Evidence map›Paper›PMID 39574694›Full record

ArticlebioRxiv : the preprint server for biology2024

Unveiling Nucleosome Dynamics: A Comparative Study Using All-Atom and Coarse-Grained Simulations Enhanced by Principal Component Analysis.

Abhik Ghosh Moulick, Rutika Patel, Augustine Onyema, Sharon M Loverde

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PubMed Full text at PMC Publisher
In one paragraph

Article in bioRxiv : the preprint server for biology, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.

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

0 citing papers in PubMed.

No citing paper in PubMed yet.

4 · The record

Corrections and comments

5 · Who and what money

Authors and funding

4 authors.

Abhik Ghosh MoulickDepartment of Chemistry, College of Staten Island, City University of New York, 2800 Victory Blvd., 6S-238, Staten Island, NY 10314.ORCID 0000-0002-1960-6729
Rutika PatelDepartment of Chemistry, College of Staten Island, City University of New York, 2800 Victory Blvd., 6S-238, Staten Island, NY 10314.
Augustine OnyemaDepartment of Chemistry, College of Staten Island, City University of New York, 2800 Victory Blvd., 6S-238, Staten Island, NY 10314.
Sharon M LoverdeDepartment of Chemistry, College of Staten Island, City University of New York, 2800 Victory Blvd., 6S-238, Staten Island, NY 10314.ORCID 0000-0002-7643-6498

Funding

Breakthrough Molecular Dynamics Research via an Anton2 SupercomputerR01GM116961 · NIGMS · CARNEGIE-MELLON UNIVERSITY · PI BLOOD, PHILIP D. · 2016 to 2023
$3.0M
Computational Methods to Characterize Structure and Dynamics of the Nucleosome Core ParticleR15GM146228 · NIGMS · COLLEGE OF STATEN ISLAND · PI LOVERDE, SHARON MARIE · 2022 to 2023
$586k
NIGMS NIH HHS R01 GM116961NIGMS NIH HHS R15 GM146228
6 · The paper itself

Abstract

This study investigates nucleosome dynamics using both all-atom and coarse-grained (CG) molecular dynamics simulations, focusing on the SIRAH force field. Simulations are performed for two nucleosomal DNA sequences-ASP and Widom-601-over six microseconds at physiological salt concentrations. Comparative analysis of structural parameters, such as groove widths and base pair geometries, reveals good agreement between atomistic and CG models, though CG simulations exhibit broader conformational sampling and greater breathing motion of DNA ends. Principal component analysis (PCA) is applied to DNA structural parameters, revealing multiple free energy minima, especially in CG simulations. These findings highlight the potential of the SIRAH CG force field for studying large-scale nucleosome dynamics, offering insights into DNA repositioning and sequence-dependent behavior.

Indexed as

all-atomCoarse-grainedNucleosomeprincipal component analysisSIRAH

Identifiers

PMID39574694
PMCPMC11580959

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.