Bin W. Zhang

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We describe methods to perform replica exchange molecular dynamics (REMD) simulations asynchronously (ASyncRE). The methods are designed to facilitate large scale REMD simulations on grid computing networks consisting of heterogeneous and distributed computing environments as well as on homogeneous high-performance clusters. We have implemented these(More)
Conditionally disordered proteins can alternate between highly ordered and less ordered configurations under physiological conditions. Whereas protein function is often associated with the ordered conformation, for some of these conditionally unstructured proteins, the opposite applies: Their activation is associated with their unfolding. An example is the(More)
Despite their importance in activated processes, transition-event durations--which are much shorter than first passage times--have not received a complete theoretical treatment. The authors therefore study the distribution rhob(t) of durations of transition events over a barrier in a one-dimensional system undergoing overdamped Langevin dynamics. The(More)
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