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Gerson E Valenzuela - One of the best experts on this subject based on the ideXlab platform.

Andriy Kovalenko - One of the best experts on this subject based on the ideXlab platform.

  • enhanced Solvation Force extrapolation for speeding up molecular dynamics simulations of complex biochemical liquids
    Journal of Chemical Physics, 2019
    Co-Authors: I P Omelyan, Andriy Kovalenko
    Abstract:

    We propose an enhanced approach to the extrapolation of mean potential Forces acting on atoms of solute macromolecules due to their interactions with solvent atoms in complex biochemical liquids. It improves and extends our previous extrapolation schemes by additionally including new techniques such as an exponential scaling transformation of coordinate space with weights complemented by an automatically adjusted balancing between the least square minimization of Force deviations and the norm of expansion coefficients in the approximation. The expensive mean potential Forces are treated in terms of the three-dimensional reference interaction site model with Kovalenko-Hirata closure molecular theory of Solvation. During the dynamics, they are calculated only after every long (outer) time interval, i.e., quite rarely to reduce the computational costs. At much shorter (inner) time steps, these Forces are extrapolated on the basis of their outer values. The equations of motion are then solved using a multiple time step integration within an optimized isokinetic Nose-Hoover chain thermostat. The new approach is applied to molecular dynamics simulations of various systems consisting of solvated organic and biomolecules of different complexity. For example, we consider hydrated alanine dipeptide, asphaltene in toluene solvent, miniprotein 1L2Y, and protein G in aqueous solution. It is shown that in all these cases, the enhanced extrapolation provides much better accuracy of the Solvation Force approximation than the existing approaches. As a result, it can be used with much larger outer time steps, leading to a significant speedup of the simulations.

  • enhanced Solvation Force extrapolation for speeding up molecular dynamics simulations of complex biochemical liquids
    arXiv: Chemical Physics, 2019
    Co-Authors: I P Omelyan, Andriy Kovalenko
    Abstract:

    We propose an enhanced approach to the extrapolation of mean potential Forces acting on atoms of solute macromolecules due to their interactions with solvent atoms in complex biochemical liquids. It improves and extends previous extrapolation schemes by including additionally new techniques such as an exponential scaling transformation of coordinate space with weights complemented by a dynamically adjusted balancing between the least square minimization of Force deviations and the norm of expansion coefficients in the approximation. The expensive mean potential Forces are treated in terms of the 3D-RISM-KH molecular theory of Solvation (three-dimensional reference interaction site model with the Kovalenko-Hirata closure). During the dynamics they are calculated only after every long enough (outer) time interval, i.e., quite rarely to reduce the computational costs. At much shorter (inner) time steps, these Forces are extrapolated on the basis of their outer values. The equations of motion are then solved using a multiple time step integration within an optimized isokinetic Nose-Hoover chain thermostat. The new approach is applied to molecular dynamics simulations of various systems consisting of solvated organic and biomolecules of different complexity. Namely, we consider hydrated alanine dipeptide, asphaltene in toluene solvent, miniprotein 1L2Y and protein G in aqueous solution. It is shown that in all these cases, the enhanced extrapolation provides much better accuracy of the Solvation Force approximation than the existing approaches. As a result, it can be used with much larger outer time steps, leading to a significant speedup of the simulations.

  • mts md of biomolecules steered with 3d rism kh mean Solvation Forces accelerated with generalized Solvation Force extrapolation
    Journal of Chemical Theory and Computation, 2015
    Co-Authors: Igor Omelyan, Andriy Kovalenko
    Abstract:

    We developed a generalized Solvation Force extrapolation (GSFE) approach to speed up multiple time step molecular dynamics (MTS-MD) of biomolecules steered with mean Solvation Forces obtained from the 3D-RISM-KH molecular theory of Solvation (three-dimensional reference interaction site model with the Kovalenko-Hirata closure). GSFE is based on a set of techniques including the non-Eckart-like transformation of coordinate space separately for each solute atom, extension of the Force-coordinate pair basis set followed by selection of the best subset, balancing the normal equations by modified least-squares minimization of deviations, and incremental increase of outer time step in motion integration. Mean Solvation Forces acting on the biomolecule atoms in conformations at successive inner time steps are extrapolated using a relatively small number of best (closest) solute atomic coordinates and corresponding mean Solvation Forces obtained at previous outer time steps by converging the 3D-RISM-KH integral e...

Robert Evans - One of the best experts on this subject based on the ideXlab platform.

