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首页> 外文学位 >Multiscale simulations of dilute-solution macromolecular dynamics in macroscopic and microscopic geometries.
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Multiscale simulations of dilute-solution macromolecular dynamics in macroscopic and microscopic geometries.

机译：宏观和微观几何形状中稀溶液大分子动力学的多尺度模拟。

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A Brownian model of DNA is developed and shown to give results in quantitative agreement with available equilibrium and non-equilibrium experimental data. A fast, accurate method of calculating the Langevin forces on the molecule is presented, as well as a semi-implicit stochastic integration scheme which allows for the use of reasonable time steps.; A new method is developed for the simulation of polymer dynamics in macroscopic devices. The method involves a splitting of the diffusion equation into internal configuration and convective fluxes. The internal configuration of the microstructure is evolved via stochastic simulation to give a δ-function representation of the distribution function. The convective update of the distribution function is performed in an orthogonal polynomial representation, taking advantage of the natural hierarchy of length scales present in the problem. We find that convective update can performed accurately by considering only the large length scale contributions.; A general method is developed for dynamic simulations of macromolecules in confined geometries. At equilibrium, we examine the stretch, diffusivity and relaxation time of DNA as a function of channel width and molecular weight. The ratio of these properties to their free-solution values form master curves when plotted against Sb/H. Scaling laws are obtained for highly confined chains. In pressure-driven flow, the DNA chains migrate toward the channel centerline in agreement with well-known experimental observations. The thickness of the resulting hydrodynamic depletion layer increases with molecular weight at constant flow strength; higher molecular weight chains therefore move with a higher average axial velocity than lower molecular weight chains. A simple kinetic theory dumbbell model of a confined flexible polymer correctly predicts the trends observed in the detailed simulations. We also examine the steady-state stretch of DNA chains as a function of channel width and flow strength. The flow strength needed to stretch a highly confined chain away from its equilibrium length is shown to increase with decreasing channel width, independent of molecular weight; this is fairly well-explained using a simple blob picture.
机译：DNA的布朗模型得以开发，并显示出与可用的平衡和非平衡实验数据定量一致的结果。提出了一种快速，准确的方法，计算在分子上的兰格文力，以及允许使用合理时间步长的半隐式随机积分方案。开发了一种用于宏观设备中聚合物动力学模拟的新方法。该方法包括将扩散方程分解为内部构造和对流。微观结构的内部结构通过随机模拟得到演化，从而给出了分布函数的δ函数表示。分布函数的对流更新以正交多项式表示形式进行，利用了问题中存在的自然的长度尺度。我们发现对流更新可以仅通过考虑大比例尺的贡献就可以准确地执行。开发了一种用于在受限几何结构中动态模拟高分子的通用方法。在平衡状态下，我们检查DNA的拉伸，扩散率和弛豫时间与通道宽度和分子量的关系。当相对于 S b / H 绘制时，这些特性与其自由溶液值的比率形成主曲线。获得高度受限链的缩放定律。在压力驱动的流动中，DNA链向通道中心线迁移，这与众所周知的实验观察结果一致。在恒定的流动强度下，所得的流体动力耗竭层的厚度随分子量的增加而增加。因此，较高分子量的链比较低分子量的链以更高的平均轴向速度运动。受限柔性聚合物的简单动力学理论哑铃模型可以正确预测在详细模拟中观察到的趋势。我们还检查了DNA链的稳态拉伸随通道宽度和流动强度的变化。已显示出将高度受限的链从平衡长度上拉开所需的流动强度会随着通道宽度的减小而增加，而与分子量无关；使用简单的斑点图片对此进行了很好的解释。

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