Vijay Pande
Publication Details
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"Cross-graining": efficient multi-scale simulation via Markov state models.
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.
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