Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison, Wisconsin 53706-1691, USA.
J Chem Phys. 2012 Jan 7;136(1):014901. doi: 10.1063/1.3672103.
This work presents an immersed boundary method that allows fast Brownian dynamics simulation of solutions of polymer chains and other Brownian objects in complex geometries with fluctuating hydrodynamics. The approach is based on the general geometry Ewald-like method, which solves the Stokes equation with distributed regularized point forces in O(N) or O(NlogN) operations, where N is the number of point forces in the system. Time-integration is performed using a midpoint algorithm and Chebyshev polynomial approximation proposed by Fixman. This approach is applied to the dynamics of a genomic DNA molecule driven by flow through a nanofluidic slit with an array of nanopits on one wall of the slit. The dynamics of the DNA molecule was studied as a function of the Péclet number and chain length (the base case being λ-DNA). The transport characteristics of the hopping dynamics in this device differ at low and high Péclet number, and for long DNA, relative to the pit size, the dynamics is governed by the segments residing in the pit. By comparing with results that neglect them, hydrodynamic interactions are shown to play an important quantitative role in the hopping dynamics.
本文提出了一种浸入边界方法，允许在具有流动流体力学的复杂几何形状中快速模拟聚合物链和其他布朗运动物体的布朗动力学解。该方法基于广义几何型 Ewald 方法，该方法通过在 O(N)或 O(NlogN)操作中使用分布式正则化点力来求解 Stokes 方程，其中 N 是系统中点力的数量。时间积分使用 Fixman 提出的中点算法和切比雪夫多项式逼近法进行。该方法应用于通过纳米通道中带有纳米凹坑阵列的壁面的流动驱动的基因组 DNA 分子的动力学。研究了 DNA 分子的动力学作为 Peclet 数和链长（基本情况是 λ-DNA）的函数。在低 Peclet 数和高 Peclet 数以及长 DNA 情况下，相对于凹坑尺寸，跳跃动力学的输运特性不同，动力学由位于凹坑中的片段控制。通过与忽略它们的结果进行比较，表明流体动力相互作用在跳跃动力学中起着重要的定量作用。
