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Determination of Kinetics and Thermodynamics of Biomolecular Processes with Trajectory Fragments

  • Alfredo E. CardenasEmail author
Chapter
Part of the Springer Series on Bio- and Neurosystems book series (SSBN, volume 8)

Abstract

Trajectory fragments algorithms are a set of methods that partition the relevant trajectory space between reactants and products into smaller regions of phase space. Many short trajectories are launched to evaluate transition probabilities between these regions. Each of the methods processes this short-trajectory data with different kinetic models and as a result long-time kinetic and thermodynamic information for the overall molecular event can be extracted. This chapter focuses on Milestoning, providing detailed analysis of the approximations involved in the algorithm and its computational implementation. Two other trajectory fragments methods (Partial Path Transition Interface Sampling and Markov State Models) are briefly discussed as well. Finally, two recent applications of trajectory fragments methods are described.

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© Springer Nature Switzerland AG 2019

Authors and Affiliations

  1. 1.Institute for Computational Engineering and SciencesUniversity of TexasAustinUSA

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