Overview
- In-depth review of the mathematical underpinnings of Markov state models
- Practical insight into applying Markov state models to molecular systems
- Points readers to freely available software for constructing Markov state models
- Includes supplementary material: sn.pub/extras
Part of the book series: Advances in Experimental Medicine and Biology (AEMB, volume 797)
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Table of contents (11 chapters)
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Front Matter
Keywords
About this book
The aim of this book volume is to explain the importance of Markov state models to molecular simulation, how they work, and how they can be applied to a range of problems.
The Markov state model (MSM) approach aims to address two key challenges of molecular simulation:
1) How to reach long timescales using short simulations of detailed molecular models.
2) How to systematically gain insight from the resulting sea of data.
MSMs do this by providing a compact representation of the vast conformational space available to biomolecules by decomposing it into states sets of rapidly interconverting conformations and the rates of transitioning between states. This kinetic definition allows one to easily vary the temporal and spatial resolution of an MSM from high-resolution models capable of quantitative agreement with (or prediction of) experiment to low-resolution models that facilitate understanding. Additionally, MSMs facilitate the calculation of quantities that are difficult to obtain from more direct MD analyses, such as the ensemble of transition pathways.
This book introduces the mathematical foundations of Markov models, how they can be used to analyze simulations and drive efficient simulations, and some of the insights these models have yielded in a variety of applications of molecular simulation.
Editors and Affiliations
Bibliographic Information
Book Title: An Introduction to Markov State Models and Their Application to Long Timescale Molecular Simulation
Editors: Gregory R. Bowman, Vijay S. Pande, Frank Noé
Series Title: Advances in Experimental Medicine and Biology
DOI: https://doi.org/10.1007/978-94-007-7606-7
Publisher: Springer Dordrecht
eBook Packages: Biomedical and Life Sciences, Biomedical and Life Sciences (R0)
Copyright Information: The Editor(s) (if applicable) and The Author(s), under exclusive license to Springer Nature B.V. 2014
Hardcover ISBN: 978-94-007-7605-0Published: 18 December 2013
Softcover ISBN: 978-94-024-0762-4Published: 18 September 2016
eBook ISBN: 978-94-007-7606-7Published: 02 December 2013
Series ISSN: 0065-2598
Series E-ISSN: 2214-8019
Edition Number: 1
Number of Pages: XII, 139
Number of Illustrations: 17 b/w illustrations, 48 illustrations in colour
Topics: Molecular Medicine, Theoretical, Mathematical and Computational Physics, Computer Appl. in Life Sciences, Physical Chemistry, Mathematics, general