Hoover, W.R.: Canonical dynamics: Equilibrium phase-space distributions. Phys. Rev. A 31, 1695

Physical Review A (Impact Factor: 2.81). 04/1985; 31(3):1695-1697. DOI: 10.1103/PhysRevA.31.1695
Source: PubMed

ABSTRACT Nose has modified Newtonian dynamics so as to reproduce both the canonical and the isothermal-isobaric probability densities in the phase space of an N-body system. He did this by scaling time (with s) and distance (with V¹D/ in D dimensions) through Lagrangian equations of motion. The dynamical equations describe the evolution of these two scaling variables and their two conjugate momenta p/sub s/ and p/sub v/. Here we develop a slightly different set of equations, free of time scaling. We find the dynamical steady-state probability density in an extended phase space with variables x, p/sub x/, V, epsilon-dot, and zeta, where the x are reduced distances and the two variables epsilon-dot and zeta act as thermodynamic friction coefficients. We find that these friction coefficients have Gaussian distributions. From the distributions the extent of small-system non-Newtonian behavior can be estimated. We illustrate the dynamical equations by considering their application to the simplest possible case, a one-dimensional classical harmonic oscillator.

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Available from: William Graham Hoover, Aug 07, 2014
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    • "In addition, some other algorithms in the Particular modules are needed. To mimic the experimental conditions, the thermostat (Nosé, 1984; Hoover, 1985) and pressure control (Berendsen et al., 1984) algorithms have been developed. The reaction field algorithm is introduced to deal with the long-range electrostatic interaction (Tironi et al., 1995). "
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    ABSTRACT: Chemical engineering systems usually involve multiple spatio-temporal scales, grouped into different levels, from the molecular scale of reactants to the industrial scale of reactors. Molecular dynamics (MD) simulation is one of the most fundamental methods for the study of such systems, but it is too costly and hence formidable for simulating large-scale behavior directly. However, there are two great potentials in extending this method. First, the logic and algorithms of traditional MD simulations can be generalized from the material level to higher levels since the elements of each level are all discrete in nature, and can be well defined, allowing an MD-style simulation based on different elements. Second, MD simulations can be accelerated by realizing the structural consistency among the problem, model, software and hardware (the so-called EMMS paradigm). These two potentials give possibilities to engineer the method of MD simulation to deal with the whole spectrum of chemical engineering phenomena.
    Chemical Engineering Science 10/2015; 121:200-216. DOI:10.1016/j.ces.2014.09.051 · 2.34 Impact Factor
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    • "Å containing 511 water molecules and 1 ion, i.e. we have 8 3 = 512 molecules in our simulation box. In the following section, we use standard NVT simulations where the temperature is controlled using Nosé-Hoover thermostat [20] [21] and the number of particles is kept constant by implementing periodic boundary conditions. In particular, we assume that our simulation box is surrounded by periodic copies of itself. "
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    ABSTRACT: Molecular dynamics (MD) simulations of ions (K$^+$, Na$^+$, Ca$^{2+}$ and Cl$^-$) in aqueous solutions are investigated. Water is described using the SPC/E model. A stochastic coarse-grained description for ion behaviour is presented and parameterized using MD simulations. It is given as a system of coupled stochastic and ordinary differential equations, describing the ion position, velocity and acceleration. The stochastic coarse-grained model provides an intermediate description between all-atom MD simulations and Brownian dynamics (BD) models. It is used to develop a multiscale method which uses all-atom MD simulations in parts of the computational domain and (less detailed) BD simulations in the remainder of the domain.
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    • "Initially, an equal number of 15 species of gases of Kr, O 2 and N 2 were loaded into the right chamber (see Fig. 2), while the other side (left chamber) was vacuum for all molecular dysemble for 10 ns. The Nose-Hoover barostat and thermostat [39] were applied to maintain the pressure and temperature at 1 atm and 300 K, with damping coefficients 1 ps "
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    ABSTRACT: Gas transport through graphene-derived membranes has gained much interest recently due to its promising potential in filtration and separation applications. In this work, we explore Kr-85 gas radionuclide sequestration from natural air in nanoporous graphene oxide membranes in which different sizes and geometries of pores were modeled on the graphene oxide sheet. This was done using atomistic simulations considering mean-squared displacement, diffusion coefficient, number of crossed species of gases through nanoporous graphene oxide , and flow through interlayer galleries. The results showed that the gas features have the densest adsorbed zone in nanoporous graphene oxide, compared with a graphene membrane, and that graphene oxide was more favorable than graphene for Kr separation. The aim of this paper is to show that for the well-defined pore size called P-7, it is possible to separate Kr-85 from a gas mixture containing Kr-85, O 2 and N 2. The results would benefit the oil industry among others.
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