Exact milestoning
نویسندگان
چکیده
منابع مشابه
A Mathematical Framework for Exact Milestoning
We give a mathematical framework for Exact Milestoning, a recently introduced algorithm for mapping a continuous time stochastic process into a Markov chain or semi-Markov process that can be efficiently simulated and analyzed. We generalize the setting of Exact Milestoning and give explicit error bounds for the error in the Milestoning equation for mean first passage times.
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Markov state models (MSMs) have become the tool of choice to analyze large amounts of molecular dynamics data by approximating them as a Markov jump process between suitably predefined states. Here we investigate "Core Set MSMs," a new type of MSMs that build on metastable core sets acting as milestones for tracing the rare event kinetics. We present a thorough analysis of Core Set MSMs based o...
متن کاملJohn von Neumann Institute for Computing Milestoning
c © 2008 by John von Neumann Institute for Computing Permission to make digital or hard copies of portions of this work for personal or classroom use is granted provided that the copies are not made or distributed for profit or commercial advantage and that copies bear this notice and the full citation on the first page. To copy otherwise requires prior specific permission by the publisher ment...
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Prediction of passive permeation rates of solutes across lipid bilayers is important to drug design, toxicology, and other biological processes such as signaling. The inhomogeneous solubility-diffusion (ISD) equation is traditionally used to relate the position-dependent potential of mean force and diffusivity to the permeability coefficient. The ISD equation is derived via the Smoluchowski equ...
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ژورنال
عنوان ژورنال: The Journal of Chemical Physics
سال: 2015
ISSN: 0021-9606,1089-7690
DOI: 10.1063/1.4913399