### Abstract

Language | English |
---|---|

Title of host publication | ASME 2008 6th International Conference on Nanochannels, Microchannels, and Minichannels |

Pages | 1587-1595 |

Number of pages | 9 |

DOIs | |

Publication status | Published - 25 Jun 2008 |

Event | ASME 2008 6th International Conference on Nanochannels, Microchannels, and Minichannels - Darmstadt, Germany Duration: 23 Jun 2008 → 25 Jun 2008 |

### Conference

Conference | ASME 2008 6th International Conference on Nanochannels, Microchannels, and Minichannels |
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Country | Germany |

City | Darmstadt |

Period | 23/06/08 → 25/06/08 |

### Fingerprint

### Keywords

- flow (dynamics)
- DNA
- modeling

### Cite this

*ASME 2008 6th International Conference on Nanochannels, Microchannels, and Minichannels*(pp. 1587-1595). [ICNMM2008-62131] https://doi.org/10.1115/ICNMM2008-62131

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*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.

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution book

TY - GEN

T1 - FALCO - fast linear corrector for modelling DNA-laden flows

AU - Benke, M.

AU - Shapiro, E.

AU - Drikakis, D.

PY - 2008/6/25

Y1 - 2008/6/25

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.

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.

KW - flow (dynamics)

KW - DNA

KW - modeling

UR - http://www.scopus.com/inward/record.url?eid=2-s2.0-77952599153&partnerID=40&md5=22186d91aecb147100ef5be296dacae0

U2 - 10.1115/ICNMM2008-62131

DO - 10.1115/ICNMM2008-62131

M3 - Conference contribution book

SN - 0-7918-4834-5

SP - 1587

EP - 1595

BT - ASME 2008 6th International Conference on Nanochannels, Microchannels, and Minichannels

ER -