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.
Author: | Konstantin Fackeldey, Marcus Weber |
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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 |