Literature DB >> 28475835

Mean Direct-Transit and Looping Times as Functions of the Potential Shape.

Alexander M Berezhkovskii1,2, Leonardo Dagdug1,2, Sergey M Bezrukov1.   

Abstract

Any trajectory of a diffusing particle making a transition between two end points of an interval can be divided into two segments, which we call direct-transit and looping parts. The former is the final segment of the trajectory, when the particle goes from one end point of the interval to the opposite end point, without retouching the starting point. The rest of the trajectory is the looping part. We study mean durations of the two parts in the presence of a symmetric linear cusp potential which, depending on the parameter values, forms either a barrier or a well between the end points. For the cusp barrier, we find that the mean direct-transit time decreases as the barrier height increases at a fixed interval length. This happens because the increase in the barrier height results in the increase of the magnitude of the force acting on the particle on both sides of the barrier. Interestingly, though the mean looping and direct-transit times are different in the case of the barrier and well potentials with equal height and depth, respectively, the mean first-passage times for the two cases are identical.

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Year:  2017        PMID: 28475835      PMCID: PMC5580047          DOI: 10.1021/acs.jpcb.7b04037

Source DB:  PubMed          Journal:  J Phys Chem B        ISSN: 1520-5207            Impact factor:   2.991


  35 in total

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4.  Diffusion model of solute dynamics in a membrane channel: mapping onto the two-site model and optimizing the flux.

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5.  Transition times in the low-noise limit of stochastic dynamics.

Authors:  Sergey V Malinin; Vladimir Y Chernyak
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6.  Single-molecule fluorescence experiments determine protein folding transition path times.

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7.  Transition path times for nucleic Acid folding determined from energy-landscape analysis of single-molecule trajectories.

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8.  Direct observation of transition paths during the folding of proteins and nucleic acids.

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9.  Fast single-molecule FRET spectroscopy: theory and experiment.

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View more
  8 in total

1.  Exact Solutions for Distributions of First-Passage, Direct-Transit, and Looping Times in Symmetric Cusp Potential Barriers and Wells.

Authors:  Alexander M Berezhkovskii; Leonardo Dagdug; Sergey M Bezrukov
Journal:  J Phys Chem B       Date:  2019-04-23       Impact factor: 2.991

2.  Communication: Transition-path velocity as an experimental measure of barrier crossing dynamics.

Authors:  Alexander M Berezhkovskii; Dmitrii E Makarov
Journal:  J Chem Phys       Date:  2018-05-28       Impact factor: 3.488

3.  A new insight into diffusional escape from a biased cylindrical trap.

Authors:  Alexander M Berezhkovskii; Leonardo Dagdug; Sergey M Bezrukov
Journal:  J Chem Phys       Date:  2017-09-14       Impact factor: 3.488

4.  First passage, looping, and direct transition in expanding and narrowing tubes: Effects of the entropy potential.

Authors:  Alexander M Berezhkovskii; Leonardo Dagdug; Sergey M Bezrukov
Journal:  J Chem Phys       Date:  2017-10-07       Impact factor: 3.488

5.  Communication: Coordinate-dependent diffusivity from single molecule trajectories.

Authors:  Alexander M Berezhkovskii; Dmitrii E Makarov
Journal:  J Chem Phys       Date:  2017-11-28       Impact factor: 3.488

6.  Membrane Permeability: Characteristic Times and Lengths for Oxygen and a Simulation-Based Test of the Inhomogeneous Solubility-Diffusion Model.

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Journal:  J Chem Theory Comput       Date:  2018-06-28       Impact factor: 6.006

7.  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

8.  Inferring potential landscapes from noisy trajectories of particles within an optical feedback trap.

Authors:  J Shepard Bryan; Prithviraj Basak; John Bechhoefer; Steve Pressé
Journal:  iScience       Date:  2022-07-19
  8 in total

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