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  • 1
    Electronic Resource
    Electronic Resource
    On the use of the quasi-Gaussian entropy theory in noncanonical ensembles. I. Prediction of temperature dependence of thermodynamic properties (1998)
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 109 (1998), S. 3004-3016 
    Details
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: In previous articles we derived and tested the quasi-Gaussian entropy theory, a description of the excess Helmholtz free energy in terms of the potential energy distribution, instead of the configurational partition function. We obtained in this way the temperature dependence of thermodynamic functions in the canonical ensemble assuming a Gaussian, Gamma or Inverse Gaussian distribution. In this article we extend the theory to describe the temperature dependence of thermodynamic properties in an exact way in the isothermal-isobaric and grand canonical ensemble, using the distribution of the appropriate heat function. For both ensembles restrictions on and implications of these distributions are discussed, and the thermodynamics assuming a Gaussian or (diverging) Gamma distribution is derived. These cases have been tested for water at constant pressure, and the results for the latter case are satisfactory. Also the distribution of the heat function of some theoretical model systems is considered.© 1998 American Institute of Physics.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1063/1.476893
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  • 2
    Electronic Resource
    Electronic Resource
    On the use of the quasi-Gaussian entropy theory in noncanonical ensembles. II. Prediction of density dependence of thermodynamic properties (1998)
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 109 (1998), S. 3017-3027 
    Details
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: In previous articles we derived and tested the quasi-Gaussian entropy theory, a description of the excess free energy in terms of the potential or full internal energy or enthalpy probability distribution, instead of the (configurational) partition function. We obtained in this way the temperature dependence of thermodynamic functions in the NVT, NpT and μVT ensembles assuming a Gaussian, Gamma or Inverse Gaussian distribution. In this article we extend the theory to describe the density dependence of thermodynamic properties, using the distribution of volume and number of particles in the isothermal-isobaric and grand canonical ensemble, respectively. In both ensembles pressure-density expressions for a Gaussian and various Gamma distributions are derived and applied to water. A Gamma description for the volume distribution turns out to be a good model in the gas range, which is in accordance with the volume distribution of an ideal gas. A Gamma description for the particle number distribution works well for liquid densities.© 1998 American Institute of Physics.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1063/1.476894
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  • 3
    Electronic Resource
    Electronic Resource
    Assessment of the validity of intermolecular potential models used in molecular dynamics simulations by extended x-ray absorption fine structure spectroscopy: A case study of Sr2+ in methanol solution (1998)
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 108 (1998), S. 9487-9497 
    Details
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: Molecular dynamics simulations have been carried out for Sr2+ in methanol using different Sr2+ Lennard-Jones parameters and methanol models. X-ray absorption fine structure (EXAFS) spectroscopy has been employed to assess the reliability of the ion-ion and ion-methanol potential functions used in the simulations. Radial distribution functions of Sr2+ in methanol have been calculated for each simulation and compared with the EXAFS experimental data. This procedure has allowed the determinations of reliable Sr2+-methanol models which have been used in longer simulations providing an accurate description of the dynamic and structural properties of this system. © 1998 American Institute of Physics.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1063/1.476398
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  • 4
    Electronic Resource
    Electronic Resource
    Extensions of the quasi-Gaussian entropy theory (1997)
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 106 (1997), S. 1893-1912 
    Details
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: In this paper we present the quasi-Gaussian entropy theory in a comprehensive and consistent way, introducing a new derivation of the theory very suited for applications to molecular systems, and addressing its use in the case of multi-phase systems. A general derivation of the possible confinement of the system within a part of phase space is given, and for water it is shown that for this a hard sphere excluded volume model can be used. To obtain the temperature dependence of the pressure, a new differential equation is derived, and besides the previously introduced Gaussian and Gamma states, in this paper we also describe a new statistical state, the Inverse Gaussian state. We discuss the properties of these different statistical states and for water compare their thermodynamics with experimental data, finding that both the Gamma and Inverse Gaussian states are excellent descriptions. © 1997 American Institute of Physics.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1063/1.473328
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  • 5
    Electronic Resource
    Electronic Resource
    Free volume properties of a simulated lipid membrane (1996)
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 104 (1996), S. 9090-9099 
    Details
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: In this paper, an extensive analysis of free volume related properties of a lipid membrane is given. Using percolation theory, and comparing the free volume properties to those of a soft polymer, additional insights are obtained. The analyses are discussed within the framework of the four region model. It is concluded that the four regions have very different free volume properties. The region containing the dense part of the lipid tails resembles a soft polymer membrane to a large extent. The middle part of the membrane is more similar to a low density alkane. The consequences of the computed free volume properties on the permeation process of small penetrants are discussed. © 1996 American Institute of Physics.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1063/1.471442
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  • 6
    Electronic Resource
    Electronic Resource
