The Experts below are selected from a list of 6798 Experts worldwide ranked by ideXlab platform

Abraham Loeb - One of the best experts on this subject based on the ideXlab platform.

  • thinking outside the Simulation Box
    Nature Physics, 2013
    Co-Authors: Abraham Loeb
    Abstract:

    Any ambitious construction project requires architects and engineers. As research shifts towards large groups that focus on the engineering aspects of linking data to existing models, architectural skills are becoming rare among young theorists.

  • on the importance of conceptual thinking outside the Simulation Box
    arXiv: History and Philosophy of Physics, 2013
    Co-Authors: Abraham Loeb
    Abstract:

    Any ambitious construction project requires architects for its design and engineers who apply the design to the real world. As scientific research shifts towards large groups which focus on the engineering aspects of linking data to existing models, architectural skills are becoming rare among young theorists. Senior researchers should mentor qualified students and postdocs to think creatively about the big picture without unwarranted loyalty to ancient blueprints from past generations of architects.

Akio Kitao - One of the best experts on this subject based on the ideXlab platform.

  • effects of water model and Simulation Box size on protein diffusional motions
    Journal of Physical Chemistry B, 2007
    Co-Authors: Kazuhiro Takemura, Akio Kitao
    Abstract:

    We performed molecular dynamics Simulations of ubiquitin with the distinct water models, TIP3P, SPC, SPC/E, and SPC/Fw, in different system sizes with different Box shapes. The translational diffusion constants of pure water linearly depend on the effective Box length, which is known as finite size effect, whereas the first and second rotational times of pure water are nearly constant. We then observed that both the overall translation and rotational motions of the protein are linearly correlated to the viscosity of pure water. As expected from the finite size effect in pure water, the translational diffusion of the protein is significantly affected by the system size, and rotational diffusion is nearly size-independent. After correction for the finite size effect, the SPC/E and SPC/Fw models reproduce both the translational and rotational motion of the protein relatively well. Thus, water models that reproduce the experimentally derived diffusional properties of pure water accurately are expected to also...

Silvia Imberti - One of the best experts on this subject based on the ideXlab platform.

  • microscopic structure of water in a water oil emulsion
    Journal of Chemical Physics, 2013
    Co-Authors: R Mancinelli, Fabio Bruni, Maria Antonietta Ricci, Silvia Imberti
    Abstract:

    We have determined the microscopic structure of water within a water/oil emulsion, by combining neutron diffraction data, exploiting the isotopic H/D substitution, and a fully atomistic Monte Carlo Simulation of a portion of a water droplet, containing the water/oil interface. The dependence of the data on the Simulation Box size and the reliability of the water-water radial distribution functions are discussed. Although water in the emulsion forms shorter and stronger hydrogen bonds compared to pure bulk water, its overall microscopic structure looks more disordered.

R. Jullien - One of the best experts on this subject based on the ideXlab platform.

  • Molecular-dynamics calculation of the thermal conductivity of vitreous silica
    Physical Review B - Condensed Matter and Materials Physics, 1999
    Co-Authors: Philippe Jund, R. Jullien
    Abstract:

    We use extensive classical molecular dynamics Simulations to calculate the thermal conductivity of a model silica glass. Apart from the potential parameters, this is done with no other adjustable quantity and the standard equations of heat transport are used directly in the Simulation Box. The calculations have been done between 10 and 1000 Kelvin and the results are in good agreement with the experimental data at temperatures above 20K. The plateau observed around 10K can be accounted for by correcting our results taking into account finite size effects in a phenomenological way.

Jean-marc Simon - One of the best experts on this subject based on the ideXlab platform.

  • Finite-size effects of Kirkwood–Buff integrals from molecular Simulations
    Molecular Simulation, 2017
    Co-Authors: Noura Dawass, Pieter Kruger, Sondre K. Schnell, Dick Bedeaux, Signe Kjelstrup, Jean-marc Simon, Thijs J. H. Vlugt
    Abstract:

    The modelling of thermodynamic properties of liquids from local density fluctuations is relevant to many chemical and biological processes. The Kirkwood–Buff (KB) theory connects the microscopic structure of isotropic liquids with macroscopic properties such as partial derivatives of activity coefficients, partial molar volumes and compressibilities. Originally, KB integrals were formulated for open and infinite systems which are difficult to access with standard Molecular Dynamics (MD) Simulations. Recently, KB integrals for finite and open systems were formulated (J Phys Chem Lett. 2013;4:235). From the scaling of KB integrals for finite subvolumes, embedded in larger reservoirs, with the inverse of the size of these subvolumes, estimates for KB integrals in the thermodynamic limit are obtained. Two system size effects are observed in MD Simulations: (1) effects due to the size of the Simulation Box and the size of the finite subvolume embedded in the Simulation Box, and (2) effects due to computing radial distribution functions (RDF) from a closed and finite system. In this study, we investigate the two effects in detail by computing KB integrals using the following methods: (1) Monte Carlo Simulations of finite subvolumes of a liquid with an analytic RDF and (2) MD Simulations of a WCA mixture for various Simulation Box sizes, but at the same thermodynamic state. We investigate the effect of the size of the Simulation Box and quantify the differences compared to KB integrals computed in the thermodynamic limit. We demonstrate that calculations of KB integrals should not be extended beyond half the size of the Simulation Box. For finite-size effects related to the RDF, we find that the Van der Vegt correction (J Chem Theory Comput. 2013;9:1347) yields the most accurate results.

  • partial molar enthalpies and reaction enthalpies from equilibrium molecular dynamics Simulation
    Journal of Chemical Physics, 2014
    Co-Authors: Sondre K. Schnell, Signe Kjelstrup, Thijs J. H. Vlugt, Ragnhild Skorpa, D Bedeaux, Jean-marc Simon
    Abstract:

    We present a new molecular Simulation technique for determining partial molar enthalpies in mixtures of gases and liquids from single Simulations, without relying on particle insertions, deletions, or identity changes. The method can also be applied to systems with chemical reactions. We demonstrate our method for binary mixtures of Weeks-Chandler-Anderson particles by comparing with conventional Simulation techniques, as well as for a simple model that mimics a chemical reaction. The method considers small subsystems inside a large reservoir (i.e., the Simulation Box), and uses the construction of Hill to compute properties in the thermodynamic limit from small-scale fluctuations. Results obtained with the new method are in excellent agreement with those from previous methods. Especially for modeling chemical reactions, our method can be a valuable tool for determining reaction enthalpies directly from a single MD Simulation.