English (United Kingdom)

https://curated-unify.zendy.io/wp-json/zendy-region/v1/featured_content/oa?rat=en

https://curated-unify.zendy.io/wp-json/zendy-region/v1/highlighted_journal/

Global: Zendy Plus annual

Presents the access of premium content as premium feature

Premium Content

Presents the keyphrase highlighting as premium feature

Keyphrase Highlighting

Presents the summarisation as premium feature

Summarisation

Insights

Presents the pdf analysis as premium feature

PDF Analysis

Presents the zaia usage as premium feature

ZAIA

Global: Zendy Tools annual

Global: Zendy Free Plan

Global: Zendy Tools monthly

Global: Zendy Plus monthly

A Markov state model of the dynamics of a protein-like chain immersed in animplicit hard sphere solvent is derived from first principles for a system ofmonomers that interact via discontinuous potentials designed to account forlocal structure and bonding in a coarse-grained sense. The model is based onthe assumption that the implicit solvent interacts on a fast time scale withthe monomers of the chain compared to the time scale for structuralrearrangements of the chain and provides sufficient friction so that the motionof monomers is governed by the Smoluchowski equation. A microscopic theory forthe dynamics of the system is developed that reduces to a Markovian model ofthe kinetics under well-defined conditions. Microscopic expressions for therate constants that appear in the Markov state model are analyzed and expressedin terms of a temperature-dependent linear combination of escape rates thatthemselves are independent of temperature. The Markov model is studied byanalyzing the eigenvalues and eigenvectors of the matrix of transition rates,and the equilibration process for a simple helix-forming system from anensemble of initially extended configurations to mainly folded configurationsis investigated as a function of temperature for a number of different chainlengths. For short chains, the relaxation is primarily single-exponential andbecomes independent of temperature in the low-temperature regime. The profileis more complicated for longer chains, where multi-exponential relaxationbehavior is seen at intermediate temperatures followed by a low temperatureregime in which the folding becomes rapid and single exponential. It isdemonstrated that the behavior of the equilibration profile as the temperatureis lowered can be understood in terms of the number of relaxation modes or``folding pathways'' that contribute to the evolution of the state populations.

Derivation of a Markov state model of the dynamics of a protein-like chain immersed in an implicit solvent