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COMPUTING THE MINIMAL REBINDING EFFECT INCLUDED IN A GIVEN KINETICS

Please always quote using this URN:urn:nbn:de:0296-matheon-13037
  • In this article we show, that the binding kinetics of a molecular system can be identi� ed by a projection of a continuous process onto a � nite number of macro states. We thus interpret binding kinetics as a projection. When projecting onto non-overlapping macro states the Markovianity is spoiled. As a consequence, the description of e.g. a receptor-ligand system by a two state kinetics is not accurate. By assigning a degree of membership to each state, we abandon the non-overlapping approach. This overlap is crucial for a correct mapping of binding e� ects by Markov State Models with regard to their long time behavior. It enables us to describe the highly discussed rebinding e� ect, where the spatial arrangement of the system has the be included. By introducing a \degree of fuzziness" we have an indicator for the strength of the rebinding e� ect, such that the minimal rebinding e� ect can be derived from an optimization problem. The fuzziness also includes some new paradigms for molecular kinetics. These new model paradigms show good agreement with experimental data.

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Metadaten
Author:Konstantin Fackeldey, Marcus Weber
URN:urn:nbn:de:0296-matheon-13037
Referee:Volker Mehrmann
Document Type:Preprint, Research Center Matheon
Language:English
Date of first Publication:2015/12/23
Release Date:2015/12/23
Tag:Rebinding; Recrossing
Institute:Zuse Institute Berlin (ZIB)
MSC-Classification:65-XX NUMERICAL ANALYSIS / 65Cxx Probabilistic methods, simulation and stochastic differential equations (For theoretical aspects, see 68U20 and 60H35) / 65C05 Monte Carlo methods
Preprint Number:1092
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