FALCO - fast linear corrector for modelling DNA-laden flows

M. Benke, E. Shapiro, D. Drikakis

Research output: Chapter in Book/Report/Conference proceedingConference contribution book

Abstract

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.
LanguageEnglish
Title of host publicationASME 2008 6th International Conference on Nanochannels, Microchannels, and Minichannels
Pages1587-1595
Number of pages9
DOIs
Publication statusPublished - 25 Jun 2008
EventASME 2008 6th International Conference on Nanochannels, Microchannels, and Minichannels - Darmstadt, Germany
Duration: 23 Jun 200825 Jun 2008

Conference

ConferenceASME 2008 6th International Conference on Nanochannels, Microchannels, and Minichannels
CountryGermany
CityDarmstadt
Period23/06/0825/06/08

Fingerprint

Corrector
Modeling
Biomolecules
Metamodel
Lagrangian multiplier
Microcavity
Molecular Simulation
Microchannel
Computational Fluid Dynamics
Analytic Solution
Dynamic Simulation
Numerical Algorithms
Computational Efficiency
Fluid Flow
Equations of Motion
Time Scales
Continuum
Model
Model-based
Motion

Keywords

  • flow (dynamics)
  • DNA
  • modeling

Cite this

Benke, M., Shapiro, E., & Drikakis, D. (2008). FALCO - fast linear corrector for modelling DNA-laden flows. In ASME 2008 6th International Conference on Nanochannels, Microchannels, and Minichannels (pp. 1587-1595). [ICNMM2008-62131] https://doi.org/10.1115/ICNMM2008-62131
Benke, M. ; Shapiro, E. ; Drikakis, D. / FALCO - fast linear corrector for modelling DNA-laden flows. ASME 2008 6th International Conference on Nanochannels, Microchannels, and Minichannels. 2008. pp. 1587-1595
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Benke, M, Shapiro, E & Drikakis, D 2008, FALCO - fast linear corrector for modelling DNA-laden flows. in ASME 2008 6th International Conference on Nanochannels, Microchannels, and Minichannels., ICNMM2008-62131, pp. 1587-1595, ASME 2008 6th International Conference on Nanochannels, Microchannels, and Minichannels, Darmstadt, Germany, 23/06/08. https://doi.org/10.1115/ICNMM2008-62131

FALCO - fast linear corrector for modelling DNA-laden flows. / Benke, M.; Shapiro, E.; Drikakis, D.

ASME 2008 6th International Conference on Nanochannels, Microchannels, and Minichannels. 2008. p. 1587-1595 ICNMM2008-62131.

Research output: Chapter in Book/Report/Conference proceedingConference contribution book

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Benke M, Shapiro E, Drikakis D. FALCO - fast linear corrector for modelling DNA-laden flows. In ASME 2008 6th International Conference on Nanochannels, Microchannels, and Minichannels. 2008. p. 1587-1595. ICNMM2008-62131 https://doi.org/10.1115/ICNMM2008-62131