  • phase behavior and structure of a fluid confined between competing solvophobic and solvophilic walls
    Physical Review E, 2012
    Co-Authors: Maria C Stewart, Robert Evans
    Abstract:

    We consider a model fluid with long-range r(-6) (dispersion) interparticle potentials confined between competing parallel walls. One wall is solvophilic and would be completely wet at bulk liquid-gas coexistence μ(co)(-), whereas the other is solvophobic and would be completely dry at μ=μ(co)(+). When the wall separation L is large and the system is below the bulk critical temperature T(C) and close to bulk liquid-gas coexistence, a delocalized interface or soft-mode phase forms with a liquid-gas interface near the center of the slit; this interacts with the walls via the power-law tails of the interparticle potentials. We use a coarse-grained effective Hamiltonian approach to derive explicit scaling expressions for the Gibbs adsorption Γ, the surface tension γ, the Solvation Force f(s), and the total susceptibility χ. These quantities depend on the dimensionless scaling variable (L/σ)(3)βδμ, where β=(k(B)T)(-1), σ is the diameter of the fluid particles and δμ=μ-μ(co) is the chemical potential deviation from bulk coexistence. Using a nonlocal density functional theory, we calculate density profiles for the asymmetrically confined fluid at different chemical potentials and for sufficiently large L confirm the scaling predictions for the four thermodynamic quantities. Since the upper critical dimension for complete wetting with power-law potentials is less than 3, we argue that our (mean-field) scaling predictions should remain valid in treatments that incorporate the effects of interfacial fluctuations. As the wall separation L is decreased at μ(co), we predict a capillary evaporation transition from the delocalized interface phase to a dilute gas state with just a thin adsorbed film of liquidlike density next to the solvophilic wall. This transition is closely connected to the first-order prewetting transition that occurs at the solvophilic wall in the semi-infinite system. We compare the phase diagram for the competing walls system with the phase diagrams for the fluid confined between identical solvophilic and identical solvophobic walls. Comparisons are also made with earlier studies of asymmetric confinement for systems with short-range Forces.

  • influence of capillary condensation on the near critical Solvation Force
    Physical Review Letters, 2000
    Co-Authors: A Drzewinski, A Maciolek, Robert Evans
    Abstract:

    We argue that in a fluid, or magnet, confined by adsorbing walls which favor liquid, or the (+) phase, the Solvation (Casimir) Force in the vicinity of the critical point is strongly influenced by capillary condensation which occurs below the bulk critical temperature T(c). At T slightly below and above T(c), a small bulk field h<0, which favors gas, or the (-) phase, leads to residual condensation and a Solvation Force which is much more attractive (at the same large wall separation) than that found exactly at the critical point. Our predictions are supported by results obtained from density-matrix renormalization-group calculations in a two-dimensional Ising strip subject to identical surface fields.

A Maciolek - One of the best experts on this subject based on the ideXlab platform.

  • Solvation Force for long ranged wall fluid potentials
    Journal of Chemical Physics, 2004
    Co-Authors: A Maciolek, A Drzewinski, Pawel Bryk
    Abstract:

    The Solvation Force of a simple fluid confined between identical planar walls is studied in two model systems with short ranged fluid–fluid interactions and long-ranged wall–fluid potentials decaying as −Az−p,z→∞, for various values of p. Results for the Ising spins system are obtained in two dimensions at vanishing bulk magnetic field h=0 by means of the density-matrix renormalization-group method; results for the truncated Lennard-Jones (LJ) fluid are obtained within the nonlocal density functional theory. At low temperatures the Solvation Force fsolv for the Ising film is repulsive and decays for large wall separations L in the same fashion as the boundary field fsolv∼L−p, whereas for temperatures larger than the bulk critical temperature fsolv is attractive and the asymptotic decay is fsolv∼L−(p+1). For the LJ fluid system fsolv is always repulsive away from the critical region and decays for large L with the the same power law as the wall–fluid potential. We discuss the influence of the critical Casi...

  • Solvation Force for long ranged wall fluid potentials
    arXiv: Statistical Mechanics, 2003
    Co-Authors: A Maciolek, A Drzewinski, Pawel Bryk
    Abstract:

    The Solvation Force of a simple fluid confined between identical planar walls is studied in two model systems with short ranged fluid-fluid interactions and long ranged wall-fluid potentials decaying as $-Az^{-p}, z\to \infty$, for various values of $p$. Results for the Ising spins system are obtained in two dimensions at vanishing bulk magnetic field $h=0$ by means of the density-matrix renormalization-group method; results for the truncated Lennard-Jones (LJ) fluid are obtained within the nonlocal density functional theory. At low temperatures the Solvation Force $f_{solv}$ for the Ising film is repulsive and decays for large wall separations $L$ in the same fashion as the boundary field $f_{solv}\sim L^{-p}$, whereas for temperatures larger than the bulk critical temperature $f_{solv}$ is attractive and the asymptotic decay is $f_{solv}\sim L^{-(p+1)}$. For the LJ fluid system $f_{solv}$ is always repulsive away from the critical region and decays for large $L$ with the the same power law as the wall-fluid potential. We discuss the influence of the critical Casimir effect and of capillary condensation on the behaviour of the Solvation Force.

