Graduate School of Integrated Sciences for Life, Hiroshima University, Higashihiroshima, Hiroshima, Japan.
Research Center for the Mathematics on Chromatin Live Dynamics, Hiroshima University, Higashihiroshima, Hiroshima, Japan.
Methods Mol Biol. 2025;2856:281-292. doi: 10.1007/978-1-0716-4136-1_17.
Biomolecules contain various heterogeneities in their structures and local chemical properties, and their functions emerge through the dynamics encoded by these heterogeneities. Molecular dynamics model-based studies will greatly contribute to the elucidation of such chemical/mechanical structure-dynamics-function relationships and the mechanisms that generate them. Coarse-grained molecular dynamics models with appropriately designed nonuniform local interactions play an important role in considering the various phenomena caused by large molecular complexes consisting of various proteins and DNA such as nuclear chromosomes. Therefore, in this chapter, we will introduce a method for constructing a coarse-grained molecular dynamics model that simulates the global behavior of each chromosome in the nucleus of a mammalian cell containing many giant chromosomes.
生物分子的结构和局部化学性质存在各种不均匀性，其功能通过这些不均匀性所编码的动力学表现出来。基于分子动力学模型的研究将极大地有助于阐明这些化学/力学结构-动力学-功能关系及其产生机制。具有适当设计的非均匀局部相互作用的粗粒分子动力学模型在考虑由各种蛋白质和 DNA 组成的大型分子复合物（如核染色体）引起的各种现象方面发挥着重要作用。因此，在本章中，我们将介绍一种构建粗粒分子动力学模型的方法，该模型可模拟哺乳动物细胞核中包含许多巨大染色体的每个染色体的整体行为。
