Evidence map›Paper›PMID 33514078›Full record

ArticleThe Journal of chemical physics2021

A new one-site coarse-grained model for water: Bottom-up many-body projected water (BUMPer). II. Temperature transferability and structural properties at low temperature.

Jaehyeok Jin, Alexander J Pak, Yining Han, Gregory A Voth

Abstract read
In one paragraph

Article in The Journal of chemical physics, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 3 papers.

0numbers the graph read from it
0cells of the map it votes in
3citing 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

3 citing papers in PubMed.

  1. Article
  2. OpenMSCG: A Software Tool for Bottom-Up Coarse-Graining.The journal of physical chemistry. B · 2023
    Article
  3. Bottom-up Coarse-Graining: Principles and Perspectives.Journal of chemical theory and computation · 2022
    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

4 authors.

Jaehyeok JinDepartment of Chemistry, Chicago Center for Theoretical Chemistry, Institute for Biophysical Dynamics, and James Franck Institute, The University of Chicago, Chicago, Illinois 60637, USA.ORCID 0000000338593545
Alexander J PakDepartment of Chemistry, Chicago Center for Theoretical Chemistry, Institute for Biophysical Dynamics, and James Franck Institute, The University of Chicago, Chicago, Illinois 60637, USA.ORCID 0000000328236480
Yining HanDepartment of Chemistry, Chicago Center for Theoretical Chemistry, Institute for Biophysical Dynamics, and James Franck Institute, The University of Chicago, Chicago, Illinois 60637, USA.ORCID 0000000265772015
Gregory A VothDepartment of Chemistry, Chicago Center for Theoretical Chemistry, Institute for Biophysical Dynamics, and James Franck Institute, The University of Chicago, Chicago, Illinois 60637, USA.ORCID 0000000232676748

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

A number of studies have constructed coarse-grained (CG) models of water to understand its anomalous properties. Most of these properties emerge at low temperatures, and an accurate CG model needs to be applicable to these low-temperature ranges. However, direct use of CG models parameterized from other temperatures, e.g., room temperature, encounters a problem known as transferability, as the CG potential essentially follows the form of the many-body CG free energy function. Therefore, temperature-dependent changes to CG interactions must be accounted for. The collective behavior of water at low temperature is generally a many-body process, which often motivates the use of expensive many-body terms in the CG interactions. To surmount the aforementioned problems, we apply the Bottom-Up Many-Body Projected Water (BUMPer) CG model constructed from Paper I to study the low-temperature behavior of water. We report for the first time that the embedded three-body interaction enables BUMPer, despite its pairwise form, to capture the growth of ice at the ice/water interface with corroborating many-body correlations during the crystal growth. Furthermore, we propose temperature transferable BUMPer models that are indirectly constructed from the free energy decomposition scheme. Changes in CG interactions and corresponding structures are faithfully recapitulated by this framework. We further extend BUMPer to examine its ability to predict the structure, density, and diffusion anomalies by employing an alternative analysis based on structural correlations and pairwise potential forms to predict such anomalies. The presented analysis highlights the existence of these anomalies in the low-temperature regime and overcomes potential transferability problems.

Identifiers

PMID33514078
PMCPMC7826166

What OpenQuestion holds

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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.