  • influence of capillary condensation on the near critical Solvation Force
    Physical Review Letters, 2000
    Co-Authors: A Drzewinski, A Maciolek, Robert Evans
    Abstract:

    We argue that in a fluid, or magnet, confined by adsorbing walls which favor liquid, or the (+) phase, the Solvation (Casimir) Force in the vicinity of the critical point is strongly influenced by capillary condensation which occurs below the bulk critical temperature T(c). At T slightly below and above T(c), a small bulk field h<0, which favors gas, or the (-) phase, leads to residual condensation and a Solvation Force which is much more attractive (at the same large wall separation) than that found exactly at the critical point. Our predictions are supported by results obtained from density-matrix renormalization-group calculations in a two-dimensional Ising strip subject to identical surface fields.

A Drzewinski - One of the best experts on this subject based on the ideXlab platform.

  • Solvation Force for long ranged wall fluid potentials
    Journal of Chemical Physics, 2004
    Co-Authors: A Maciolek, A Drzewinski, Pawel Bryk
    Abstract:

    The Solvation Force of a simple fluid confined between identical planar walls is studied in two model systems with short ranged fluid–fluid interactions and long-ranged wall–fluid potentials decaying as −Az−p,z→∞, for various values of p. Results for the Ising spins system are obtained in two dimensions at vanishing bulk magnetic field h=0 by means of the density-matrix renormalization-group method; results for the truncated Lennard-Jones (LJ) fluid are obtained within the nonlocal density functional theory. At low temperatures the Solvation Force fsolv for the Ising film is repulsive and decays for large wall separations L in the same fashion as the boundary field fsolv∼L−p, whereas for temperatures larger than the bulk critical temperature fsolv is attractive and the asymptotic decay is fsolv∼L−(p+1). For the LJ fluid system fsolv is always repulsive away from the critical region and decays for large L with the the same power law as the wall–fluid potential. We discuss the influence of the critical Casi...

  • Solvation Force for long ranged wall fluid potentials
    arXiv: Statistical Mechanics, 2003
    Co-Authors: A Maciolek, A Drzewinski, Pawel Bryk
    Abstract:

    The Solvation Force of a simple fluid confined between identical planar walls is studied in two model systems with short ranged fluid-fluid interactions and long ranged wall-fluid potentials decaying as $-Az^{-p}, z\to \infty$, for various values of $p$. Results for the Ising spins system are obtained in two dimensions at vanishing bulk magnetic field $h=0$ by means of the density-matrix renormalization-group method; results for the truncated Lennard-Jones (LJ) fluid are obtained within the nonlocal density functional theory. At low temperatures the Solvation Force $f_{solv}$ for the Ising film is repulsive and decays for large wall separations $L$ in the same fashion as the boundary field $f_{solv}\sim L^{-p}$, whereas for temperatures larger than the bulk critical temperature $f_{solv}$ is attractive and the asymptotic decay is $f_{solv}\sim L^{-(p+1)}$. For the LJ fluid system $f_{solv}$ is always repulsive away from the critical region and decays for large $L$ with the the same power law as the wall-fluid potential. We discuss the influence of the critical Casimir effect and of capillary condensation on the behaviour of the Solvation Force.

  • influence of capillary condensation on the near critical Solvation Force
    Physical Review Letters, 2000
    Co-Authors: A Drzewinski, A Maciolek, Robert Evans
    Abstract:

    We argue that in a fluid, or magnet, confined by adsorbing walls which favor liquid, or the (+) phase, the Solvation (Casimir) Force in the vicinity of the critical point is strongly influenced by capillary condensation which occurs below the bulk critical temperature T(c). At T slightly below and above T(c), a small bulk field h<0, which favors gas, or the (-) phase, leads to residual condensation and a Solvation Force which is much more attractive (at the same large wall separation) than that found exactly at the critical point. Our predictions are supported by results obtained from density-matrix renormalization-group calculations in a two-dimensional Ising strip subject to identical surface fields.