Related papers: The colon-pile
Diverse processes--e.g. bioremediation, biofertilization, and microbial drug delivery--rely on bacterial migration in disordered, three-dimensional (3D) porous media. However, how pore-scale confinement alters bacterial motility is unknown…
The transition from monolayers to multilayered structures in bacterial colonies is a fundamental step in biofilm development. Observed across different morphotypes and species, this transition is triggered within freely growing bacterial…
The spreading of bacterial populations is central to processes in agriculture, the environment, and medicine. However, existing models of spreading typically focus on cells in unconfined settings--despite the fact that many bacteria inhabit…
Motile organisms can form stable agglomerates such as cities or colonies. In the outbreak of a highly contagious disease, the control of large-scale epidemic spread depends on factors like the number and size of agglomerates, travel rate…
In growing active matter systems, a large collection of engineered or living autonomous units metabolize free energy and create order at different length scales as they proliferate and migrate collectively. One such example is bacterial…
We investigate the emergence of global alignment in colonies of dividing rod-shaped cells under confinement. Using molecular dynamics simulations and continuous modeling, we demonstrate that geometrical anisotropies in the confining…
Swimming microbes, such as bacteria and algae, live in diverse habitats including soil, ocean and human body which are characterized by structural boundaries and heterogeneous fluid flows. Although much progress has been made in…
Fluid flow has a major effect on the aggregation and fragmentation of bacterial colonies. Yet, a generic framework to understand and predict how hydrodynamics affects colony size remains elusive. This study investigates how fluid flow…
Kinetic equations, which explicitly take into account the branching nature of sandpile avalanches, are derived. The dynamics of the sandpile model is described by the generating functions of a branching process. Having used the results…
Proliferation and motility are ubiquitous drivers of activity in biological systems. Here, we study a dense binary mixture of motile and proliferating particles with exclusively repulsive interactions, where homeostasis in the proliferating…
Nonequilibrium phase transitions between an active and an absorbing state are found in models of populations, epidemics, autocatalysis, and chemical reactions on a surface. While absorbing-state phase transitions fall generically in the DP…
Collective and directed motility or swarming is an emergent phenomenon displayed by many self-organized assemblies of active biological matter such as clusters of embryonic cells during tissue development, cancerous cells during tumor…
Social insects are ecologically and evolutionarily most successful organisms on earth, which can achieve robust collective behaviors through local interactions among group members. Colony migration has been considered as a leading example…
A big challenge in current biology is to understand the exact self-organization mechanism underlying complex multi-physics coupling developmental processes. With multiscale computations of from subcellular gene expressions to cell…
While it is well established that self-propelled particles with alignment interactions can exhibit orientational order, the impact of self-replication and annihilation, which are key characteristics in cellular systems, on spatiotemporal…
Controlling the phases of matter is a challenge that spans from condensed materials to biological systems. Here, by imposing a geometric boundary condition, we study controlled collective motion of Escherichia coli bacteria. A circular…
Many types of mammalian cells exert active contractile forces and mechanically deform their elastic substrate, to accomplish biological functions such as cell migration. These substrate deformations provide a mechanism by which cells can…
The notion of Self-organized criticality (SOC) had been conceived to interpret the spontaneous emergence of long range correlations in nature. Since then many different models had been introduced to study SOC. All of them have few common…
We show that the probability distribution of the residence-times of sand grains in sandpile models, in the scaling limit, can be expressed in terms of the survival probability of a single diffusing particle in a medium with absorbing…
A simulation approach to the stochastic growth of bacterial towers is presented, in which a non-uniform and finite nutrient supply essentially determines the emerging structure through elementary chemotaxis. The method is based on cellular…