Evidence map›Paper›PMID 31319036›Full record

ArticleThe journal of physical chemistry letters2019

Understanding Missing Entropy in Coarse-Grained Systems: Addressing Issues of Representability and Transferability.

Jaehyeok Jin, Alexander J Pak, Gregory A Voth

Abstract read
In one paragraph

Article in The journal of physical chemistry letters, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers.

0numbers the graph read from it
0cells of the map it votes in
20citing 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

20 citing papers in PubMed.

  1. Article
  2. Article
  3. Article
  4. Article
  5. Changing Your Martini Can Still Give You a Hangover.Journal of chemical theory and computation · 2024
    Article
  6. Article
  7. OpenMSCG: A Software Tool for Bottom-Up Coarse-Graining.The journal of physical chemistry. B · 2023
    Article
  8. Review
  9. Article
  10. Article
  11. Bottom-up Coarse-Graining: Principles and Perspectives.Journal of chemical theory and computation · 2022
    Review
  12. Article
  13. Article
  14. Accurate model of liquid-liquid phase behavior of intrinsically disordered proteins from optimization of single-chain properties.Proceedings of the National Academy of Sciences of the United States of America · 2021
    Article
  15. Article
  16. Article
  17. Article
  18. ACS omega · 2020
    Article
  19. Article
  20. Temperature and Phase Transferable Bottom-up Coarse-Grained Models.Journal of chemical theory and computation · 2020
    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.

Jaehyeok JinDepartment of Chemistry, James Franck Institute, and Institute for Biophysical Dynamics , The University of Chicago , 5735 South Ellis Avenue , Chicago , Illinois 60637 , United States.
Alexander J PakDepartment of Chemistry, James Franck Institute, and Institute for Biophysical Dynamics , The University of Chicago , 5735 South Ellis Avenue , Chicago , Illinois 60637 , United States.
Gregory A VothDepartment of Chemistry, James Franck Institute, and Institute for Biophysical Dynamics , The University of Chicago , 5735 South Ellis Avenue , Chicago , Illinois 60637 , United States.ORCID http://orcid.org/0000-0002-3267-6748

Funding

Computational Insights into Assembly, Budding, and Maturation during HIV-1 ReplicationF32AI150477 · NIAID · UNIVERSITY OF CHICAGO · PI PAK, ALEXANDER · 2019 to 2019
$64k
NIAID NIH HHS F32 AI150477
6 · The paper itself

Abstract

Coarse-grained (CG) models facilitate efficient simulation of complex systems by integrating out the atomic, or fine-grained (FG), degrees of freedom. Systematically derived CG models from FG simulations often attempt to approximate the CG potential of mean force (PMF), an inherently multidimensional and many-body quantity, using additive pairwise contributions. However, they currently lack fundamental principles that enable their extensible use across different thermodynamic state points, i.e., transferability. In this work, we investigate the explicit energy-entropy decomposition of the CG PMF as a means to construct transferable CG models. In particular, despite its high-dimensional nature, we find for liquid systems that the entropic component to the CG PMF can similarly be represented using additive pairwise contributions, which we show is highly coupled to the CG configurational entropy. This approach formally connects the missing entropy that is lost due to the CG representation, i.e., translational, rotational, and vibrational modes associated with the missing degrees of freedom, to the CG entropy. By design, the present framework imparts transferable CG interactions across different temperatures due to the explicit definition of an additive entropic contribution. Furthermore, we demonstrate that transferability across composition state points, such as between bulk liquids and their mixtures, is also achieved by designing combining rules to approximate cross-interactions from bulk CG PMFs. Using the predicted CG model for liquid mixtures, structural correlations of the fitted CG model were found to corroborate a high-fidelity combining rule. Our findings elucidate the physical nature and compact representation of CG entropy and suggest a new approach for overcoming the transferability problem. We expect that this approach will further extend the current view of CG modeling into predictive multiscale modeling.

Identifiers

PMID31319036
PMCPMC6782054

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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.