Person: Martín Roca, José
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First Name
José
Last Name
Martín Roca
Affiliation
Universidad Complutense de Madrid
Faculty / Institute
Ciencias Físicas
Department
Estructura de la Materia, Física Térmica y Electrónica
Area
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Item Rheology of Pseudomonas fluorescens biofilms: From experiments to predictive DPD mesoscopic modeling(Journal of chemical physics, 2023) Martín Roca, José; Bianco, Valentino; Alarcón, Francisco; Monnappa, Ajay K.; Natale, Paolo; Monroy, Francisco; Orgaz Martín, Belén; López Montero, Iván; Valeriani, ChantalBacterial 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.Item Characterization of MIPS in a suspension of repulsive active Brownian particles through dynamical features(Journal of chemical physics, 2021) Martín Roca, José; Martínez, Raúl; Alexander, Lachlan C.; Díez, Ángel Luis; Aarts, Dirk G. A. L.; Alarcón, Francisco; Ramírez, Jorge; Valeriani, ChantalWe study a two-dimensional system composed by Active Brownian Particles (ABPs), focusing on the onset of Motility Induced Phase Separation (MIPS), by means of molecular dynamics simulations. For a pure hard-disk system with no translational diffusion, the phase diagram would be completely determined by their density and Peclet number. In our model, two additional effects are present: translational noise and the overlap of particles; we study the effects of both in the phase space. As we show, the second effect can be mitigated if we use, instead of the standard Weeks-Chandler-Andersen potential, a stiffer potential: the pseudo-hard sphere potential. Moreover, in determining the boundary of our phase space, we explore different approaches to detect MIPS and conclude that observing dynamical features, via the non-Gaussian parameter, is more efficient than observing structural ones, such as through the local density distribution function. We also demonstrate that the Vogel-Fulcher equation successfully reproduces the decay of the diffusion as a function of density, with the exception of very high densities. Thus, in this regard, the ABP system behaves similar to a fragile glass.