Polson James M, Rehel Desiree A
Department of Physics, University of Prince Edward Island, 550 University Ave., Charlottetown, Prince Edward Island C1A 4P3, Canada.
Soft Matter. 2021 Jun 16;17(23):5792-5805. doi: 10.1039/d1sm00308a.
Motivated by recent nanofluidics experiments, we use Brownian dynamics and Monte Carlo simulations to study the conformation, organization and dynamics of two polymer chains confined to a single box-like cavity. The polymers are modeled as flexible bead-spring chains, and the box has a square cross-section of side length L and a height that is small enough to compress the polymers in that dimension. For sufficiently large L, the system behaviour approaches that of an isolated polymer in a slit. However, the combined effects of crowding and confinement on the polymer organization, conformation and equilibrium dynamics become significant when where is the transverse radius of gyration for a slit geometry. In this regime, the centre-of-mass probability distribution in the transverse plane exhibits a depletion zone near the centre of the cavity (except at very small L) and a 4-fold symmetry with quasi-discrete positions. Reduction in polymer size with decreasing L arises principally from confinement rather than inter-polymer crowding. By contrast, polymer diffusion and internal motion are strongly affected by inter-polymer crowding. The two polymers tend to occupy opposite positions relative to the box centre, about which they diffuse relatively freely. Qualitatively, this static and dynamical behaviour differs significantly from that previously observed for confinement of two polymers to a narrow channel. The simulation results for a suitably chosen box width are qualitatively consistent with results from a recent experimental study of two λ-DNA chains confined to a nanofluidic cavity.
受近期纳米流体学实验的启发，我们使用布朗动力学和蒙特卡罗模拟来研究限制在单个盒状腔体内的两条聚合物链的构象、组织和动力学。聚合物被建模为柔性珠弹簧链，盒子的横截面为边长为L的正方形，其高度足够小，可在该维度上压缩聚合物。对于足够大的L，系统行为接近狭缝中孤立聚合物的行为。然而，当（其中是狭缝几何形状的横向回转半径）时，拥挤和限制对聚合物组织、构象和平衡动力学的综合影响变得显著。在这种情况下，横向平面内的质心概率分布在腔体中心附近呈现耗尽区（非常小的L除外），并具有准离散位置的四重对称性。聚合物尺寸随L减小而减小主要源于限制而非聚合物间的拥挤。相比之下，聚合物扩散和内部运动受聚合物间拥挤的强烈影响。两条聚合物倾向于相对于盒子中心占据相反位置，围绕该中心它们相对自由地扩散。定性地说，这种静态和动态行为与之前观察到的将两条聚合物限制在狭窄通道中的行为有显著差异。对于适当选择的盒宽，模拟结果与最近对两条限制在纳米流体腔体内的λ-DNA链的实验研究结果在定性上是一致的。
