Advances in Experimental Medicine and Biology

An Introduction to Markov State Models and Their Application to Long Timescale Molecular Simulation

Editors: Bowman, Gregory R., Pande, Vijay S., Noé, Frank (Eds.)

  • 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
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eBook $159.00
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  • ISBN 978-94-007-7606-7
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Hardcover $209.00
price for USA
  • ISBN 978-94-007-7605-0
  • Free shipping for individuals worldwide
  • Usually dispatched within 3 to 5 business days.
Softcover $209.00
price for USA
  • Customers within the U.S. and Canada please contact Customer Service at 1-800-777-4643, Latin America please contact us at +1-212-460-1500 (Weekdays 8:30am – 5:30pm ET) to place your order.
  • Due: November 4, 2016
  • ISBN 978-94-024-0762-4
  • Free shipping for individuals worldwide
About this Textbook

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.

Table of contents (11 chapters)

  • Introduction and Overview of This Book

    Bowman, Gregory R. (et al.)

    Pages 1-6

  • An Overview and Practical Guide to Building Markov State Models

    Bowman, Gregory R.

    Pages 7-22

  • Markov Model Theory

    Sarich, Marco (et al.)

    Pages 23-44

  • Estimation and Validation of Markov Models

    Prinz, Jan-Hendrik (et al.)

    Pages 45-60

  • Uncertainty Estimation

    Noé, Frank (et al.)

    Pages 61-74

Buy this book

eBook $159.00
price for USA (gross)
  • ISBN 978-94-007-7606-7
  • Digitally watermarked, DRM-free
  • Included format: PDF, EPUB
  • ebooks can be used on all reading devices
  • Immediate eBook download after purchase
Hardcover $209.00
price for USA
  • ISBN 978-94-007-7605-0
  • Free shipping for individuals worldwide
  • Usually dispatched within 3 to 5 business days.
Softcover $209.00
price for USA
  • Customers within the U.S. and Canada please contact Customer Service at 1-800-777-4643, Latin America please contact us at +1-212-460-1500 (Weekdays 8:30am – 5:30pm ET) to place your order.
  • Due: November 4, 2016
  • ISBN 978-94-024-0762-4
  • Free shipping for individuals worldwide
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Bibliographic Information

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
Series Volume
797
Copyright
2014
Publisher
Springer Netherlands
Copyright Holder
Springer Science+Business Media Dordrecht
eBook ISBN
978-94-007-7606-7
DOI
10.1007/978-94-007-7606-7
Hardcover ISBN
978-94-007-7605-0
Softcover ISBN
978-94-024-0762-4
Series ISSN
0065-2598
Edition Number
1
Number of Pages
XII, 139
Number of Illustrations and Tables
17 b/w illustrations, 48 illustrations in colour
Topics