Evidence map›Paper›PMID 32113343›Full record

ArticleThe Journal of chemical physics2020

Microcanonical coarse-graining of the kinetic Ising model.

Daniel Sigg, Vincent A Voelz, Vincenzo Carnevale

Abstract read
In one paragraph

Article in The Journal of chemical physics, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 1 paper.

0numbers the graph read from it
0cells of the map it votes in
1citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

1 citing paper in PubMed.

  1. Article
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

3 authors.

Daniel SiggdPET, Spokane, Washington 99223, USA.ORCID 0000000349442988
Vincent A VoelzDepartment of Chemistry, Temple University, Philadelphia, Pennsylvania 19122, USA.ORCID 0000000210542124
Vincenzo CarnevaleInstitute for Computational Molecular Science, College of Science and Technology, Temple University, Philadelphia, Pennsylvania 19122, USA.ORCID 0000000219188280

Funding

Regulation of the Intestinal Ca2+ Channels TRPV6R01GM093290 · NIGMS · UNIV OF MED/DENT OF NJ-NJ MEDICAL SCHOOL · PI CARNEVALE, VINCENZO, ROHACS, TIBOR · 2011 to 2025
$4.9M
Markov State Model approaches for folding, binding and designR01GM123296 · NIGMS · TEMPLE UNIV OF THE COMMONWEALTH · PI VOELZ, VINCENT · 2017 to 2025
$3.1M
Molecular mechanism of TRPV1 activationR01GM131048 · NIGMS · TEMPLE UNIV OF THE COMMONWEALTH · PI CARNEVALE, VINCENZO, ROHACS, TIBOR · 2019 to 2022
$1.4M
Computer Cluster for Computational Biology and BiophysicsS10OD020095 · OD · TEMPLE UNIV OF THE COMMONWEALTH · PI LEVY, RONALD · 2015 to 2015
$442k
NIGMS NIH HHS R01 GM093290NIGMS NIH HHS R01 GM123296NIGMS NIH HHS R01 GM131048NIH HHS S10 OD020095
6 · The paper itself

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.

Identifiers

PMID32113343
PMCPMC7042020

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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.