稀溶液中线形DNA分子链结构及扩散的布朗动力学模拟

Brownian dynamics simulation of conformation and diffusion of linear DNA chain in dilute solution

通过构建全参数化的珠-弹簧分子链模型,并运用一种高效稳定的半隐式预测-校验积分算法求解描述稀溶液中DNA分子链结构演化的随机动力学方程组,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对分子链的回旋半径、质心扩散系数以及相应标度指数的影响.模拟结果能够验证良溶剂中分子链Zimm模型的标度规律,并揭示出3种非线性作用对稀溶液中分子链静态结构属性和动力学属性不同的影响程度和变化趋势.分子链柔性对稀溶液中DNA结构、扩散系数以及标度指数影响都很小.溶剂品质的提高可显著增大分子链的回旋半径,减小其扩散系数,并且使两者随链长的标度指数显著增加.流体动力学作用不改变分子链的结构,但显著影响其扩散系数.随着流体作用的增强,分子链的质心扩散系数增大,随链长变化的标度指数减小.

By constructing a full-parameterized bead-spring chain model and applying a highly efficient second-order semi-implicit predictor-corrector algorithm,the influence of three nonlinear interactions including excluded volume interaction,finite extensible nonlinear elastic interaction and fluctuating hydrodynamic interaction on the radius of gyration,diffusion coefficient and their scaling exponents are studied systematically.Simulation results validate the scaling law of Zimm model in good solvent and demonstrate different degrees and directions of these nonlinear effects.Chain flexibility has little influence on conformation and diffusion coefficient.The higher solvent quality clearly increases the radius of gyration and decreases the diffusion coefficient,and makes both quantities increase with the scaling exponents.In addition,the hydrodynamic interaction has little influence on the conformation of DNA chain,but it increases the diffusion coefficient and decreases its scaling exponent greatly.