Trebotich D, Miller G H, Bybee M D
Center for Applied Scientific Computing, Lawrence Livermore National Laboratory, P.O. Box 808, L-560, Livermore, CA 94551, USA.
J Nanosci Nanotechnol. 2008 Jul;8(7):3749-56.
We present a hybrid fluid-particle algorithm to simulate flow and transport of DNA-laden fluids in microdevices. Relevant length scales in microfluidic systems range from characteristic channel sizes of millimeters to micron scale geometric variation (e.g., post arrays) to 10 nanometers for the length of a single rod in a bead-rod polymer representation of a biological material such as DNA. The method is based on a previous fluid-particle algorithm in which long molecules are represented as a chain of connected rods, but in which the physically unrealistic behavior of rod crossing occurred. We have extended this algorithm to include screened Coulombic forces between particles by implementing a Debye-Hückel potential acting between rods. In the method an unsteady incompressible Newtonian fluid is discretized with a second-order finite difference method in the interior of the Cartesian grid domain; an embedded boundary volume-of-fluid formulation is used near boundaries. The bead-rod polymer model is fully coupled to the solvent through body forces representing hydrodynamic drag and stochastic thermal fluctuations. While intra-polymer interactions are modeled by a soft potential, polymer-structure interactions are treated as perfectly elastic collisions. We demonstrate this method on flow and transport of a polymer through a post array microchannel in 2D where the polymer incorporates more realistic physical parameters of DNA, and compare to previous simulations where rods are allowed to cross. We also show that the method is capable of simulating 3D flow in a packed bed micro-column.
我们提出了一种混合流体-粒子算法，用于模拟微器件中载有DNA的流体的流动和输运。微流体系统中的相关长度尺度范围很广，从毫米级的特征通道尺寸到微米级的几何变化（例如柱阵列），再到生物材料（如DNA）的珠-杆聚合物表示中单个杆的长度的10纳米。该方法基于先前的流体-粒子算法，在该算法中，长分子被表示为相连杆的链，但其中发生了杆交叉这种不符合物理实际的行为。我们通过在杆之间施加德拜-休克尔势来扩展此算法，以纳入粒子间的屏蔽库仑力。在该方法中，笛卡尔网格域内部的非稳态不可压缩牛顿流体用二阶有限差分法离散；边界附近使用嵌入式边界流体体积公式。珠-杆聚合物模型通过表示流体动力阻力和随机热涨落的体力与溶剂完全耦合。虽然聚合物内相互作用由软势建模，但聚合物-结构相互作用被视为完全弹性碰撞。我们在二维的柱阵列微通道中对聚合物的流动和输运演示了此方法，其中聚合物纳入了更符合实际的DNA物理参数，并与先前允许杆交叉的模拟进行了比较。我们还表明该方法能够模拟填充床微柱中的三维流动。
