An Efficient Multi-Scale Modelling Approach for ssDNA Motion in Fluid Flow

作     者：M. Benke E. Shapiro D. Drikakis 

作者机构：Fluid Mechanics and Computational Science Group Department of Aerospace Sciences Cranfield University 

出 版 物：《Journal of Bionic Engineering》 (仿生工程学报（英文版）)

年 卷 期：2008年第5卷第4期

页      面：299-307页

核心收录：

学科分类：080704[工学-流体机械及工程] 08[工学] 0807[工学-动力工程及工程热物理] 

基　　金：supported in part by the European Commission under the 6th Framework Program (Project: DINAMICS  NMP4-CT-2007-026804) 

主　　题：multi-scale modelling DNA macromolecule transport meta-modelling particle corrector 

摘      要：The paper presents a multi-scale modelling approach for simulating macromolecules in fluid flows. Macromolecule transport at low number densities is frequently encountered in biomedical devices, such as separators, detection and analysis systems. Accurate modelling of this process is challenging due to the wide range of physical scales involved. The continuum approach is not valid for low solute concentrations, but the large timescales of the fluid flow make purely molecular simulations prohibitively expensive. A promising multi-scale modelling strategy is provided by the meta-modelling approach considered in this paper. Meta-models are based on the coupled solution of fluid flow equations and equations of motion for a simplified mechanical model of macromolecules. The approach enables simulation of individual macromolecules at macroscopic time scales. Meta-models often rely on particle-corrector algorithms, which impose length constraints on the mechanical model. Lack of robustness of the particle-corrector algorithm employed can lead to slow convergence and numerical instability. A new FAst Linear COrrector （FALCO） algorithm is introduced in this paper, which significantly improves computational efficiency in comparison with the widely used SHAKE algorithm. Validation of the new particle corrector against a simple analytic solution is performed and improved convergence is demonstrated for ssDNA motion in a lid-driven micro-cavity.