TY - GEN
T1 - FALCO - Fast linear corrector for modelling DNA-laden flows
AU - Benke, M.
AU - Shapiro, E.
AU - Drikakis, D.
N1 - Copyright:
Copyright 2013 Elsevier B.V., All rights reserved.
PY - 2008
Y1 - 2008
N2 - The paper concerns the development of a numerical algorithm for improving the efficiency of computational fluid dynamics simulations of transport of biomolecules in microchannels at low number densities. For this problem, the continuum approach based on the concentration field model becomes invalid, whereas time scales involved make purely molecular simulations prohibitively computationally expensive. In this context, meta-models based on coupled solution of fluid flow equations and equations of motion for a simplified mechanical model of biomolecules provide a viable alternative. Meta-models often rely on particle-corrector algorithms, which impose length constraints on the mechanical DNA model. Particle-corrector algorithms are not sufficiently robust, thus resulting in slow convergence. A new geometrical particle corrector algorithm - called FALCO - is proposed in this paper, which significantly improves computational efficiency in comparison with the widely used SHAKE algorithm. It is shown that the new corrector can be related to the SHAKE algorithm by an appropriate choice of Lagrangian multipliers. Validation of the new particle corrector against a simple analytic solution is performed and the improved convergence is demonstrated for a macromolecule motion in a micro-cavity. This work has been supported in part by the European Commission under the 6th Framework Program (Project: DINAMICS, NMP4-CT-2007-026804).
AB - The paper concerns the development of a numerical algorithm for improving the efficiency of computational fluid dynamics simulations of transport of biomolecules in microchannels at low number densities. For this problem, the continuum approach based on the concentration field model becomes invalid, whereas time scales involved make purely molecular simulations prohibitively computationally expensive. In this context, meta-models based on coupled solution of fluid flow equations and equations of motion for a simplified mechanical model of biomolecules provide a viable alternative. Meta-models often rely on particle-corrector algorithms, which impose length constraints on the mechanical DNA model. Particle-corrector algorithms are not sufficiently robust, thus resulting in slow convergence. A new geometrical particle corrector algorithm - called FALCO - is proposed in this paper, which significantly improves computational efficiency in comparison with the widely used SHAKE algorithm. It is shown that the new corrector can be related to the SHAKE algorithm by an appropriate choice of Lagrangian multipliers. Validation of the new particle corrector against a simple analytic solution is performed and the improved convergence is demonstrated for a macromolecule motion in a micro-cavity. This work has been supported in part by the European Commission under the 6th Framework Program (Project: DINAMICS, NMP4-CT-2007-026804).
UR - http://www.scopus.com/inward/record.url?scp=77952599153&partnerID=8YFLogxK
U2 - 10.1115/ICNMM2008-62131
DO - 10.1115/ICNMM2008-62131
M3 - Conference contribution
AN - SCOPUS:77952599153
SN - 0791848345
SN - 9780791848340
T3 - Proceedings of the 6th International Conference on Nanochannels, Microchannels, and Minichannels, ICNMM2008
SP - 1587
EP - 1595
BT - Proceedings of the 6th International Conference on Nanochannels, Microchannels, and Minichannels, ICNMM2008
T2 - 6th International Conference on Nanochannels, Microchannels, and Minichannels, ICNMM2008
Y2 - 23 June 2008 through 25 June 2008
ER -