Evidence map›Paper›PMID 36976890›Full record

ArticleJournal of chemical information and modeling2023

Soft Matter under Pressure: Pushing Particle-Field Molecular Dynamics to the Isobaric Ensemble.

Samiran Sen, Morten Ledum, Sigbjørn Løland Bore, Michele Cascella

Open access · hybridAbstract read
In one paragraph

Article in Journal of chemical information and modeling, 2023. 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
1.5field-weighted citation impact, top 18% of its field
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, 10 citations in OpenAlex.

  1. Article
  2. Article
  3. 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

4 authors at 1 institution in 1 country.

Samiran SenHylleraas Centre for Quantum Molecular Sciences and Department of Chemistry, University of Oslo, P.O. Box 1033 Blindern, 0315 Oslo, Norway.ORCID 0000-0002-1922-7796
Morten LedumHylleraas Centre for Quantum Molecular Sciences and Department of Chemistry, University of Oslo, P.O. Box 1033 Blindern, 0315 Oslo, Norway.ORCID 0000-0003-4244-4876
Sigbjørn Løland BoreHylleraas Centre for Quantum Molecular Sciences and Department of Chemistry, University of Oslo, P.O. Box 1033 Blindern, 0315 Oslo, Norway.ORCID 0000-0002-8620-4885
Michele CascellaHylleraas Centre for Quantum Molecular Sciences and Department of Chemistry, University of Oslo, P.O. Box 1033 Blindern, 0315 Oslo, Norway.ORCID 0000-0003-2266-5399
University of Oslo · NO

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

Hamiltonian hybrid particle-field molecular dynamics is a computationally efficient method to study large soft matter systems. In this work, we extend this approach to constant-pressure (NPT) simulations. We reformulate the calculation of internal pressure from the density field by taking into account the intrinsic spread of the particles in space, which naturally leads to a direct anisotropy in the pressure tensor. The anisotropic contribution is crucial for reliably describing the physics of systems under pressure, as demonstrated by a series of tests on analytical and monatomic model systems as well as realistic water/lipid biphasic systems. Using Bayesian optimization, we parametrize the field interactions of phospholipids to reproduce the structural properties of their lamellar phases, including area per lipid, and local density profiles. The resulting model excels in providing pressure profiles in qualitative agreement with all-atom modeling, and surface tension and area compressibility in quantitative agreement with experimental values, indicating the correct description of long-wavelength undulations in large membranes. Finally, we demonstrate that the model is capable of reproducing the formation of lipid droplets inside a lipid bilayer.

Indexed as

Lipid BilayersMolecular Dynamics SimulationBayes TheoremPhospholipidsSurface TensionLipid BilayersPhospholipids

Identifiers

PMID36976890
PMCPMC10091448
OpenAlexW4361029758

What OpenQuestion holds

Textmetadata
LicenceCC BY
Read underepoch 390

Registered trials

None linked

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.