First passage time distribution in stochastic processes with moving and static absorbing boundaries with application to biological rupture experiments.

The Journal of Chemical Physics
Zhonghan HuB J Berne

Abstract

We develop and investigate an integral equation connecting the first passage time distribution of a stochastic process in the presence of an absorbing boundary condition and the corresponding Green's function in the absence of the absorbing boundary. Analytical solutions to the integral equations are obtained for three diffusion processes in time-independent potentials which have been previously investigated by other methods. The integral equation provides an alternative way to analytically solve the three diffusion-controlled reactive processes. In order to help analyze biological rupture experiments, we further investigate the numerical solutions of the integral equation for a diffusion process in a time-dependent potential. Our numerical procedure, based on the exact integral equation, avoids the adiabatic approximation used in previous analytical theories and is useful for fitting the rupture force distribution data from single-molecule pulling experiments or molecular dynamics simulation data, especially at larger pulling speeds, larger cantilever spring constants, and smaller reaction rates. Stochastic simulation results confirm the validity of our numerical procedure. We suggest combining a previous analytical theory wit...Continue Reading

References

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Citations

Oct 10, 2014·Chemical Communications : Chem Comm·Zhonghan Hu
Aug 10, 2013·The Journal of Chemical Physics·Hiroshi FujisakiAkinori Kidera
Apr 8, 2014·Proceedings of the National Academy of Sciences of the United States of America·Rob MorrisJuan Carlos Izpisua Belmonte
Oct 29, 2014·The European Physical Journal. E, Soft Matter·V K Gupta
Jun 19, 2016·Proceedings of the National Academy of Sciences of the United States of America·Michael HinczewskiD Thirumalai
Aug 1, 2014·Nature Communications·Jakob T BullerjahnKlaus Kroy
Sep 26, 2012·Physical Review Letters·Christian KappelHelmut Grubmüller
Aug 16, 2013·Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics·Diandrew Lexter Dy, Jose Perico Esguerra
Feb 18, 2017·Physical Review. E·Deepika Janakiraman
Apr 8, 2017·The Journal of Chemical Physics·Stefan Jaschonek, Gregor Diezemann
Mar 22, 2018·Physical Chemistry Chemical Physics : PCCP·Markus SelmkeHaw Yang
Mar 3, 2017·The Journal of Chemical Physics·Yunyun LiFabio Marchesoni
Feb 20, 2019·Physical Review. E·Axel Masó-PuigdellosasVicenç Méndez
Apr 17, 2018·Royal Society Open Science·Giacomo BoncioliniNicolas Noiray
Mar 13, 2021·Physical Review Letters·Harish CharanItamar Procaccia
Dec 15, 2017·Langmuir : the ACS Journal of Surfaces and Colloids·Keith M CarrollUrs Duerig

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Methods Mentioned

BETA
atomic force spectroscopy

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