Titlebook: New Algorithms for Macromolecular Simulation; Benedict Leimkuhler,Christophe Chipot,Robert Skeel Book 2006 Springer-Verlag Berlin Heidelbe

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Biomolecular Sampling: Algorithms, Test Molecules, and Metricsnd scale with timestep and system size. Presented, herein, are a set of sampling algorithms, test molecules, and metrics. We make the sampling methods discussed available via the open source and freely distributed . molecular simulation framework.

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Free Energy Calculations in Biological Systems. How Useful Are They in Practice?nds — in connection with the blood-brain barrier, the folding of a short hydrophobic peptide, and the association of transmembrane α-helical domains, in line with the “two-stage” model of membrane protein folding. Current strategies for improving the reliability of free energy calculations, while ma

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Lecture Notes in Computational Science and Engineeringhttp://image.papertrans.cn/n/image/664769.jpg

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New Algorithms for Macromolecular Simulation978-3-540-31618-3Series ISSN 1439-7358 Series E-ISSN 2197-7100

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The Targeted Shadowing Hybrid Monte Carlo (TSHMC) MethodFollowing . & . [14], . [13], and . [1] as well as work of one of the authors on dissipative particle dynamics [4] and modified equations [23], we suggest a modified Metropolis criterion and a more flexible momentum update to improve the acceptance rate and the flexibility of the thermal coupling in standard hybrid Monte Carlo simulations.

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Modeling and Simulation Based Approaches for Investigating Allosteric Regulation in Enzymesdels, tools and/or protocols, including homology-based modeling (HM) and molecular dynamics (MD) simulations. We demonstrate how these . methods can be used to advance our understanding of complex processes using the allosteric regulation of soluble guanynyl cyclase (sGC) as an example. Future directions for the sGC research are also identified.

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llection of unbounded FIFO queues. Their intended use is to serve as a symbolic representation of the possible queue contents that can occur in the state space of a protocol modeled by finite-state machines communicating through unbounded queues. This is done with the help of a loop-first search, a