Huang Aiqun, Reisner Walter, Bhattacharya Aniket
University of Central Florida, 4000 Central Florida Blvd, Orlando, FL 32816, USA.
McGill University, 845 Rue Sherbrooke O, Montréal, QC H3A 0G4, Canada.
Polymers (Basel). 2016 Sep 29;8(10):352. doi: 10.3390/polym8100352.
We use Brownian dynamics (BD) simulation of a coarse-grained (CG) bead-spring model of DNA to study the nonequilibrim dynamics of a single DNA molecule confined inside a rectangular nanochannel being squeezed with a sliding gasket piston or "nanodozer". From our simulations we extract the nonequilibrim density profile c ( x , t ) of the squeezed molecule along the channel axis (-coordinate) and then analyze the non-equilibrium profile using a recently introduced phenomenological Nonlinear Partial Differential Equation (NPDE) model. Since the NPDE approach also fits the experimental results well and is numerically efficient to implement, the combined BD + NPDE methods can be a powerful approach to analyze details of the confined molecular dynamics. In particular, the overall excellent agreement between the two complementary sets of data provides a strategy for carrying out large scale simulation on semi-flexible biopolymers in confinement at biologically relevant length scales.
我们使用DNA粗粒化（CG）珠簧模型的布朗动力学（BD）模拟，来研究单个DNA分子在矩形纳米通道内的非平衡动力学，该纳米通道由滑动垫片活塞或“纳米推土机”挤压。通过模拟，我们提取了被挤压分子沿通道轴（x坐标）的非平衡密度分布c(x,t)，然后使用最近引入的唯象非线性偏微分方程（NPDE）模型分析非平衡分布。由于NPDE方法也能很好地拟合实验结果且在数值上易于实现，BD + NPDE组合方法可能是分析受限分子动力学细节的有力方法。特别是，两组互补数据之间总体上的良好一致性，为在生物学相关长度尺度下对受限半柔性生物聚合物进行大规模模拟提供了一种策略。
