Toward the cellular-scale simulation of motor-driven cytoskeletal assemblies.
Toward the cellular-scale simulation of motor-driven cytoskeletal assemblies.
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DOI：
10.7554/elife.74160
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发表时间：
2022-05-26
期刊：
影响因子：
7.7
通讯作者：
Shelley, Michael
中科院分区：
文献类型：
--
作者：
Yan, Wen;Ansari, Saad;Lamson, Adam;Glaser, Matthew A.;Blackwell, Robert;Betterton, Meredith D.;Shelley, Michael
细胞骨架——聚合丝、分子马达和交联剂的集合——是活性物质的一个基本例子，并在细胞中组装成指导基本生物功能的细胞器。细胞骨架组装的模拟是模拟细胞过程和理解其惊人的材料特性的重要工具。在这里，我们提出了aLENS（生活集成模拟器），这是一种新的计算框架，旨在克服传统模拟方法的局限性。我们用坚持热力学能量景观的交联动力学来模拟分子马达，并在有效和稳定地加强细丝之间的硬体排斥的同时整合系统动力学。在施加空间约束时完全避免了分子势。利用并行计算，我们模拟了成千上万的细胞骨架细丝和交联马达，重现了束形成和屈曲等紧急现象。这个模拟框架可以帮助阐明运动类型、热波动、内应力和约束如何决定细胞骨架活性物质的进化。
The cytoskeleton – a collection of polymeric filaments, molecular motors, and crosslinkers – is a foundational example of active matter, and in the cell assembles into organelles that guide basic biological functions. Simulation of cytoskeletal assemblies is an important tool for modeling cellular processes and understanding their surprising material properties. Here, we present aLENS (a Living Ensemble Simulator), a novel computational framework designed to surmount the limits of conventional simulation methods. We model molecular motors with crosslinking kinetics that adhere to a thermodynamic energy landscape, and integrate the system dynamics while efficiently and stably enforcing hard-body repulsion between filaments. Molecular potentials are entirely avoided in imposing steric constraints. Utilizing parallel computing, we simulate tens to hundreds of thousands of cytoskeletal filaments and crosslinking motors, recapitulating emergent phenomena such as bundle formation and buckling. This simulation framework can help elucidate how motor type, thermal fluctuations, internal stresses, and confinement determine the evolution of cytoskeletal active matter.