Stochastic simulations of DNA in flow: Dynamics and the effects of hydrodynamic interactions
Stochastic simulations of DNA in flow: Dynamics and the effects of hydrodynamic interactions
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DOI：
10.1063/1.1466831
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发表时间：
2002-05-01
影响因子：
4.4
通讯作者：
Graham, MD
中科院分区：
文献类型：
--
作者：
Jendrejack, RM;de Pablo, JJ;Graham, MD
我们提出了一个用于染色 lambda 噬菌体 DNA 的完全参数化的珠弹簧链模型。该模型考虑了分子的有限延展性、排除的体积效应和波动的流体动力相互作用 (HI)。参数是根据 21 mum 染色的 lambda 噬菌体 DNA 的平衡实验数据确定的，并且可以定量预测分子的非平衡行为。然后该模型可用于预测高达 126 mm 的 DNA 分子的平衡和非平衡行为。特别是，HI 模型给出的结果与较宽分子量范围内的实验扩散率数据定量一致。当珠粒摩擦系数适合特定分子量下的实验松弛时间时，剪切流和拉伸流中的拉伸可以通过该分子量下的自由排水模型或 HI 模型充分预测，尽管这两个模型的拟合珠粒摩擦系数有显着差异。在剪切流中，我们发现高剪切速率 (gamma) 下的两种状态遵循不同的缩放行为。在第一个例子中，粘度和第一法向应力系数分别大致分别为 gamma(-6/11) 和 gamma(-14/11)。在较高的剪切速率下，它们变成伽玛（-2/3）和伽玛（-4/3）。这些机制适用于自由排水模型和 HI 模型，并且可以根据链端扩散的缩放参数来理解。 (C) 2002 年美国物理研究所。
We present a fully parametrized bead-spring chain model for stained lambda-phage DNA. The model accounts for the finite extensibility of the molecule, excluded volume effects, and fluctuating hydrodynamic interactions (HI). Parameters are determined from equilibrium experimental data for 21 mum stained lambda-phage DNA, and are shown to quantitatively predict the non-equilibrium behavior of the molecule. The model is then used to predict the equilibrium and nonequilibrium behavior of DNA molecules up to 126 mum. In particular, the HI model gives results that are in quantitative agreement with experimental diffusivity data over a wide range of molecular weights. When the bead friction coefficient is fit to the experimental relaxation time at a particular molecular weight, the stretch in shear and extensional flows is adequately predicted by either a free-draining or HI model at that molecular weight, although the fitted bead friction coefficients for the two models differ significantly. In shear flow, we find two regimes at high shear rate (gamma) that follow different scaling behavior. In the first, the viscosity and first normal stress coefficient scale roughly as gamma(-6/11) and gamma(-14/11), respectively. At higher shear rates, these become gamma(-2/3) and gamma(-4/3). These regimes are found for both free-draining and HI models and can be understood based on scaling arguments for the diffusion of chain ends. (C) 2002 American Institute of Physics.