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Unraveling internal friction in a coarse-grained protein model

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dc.contributor.authorMonago Díaz, Carlos Sebastián
dc.contributor.authorTorre Rodríguez, Jaime Arturo de la
dc.contributor.authorDelgado-Buscalioni, Rafael
dc.date.accessioned2025-06-27T14:37:40Z
dc.date.available2025-06-27T14:37:40Z
dc.date.issued2025-03-19
dc.descriptionThis is an Accepted Manuscript of an article published by AIP Publishing in "The Journal of Chemical Physics 162.11 (2025)", available at: https://doi.org/10.1063/5.0255498
dc.description.abstractUnderstanding the dynamic behavior of complex biomolecules requires simplified models that not only make computations feasible but also reveal fundamental mechanisms. Coarse-graining (CG) achieves this by grouping atoms into beads, whose stochastic dynamics can be derived using the Mori–Zwanzig formalism, capturing both reversible and irreversible interactions. In liquid, the dissipative bead–bead interactions have so far been restricted to hydrodynamic couplings. However, friction does not only arise from the solvent but, notably, from the internal degrees of freedom missing in the CG beads. This leads to an additional “internal friction” whose relevance is studied in this contribution. By comparing with all-atom molecular dynamics (MD), we neatly show that in order to accurately reproduce the dynamics of a globular protein in water using a CG model, not only a precise determination of elastic couplings and the Stokesian self-friction of each bead is required. Critically, the inclusion of internal friction between beads is also necessary for a faithful representation of protein dynamics. We propose to optimize the parameters of the CG model through a self-averaging method that integrates the CG dynamics with an evolution equation for the CG parameters. This approach ensures that selected quantities, such as the radial distribution function and the time correlation of bead velocities, match the corresponding MD values.en
dc.description.versionversión final
dc.identifier.citationMonago, C., de la Torre, J. A., Delgado-Buscalioni, R., Español, P. "Unraveling internal friction in a coarse-grained protein model", The Journal of Chemical Physics 162.11 (2025), https://doi.org/10.1063/5.0255498
dc.identifier.doihttps://doi.org/10.1063/5.0255498
dc.identifier.issn0021-9606
dc.identifier.urihttps://hdl.handle.net/20.500.14468/26948
dc.journal.issue11
dc.journal.titleThe Journal of chemical physics
dc.journal.volume162
dc.language.isoen
dc.page.final13
dc.page.initial1
dc.publisherAIP Publishing
dc.relation.centerFacultades y escuelas::Facultad de Ciencias
dc.relation.departmentFÍSICA FUNDAMENTAL
dc.rightsinfo:eu-repo/semantics/embargoedAccess
dc.rights.uriAtribución-NoComercial-SinDerivadas 4.0 Internacional
dc.subject12 Matemáticas
dc.subject23 Química::2307 Química física
dc.subject24 Ciencias de la Vida
dc.subject25 Ciencias de la Tierra y del Espacio
dc.subject.keywordsMolecular dynamicsen
dc.subject.keywordsLaws of frictionen
dc.subject.keywordsElectrostaticsen
dc.subject.keywordsKnowledge representationen
dc.subject.keywordsHydrodynamicsen
dc.subject.keywordsCoarse-grain modelen
dc.subject.keywordsProteinsen
dc.subject.keywordsNonequilibrium statistical mechanicsen
dc.subject.keywordsStochastic processesen
dc.subject.keywordsClassical statistical mechanicsen
dc.titleUnraveling internal friction in a coarse-grained protein modelen
dc.typeartículoes
dc.typejournal articleen
dspace.entity.typePublication
relation.isAuthorOfPublicationc5b33272-3c0a-4717-a474-277054209364
relation.isAuthorOfPublication488cdc69-4873-4328-9762-aa4d769eb267
relation.isAuthorOfPublication.latestForDiscoveryc5b33272-3c0a-4717-a474-277054209364
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