On mesoscale modelling of dsDNA molecules in fluid flow

M. Benke, E. Shapiro, D. Drikakis

Research output: Contribution to journalArticle

4 Citations (Scopus)

Abstract

The paper presents a new mesoscale modelling approach to investigation of dsDNA molecules motion in fluid flow. The proposed method includes the effects of inertia and is capable of capturing accurately dsDNA relaxation and stretching phenomena. The accuracy of the proposed method is explored through comparisons with published experimental data. For the simulation of disengaged dsDNA molecules, a novel correction to the elastic force formulation is suggested. The proposed adjustment offers a significant improvement in the prediction of dsDNA length for both relaxation in resting buffer and extension using hydrodynamic focusing. Analysis of the individual contributions to the force acting on the dsDNA molecules demonstrates that the dynamics of dsDNA extension observed experimentally is dominated by the hydrodynamic drag force.
LanguageEnglish
Pages697-704
Number of pages8
JournalJournal of Computational and Theoretical Nanoscience
Volume10
Issue number3
DOIs
Publication statusPublished - 1 Mar 2013

Fingerprint

fluid flow
Fluid Flow
Flow of fluids
Molecules
Hydrodynamics
hydrodynamics
Modeling
molecules
Drag Force
inertia
Inertia
Stretching
drag
Drag
Buffer
Adjustment
Buffers
buffers
adjusting
Experimental Data

Keywords

  • DNA mechanics
  • dynamic behavior of DNA
  • mesoscale modeling of DNA

Cite this

Benke, M. ; Shapiro, E. ; Drikakis, D. / On mesoscale modelling of dsDNA molecules in fluid flow. In: Journal of Computational and Theoretical Nanoscience. 2013 ; Vol. 10, No. 3. pp. 697-704.
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On mesoscale modelling of dsDNA molecules in fluid flow. / Benke, M.; Shapiro, E.; Drikakis, D.

In: Journal of Computational and Theoretical Nanoscience, Vol. 10, No. 3, 01.03.2013, p. 697-704.

Research output: Contribution to journalArticle

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