**Courant Lecture Notes**

Volume: 24;
2013;
128 pp;
Softcover

MSC: Primary 60; 47; 92;

Print ISBN: 978-0-8218-4359-8

Product Code: CLN/24

List Price: $34.00

Individual Member Price: $27.20

**Electronic ISBN: 978-1-4704-1439-9
Product Code: CLN/24.E**

List Price: $34.00

Individual Member Price: $27.20

#### You may also like

#### Supplemental Materials

# Metastability and Markov State Models in Molecular Dynamics: Modeling, Analysis, Algorithmic Approaches

Share this page
*Christof Schütte; Christof Schütte; Marco Sarich*

A co-publication of the AMS and the Courant Institute of Mathematical Sciences at New York University

Applications in modern biotechnology and
molecular medicine often require simulation of biomolecular systems in
atomic representation with immense length and timescales that are far
beyond the capacity of computer power currently available. As a
consequence, there is an increasing need for reduced models that
describe the relevant dynamical properties while at the same time
being less complex. In this book the authors exploit the existence of
metastable sets for constructing such a reduced molecular dynamics
model, the so-called Markov state model (MSM), with good approximation
properties on the long timescales.

With its many examples and illustrations, this book is addressed to
graduate students, mathematicians, and practical computational
scientists wanting an overview of the mathematical background for the
ever-increasing research activity on how to construct MSMs for very
different molecular systems ranging from peptides to proteins, from
RNA to DNA, and via molecular sensors to molecular aggregation. This
book bridges the gap between mathematical research on molecular
dynamics and its practical use for realistic molecular systems by
providing readers with tools for performing in-depth analysis of
simulation and data-analysis methods.

Titles in this series are co-published with the Courant Institute of Mathematical Sciences at New York University.

#### Table of Contents

# Table of Contents

## Metastability and Markov State Models in Molecular Dynamics: Modeling, Analysis, Algorithmic Approaches

- Cover Cover11
- Title page iii4
- Contents v6
- Introduction vii8
- Transfer operator approach to conformation dynamics 112
- Dynamics 516
- Metastability 1526
- Transfer operators and generators 2536
- Projected transfer operators 6172
- Transition path theory 99110
- Concluding remarks 115126
- Appendix A. Some mathematical aspects of transfer operators 117128
- Appendix B. Definition of exit rates 121132
- Bibliography 123134
- Back Cover Back Cover1141

#### Readership

Graduate students and research mathematicians interested in molecular dynamics.