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Rheology of Pseudomonas fluorescens biofilms: From experiments to predictive DPD mesoscopic modeling

dc.contributor.authorMartín Roca, José
dc.contributor.authorBianco, Valentino
dc.contributor.authorAlarcón, Francisco
dc.contributor.authorMonnappa, Ajay K.
dc.contributor.authorNatale, Paolo
dc.contributor.authorMonroy, Francisco
dc.contributor.authorOrgaz Martín, Belén
dc.contributor.authorLópez Montero, Iván
dc.contributor.authorValeriani, Chantal
dc.date.accessioned2023-06-22T11:16:12Z
dc.date.available2023-06-22T11:16:12Z
dc.date.issued2023-02-21
dc.descriptionB.O., I.L.-M., and C.V. acknowledge funding from Grant UCM/Santander PR26/16. C.V acknowledges funding from MINECO grants EUR2021-122001, PID2019-105343GB-I00, IHRC22/00002. F.M. acknowledges funding from MINECO under Grant Nos. PID2019-105606RB-I00, FIS2016-78847-P, PID2019-108391RB-I00, and FIS2015-70339; from the REACT-EU program PR38-21-28 ANTICIPA-CM, a grant by the Comunidad de Madrid and European Union under the FEDER Program; from EU in response to COVID-19 pandemics; and from Comunidad de Madrid under Grant Nos. S2018/NMT-4389 and Y2018/BIO-5207. C.V. acknowledges funding from MINECO under Grant No. PID2019-105343GB-I00. F.A acknowledges the support from the "Juan de la Cierva" program (Grant No. FJCI-2017-33580). A.K.M. is recipient of a Sara Borrell fellowship (Grant No. CD18/00206) financed by the Spanish Ministry of Health. V.B. acknowledges the support from the European Commission through Marie Sklodowska-Curie Fellowship No. 748170 ProFrost. Support from MINECO (Grant No. IRHC22/00002) is also acknowledged. The authors acknowledge the computer resources from the Red Española de Supercomputación (RES) under Grant Nos. FI-2020-1-0015 and FI-2020-2-0032 and from the Vienna Scientific Cluster (VSC).
dc.description.abstractBacterial biofilms mechanically behave as viscoelastic media consisting of micron-sized bacteria cross-linked to a self-produced network of extracellular polymeric substances (EPSs) embedded in water. Structural principles for numerical modeling aim at describing mesoscopic viscoelasticity without losing details on the underlying interactions existing in wide regimes of deformation under hydrodynamic stress. Here, we approach the computational challenge to model bacterial biofilms for predictive mechanics in silico under variable stress conditions. Up-to-date models are not entirely satisfactory due to the plethora of parameters required to make them functioning under the effects of stress. As guided by the structural depiction gained in a previous work with Pseudomonas fluorescens [Jara et al., Front. Microbiol. 11, 588884 (2021)], we propose a mechanical modeling by means of Dissipative Particle Dynamics (DPD), which captures the essentials of topological and compositional interactions between bacterial particles and cross-linked EPS-embedding under imposed shear. The P. fluorescens biofilms have been modeled under mechanical stress mimicking shear stresses as undergone in vitro. The predictive capacity for mechanical features in DPD-simulated biofilms has been investigated by varying the externally imposed field of shear strain at variable amplitude and frequency. The parametric map of essential biofilm ingredients has been explored by making the rheological responses to emerge among conservative mesoscopic interactions and frictional dissipation in the underlying microscale. The proposed coarse grained DPD simulation qualitatively catches the rheology of the P. fluorescens biofilm over several decades of dynamic scaling. Published under an exclusive license by AIP Publishing.
dc.description.departmentDepto. de Estructura de la Materia, Física Térmica y Electrónica
dc.description.facultyFac. de Ciencias Físicas
dc.description.refereedTRUE
dc.description.sponsorshipUniversidad Complutense de Madrid (UCM)
dc.description.sponsorshipMinisterio de Economía y Competitividad
dc.description.sponsorshipREACT-EU program
dc.description.sponsorshipComunidad de Madrid
dc.description.sponsorship"Juan de la Cierva" program
dc.description.sponsorshipEuropean Union under the FEDER Program
dc.description.sponsorshipSara Borrell fellowship - Spanish Ministry of Health
dc.description.sponsorshipEuropean Commission through Marie Sklodowska-Curie Fellowship
dc.description.sponsorshipRed Española de Supercomputación (RES)
dc.description.sponsorshipVienna Scientific Cluster (VSC)
dc.description.sponsorshipBanco Santander
dc.description.statuspub
dc.eprint.idhttps://eprints.ucm.es/id/eprint/78271
dc.identifier.doi10.1063/5.0131935
dc.identifier.issn0021-9606
dc.identifier.officialurlhttp://dx.doi.org/10.1063/5.0131935
dc.identifier.relatedurlhttps://pubs.aip.org/aip/jcp/
dc.identifier.urihttps://hdl.handle.net/20.500.14352/72267
dc.issue.number7
dc.journal.titleJournal of chemical physics
dc.language.isoeng
dc.publisherAmerican Institute of Physics
dc.relation.projectIDPR26/16
dc.relation.projectIDEUR2021-122001
dc.relation.projectIDPID2019-105343GB-I00
dc.relation.projectIDIHRC22/00002
dc.relation.projectIDPID2019-105606RB-I00
dc.relation.projectIDFIS2016-78847-P
dc.relation.projectIDPID2019-108391RB-I00
dc.relation.projectIDFIS2015-70339
dc.relation.projectIDS2018/NMT-4389
dc.relation.projectIDY2018/BIO-5207
dc.relation.projectIDPR38-21-28 ANTICIPA-CM
dc.relation.projectIDS2018/NMT-4389
dc.relation.projectIDFJCI-2017-33580
dc.relation.projectIDCD/1800206
dc.relation.projectID748170 ProFrost
dc.relation.projectIDIRHC22/00002
dc.relation.projectIDFI-2020-1-0015
dc.relation.projectIDFI-2020-2-0032
dc.rights.accessRightsrestricted access
dc.subject.cdu539.1
dc.subject.keywordImmersed boundary method
dc.subject.keywordMechanical-properties
dc.subject.keywordVariable viscosity
dc.subject.keywordParticle
dc.subject.keywordViscoelasticity
dc.subject.keywordMicrostructure
dc.subject.keywordPolysaccharide
dc.subject.keywordHydrogels
dc.subject.ucmFísica nuclear
dc.subject.unesco2207 Física Atómica y Nuclear
dc.titleRheology of Pseudomonas fluorescens biofilms: From experiments to predictive DPD mesoscopic modeling
dc.typejournal article
dc.volume.number158
dspace.entity.typePublication
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relation.isAuthorOfPublication.latestForDiscoverya49a9cc0-df5e-4064-b273-0190370cb821

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