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arXiv 2109.03516cond-mat.stat-mechcond-mat.softphysics.chem-ph
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生物分子机器的非平衡稳态模型

Modeling of biomolecular machines in non-equilibrium steady states

Thomas Speck

摘要:

数值计算已经成为所有现代定量科学的支柱。任何计算都涉及建模-即使这一步通常并不明确-并且任何模型都必须忽略细节,同时仍然保持物理准确性。平衡统计力学指导了遵循细致平衡的动力学模型和数值方法的发展。对于偏离热平衡的系统,缺少这样一个普遍的理论框架。对于一类受马尔可夫动力学和局部细致平衡约束的驱动系统,随机热力学已经发展到填补这一空白,并提供基本的约束和指导原则。下一步是将随机热力学从简单模型系统推进到具有数万甚至数百万自由度的复杂系统。生物分子在化学梯度和机械力的存在下工作是这一挑战的主要例子。在这个角度来看,我们给出了一个介绍等温随机热力学面向系统的多尺度建模的构象动力学的生物分子和合成机器,我们概述了一些开放的挑战。

英文摘要:

Numerical computations have become a pillar of all modern quantitative sciences. Any computation involves modeling--even if often this step is not made explicit--and any model has to neglect details while still being physically accurate. Equilibrium statistical mechanics guides both the development of models and numerical methods for dynamics obeying detailed balance. For systems driven away from thermal equilibrium such a universal theoretical framework is missing. For a restricted class of driven systems governed by Markov dynamics and local detailed balance, stochastic thermodynamics has evolved to fill this gap and to provide fundamental constraints and guiding principles. The next step is to advance stochastic thermodynamics from simple model systems to complex systems with ten thousands or even millions degrees of freedom. Biomolecules operating in the presence of chemical gradients and mechanical forces are a prime example for this challenge. In this Perspective, we give an introduction to isothermal stochastic thermodynamics geared towards the systematic multiscale modeling of the conformational dynamics of biomolecular and synthetic machines, and we outline some of the open challenges.

机构、总结、中文摘要均由AI分析而来,可能存在错误,请以论文正文为准。

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