    Prediction of the liquid–vapor equilibrium pressure using the quasi-Gaussian entropy theory (1996)
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 105 (1996), S. 7022-7025 
    Details
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: We derived a method to evaluate the liquid–vapor equilibrium pressure, with high accuracy over a large range of temperature, using the quasi-Gaussian entropy theory. The final expression that we obtain for the equilibrium pressure as a function of the temperature can be considered as a very accurate approximate solution of the Clausius–Clapeyron equation. The method was applied to water, methanol and mercury, and was compared to two usual approximations of the Clausius–Clapeyron equation. © 1996 American Institute of Physics.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1063/1.472503
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  • 7
    Electronic Resource
    Electronic Resource
    Free energy of hydrophobic hydration: A molecular dynamics study of noble gases in water (1986)
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 85 (1986), S. 6720-6727 
    Details
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: The potential utility and limitations of two methods to determine free energy differences from molecular dynamics simulations (MD) are studied. The computation of the free energy of hydration of the inert gases serves as a simple but illustrative example. Good results are obtained for the inert gases from a perturbation treatment, using a reference ensemble obtained from a MD simulation of a cavity in water, if these atoms are comparable in size to the cavity and the calculated free energy differences are small. This limits the applicability of the perturbation treatment of a small number of cases. Larger free energy differences can be obtained with reasonable accuracy from MD simulations with continuously changing interaction parameters. This integration method is more generally applicable, but makes an additional simulation necessary.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1063/1.451846
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  • 8
    Electronic Resource
    Electronic Resource
    Molecular dynamics simulation of the transport of small molecules across a polymer membrane (1992)
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 96 (1992), S. 4699-4704 
    Details
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: The transport of small molecules through a polymer membrane is modeled using the computer simulation technique of molecular dynamics (MD). The transport coefficient is derived from a combination of the excess free energy and the diffusion constant. Both properties are derived from MD simulations, applied to helium and methane in polydimethylsiloxane (PDMS). The diffusional process appears to have the character of a jump diffusion for methane and less so for helium. Jumps are allowed by fluctuations of the size and shape of holes. Experimental diffusion constants are well reproduced. The excess free energies, determined by a particle insertion method, are lower by 5–7 kJ/mol than experimental values. It is shown that, as a result of a higher solubility, methane has a higher permeability constant than helium, despite its lower diffusion constant.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1063/1.462806
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  • 9
    Electronic Resource
    Electronic Resource
    Free energy of ionic hydration: Analysis of a thermodynamic integration technique to evaluate free energy differences by molecular dynamics simulations (1988)
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 89 (1988), S. 5876-5886 
    Details
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: The thermodynamic integration technique to evaluate free energy differences by molecular dynamics simulations is analyzed. The hydration of the ions Na+ , K+ , Ca++ , F−, Cl−, and Br− is used as the process to illustrate the potential utility of the method. A neon–water system is used as a reference system. The parameters that influence the performance and accuracy of the thermodynamic integration, in which the potential interaction parameters are gradually and continuously changed, are studied. These parameters include the total simulation time, the magnitude of the time step for the numerical integration of the equations of motion, the system size, and the cutoff radii for the intermolecular interactions. Fast convergence is found for the Gibbs free energy difference between Ne and Na+ with respect to total simulation time. The time step and system size are relatively unimportant. The use of cutoff radii, for the ion–water but especially unfortunately also the water–water intermolecular interactions, seriously influences the results obtained. A simple correction for the use of cutoff radii cannot be made. Results are compared to experimental values.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1063/1.455539
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  • 10
    Electronic Resource
    Electronic Resource
    Molecular dynamics simulation of a smectic liquid crystal with atomic detail (1988)
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 89 (1988), S. 3718-3732 
    Details
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: A molecular dynamics simulation of a sodium–decanoate/decanol/water system is reported. The system is treated in full atomic detail, with the exception of CH2 and CH3 groups that are considered to be "united atoms,'' and is a refinement of a previous model membrane [Mol. Phys. 11, 1 (1983)]. The long-range Coulomb interactions were included specifically. The order parameters of the chain units of the lipids and diffusion constants of components in the system calculated from the simulation agree well with those reported in experiments on this model membrane. The overall structure of the membrane shows considerable disorder, with a broad lipid–water interface, extending over approximately 1 nm. The distribution of the components is such that an almost complete charge cancellation occurs throughout the system, which is in contradiction with the generally assumed electrical double layer structure for membranes. A counterion condensation of 70% is observed. Both the translational and the rotational motions of water are slowed down compared to bulk water. The penetration of water into the hydrocarbon region of the membrane is substantial. Pair correlations of various atom pairs, and dihedral statistics and transition rates of the dihedrals in the lipids are reported. The distributions of chain segments of the lipids, of water molecules, and of sodium ions are compared with theoretical predictions.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1063/1.454893
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