Evidence map›Paper›PMID 32975948›Full record

ArticleJournal of chemical theory and computation2020

Temperature and Phase Transferable Bottom-up Coarse-Grained Models.

Jaehyeok Jin, Alvin Yu, Gregory A Voth

Abstract read
In one paragraph

Article in Journal of chemical theory and computation, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.

0numbers the graph read from it
0cells of the map it votes in
19citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

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

19 citing papers in PubMed.

  1. Article
  2. Article
  3. Article
  4. Article
  5. Article
  6. Article
  7. Article
  8. OpenMSCG: A Software Tool for Bottom-Up Coarse-Graining.The journal of physical chemistry. B · 2023
    Article
  9. Article
  10. Article
  11. Article
  12. Article
  13. Bottom-up Coarse-Graining: Principles and Perspectives.Journal of chemical theory and computation · 2022
    Review
  14. Article
  15. Article
  16. "Dividing and Conquering" and "Caching" in Molecular Modeling.International journal of molecular sciences · 2021
    Review
  17. Article
  18. Article
  19. Review
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.

Jaehyeok JinDepartment of Chemistry, Chicago Center for Theoretical Chemistry, James Franck Institute, and Institute for Biophysical Dynamics, The University of Chicago, 5735 S. Ellis Avenue, Chicago, Illinois 60637, United States.ORCID http://orcid.org/0000-0003-3859-3545
Alvin YuDepartment of Chemistry, Chicago Center for Theoretical Chemistry, James Franck Institute, and Institute for Biophysical Dynamics, The University of Chicago, 5735 S. Ellis Avenue, Chicago, Illinois 60637, United States.
Gregory A VothDepartment of Chemistry, Chicago Center for Theoretical Chemistry, James Franck Institute, and Institute for Biophysical Dynamics, The University of Chicago, 5735 S. Ellis Avenue, Chicago, Illinois 60637, United States.ORCID http://orcid.org/0000-0002-3267-6748

Funding

Computational and Theoretical Studies of Retroviral Replication - ResubmissionF32AI150208 · NIAID · UNIVERSITY OF CHICAGO · PI YU, ALVIN · 2020 to 2022
$147k
NIAID NIH HHS F32 AI150208
6 · The paper itself

Abstract

Despite the high fidelity of bottom-up coarse-grained (CG) approaches to recapitulate the structural correlations in atomistic simulations, the general use of bottom-up CG methods is limited because of the nontransferable nature of these CG models under different thermodynamic conditions. Because bottom-up CG potentials usually correspond to configuration-dependent free energies of the system, recent studies have focused on adjusting enthalpic or entropic contributions to account for issues with transferability. However, these approaches can require a manual adjustment of the CG interaction a priori and are usually limited to constant volume ensembles. To overcome these limitations, we construct temperature and phase transferable CG models under constant pressure by developing the ultra-coarse-graining (UCG) methodology in the mean-field limit. In the mean-field ansatz, an embedded semi-global order parameter recapitulates global changes to the system by automatically adjusting the effective CG interactions, thus bridging free energy decompositions with UCG theory. The method presented is designed to faithfully capture structural correlations under different thermodynamic conditions, using a single UCG model. Specifically, we test the applicability of the developed theory in three distinct cases: (1) different temperatures at constant pressure in liquids, (2) different temperatures across thermodynamic phases, and (3) liquid/vapor interfaces. We demonstrate that the systematic construction of both temperature and phase transferable bottom-up CG models is possible using this generalized UCG theory. Based on our findings, this approach significantly extends the transferability and applicability of the bottom-up CG theory and method.

Identifiers

PMID32975948
PMCPMC8631167

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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.