Parameter-free prediction of DNA dynamics in planar extensional flow of semidilute solutions

被引:29
作者
Sasmal, Chandi [1 ]
Hsiao, Kai-Wen [2 ]
Schroeder, Charles M. [2 ]
Prakash, J. Ravi [1 ]
机构
[1] Monash Univ, Dept Chem Engn, Melbourne, Vic 3800, Australia
[2] Univ Illinois, Dept Chem & Biomol Engn, Urbana, IL 61801 USA
基金
澳大利亚研究理事会; 美国国家科学基金会;
关键词
EXCLUDED-VOLUME INTERACTIONS; DILUTE POLYMER-SOLUTIONS; BROWNIAN DYNAMICS; MONTE-CARLO; HYDRODYNAMIC PROPERTIES; VISCOMETRIC FUNCTIONS; FLEXIBLE POLYMERS; ROUSE CHAINS; CONCENTRATION-DEPENDENCE; ELONGATIONAL FLOW;
D O I
10.1122/1.4972237
中图分类号
O3 [力学];
学科分类号
08 ; 0801 ;
摘要
The dynamics of individual Deoxyribonucleic acid (DNA) molecules in semidilute solutions undergoing planar extensional flow is simulated using a multiparticle Brownian dynamics algorithm, which incorporates hydrodynamic and excluded volume interactions in the context of a coarse-grained bead-spring chain model for DNA. The successive fine-graining protocol [P. Sunthar and J. R. Prakash, Macromolecules 38, 617-640 (2005); R. Prabhakar et al., J. Rheol. 48, 1251-1278 (2004)], in which simulation data acquired for bead-spring chains with increasing values of the number of beads Nb, is extrapolated to the number of Kuhn steps NK in DNA (while keeping key physical parameters invariant), is used to obtain parameter-free predictions for a range of Weissenberg numbers and Hencky strain units. A systematic comparison of simulation predictions is carried out with the experimental observations of Hsiao et al. [J. Rheol. (in press)], who have recently used single molecule techniques to investigate the dynamics of dilute and semidilute solutions of lambda-phage DNA in planar extensional flow. In particular, they examine the response of individual chains to step-strain deformation followed by cessation of flow, thereby capturing both chain stretch and relaxation in a single experiment. The successive fine-graining technique is shown to lead to quantitatively accurate predictions of the experimental observations in the stretching and relaxation phases. Additionally, the transient chain stretch following a step strain deformation is shown to be much smaller in semidilute solutions than in dilute solutions, in agreement with experimental observations. (C) 2016 The Society of Rheology.
引用
收藏
页码:169 / 186
页数:18
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