Kirmizialtin Serdal, Makarov Dmitrii E
Department of Chemistry and Biochemistry, University of Texas at Austin, Austin, Texas, 78712, USA.
J Chem Phys. 2008 Mar 7;128(9):094901. doi: 10.1063/1.2835605.
The dynamics of molecular knots is implicated in a broad range of phenomena, from DNA replication to relaxation of polymer melts. Motivated by the recent experiments, in which biopolymer knots have been observed and manipulated at a single-molecule level, we have used computer simulations to study the dynamics of "friction knots" joining individual polymer strands. A friction knot splicing two ropes becomes jammed when the ropes are pulled apart. In contrast, molecular friction knots eventually become undone by thermal motion. We show that depending on the knot type and on the polymer structure, a microscopic friction knot can be strong (the time tau the knot stays tied increases with the force F applied to separate the strands) or weak (tau decreases with increasing F). The strong knot behavior is a microscopic analog of macroscopic knot jamming. We further describe a simple model explaining these behaviors.
分子结的动力学与从DNA复制到聚合物熔体松弛等广泛的现象有关。受近期实验的启发，在这些实验中已在单分子水平上观察和操纵了生物聚合物结，我们使用计算机模拟来研究连接单个聚合物链的“摩擦结”的动力学。当两根绳子被拉开时，拼接两根绳子的摩擦结会卡住。相比之下，分子摩擦结最终会因热运动而解开。我们表明，根据结的类型和聚合物结构，微观摩擦结可以是强的（结保持系住的时间τ随着用于分开链的力F增加而增加）或弱的（τ随着F增加而减小）。强结行为是宏观结卡住的微观类似物。我们进一步描述了一个解释这些行为的简单模型。
