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Transition Path Sampling Simulations of Biological Systems

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Atomistic Approaches in Modern Biology

Part of the book series: Topics in Current Chemistry ((TOPCURRCHEM,volume 268))

Abstract

Transition path sampling is a computational method for the simulation of rare but important events occurring in complex systems. Based on a statistical mechanics in trajectory space, transition path sampling can be applied to identify mechanisms and determine rate constants. Here we review the basic ideas and algorithms of transition path sampling and discuss some recent applications of this methodology to problems in molecular biology including protein folding, enzyme catalysis, and processes occurring in lipid bilayers.

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Abbreviations

DPS:

Discrete path sampling

FFS:

Forward flux sampling

MC:

Monte Carlo

MD:

Molecular dynamics

TIS:

Transition interface sampling

TPS:

Transition path sampling

TS:

Transition state

TSE:

Transition state ensemble

TST:

Transition state theory

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Author information

Authors and Affiliations

  1. Faculty of Physics, University of Vienna, Boltzmanngasse 5, 1090, Vienna, Austria

    Christoph Dellago

  2. van't Hoff Institute for Molecular Sciences, University of Amsterdam, Nieuwe Achtergracht 166, 1018 WV, Amsterdam, The Netherlands

    Peter G. Bolhuis

Authors
  1. Christoph Dellago
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  2. Peter G. Bolhuis
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Corresponding author

Correspondence to Christoph Dellago .

Editor information

Markus Reiher

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© 2006 Springer-Verlag Berlin Heidelberg

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Dellago, C., Bolhuis, P.G. (2006). Transition Path Sampling Simulations of Biological Systems. In: Reiher, M. (eds) Atomistic Approaches in Modern Biology. Topics in Current Chemistry, vol 268. Springer, Berlin, Heidelberg . https://doi.org/10.1007/128_085

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