Model chromatin flows: numerical analysis of linear and nonlinear hydrodynamics inside a sphere
Model chromatin flows: numerical analysis of linear and nonlinear hydrodynamics inside a sphere
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DOI：
10.1140/epje/s10189-023-00327-1
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发表时间：
2023-08-01
影响因子：
1.8
通讯作者：
Grosberg，Alexander Y. Y.
中科院分区：
文献类型：
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作者：
Eshghi，Iraj;Zidovska，Alexandra;Grosberg，Alexander Y. Y.
我们在模拟细胞核的受限几何形状内求解了活跃染色质动力学的流体动力学模型。使用分析和数值方法，我们描述的染色质聚合物的行为具有极性对称的电机的活动驱动，无论是在线性响应制度，以及在长期的，完全非线性制度的流量。边界的引入诱导了染色质流动中的特定几何形状，我们使用矢量球谐函数来描述，该工具大大简化了我们的分析和数值方法。我们发现，长期的行为，这个模型在禁闭是占主导地位的稳定，横向流动的染色质循环周围的球形域。这些循环流被发现是强大的扰动，其特征尺寸由域的大小。这使我们进一步了解细胞核中的活性染色质动力学，并为进一步开发更复杂的活性染色质动力学模型提供了基础。图形摘要
We solve a hydrodynamic model of active chromatin dynamics, within a confined geometry simulating the cell nucleus. Using both analytical and numerical methods, we describe the behavior of the chromatin polymer driven by the activity of motors having polar symmetry, both in the linear response regime as well as in the long-term, fully nonlinear regime of the flows. The introduction of a boundary induces a particular geometry in the flows of chromatin, which we describe using vector spherical harmonics, a tool which greatly simplifies both our analytical and numerical approaches. We find that the long-term behavior of this model in confinement is dominated by steady, transverse flows of chromatin which circulate around the spherical domain. These circulating flows are found to be robust to perturbations, and their characteristic size is set by the size of the domain. This gives us further insight into active chromatin dynamics in the cell nucleus, and provides a foundation for development of further, more complex models of active chromatin dynamics.Graphical abstract