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An efficient multi-scale modelling approach for ssDNA motion in fluid flow

By Matyas Benke, Evgeniy Shapiro and Dimitris Drikakis

Abstract

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

Topics: Multi-scale modelling, DNA, Macromolecule transport, Meta-modelling, Particle corrector.
Publisher: Elsevier Science B.V., Amsterdam
Year: 2008
DOI identifier: 10.1016/S1672-6529(08)60174-2
OAI identifier: oai:dspace.lib.cranfield.ac.uk:1826/3078
Provided by: Cranfield CERES
Journal:

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