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Computation 2018, 6(1), 20; https://doi.org/10.3390/computation6010020

Implications of PCCA+ in Molecular Simulation

Numerical Analysis and Modelling, Konrad-Zuse-Zentrum für Informationstechnik Berlin (ZIB), Takustraße 7, 14195 Berlin, Germany
Received: 8 January 2018 / Revised: 16 February 2018 / Accepted: 16 February 2018 / Published: 19 February 2018
(This article belongs to the Special Issue Computation in Molecular Modeling)
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Abstract

Upon ligand binding or during chemical reactions the state of a molecular system changes in time. Usually we consider a finite set of (macro-) states of the system (e.g., ‘bound’ vs. ‘unbound’), although the process itself takes place in a continuous space. In this context, the formula χ = X A connects the micro-dynamics of the molecular system to its macro-dynamics. χ can be understood as a clustering of micro-states of a molecular system into a few macro-states. X is a basis of an invariant subspace of a transfer operator describing the micro-dynamics of the system. The formula claims that there is an unknown linear relation A between these two objects. With the aid of this formula we can understand rebinding effects, the electron flux in pericyclic reactions, and systematic changes of binding rates in kinetic ITC experiments. We can also analyze sequential spectroscopy experiments and rare event systems more easily. This article provides an explanation of the formula and an overview of some of its consequences. View Full-Text
Keywords: Robust Perron Cluster Analysis; membership function; invariant subspace Robust Perron Cluster Analysis; membership function; invariant subspace
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Weber, M. Implications of PCCA+ in Molecular Simulation. Computation 2018, 6, 20.

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