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Molecular dynamics

Portland State University

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Full-Text Articles in Physics

Entropy Production And Volume Contraction In Thermostated Hamiltonian Dynamics, John D. Ramshaw Nov 2017

Entropy Production And Volume Contraction In Thermostated Hamiltonian Dynamics, John D. Ramshaw

Physics Faculty Publications and Presentations

Patra et al. [Int. J. Bifurcat. Chaos 26, 1650089 (2016)] recently showed that the time-averaged rates of entropy production and phase-space volume contraction are equal for several different molecular dynamics methods used to simulate nonequilibrium steady states in Hamiltonian systems with thermostated temperature gradients. This equality is a plausible statistical analog of the second law of thermodynamics. Here we show that those two rates are identically equal in a wide class of methods in which the thermostat variables z are determined by ordinary differential equations of motion (i.e., methods of the Nosé-Hoover or integral feedback control type). This …


Erratum: "Environmental Swap Energy And Role Of Configurational Entropy In Transfer Of Small Molecules From Water Into Alkanes", Pavel Smejtek, Robert Campbell Word Jun 2005

Erratum: "Environmental Swap Energy And Role Of Configurational Entropy In Transfer Of Small Molecules From Water Into Alkanes", Pavel Smejtek, Robert Campbell Word

Physics Faculty Publications and Presentations

Presents correction to an article related to configurational entropy in transfer of small molecules from water into alkanes, published in the 2005 issue of "The Journal Chemical Physics" and is available online at: http://archives.pdx.edu/ds/psu/8364


Environmental Swap Energy And Role Of Configurational Entropy In Transfer Of Small Molecules From Water Into Alkanes, Pavel Smejtek, Robert Campbell Word Jan 2004

Environmental Swap Energy And Role Of Configurational Entropy In Transfer Of Small Molecules From Water Into Alkanes, Pavel Smejtek, Robert Campbell Word

Physics Faculty Publications and Presentations

We studied the effect of segmented solvent molecules on the free energy of transfer of small molecules from water into alkanes (hexane, heptane, octane, decane, dodecane, tetradecane, and hexadecane). For these alkanes we measured partition coefficients of benzene, 3-methylindole (3MI), 2,3,4,6-tetrachlorophenol (TeCP), and 2,4,6-tribromophenol (TriBP) at 3, 11, 20, 3, and 47 °C. For 3MI, TeCP, and TriBP the dependence of free energy of transfer on length of alkane chains was found to be very different from that for benzene. In contrast to benzene, the energy of transfer for 3MI, TeCP, and TriBP was independent of the number of carbons …


Decay Of Molecules At Spherical Surfaces: Nonlocal Effects, P.T. Leung Apr 1990

Decay Of Molecules At Spherical Surfaces: Nonlocal Effects, P.T. Leung

Physics Faculty Publications and Presentations

The decay rates for molecules in the vicinity of a metallic sphere are investigated in a phenomenological approach for very close molecule-surface distances d. The Fuchs-Claro model [Phys. Rev. B 35, 3722 (1987)] is adopted to describe the polarizability of the sphere with the nonlocal dielectric response being accounted for within the hydrodynamic description. The results show significant differences when compared with those obtained previously within a local description for dlsim50 Aring, with extra resonances observed in the high-frequency regime, a phenomenon similar to that noted previously by Ruppin (1982), in his calculation of the extinction cross section for such …


Energy-Transfer Theory For The Classical Decay Rates Of Molecules At Rough Metallic Surfaces, P.T. Leung, Thomas F. George Sep 1987

Energy-Transfer Theory For The Classical Decay Rates Of Molecules At Rough Metallic Surfaces, P.T. Leung, Thomas F. George

Physics Faculty Publications and Presentations

The problem of the decay rates for molecules at rough metallic surfaces is considered, where the classical electromagnetic energy-transfer theory of Chance, Prock, and Silbey for a flat surface is generalized to the case of a rough boundary. A dynamical theory is constructed through the combination of the Sommerfeld antenna theory and the integral equation formalism of Maxwell's equations at rough boundaries established mainly by Maradudin, Mills, and Agarwal. Perturbative solutions are obtained and numerical results are given with reference to a shallow sinusoidal grating surface. The results, when compared with those obtained previously from the application of the image …


An Approximate Variational Method For Improved Thermodynamics Of Molecular Fluids, M. S. Shaw, J. D. Johnson, John D. Ramshaw Jan 1986

An Approximate Variational Method For Improved Thermodynamics Of Molecular Fluids, M. S. Shaw, J. D. Johnson, John D. Ramshaw

Physics Faculty Publications and Presentations

For a certain class of thermodynamic perturbation theories, a generalization of the Gibbs-Bogoliubov inequality holds through second order of perturbation theory and for a subset of terms the inequality is true to infinite order. Using this approximate variational principle, a perturbation theory is chosen for which the Helmholtz free energy of the reference system is minimized under the constraint that the first order term is identically zero. We apply these ideas to the determination of effective spherical potentials that accurately reproduce the thermodynamics of nonspherical molecular potentials. For a diatomic-Lennard-Jones (DLJ) potential with l ∕σ = 0.793, the resulting spherical …


Brownian Motion In A Flowing Fluid, John D. Ramshaw Sep 1979

Brownian Motion In A Flowing Fluid, John D. Ramshaw

Physics Faculty Publications and Presentations

A phenomenological theory is developed for Brownian motion in a flowing incompressible fluid. The Brownian particles are regarded as an ideal gas subject to a position- and time-dependent force field that represents interactions with the host fluid. This approach immediately leads to deterministic partial differential equations of motion for the Brownian particles. These equations are then examined in the limit of large friction, in which they imply an expression for the diffusional mass flux of Brownian particles. This expression is a sum of terms representing concentration, forced, thermal, and pressure diffusion. Comparisons are made with earlier work, and with the …