arXiv subjects

Francisco Alarcon Oseguera

Publications and source records attributed to Francisco Alarcon Oseguera.

3 recordsLinked to original sources

arXiv2021

Collective motion of run-and-tumble particles drives aggregation in one-dimensional systems

Active matter deals with systems whose particles consume energy at the individual level in order to move. To unravel features such as the emergence of collective structures several models have been suggested, such as the on-lattice model of run-and-tumble particles implemented via the Persistent Exclusion Process (PEP). In our work, we study a one dimensional system of run-and-tumble repulsive or attractive particles, both on and off lattice. Additionally, we implement a cluster motility dynamics in the on-lattice case (since in the off-lattice case cluster motility arises from the individual particle dynamics). While we observe important differences between discrete and continuous dynamics, few common features are of particular importance. Increasing particle density drives aggregation across all different systems explored. For non-attractive particles, the effects of particle activity on aggregation are largely independent of the details of the dynamics. On the contrary, once attractive interactions are introduced, the steady state, which is completely determined by the interplay between these and the particles' activity, becomes highly dependent on the details of the dynamics.

cond-mat.soft↗

arXiv2021

In-silico modeling of early-stage biofilm formation

Several bacteria and bacteria strands form biofilms in different environmental conditions, e.g. pH, temperature, nutrients, etc. Biofilm growth, therefore, is an extremely robust process. Because of this, while biofilm growth is a complex process affected by several variables, insights into biofilm formation could be obtained studying simple schematic models. In this manuscript, we describe a hybrid molecular dynamics and Monte Carlo model for the simulation of the early stage formation of a biofilm, to explicitly demonstrate that it is possible to account for most of the processes expected to be relevant. The simulations account for the growth and reproduction of the bacteria, for their interaction and motility, for the synthesis of extracellular polymeric substances and Psl trails. We describe the effect of these processes on the early stage formation of biofilms, in two dimensions, and also discuss preliminary three-dimensional results.

cond-mat.soft↗

arXiv2021

Self-adaptation of Pseudomonas fluorescens biofilms to hydrodynamic stress

In some conditions, bacteria self-organise into biofilms, supracellular structures made of a self-produced embedding matrix, mainly composed on polysaccharides, DNA, proteins and lipids. It is known that bacteria change their colony/matrix ratio in the presence of external stimuli such as hydrodynamic stress. However, little is still known about the molecular mechanisms driving this self-adaptation. In this work, we monitor structural features of Pseudomonas fluorescens biofilms grown with and without hydrodynamic stress. Our measurements show that the hydrodynamic stress concomitantly increases the cell density population and the matrix production. At short growth timescales, the matrix mediates a weak cell-cell attractive interaction due to the depletion forces originated by the polymer constituents. Using a population dynamics model, we conclude that hydrodynamic stress causes a faster diffusion of nutrients and a higher incorporation of planktonic bacteria to the already formed microcolonies. This results in the formation of more mechanically stable biofilms due to an increase of the number of crosslinks, as shown by computer simulations. The mechanical stability also lies on a change in the chemical compositions of the matrix, which becomes enriched in carbohydrates, known to display adhering properties. Overall, we demonstrate that bacteria are capable of self-adapting to hostile hydrodynamic stress by tailoring the biofilm chemical composition, thus affecting both the mesoscale structure of the matrix and its viscoelastic properties that ultimately regulate the bacteria-polymer interactions.

cond-mat.soft↗