Markovian and Non-Markovian Modeling of Membrane Dynamics with Milestoning
Markovian and Non-Markovian Modeling of Membrane Dynamics with Milestoning
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DOI：
10.1021/acs.jpcb.6b01890
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发表时间：
2016-08-25
影响因子：
3.3
通讯作者：
Elber, Ron
中科院分区：
文献类型：
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作者：
Cardenas, Alfredo E.;Elber, Ron
我们利用详细的原子模拟和里程碑理论来提取膜动力学和热力学的粗粒度模型。磷酸基位移的非马尔可夫理论和马尔可夫理论用于粗略表示膜运动。这两种模型的构建使得检验它们的一致性和准确性成为可能。对磷酸基团沿膜平面法线的平衡和波动进行了估计，并构建和求解了马尔可夫方程。构建的最优马尔可夫模型完全再现了非马尔可夫模型的平衡和平均首次通过时间（MFPT）。这两个模型的平衡解与直接分子动力学模拟得到的分布进行了比较。动力学的情况比较复杂。质量密度的多个局部弛豫时间得到了说明，强调了这一过程的非马尔可夫特性。在马尔可夫模型中，一个状态只有一个弛豫时间。将粒子动力学映射到场密度动力学提供了一种粗粒化复杂系统（如膜）的新方法，可以在原子细节模型和宏观膜现象学描述之间架起一座桥梁。
We exploit atomically detailed simulations and the milestoning theory to extract coarse grained models of membrane kinetics and thermodynamics. Non-Markovian and Markovian theories for the phosphate group displacements are used to coarsely represent membrane motions. The construction of the two models makes it possible to examine their consistency and accuracy. The equilibrium and fluctuations of the phosphate groups along the normal to the membrane plane are estimated, and milestoning equations are constructed and solved. An optimal Markovian model is constructed that reproduces exactly the equilibrium and mean first passage time (MFPT) of the non-Markovian model. The equilibrium solution of both models is favorably compared to distributions obtained from straightforward molecular dynamics simulations. The picture for the kinetics is complex. Multiple local relaxation times of the mass density are illustrated emphasizing the non-Markovian characteristics of the process. In Markovian modeling, only a single relaxation time is assumed for a state. Mapping of particle dynamics to the dynamics of a field density offers a new way of coarse graining complex systems as membranes that may bridge between atomically detailed models and phenomenological descriptions of macroscopic membranes.