem. Phys. 114, 9998 (2001). (abstract)

Smith W. R., Lisal M., Missen R. W.
The Pitzer-Lee-Kesler-Teja (PLKT) strategy and its implementation by meta-computing software.
Chem. Eng. Ed. 35, 68-73 (2001).

2000

Strnad M., Nezbeda I.
Parallelized sampling of the Gibbs ensemble.
Mol. Phys. 98, 1887-1894 (2000). (abstract)

Kolafa J., Nezbeda I.
Effect of short- and long-range forces on the structure of water. II. Orientational ordering and the dielectric constant.
Mol. Phys. 98, 1505-1520 (2000). (abstract * fulltext & and supplementary material)

Kolafa J., Bywater B., Perram J. W.
Essential motions and energetic contributions of individual residues on a peptide bound to an SH3 domain.
Biophys. J. 79, 646-655 (2000). (abstract )

Nezbeda I.
Solubility of apolar fluids in water: A simple molecular model and theory.
Fluid Phase Equil., 170, 13-22 (2000). (abstract)

Lisal M., Smith W. R., Nezbeda I.
Molecular simulation of multicomponent reaction and phase equilibria: Reaction-ensemble Monte Carlo (MC) simulation of the MTBE ternary system.
AIChE J., 46, 866-875 (2000). (abstract)

Nezbeda I.
On the role of short- and long-range forces in aqueous systems.
J. Mol. Liquids, 85, 249-255 (2000).

Lisal M., Aim K., Fischer J.
Vapour-liquid equilibria of dipolar two-centre Lennard-Jones fluids from a physically based equation of state.
Mol. Simul., in press.????

Jirasek V., Labik S., Malijevsky A., Lisal M.
An integral equation and Monte Carlo study of homo- and hetero-nuclear square-well diatomic fluids.
Molec. Phys. 98, 2033-2043 (2000).

1999

Lisal M., Smith W. R., Nezbeda I.
The accurate computer simulation of phase equilibrium for complex fluid mixtures. Application to binaries involving isobutene, methanol, methyl tert-butyl ether, and n-butane.
J. Phys. Chem. B, 103, 10496-10505 (1999). (abstract)

Nezbeda I., Kolafa J.
Effect of short- and long-range forces on the structure of water: Temperature and density dependence.
Mol. Phys., 97, 1105-1116 (1999). (PDF fulltext)

Lisal M, Nezbeda I., Smith W. R.
The reaction ensemble method for the computer simulation of chemical and phase equilibria. II. the Br₂+Cl₂+BrCl system.
J. Chem. Phys., 110, 8597-8604 (1999). (abstract)

Kolafa J., Nezbeda I., Pavlicek J., Smith W. R.
Global phase diagrams of model and real binary fluid mixtures. II. Non-Lorentz-Berthelot mixture of attractive hard spheres.
Phys. Chem. Chem. Phys., 1, 4233-4240 (1999). (abstract)

Predota M., Nezbeda I.
Hydrophobic hydration at the level of primitive models.
Mol. Phys., 96, 1237-1248 (1999). (abstract)

Strnad M., Nezbeda I.
An extended Gibbs ensemble.
Mol. Simul., 22, 193-198 (1999). (abstract)

Nezbeda I., Pavlicek J., Kolafa J., Galindo A., Jackson G.
Global phase behavior of model mixtures of water and n-alkanols.
Fluid Phase Equil., 158-160, 193-199 (1999). (abstract)

Lisal M., Nezbeda I., Vortler H. L.
Fluid-solid boundary of the compressed exp-6 fluids.
Fluid Phase Equil., 154, 49-54 (1999). (abstract)

Lisal M., Nezbeda I.
Pure fluids of homonuclear and heteronuclear square-well diatomics. I. Computer simulation study.
Mol. Phys., 96, 335-347 (1999). (abstract)

Mao Y., Woenckhaus J., Kolafa J., Ratner M. A., Jarrold M. F.
Thermal unfolding of unsolvated cytochrome c: Experiment and molecular dynamics simulations
J. Am. Chem. Soc., 121, 2712-2721 (1999) (abstract)

Kolafa J.
Azeotropic phenomena in the global phase diagram of the Redlich-Kwong equation of state
Phys. Chem. Chem. Phys., 1, 5665 (1999) ( PDF fulltext)

Lisal M., Budinsky R., Vacek V., Aim K.
Vapor-liquid equilibria of alternative refrigerants by molecular dynamics simulations
Intl. J. Thermophys., 20, 163-174 (1999)

Lisal M., Aim K.
Vapor-liquid equilibrium, fluid state, and zero-pressure solid properties of chlorine from anisotropic interaction potential by molecular dynamics
Fluid Phase Equil., 161, 241-256 (1999)

1998

Smith W. R., Nezbeda I., Strnad M., Triska B., Labik S., Malijevsky A.
Generalized thermodynamic perturbation theory for polyatomic fluid mixtures. I. Formulation and results for chemical potentials.
J. Chem. Phys., 109, 1052-1061 (1998).

Kolafa J., Nezbeda I., Pavlicek J., Smith W. R.
Global phase diagrams of model and real binary fluid mixtures: Lorentz-Berthelot mixture of attractive hard spheres.
Fluid Phase Equil., 146, 103-121 (1998). (abstract) (PDF fulltext)

Strnad M., Nezbeda I.
Extended primitive models of water revisited.
Mol. Phys., 93, 25-30 (1998).

Nezbeda I.
Structure of water: Short-ranged versus long-ranged forces.
Czech. J. Phys. B48, 117-122 (1998).

Kolafa J., Ratner M.
Oligomers of poly(ethylene oxide): Molecular dynamics with a polarizable force field
Mol. Simul. 21, 1-26 (1998) (PDF fulltext)

1997

Nezbeda I., Kolafa J., Smith W.R.
Molecular theory of phase equilibria in model and real associated mixtures. III. Binary solutions of inert gases and n-alkanes in ammonia and methanol.
Fluid Phase Equil., 130, 133-156 (1997).

Nezbeda I.
Fluids of pseudo-hard bodies.
Mol. Phys., 90, 661-664 (1997).

Nezbeda I., Kolafa J., Smith W. R.
On global phase diagrams of binary mixtures. I. Systematic basis for describing types of phase equilibrium phenomena.
J. Chem. Soc., Faraday Trans., 93, 3073-3080 (1997). (PDF fulltext)

Slovak J., Nezbeda I.
Extended 5-site primitive models of water: Theory and computer simulations.
Mol. Phys., 91, 1125-1136 (1997).

Vortler H. L, Nezbeda I., Lisal M.
The exp-6 potential fluid at very high pressures. Computer simulations and theory.
Mol. Phys., 92, 813-824 (1997).

Lisal M., Vacek V.
Effective potentials for liquid simulation of the alternative refrigerants HFC-134a (CF₃CH₂F) and HFC-125 (CF₃CHF₂).
Fluid Phase Equil. 127, 83-102 (1997).

Lisal M., Budinsky R., Vacek V.
Vapour-liquid equilibria for dipolar two-centre Lennard-Jones fluids by Gibbs-Duhem integration.
Fluid Phase Equil. 135, 193-207 (1997).

Lisal M., Vacek V.
Direct evaluation of solid-liquid equilibria by molecular dynamics using Gibbs-Duhem integration.
Molec. Simul. 19, 43-61 (1997).

Review papers, monographs, and textbooks

Nezbeda I., Kolafa J., Kotrla M.
Introduction to computer simulations. Monte Carlo and molecular dynamics methods.
(Karolinum - Charles University Press, 1999; in Czech). ( Contents, demo, errata etc. )