Evidence map›Paper›PMID 39579131›Full record

ArticleJournal of chemical theory and computation2024

Thermodynamic Transferability in Coarse-Grained Force Fields Using Graph Neural Networks.

Emily Shinkle, Aleksandra Pachalieva, Riti Bahl, Sakib Matin, Brendan Gifford, Galen T Craven, Nicholas Lubbers

Abstract read
In one paragraph

Article in Journal of chemical theory and computation, 2024. 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.

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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

7 authors.

Emily ShinkleComputer, Computational, and Statistical Sciences Division, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, United States.ORCID 0000-0003-2255-0540
Aleksandra PachalievaEarth and Environmental Sciences Division, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, United States.ORCID 0000-0003-1246-0410
Riti BahlDepartment of Mathematics, Emory University, Atlanta, Georgia 30322, United States.
Sakib MatinTheoretical Division, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, United States.
Brendan GiffordTheoretical Division, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, United States.ORCID 0000-0002-4116-711X
Galen T CravenTheoretical Division, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, United States.
Nicholas LubbersComputer, Computational, and Statistical Sciences Division, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, United States.ORCID 0000-0002-9001-9973

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

Coarse-graining is a molecular modeling technique in which an atomistic system is represented in a simplified fashion that retains the most significant system features that contribute to a target output while removing the degrees of freedom that are less relevant. This reduction in model complexity allows coarse-grained molecular simulations to reach increased spatial and temporal scales compared with corresponding all-atom models. A core challenge in coarse-graining is to construct a force field that represents the interactions in the new representation in a way that preserves the atomistic-level properties. Many approaches to building coarse-grained force fields have limited transferability between different thermodynamic conditions as a result of averaging over internal fluctuations at a specific thermodynamic state point. Here, we use a graph-convolutional neural network architecture, the Hierarchically Interacting Particle Neural Network with Tensor Sensitivity (HIP-NN-TS), to develop a highly automated training pipeline for coarse-grained force fields, which allows for studying the transferability of coarse-grained models based on the force-matching approach. We show that this approach yields not only highly accurate force fields but also that these force fields are more transferable through a variety of thermodynamic conditions. These results illustrate the potential of machine learning techniques, such as graph neural networks, to improve the construction of transferable coarse-grained force fields.

Identifiers

PMID39579131
PMCPMC11635977

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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.