We 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 Péclet 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.

In this work we study microwimmers, whether colloids or polymers, embedded in bulk or in confinement. We explicitly consider hydrodynamic interactions and simulate the swimmers via an implementation inspired by the squirmer model. Concerning the surrounding fluid, we employ a Dissipative Particle Dynamics scheme. Differently from the Lattice-Boltzmann technique, on the one side this approach allows us to properly deal not only with hydrodynamics but also with thermal fluctuations. On the other side, this approach enables us to study microwimmers with complex shapes, ranging from spherical colloids to polymers. To start with, we study a simple spherical colloid. We analyze the features of the velocity fields of the surrounding solvent, when the colloid is a pusher, a puller or a neutral swimmer either in bulk or confined in a cylindrical channel. Next, we characterise its dynamical behaviour by computing the mean square displacement and the long time diffusion when the active colloid is in bulk or in a channel (varying its radius) and analyze the orientation autocorrelation function in the latter case. While the three studied squirmer types are characterised by the same bulk diffusion, the cylindrical confinement considerably modulates the diffusion and the orientation autocorrelation function. Finally, we focus our attention on a more complex shape: an active polymer. We first characterise the structural features computing its radius of gyration when in bulk or in cylindrical confinement, and compare to known results obtained without hydrodynamics. Next, we characterise the dynamical behaviour of the active polymer by computing its mean square displacement and the long time diffusion. On the one hand, both diffusion and radius of gyration decrease due to the hydrodynamic interaction when the system is in bulk. On the other hand, the effect of confinement is to decrease the radius of gyration, disturbing the motion of the polymer and thus reducing its diffusion.

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In this work we study a two-dimensional system composed by Active Brownian Particles (ABPs) interacting via a repulsive potential with two-length-scales, a soft shell and a hard-core. Depending on the ratio between the strength of the soft shell barrier and the activity, we find two regimes: If this ratio is much larger or smaller than 1, the observed behavior is comparable with ABPs interacting via a single length-scale potential. If this ratio is similar to 1, the two length-scales are relevant for both structure and dynamical properties. On the structural side, when the system exhibits a motility induced phase separation, the dense phase is characterised by new and more complex structures compared with the hexatic phase observed in single length-scale systems.On the dynamical side, as far as we are aware, this is the first representation of an anomalous dynamics in active particles.

A bacterial biofilm is a living example of an actively viscoelastic medium as consists of micron-sized bacteria crosslinked to a self-produced network of Extracellular Polymeric Substances (EPS) embedded in water. Besides experimental in vivo and in vitro approaches to predictive biofilm mechanics, one could also think of developing a numerical model to characterise biofilm's viscoelasticity with the goal of avoiding perturbing deformations, or breaking once formed under given hydrodynamic stress, or simply to circumvent pathogen laboratory hazard by synthesizing in silico a forecasting simulation platform. However, 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 the previous work, we propose a bacterial biofilm mechanical modeling by means of the numerical coarse-grain model of dissipative particle dynamics (DPD). The modelled Pseudomonas fluorescens biofilms have been constituted with increasing mechanical stress mimicking real biofilms undergoing shear. The mesoscopic DPD-model consists of bacteria embedded in a crosslinked polymer matrix whose mechanical features are made to depend on the mesh topology and composition. We investigate its predictive capacity of mechanical features as varying an externally imposed shear strain field. We also compare with rheological experiments performed on a P. fluorescens biofilms grown under static and shaking conditions that resemble scenarios of hydrodynamic stress. The proposed coarse grained DPD simulation qualitatively catches the rheology of the P. fluorescens biofilm over several decades of dynamic scaling.