From quantum to subcellular scales: multi-scale simulation approaches and the SIRAH force field.
QM/MM/CG
SIRAH
coarse-grain
hybrid
molecular dynamics
Journal
Interface focus
ISSN: 2042-8898
Titre abrégé: Interface Focus
Pays: England
ID NLM: 101531990
Informations de publication
Date de publication:
06 Jun 2019
06 Jun 2019
Historique:
accepted:
11
02
2019
entrez:
9
5
2019
pubmed:
9
5
2019
medline:
9
5
2019
Statut:
ppublish
Résumé
Modern molecular and cellular biology profits from astonishing resolution structural methods, currently even reaching the whole cell level. This is encompassed by the development of computational methods providing a deep view into the structure and dynamics of molecular processes happening at very different scales in time and space. Linking such scales is of paramount importance when aiming at far-reaching biological questions. Computational methods at the interface between classical and coarse-grained resolutions are gaining momentum with several research groups dedicating important efforts to their development and tuning. An overview of such methods is addressed herein, with special emphasis on the SIRAH force field for coarse-grained and multi-scale simulations. Moreover, we provide proof of concept calculations on the implementation of a multi-scale simulation scheme including quantum calculations on a classical fine-grained/coarse-grained representation of double-stranded DNA. This opens the possibility to include the effect of large conformational fluctuations in chromatin segments on, for instance, the reactivity of particular base pairs within the same simulation framework.
Identifiants
pubmed: 31065347
doi: 10.1098/rsfs.2018.0085
pii: rsfs20180085
pmc: PMC6501346
doi:
Types de publication
Journal Article
Review
Langues
eng
Pagination
20180085Déclaration de conflit d'intérêts
We declare we have no competing interests.
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