TY - JOUR
T1 - An Efficient Multi-Scale Modelling Approach for ssDNA Motion in Fluid Flow
AU - Benke, M.
AU - Shapiro, E.
AU - Drikakis, D.
N1 - Funding Information:
This work is supported in part by the European Commission under the 6th Framework Program (Project: DINAMICS, NMP4-CT-2007-026804).
Copyright:
Copyright 2009 Elsevier B.V., All rights reserved.
PY - 2008/12
Y1 - 2008/12
N2 - 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.
AB - 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.
KW - DNA
KW - macromolecule transport
KW - meta-modelling
KW - multi-scale modelling
KW - particle corrector
UR - http://www.scopus.com/inward/record.url?scp=58049188825&partnerID=8YFLogxK
U2 - 10.1016/S1672-6529(08)60174-2
DO - 10.1016/S1672-6529(08)60174-2
M3 - Article
AN - SCOPUS:58049188825
SN - 1672-6529
VL - 5
SP - 299
EP - 307
JO - Journal of Bionic Engineering
JF - Journal of Bionic Engineering
IS - 4
ER -