Kasson Peter M, Pande Vijay S
Departments of Chemistry and Structural Biology, Stanford University Stanford, CA 94305, USA.
Pac Symp Biocomput. 2010:260-8.
Accurate and efficient methods to simulate biomolecular systems at multiple levels of detail simultaneously are an ongoing challenge for the simulation community. Here we present a new method for multi-scale simulation where a complex system can be partitioned into two loosely-coupled sub-systems, one coarse-grained and one atomistic. If the coupling between the coarse-grained and atomistic systems can be encoded into discrete states that interconvert slowly, we can construct a Markov state model where we approximate any given transition P[(s(i),t(j))->(s(k),t(1))] in the joint space of the coarse-grained and atomistic systems as the product of two orthogonal transitions P(s(i)->s(k) mid R: t(j)) and P(t(j)->t(1) mid R: s(j)). We provide a formalism for constructing such models and describe how they may be applied to multi-scale simulation of membrane proteins. This "cross-graining" methodology may provide a general means to efficiently simulate mixed-scale systems.
对于模拟社区来说，能够同时在多个细节层次上准确、高效地模拟生物分子系统仍是一项持续的挑战。在此，我们提出一种新的多尺度模拟方法，其中一个复杂系统可被划分为两个松散耦合的子系统，一个是粗粒度的，另一个是原子级的。如果粗粒度系统与原子级系统之间的耦合能够被编码为缓慢相互转换的离散状态，那么我们就可以构建一个马尔可夫状态模型，在该模型中，我们将粗粒度系统与原子级系统联合空间中任何给定的跃迁P[(s(i),t(j))->(s(k),t(1))]近似为两个正交跃迁P(s(i)->s(k) mid R: t(j))和P(t(j)->t(1) mid R: s(j))的乘积。我们提供了构建此类模型的形式体系，并描述了如何将它们应用于膜蛋白的多尺度模拟。这种“交叉粒度”方法可能为高效模拟混合尺度系统提供一种通用手段。
