论文标题
使用CytoSIM模拟细胞骨架系统的典型工作流程
A typical workflow to simulate cytoskeletal systems with Cytosim
论文作者
论文摘要
现在，许多细胞骨架系统众所周知，可以允许其精确的定量建模。微管和肌动蛋白丝的表征很好，相关蛋白通常是已知的，并且它们的丰度以及这些元素之间的相互作用。因此，计算机模拟可用于精确地研究系统的集体行为，以互补的实验。 Cytosim是一种开源细胞骨架仿真套件，旨在处理具有相关蛋白（例如分子电动机）的柔性丝状系统。它还提供了模拟电动机的被动交联，可扩散的交联，成核器，切割器和离散版本的电动机，这些版本仅在细丝上踏上无占用的晶格位点。其他物体通过提供球形或更复杂的几何形状来补充细丝，这些几何形状可用于表示细胞中的染色体，细胞核或囊泡。 Cytosim提供了简单的命令行工具，用于运行模拟并显示其结果，这些工具是多才多艺的，不需要编程技能。在此工作流程中，逐步说明被提供给：i）在新计算机上安装必要的环境，ii）配置Cytosim以模拟2D Actomyosin网络的收缩，iii）产生系统的视觉表示。接下来，通过系统地改变关键参数来探测系统：交联的数量。最后，系统的视觉表示与收缩性的数值定量相辅相成，以在图中查看收缩力如何取决于系统的组成。总体而言，这些不同的步骤构成了一个典型的工作流程，可以在很少的修改中应用，以解决细胞骨架领域的许多其他问题。
Many cytoskeletal systems are now sufficiently well known to permit their precise quantitative modelling. Microtubule and actin filaments are well characterized, and the associated proteins are often known, as well as their abundance and the interactions between these elements. Thus, computer simulations can be used to investigate the collective behavior of the system precisely, in a way that is complementary to experiments. Cytosim is an Open Source cytoskeleton simulation suite designed to handle large systems of flexible filaments with associated proteins such as molecular motors. It also offers the possibility to simulate passive crosslinkers, diffusible crosslinkers, nucleators, cutters and discrete versions of the motors that only step on unoccupied lattice sites on a filament. Other objects complement the filaments by offering spherical or more complicated geometry that can be used to represent chromosomes, nucleus or vesicles in the cell. Cytosim offers simple command-line tools for running a simulation and displaying its results, that are versatile and do not require programming skills. In this workflow, step-by-step instructions are given to: i) install the necessary environment on a new computer, ii) configure Cytosim to simulate the contraction of a 2D actomyosin network, iii) produce a visual representation of the system. Next, the system is probed by systematically varying a key parameter: the number of crosslinkers. Finally, the visual representation of the system is complemented by a numerical quantification of contractility to view, in a graph, how contractility depends on the composition of the system. Overall, these different steps constitute a typical workflow that can be applied with few modifications, to tackle many other problems in the cytoskeletal field.
