TensorCalculator: exploring the evolution of mechanical stress in the CCMV capsid
TensorCalculator: exploring the evolution of mechanical stress in the CCMV capsid
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DOI：
10.1088/1361-648x/aaa0f6
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发表时间：
2018-01-31
影响因子：
2.7
通讯作者：
Barsegov, Valeri
中科院分区：
文献类型：
--
作者：
Kononova, Olga;Maksudov, Farkhad;Barsegov, Valeri
提出了一种精确计算柯西应力张量、应力不变量、主应力分量、von Mises张量和Tresca张量的新方法。该方法基于原子应力方法，该方法允许计算应力张量，广泛用于材料特性的连续力学建模，使用离散原子和基于c - α的生物颗粒粗粒度结构模型的MD模拟输出。将该方法映射到软件包TensorCalculator中，成功地应用于豇豆绿斑病毒（CCMV）空壳，以探索软病毒衣壳中机械应力的演变。我们发现在CCMV结构的各个部分存在不均匀的应力分布，并且应力从病毒结构的一个部分传递到另一个部分，这也表明了熵效应的重要性，这在有限元分析和弹性网络建模中经常被忽略。我们用第一主应力分量制定了弹性变形的判据。此外，我们表明von Mises和Tresca应力张量可以用来预测病毒衣壳机械失效的开始，这导致整体结构崩溃。TensorCalculator可用于研究病毒衣壳和其他大尺寸蛋白质组件缺陷的应力演化和动力学。
A new computational methodology for the accurate numerical calculation of the Cauchy stress tensor, stress invariants, principal stress components, von Mises and Tresca tensors is developed. The methodology is based on the atomic stress approach which permits the calculation of stress tensors, widely used in continuum mechanics modeling of materials properties, using the output from the MD simulations of discrete atomic and C-alpha-based coarsegrained structural models of biological particles. The methodology mapped into the software package TensorCalculator was successfully applied to the empty cowpea chlorotic mottle virus (CCMV) shell to explore the evolution of mechanical stress in this mechanically-tested specific example of a soft virus capsid. We found an inhomogeneous stress distribution in various portions of the CCMV structure and stress transfer from one portion of the virus structure to another, which also points to the importance of entropic effects, often ignored in finite element analysis and elastic network modeling. We formulate a criterion for elastic deformation using the first principal stress components. Furthermore, we show that von Mises and Tresca stress tensors can be used to predict the onset of a viral capsid's mechanical failure, which leads to total structural collapse. TensorCalculator can be used to study stress evolution and dynamics of defects in viral capsids and other large-size protein assemblies.