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PreprintCited by 39Protein Structure and DynamicsAdvanced Physical and Chemical Molecular InteractionsRNA and protein synthesis mechanisms

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GENESIS CGDYN: large-scale coarse-grained MD simulation with dynamic load balancing for heterogeneous biomolecular systems

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Sugita, Yuji, Jung, Jaewoon, Tan, Cheng·2023·Nature Communications
DOI 10.21203/rs.3.rs-3327216/v1PMC PMC11032353

Preprint — published as 10.1038/s41467-024-47654-1

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Abstract

Residue-level coarse-grained (CG) molecular dynamics (MD) simulation is widely used to investigate slow biological processes that involve multiple proteins, nucleic acids, and their complexes. Biomolecules in a large simulation system are distributed non-uniformly, limiting computational efficiency with conventional methods. Here, we develop a hierarchical domain decomposition scheme with dynamic load balancing for heterogeneous biomolecular systems to keep computational efficiency even after drastic changes in particle distribution. The new schemes are applied to intrinsically disordered protein (IDP) droplet fusions. The droplet shape changes correlate with mixing IDP chains from two droplets. We also simulate formations of large IDP droplets, whose sizes are almost equivalent to those observed in microscopy. The methods have been implemented in CGDYN of the GENESIS software, which provides a new tool for investigating mesoscopic biological phenomena using the residue-level CG models.

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Metadata

Authors
Sugita, Y., Jung, J., & Tan, C.
Affiliations
  • RIKEN (JP)
  • RIKEN Center for Computational Science (JP)
Corresponding author
Sugita, Yuji
ORCID
Venue
Nature Communications
Publisher
Springer Science and Business Media LLC
Published
2023-09-25
Volume
15
Issue
1
Pages
3370-3370
ISSN
2041-1723 (ISSN-L)
DOI
10.21203/rs.3.rs-3327216/v1
PMC
PMC11032353
OpenAlex
W4394979883
Cited by
39
References
1
Citations by year
2026: 11 · 2025: 19 · 2024: 9
FWCI
5.29
Type
journal article
Language
en
Open access
Licence
Locations
  • Nature Communications (publishedVersion, cc-by)
  • bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by)
  • Research Square (acceptedVersion, cc-by)
  • PubMed Central (publishedVersion, cc-by)
  • PubMed (publishedVersion)
  • RePEc: Research Papers in Economics (submittedVersion)
  • DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
Funders
  • Ministry of Education, Culture, Sports, Science and Technology (JPMXP1020200101, 21H05282, 19H05645, JPMXP1122714694, hp210177, JPMXP1020230327, 21H05249, hp200135)
  • Japan Society for the Promotion of Science (21H05249, JPMXP1020200101, JPMXP1020230327, 21H05282, JPMXP1122714694, 19H05645)
  • RIKEN (hp200028, hp210177, 19H05645, hp200135, hp230212)
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
  • Physical Sciences › Chemistry › Physical and Theoretical Chemistry › Advanced Physical and Chemical Molecular Interactions
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA and protein synthesis mechanisms
Keywords
dynamic load balancing, hierarchical domain decomposition, intrinsically disordered proteins, protein droplets, droplet fusion, Ostwald ripening
MeSH terms
Nucleic Acids, Proteins, Software, Molecular Dynamics Simulation

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