Literature DB >> 23277928

First passage times in homogeneous nucleation and self-assembly.

Romain Yvinec1, Maria R D'Orsogna, Tom Chou.   

Abstract

Motivated by nucleation and molecular aggregation in physical, chemical, and biological settings, we present a thorough analysis of the general problem of stochastic self-assembly of a fixed number of identical particles in a finite volume. We derive the backward Kolmogorov equation (BKE) for the cluster probability distribution. From the BKE, we study the distribution of times it takes for a single maximal cluster to be completed, starting from any initial particle configuration. In the limits of slow and fast self-assembly, we develop analytical approaches to calculate the mean cluster formation time and to estimate the first assembly time distribution. We find, both analytically and numerically, that faster detachment can lead to a shorter mean time to first completion of a maximum-sized cluster. This unexpected effect arises from a redistribution of trajectory weights such that upon increasing the detachment rate, paths that take a shorter time to complete a cluster become more likely.

Entities:  

Year:  2012        PMID: 23277928     DOI: 10.1063/1.4772598

Source DB:  PubMed          Journal:  J Chem Phys        ISSN: 0021-9606            Impact factor:   3.488


  7 in total

1.  Kinetics of aggregation with a finite number of particles and application to viral capsid assembly.

Authors:  Nathanael Hoze; David Holcman
Journal:  J Math Biol       Date:  2014-08-08       Impact factor: 2.259

Review 2.  How and why to build a mathematical model: A case study using prion aggregation.

Authors:  Mikahl Banwarth-Kuhn; Suzanne Sindi
Journal:  J Biol Chem       Date:  2020-01-31       Impact factor: 5.157

3.  Slack reactants: A state-space truncation framework to estimate quantitative behavior of the chemical master equation.

Authors:  Jinsu Kim; Jason Dark; German Enciso; Suzanne Sindi
Journal:  J Chem Phys       Date:  2020-08-07       Impact factor: 3.488

4.  Speed limits of protein assembly with reversible membrane localization.

Authors:  Bhavya Mishra; Margaret E Johnson
Journal:  J Chem Phys       Date:  2021-05-21       Impact factor: 3.488

5.  Generalizing a mathematical model of prion aggregation allows strain coexistence and co-stability by including a novel misfolded species.

Authors:  Paul Lemarre; Laurent Pujo-Menjouet; Suzanne S Sindi
Journal:  J Math Biol       Date:  2018-08-16       Impact factor: 2.259

6.  Stochastic yield catastrophes and robustness in self-assembly.

Authors:  Florian M Gartner; Isabella R Graf; Patrick Wilke; Philipp M Geiger; Erwin Frey
Journal:  Elife       Date:  2020-02-05       Impact factor: 8.140

7.  A kinetic approach to the sequence-aggregation relationship in disease-related protein assembly.

Authors:  Bogdan Barz; David J Wales; Birgit Strodel
Journal:  J Phys Chem B       Date:  2014-01-17       Impact factor: 2.991

  7 in total

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