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The experiments conducted by various scientific groups indicate that, in dense two-dimensional systems of elongated particles subjected to vibration, the pattern formation is possible. Computer simulations have evidenced that the random…
Interactions between neighboring cells are essential for generating or refining patterns in a number of biological systems. We propose a discrete filtering approach to predict how networks of cells modulate spatially varying input signals…
Recent experimental and theoretical studies suggest that crystallization and glass-like solidification are useful analogies for understanding cell ordering in confluent biological tissues. It remains unexplored how cellular ordering…
From cytoskeletal networks to tissues, many biological systems behave as active materials. Their composition and stress-generation is affected by chemical reaction networks. In such systems, the coupling between mechanics and chemistry…
In nature, microorganisms must often cope with hostile environmental conditions. To do so they have developed sophisticated cooperative behavior and intricate communication capabilities, such as: direct cell-cell physical interactions via…
Spatiotemporal patterns are common in biological systems. For electrically-coupled cells previous studies of pattern formation have mainly used external forcing as the main bifurcation parameter. The purpose of this paper is to show that…
During colony growth, complex interactions regulate the bacterial orientation, leading to the formation of large-scale ordered structures, including topological defects and microdomains. These structures may benefit bacterial strains,…
Colonies of the social bacterium Myxococcus xanthus go through a morphological transition from a thin colony of cells to three-dimensional droplet-like fruiting bodies as a strategy to survive starvation. The biological pathways that…
Concentrated suspensions of swimming microorganisms and other forms of active matter are known to display complex, self-organized spatio-temporal patterns on scales large compared to those of the individual motile units. Despite intensive…
Recent 3D organ reconstitution studies show that a group of stem cells can establish a body axis and acquire different fates in a spatially organized manner. How such symmetry breaking happens in the absence of external spatial cues, and…
We present and analyze mechanisms for the patterned deposition of particles in a spatio-temporally driven lattice. The working principle is based on the breaking of the spatio-temporal translation symmetry, which is responsible for the…
In this review, we discuss modularity and hierarchy in biological systems. We review examples from protein structure, genetics, and biological networks of modular partitioning of the geometry of biological space. We review theories to…
Mechanical interactions among cells in a growing microbial colony can significantly influence the colony's spatial genetic structure and, thus, evolutionary outcomes such as the fates of rare mutations. Here, we computationally investigate…
Rhythmic and sequential segmentation of the embryonic body plan is a vital developmental patterning process in all vertebrate species. However, a theoretical framework capturing the emergence of dynamic patterns of gene expression from the…
We present results of experiments on the dynamics of Dictyostelium discoideum in a novel set-up which constraints cell motion to a plane. After aggregation, the amoebae collect into round ''pancake" structures in which the cells rotate…
Polariton condensates have proved to be model systems to investigate topological defects, as they allow for direct and non-destructive imaging of the condensate complex order parameter. The fundamental topological excitations of such…
We report the emergence of large zigzag bands in a population of reversibly actuated magnetic rotors that behave as active shakers, namely squirmers that shake the fluid around them without moving. The shakers collectively organize into…
A model for a monolayer of two types of particles spontaneously forming ordered patterns is studied by a mesoscopic theory and by MC simulations. We assume hard-cores of the same size for both components, short-range attraction long-range…
We consider collective dynamics of self-propelling particles in two dimensions. They can align themselves according to the direction of propulsion of their neighbours, together with a random perturbation (i.e. rotational fluctuation). They…
A continuous route from a disordered soup of simple chemical feedstocks to a functional protocell -- a compartment that metabolizes, grows, and propagates -- remains elusive. Here, we show that a homogeneous aqueous chemical mixture…