Bridging fluctuating hydrodynamics and molecular dynamics simulations of fluids.
Bridging fluctuating hydrodynamics and molecular dynamics simulations of fluids.
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桥接流体的波动流体动力学和分子动力学模拟。
DOI：
10.1063/1.3106717
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发表时间：
2009
期刊：
影响因子：
--
通讯作者：
J. Chu
中科院分区：
文献类型：
--
作者：
N. Voulgarakis;J. Chu
一种新的多尺度粗粒化（CG）方法的发展，以桥梁分子和流体动力学模型的流体。在这项工作中考虑的流体动力学表示是基于波动流体动力学（FH）方程。该方法的本质是从分子动力学（MD）模拟的快照的位置和速度矢量映射到流体动力学表示的欧拉细胞上的场变量。通过明确考虑的有效长度尺度d（摩尔），表征分子的体积，计算的密度波动从MD通过我们的映射程序具有体积依赖性，对应于一个冷液体的巨正则系综，即使当一个小的细胞长度（5-10 A）被用于流体动力学表示。对于TIP 3 P水在300 K和1大气压，d（mol）被发现是2.4 A，对应于排除的半径的水分子所揭示的其中心的质量径向分布函数。通过匹配密度波动和自相关函数的动量场计算从FH方程与MD模拟计算，声速和剪切和体积粘度的CG流体动力学模型可以直接从MD确定。在此基础上，提出了一种新的交错离散格式，利用中心差分法求解三维空间中等温压缩流体的FH方程。该格式在满足涨落耗散定理方面具有很高的精度。由于场变量和通量之间的因果关系被捕获，我们证明了交错离散方案也预测正确的物理行为，在模拟瞬态流体流动。在这项工作中提出的技术也可以用来设计多尺度的策略，模拟复杂的流体和大分子溶液。
A new multiscale coarse-graining (CG) methodology is developed to bridge molecular and hydrodynamic models of a fluid. The hydrodynamic representation considered in this work is based on the equations of fluctuating hydrodynamics (FH). The essence of this method is a mapping from the position and velocity vectors of a snapshot of a molecular dynamics (MD) simulation to the field variables on Eulerian cells of a hydrodynamic representation. By explicit consideration of the effective lengthscale d(mol) that characterizes the volume of a molecule, the computed density fluctuations from MD via our mapping procedure have volume dependence that corresponds to a grand canonical ensemble of a cold liquid even when a small cell length (5-10 A) is used in a hydrodynamic representation. For TIP3P water at 300 K and 1 atm, d(mol) is found to be 2.4 A, corresponding to the excluded radius of a water molecule as revealed by its center-of-mass radial distribution function. By matching the density fluctuations and autocorrelation functions of momentum fields computed from solving the FH equations with those computed from MD simulation, the sound velocity and shear and bulk viscosities of a CG hydrodynamic model can be determined directly from MD. Furthermore, a novel staggered discretization scheme is developed for solving the FH equations of an isothermal compressive fluid in a three dimensional space with a central difference method. This scheme demonstrates high accuracy in satisfying the fluctuation-dissipation theorem. Since the causative relationship between field variables and fluxes is captured, we demonstrate that the staggered discretization scheme also predicts correct physical behaviors in simulating transient fluid flows. The techniques presented in this work may also be employed to design multiscale strategies for modeling complex fluids and macromolecules in solution.
DOI：
10.1209/0295-5075/19/3/001
发表时间：
1992-06-01
期刊：
EUROPHYSICS LETTERS
影响因子：
--
作者：
HOOGERBRUGGE, PJ;KOELMAN, JMVA
通讯作者：
KOELMAN, JMVA