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The Concept of Cooperative Dynamics in Simulations of Soft Matter
Frontiers in Physics ( IF 3.1 ) Pub Date : 2020-11-10 , DOI: 10.3389/fphy.2020.607480
Piotr Polanowski , Andrzej Sikorski

In this review we compiled recent advances concerning the cooperative motion in crowded soft matter systems. We tried to answer the question how to perform dynamic Monte Carlo simulations of dense macromolecular systems effectively. This problem is not simple due to the fact that the movement in such systems is strictly correlated which leads to cooperative phenomena. The influence of crowding was found interesting especially for two-dimensional cases, e.g., in membranes where the presence of macromolecules, proteins and cytoskeleton often changed the mean-square displacement as a function of the lag time and anomalous diffusion appeared. Simple models are frequently used to shed a light on molecular transport in biological systems. The emphasis was given to the Dynamic Lattice Liquid model. The latter model became a basis for a parallel algorithm that takes into account coincidences of elementary molecular motion attempts resulting in local cooperative structural transformations. The emphasis is put on influence of the model of molecular transport on the diffusion. The comparison to alternative approaches like single agent model was carried out.



中文翻译:

软物质模拟中的合作动力学概念

在这篇综述中,我们汇总了有关拥挤软物质系统中的合作运动的最新进展。我们试图回答这个问题,即如何有效地执行稠密大分子系统的动态蒙特卡洛模拟。由于这样的系统中的运动严格相关,导致协作现象,所以这个问题并不简单。发现拥挤的影响尤其对于二维情况而言是有趣的,例如,在膜中,大分子,蛋白质和细胞骨架的存在经常根据滞后时间和异常扩散而改变均方位移。简单模型经常被用来阐明生物系统中的分子运输。重点放在了动态晶格液体模型上。后一种模型成为并行算法的基础,该算法考虑了导致局部协作结构转换的基本分子运动尝试的重合。重点放在分子运输模型对扩散的影响上。与其他方法(如单代理模型)进行了比较。

更新日期:2020-11-27
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