Literature DB >> 32113343

Microcanonical coarse-graining of the kinetic Ising model.

Daniel Sigg1, Vincent A Voelz2, Vincenzo Carnevale3.   

Abstract

We propose a scheme for coarse-graining the dynamics of the 2-D kinetic Ising model onto the microcanonical ensemble. At subcritical temperatures, 2-D and higher-dimensional Ising lattices possess two basins of attraction separated by a free energy barrier. Projecting onto the microcanonical ensemble has the advantage that the dependence of the crossing rate constant on environmental conditions can be obtained from a single Monte Carlo trajectory. Using various numerical methods, we computed the forward rate constants of coarse-grained representations of the Ising model and compared them with the true value obtained from brute force simulation. While coarse-graining preserves detailed balance, the computed rate constants for barrier heights between 5 kT and 9 kT were consistently 50% larger than the true value. Markovianity testing revealed loss of dynamical memory, which we propose accounts for coarse-graining error. Committor analysis did not support the alternative hypothesis that microcanonical projection is incompatible with an optimal reaction coordinate. The correct crossing rate constant was obtained by spectrally decomposing the diffusion coefficient near the free energy barrier and selecting the slowest (reactive) component. The spectral method also yielded the correct rate constant in the 3-D Ising lattice, where coarse-graining error was 6% and memory effects were diminished. We conclude that microcanonical coarse-graining supplemented by spectral analysis of short-term barrier fluctuations provides a comprehensive kinetic description of barrier crossing in a non-inertial continuous-time jump process.

Entities:  

Year:  2020        PMID: 32113343      PMCID: PMC7042020          DOI: 10.1063/1.5139228

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


  25 in total

1.  New Monte Carlo technique for studying phase transitions.

Authors: 
Journal:  Phys Rev Lett       Date:  1988-12-05       Impact factor: 9.161

2.  Hit and miss of classical nucleation theory as revealed by a molecular simulation study of crystal nucleation in supercooled sulfur hexafluoride.

Authors:  Jean-Marc Leyssale; Jérôme Delhommelle; Claude Millot
Journal:  J Chem Phys       Date:  2007-07-28       Impact factor: 3.488

3.  Voltage-dependent gating at the KcsA selectivity filter.

Authors:  Julio F Cordero-Morales; Luis G Cuello; Eduardo Perozo
Journal:  Nat Struct Mol Biol       Date:  2006-03-12       Impact factor: 15.369

4.  Diffusion along the splitting/commitment probability reaction coordinate.

Authors:  Alexander M Berezhkovskii; Attila Szabo
Journal:  J Phys Chem B       Date:  2013-07-03       Impact factor: 2.991

5.  Kramers' diffusion theory applied to gating kinetics of voltage-dependent ion channels.

Authors:  D Sigg; H Qian; F Bezanilla
Journal:  Biophys J       Date:  1999-02       Impact factor: 4.033

6.  Microcanonical ensemble Monte Carlo method for discrete systems.

Authors: 
Journal:  Phys Rev E Stat Phys Plasmas Fluids Relat Interdiscip Topics       Date:  1996-04

7.  Total charge movement per channel. The relation between gating charge displacement and the voltage sensitivity of activation.

Authors:  D Sigg; F Bezanilla
Journal:  J Gen Physiol       Date:  1997-01       Impact factor: 4.086

8.  A linkage analysis toolkit for studying allosteric networks in ion channels.

Authors:  Daniel Sigg
Journal:  J Gen Physiol       Date:  2012-12-17       Impact factor: 4.086

9.  Voltage-dependent gating in a "voltage sensor-less" ion channel.

Authors:  Harley T Kurata; Markus Rapedius; Marc J Kleinman; Thomas Baukrowitz; Colin G Nichols
Journal:  PLoS Biol       Date:  2010-02-23       Impact factor: 8.029

10.  History-dependent Dynamics in a Generic Model of Ion Channels - an Analytic Study.

Authors:  Daniel Soudry; Ron Meir
Journal:  Front Comput Neurosci       Date:  2010-04-08       Impact factor: 2.380

View more
  1 in total

1.  Optimal Population Coding for Dynamic Input by Nonequilibrium Networks.

Authors:  Kevin S Chen
Journal:  Entropy (Basel)       Date:  2022-04-25       Impact factor: 2.738

  1 in total

北京卡尤迪生物科技股份有限公司 © 2022-2023.