全伸展DNA链折叠过程中三种非线性作用的布朗动力学模拟

引用本文: 张勇, 肖忠党. 全伸展DNA链折叠过程中三种非线性作用的布朗动力学模拟[J]. 物理化学学报, 2011, 27(11): 2705-2710. doi: 10.3866/PKU.WHXB20111111 shu

Citation: ZHANG Yong, XIAO Zhong-Dang. Brownian Dynamics Simulation of Three Nonlinear Interactions on the Folding Process of Single Completely Stretched DNA Chain[J]. Acta Physico-Chimica Sinica, 2011, 27(11): 2705-2710. doi: 10.3866/PKU.WHXB20111111 shu

全伸展DNA链折叠过程中三种非线性作用的布朗动力学模拟

张勇 ^1,2, ,
肖忠党 ^1,

基金项目:
国家自然科学基金(20875014, 30901285)资助项目 (20875014, 30901285)

摘要: 脱氧核糖核酸(DNA)单分子链从完全拉伸状态折叠到平衡状态的动力学过程是溶液中DNA单分子力学的重要特征之一. 通过构建全参数化的珠子-弹簧分子链模型, 并运用一种高效平衡的半隐式预测——校验积分算法, 系统研究了体积排斥作用、有限伸长弹性作用和涨落流体动力学作用等三种非线性作用对稀溶液中DNA分子链折叠过程相对回旋半径和驰豫时间的影响程度和变化趋势. 模拟结果发现: 体积排斥作用不影响分子链的折叠驰豫时间, 但能显著减小平衡时的相对回旋半径; 流体动力学作用不影响分子链的相对回旋半径, 但明显缩短折叠过程的驰豫时间; 有限伸长弹性作用能明显减小短链的相对回旋半径, 能显著延长长链的折叠驰豫时间. 模拟数据进一步表明: 完全伸展的DNA分子链在折叠过程中的相对回旋半径随时间平滑变化,且折叠驰豫时间随长度的标度指数对上述三种非线性作用都具有两种不同的长度依赖性.

关键词:

English

Brownian Dynamics Simulation of Three Nonlinear Interactions on the Folding Process of Single Completely Stretched DNA Chain

ZHANG Yong ^1,2, ,
XIAO Zhong-Dang ^1,

1.
1. State Key Laboratory of Bioelectronics, School of Biological Science & Medical Engineering, Southeast University, Nanjing 211189, P. R. China;
2. Department of Physics, Southeast University, Nanjing 211189, P. R. China
Received Date: 23 May 2011
Available Online: 27 October 2011
Fund Project:
国家自然科学基金(20875014, 30901285)资助项目

Abstract: The folding dynamics of a completely stretched dexoxyribonucleic acid (DNA) molecule chain is an important feature of single DNA mechanics. By constructing a fully parameterized bead-spring chain model and applying a highly efficient second order semi-implicit predictor-corrector al rithm, we studied the influence of three nonlinear interactions including the excluded volume interaction, the finite extensible nonlinear elastic interaction, and the fluctuating hydrodynamic interaction on the folding process. Simulation results show that the excluded volume interaction decreases the relative radius of gyration of the DNA chain obviously but has no influence on the relaxation time. Instead, the hydrodynamic interaction clearly decreases the relaxation time but it does not change the relative radius of gyration. In addition, the finite extensible elastic interaction was found to decrease the relative radius of gyration of the short chain clearly and increase the relaxation time of the long chain obviously. Furthermore, we obtained a smooth change for the relative radius of gyration with time. The scaling exponent of the relaxation time with the length of chain has two different values under all three nonlinear interactions. These results complete our understanding about single DNA molecule chain mechanics in solution.

Key words:

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全伸展DNA链折叠过程中三种非线性作用的布朗动力学模拟

English

Brownian Dynamics Simulation of Three Nonlinear Interactions on the Folding Process of Single Completely Stretched DNA Chain

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通讯作者: 陈斌, bchen63@163.com

中国化学会秘书处

全伸展DNA链折叠过程中三种非线性作用的布朗动力学模拟

English

Brownian Dynamics Simulation of Three Nonlinear Interactions on the Folding Process of Single Completely Stretched DNA Chain

CCS Chemistry：嵌段共聚物自组装成 “三明治”二维有机材料，实现纳米级压力传感功能

CCS Chemistry：颜徐州、鲍哲南： 你的皮肤可能是一片SPMs

CCS Chemistry：工作高效不疲劳，只须让催化剂动起来

CCS Chemistry：静电组装导向聚合- 聚电解质纳米凝胶量化制备新策略

CCS Chemistry：金黄色葡萄球菌醛基脱氢酶是如何识别特异性底物的？

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