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Computational Methods to Study the Structure and Dynamics of Biomolecules and Biomolecular Processes pp 281–303Cite as

Determination of Kinetics and Thermodynamics of Biomolecular Processes with Trajectory Fragments

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Part of the book series: Springer Series on Bio- and Neurosystems ((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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  1. Institute for Computational Engineering and Sciences, University of Texas, Austin, TX, 78712, USA

    Alfredo E. Cardenas

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Correspondence to Alfredo E. Cardenas .

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  1. Faculty of Chemistry, University of Gdańsk, Gdańsk, Poland

    Adam Liwo

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Cardenas, A.E. (2019). Determination of Kinetics and Thermodynamics of Biomolecular Processes with Trajectory Fragments. In: Liwo, A. (eds) Computational Methods to Study the Structure and Dynamics of Biomolecules and Biomolecular Processes. Springer Series on Bio- and Neurosystems, vol 8. Springer, Cham. https://doi.org/10.1007/978-3-319-95843-9_9

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