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In the present work we simulate the basic two-dimensional dynamics of swarming E. coli bacteria on the surface of a moderately soft agar plate. Individual bacteria are modelled by self-propelled ridged bodies (agents), which interact with…

The paper considers some class of dynamical systems that called density systems. For such systems the derivative of quadratic function depends on so-called density function. The density function is used to set the properties of phase space,…

At the macroscopic scale, many important models of collective motion fall into the class of kinematic flows for which both velocity and diffusion terms depend only on particle density. When total particle numbers are fixed and finite,…

Dense bacterial suspensions at fluid interfaces provide a natural platform to explore active turbulence in a dimensional mismatch: active units are restricted to a two-dimensional surface, while the induced flows extend into the surrounding…

Biofilament-motor protein complexes are ubiquitous in biology and drive the transport of cargo vital for many fundamental cellular processes. As they move, motor proteins exert compressive forces on the filaments to which they are attached,…

Mixtures of active and passive particles are predicted to exhibit a variety of nonequilibrium phases. Here we report a dynamic clustering phase in mixtures of colloids and motile bacteria. We show that colloidal clustering results from a…

Bacterial flagellar swarming enables dense microbial populations to migrate collectively across surfaces, often resulting in emergent, coordinated behaviors. However, probing the underlying energetics of swarming at the single cluster level…

In biological tissues, it is now well-understood that mechanical cues are a powerful mechanism for pattern regulation. While much work has focused on interactions between cells and external substrates, recent experiments suggest that cell…

Bacteria organize in a variety of collective states, from swarming, which has been attributed to rapid surface exploration, to biofilms, which are highly dense immobile communities attributed to stress resistance. It has been suggested that…

In this perspective article, we discuss bacterial populations as a model system of active matter. It allows for the exploration and characterization of various phases of active matter and brings rich implications for both physics and…

Unlike coffee and cream that homogenize when stirred, growing micro-organisms (e.g., bacteria, baker's yeast) can actively kill each other and avoid mixing. How do such antagonistic interactions impact the growth and survival of competing…

Biological systems are majorly dependent on their property of bistability in order to exhibit nongenetic heterogeneity in terms of cellular morphology and physiology. Spatial patterns of phenotypically heterogeneous cells, arising due to…

Mixing of two fluids can lead to the formation of a precipitate. If one of the fluids is injected into a confined space filled with the other, a created precipitate disrupts the flow locally and forms complex spatiotemporal patterns. The…

Although the pattern formation on polymer gels has been considered as a result of the mechanical instability due to the volume phase transition, we found a macroscopic surface pattern formation not caused by the mechanical instability. It…

In this paper we study the dynamics of stochastic microorganism flocculation models. Given the strong influence of environmental and seasonal fluctuations that are present in these models, we propose a stochastic model that includes…

Bacteria can adjust the structure of colonies and biofilms to enhance their survival rate under external stress. Here, we explore the link between bacterial interaction forces and colony structure. We show that the activity of extracellular…

We introduce a general theoretical framework to study the shape dynamics of actively growing and remodeling surfaces. Using this framework we develop a physical model for growing bacterial cell walls and study the interplay of cell shape…

It is known from both experiments and molecular dynamics simulations that chemically patterning a solid surface has an effect on the flow of an adjacent liquid. This fact is in stark contrast with predictions of classical fluid mechanics…

There are rich emergent phase behaviors in non-equilibrium active systems. Flocking and clustering are two representative dynamic phases. The relationship between these two phases is still unclear. In the paper, we numerically investigate…

We derive from first principles a three-dimensional theory of self-propelled particle swarming in a viscous fluid environment. Our model predicts emergent collective behavior that depends critically on fluid opacity, mechanism of…