Coarse-graining bistability with the Martini force field

An increasing interest in molecular structures whose long term dynamics resemble those of bistable mechanical systems promotes the search of possible candidates that may operate as two-state switching units. Of particular interest are the systems that are capable to exhibit such bistable effects as...

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Bibliographic Details
Published inarXiv.org
Main Authors Muratov, Alexander D, Avetisov, Vladik A
Format Paper
LanguageEnglish
Published Ithaca Cornell University Library, arXiv.org 01.11.2024
Subjects
Bistability
Dynamic structural analysis
Mechanical systems
Molecular dynamics
Molecular structure
Pyridines
Stochastic resonance
Synchronism
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Summary:An increasing interest in molecular structures whose long term dynamics resemble those of bistable mechanical systems promotes the search of possible candidates that may operate as two-state switching units. Of particular interest are the systems that are capable to exhibit such bistable effects as spontaneous vibrations, stochastic resonance and spontaneous synchronization. Previously, in all-atom molecular dynamics simulations it has been demonstrated that short pyridine-furan springs show these bistable phenomena. In this article we introduce a coarse-grained model of such springs and investigate the possibility to observe the bistability effects, such as spontaneous vibrations. Our findings allow the studies of short pyridine-furan springs at large time and length scales and open field for further computational research of large bistable systems.
ISSN:2331-8422