Effect of internal viscosity on Brownian dynamics of DNA molecules in shear flow

DOI10.1016/J.COMPBIOLCHEM.2007.02.010zbMATH Open1124.92004arXivq-bio/0703003OpenAlexW2029970659WikidataQ51036517 ScholiaQ51036517MaRDI QIDQ2373299FDOQ2373299

Authors: Xiao-Dong Yang, R. V. N. Melnik 

Publication date: 17 July 2007

Published in: Computational Biology and Chemistry (Search for Journal in Brave)

Abstract: The results of Brownian dynamics simulations of a single DNA molecule in shear flow are presented taking into account the effect of internal viscosity. The dissipative mechanism of internal viscosity is proved necessary in the research of DNA dynamics. A stochastic model is derived on the basis of the balance equation for forces acting on the chain. The Euler method is applied to the solution of the model. The extensions of DNA molecules for different Weissenberg numbers are analyzed. Comparison with the experimental results available in the literature is carried out to estimate the contribution of the effect of internal viscosity.

Full work available at URL: https://arxiv.org/abs/q-bio/0703003

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zbMATH Keywords

Brownian dynamicsDumbbell modelDNA molecules in shear flowEffect of internal viscosity

Mathematics Subject Classification ID

Biochemistry, molecular biology (92C40) Brownian motion (60J65) Biophysics (92C05)

Cites Work

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Cited In (4)

• Do internal viscosity models satisfy the fluctuation-dissipation theorem?
• DNA-RNA transcription as an impact of viscosity
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• First passage time for multivariate jump-diffusion processes in finance and other areas of applications

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