Force distribution in a semiflexible loop.
Force distribution in a semiflexible loop.
复制标题
半柔性环中的力分布。
DOI：
10.1103/physreve.93.043315
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发表时间：
2016
期刊：
影响因子：
--
通讯作者：
Kim,HaroldD
中科院分区：
文献类型：
--
作者：
Waters,JamesT;Kim,HaroldD
经历热波动的环路在自然界中很普遍。环状或交联聚合物、环状大分子和蛋白质介导的DNA环都属于这一类。这些分子的稳定性通常用自由能（平均量）来描述，但它也可能受到这些系统内作用的局部波动力的影响。因此，这些力的完整分布可以让我们深入了解超越热力学预测能力的机械化学。在本文中，我们研究了受限于环状状态的不可延伸的半柔性聚合物所施加的力。通过使用称为“相空间采样”的模拟方法，我们生成了位置和动量空间中链构象的平衡分布。我们使用拉格朗日力学计算了该链系综中环路两端之间的约束力，并表明这些力的平均值等于热力学力。通过分析对力的动力学和潜在贡献，我们发现平均力作用在增加延伸的方向上，不是因为弯曲应力，而是尽管如此。此外，我们还获得了作为链长度、延伸度和刚度函数的约束力分布。值得注意的是，增加轮廓长度会降低平均力，但额外的自由度会导致约束力的波动增加。力分布是不对称的，并且比高斯分布下降得不太剧烈。我们的工作举例说明了一个系统，其中以纯热力学框架无法预见的方式发生大幅波动，并提供了可用于有效、无偏模拟约束系统的计算工具。
Loops undergoing thermal fluctuations are prevalent in nature. Ringlike or cross-linked polymers, cyclic macromolecules, and protein-mediated DNA loops all belong to this category. Stability of these molecules are generally described in terms of free energy, an average quantity, but it may also be impacted by local fluctuating forces acting within these systems. The full distribution of these forces can thus give us insights into mechanochemistry beyond the predictive capability of thermodynamics. In this paper, we study the force exerted by an inextensible semiflexible polymer constrained in a looped state. By using a simulation method termed “phase-space sampling,” we generate the equilibrium distribution of chain conformations in both position and momentum space. We compute the constraint forces between the two ends of the loop in this chain ensemble using Lagrangian mechanics, and show that the mean of these forces is equal to the thermodynamic force. By analyzing kinetic and potential contributions to the forces, we find that the mean force acts in the direction of increasing extension not because of bending stress, but in spite of it. Furthermore, we obtain a distribution of constraint forces as a function of chain length, extension, and stiffness. Notably, increasing contour length decreases the average force, but the additional freedom allows fluctuations in the constraint force to increase. The force distribution is asymmetric and falls off less sharply than a Gaussian distribution. Our work exemplifies a system where large-amplitude fluctuations occur in a way unforeseen by a purely thermodynamic framework, and offers computational tools useful for efficient, unbiased simulation of a constrained system.