Literature DB >> 34241169

Crowding breaks the forward/backward symmetry of transition times in biased random walks.

Jaeoh Shin1, Alexander M Berezhkovskii2, Anatoly B Kolomeisky1.   

Abstract

Microscopic mechanisms of natural processes are frequently understood in terms of random walk models by analyzing local particle transitions. This is because these models properly account for dynamic processes at the molecular level and provide a clear physical picture. Recent theoretical studies made a surprising discovery that in complex systems, the symmetry of molecular forward/backward transition times with respect to local bias in the dynamics may be broken and it may take longer to go downhill than uphill. The physical origins of these phenomena remain not fully understood. Here, we explore in more detail the microscopic features of the symmetry breaking in the forward/backward transition times by analyzing exactly solvable discrete-state stochastic models. In particular, we consider a specific case of two random walkers on a four-site periodic lattice as the way to represent the general systems with multiple pathways. It is found that the asymmetry in transition times depends on several factors that include the degree of deviation from equilibrium, the particle crowding, and methods of measurements of dynamic properties. Our theoretical analysis suggests that the asymmetry in transition times can be explored experimentally for determining the important microscopic features of natural processes by quantitatively measuring the local deviations from equilibrium and the degrees of crowding.

Entities:  

Year:  2021        PMID: 34241169      PMCID: PMC8411889          DOI: 10.1063/5.0053634

Source DB:  PubMed          Journal:  J Chem Phys        ISSN: 0021-9606            Impact factor:   4.304


  14 in total

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Journal:  Phys Rev E Stat Nonlin Soft Matter Phys       Date:  2006-04-21

3.  The theory of ion transport through membrane channels.

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Review 4.  Random walk models in biology.

Authors:  Edward A Codling; Michael J Plank; Simon Benhamou
Journal:  J R Soc Interface       Date:  2008-08-06       Impact factor: 4.118

Review 5.  Single-Molecule Studies in Live Cells.

Authors:  Ji Yu
Journal:  Annu Rev Phys Chem       Date:  2016-04-08       Impact factor: 12.703

6.  Asymmetry of forward/backward transition times as a non-equilibrium measure of complexity of microscopic mechanisms.

Authors:  Jaeoh Shin; Anatoly B Kolomeisky
Journal:  J Chem Phys       Date:  2020-09-28       Impact factor: 3.488

7.  Biased Random Walk in Crowded Environment: Breaking Uphill/Downhill Symmetry of Transition Times.

Authors:  Jaeoh Shin; Alexander M Berezhkovskii; Anatoly B Kolomeisky
Journal:  J Phys Chem Lett       Date:  2020-05-27       Impact factor: 6.475

8.  Mechanisms of Protein Search for Targets on DNA: Theoretical Insights.

Authors:  Alexey A Shvets; Maria P Kochugaeva; Anatoly B Kolomeisky
Journal:  Molecules       Date:  2018-08-22       Impact factor: 4.411

9.  Experimental evidence of symmetry breaking of transition-path times.

Authors:  J Gladrow; M Ribezzi-Crivellari; F Ritort; U F Keyser
Journal:  Nat Commun       Date:  2019-01-04       Impact factor: 14.919

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  1 in total

1.  Inferring entropy production rate from partially observed Langevin dynamics under coarse-graining.

Authors:  Aishani Ghosal; Gili Bisker
Journal:  Phys Chem Chem Phys       Date:  2022-10-12       Impact factor: 3.945

  1 in total

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