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Many cellular and subcellular biological processes can be described in terms of diffusing and chemically reacting species (e.g. enzymes). Such reaction-diffusion processes can be mathematically modelled using either deterministic…
An evolving yeast colony is simulated by means of a cellular automaton that takes care of many important features of the system under study. A complete survey of the properties of the colony is done and a set of scaling relations is found,…
We study colonies of non-motile, rod-shaped bacteria growing on solid substrates. In our model, bacteria interact purely mechanically, by pushing each other away as they grow, and consume a diffusing nutrient. We show that mechanical…
We present a two-species population model in a well-mixed environment where the dynamics involves, in addition to birth and death, changes due to environmental factors and inter-species interactions. The novel dynamical components are…
Spatio-temporal extensions of familiar compartment models for disease transmission incorporating diffusive behavior, or interactions between individuals at separate locations, are explored. The models considered have the character of…
A mathematical model of Min oscillation in Escherichia coli is numerically studied. The oscillatory state and hysteretic transition are explained with simpler coupled differential equations. Next, we propose a simple model of cell growth…
Bacterial colonies growing on surfaces are shaped by mechanical stresses transmitted through the community, governed by the balance between cell growth and steric and cell-substrate interactions. Using overdamped dynamics simulations of…
Biological pattern formation is one of the most intriguing phenomena in nature. Simplest examples of such patterns are represented by travelling waves and stationary periodic patterns which occur during various biological processes…
We study bacterial diffusion in disordered porous media. Interactions with obstacles, at unknown locations, make this problem challenging. We approach it by abstracting the environment to cell states with memoryless transitions. With this,…
Several different enzymes display an apparent diffusion coefficient that increases with the concentration of their substrate. Moreover, their motion becomes directed in substrate gradients. Currently, there are several competing models for…
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…
In bacterial populations, cells are able to cooperate in order to yield complex collective functionalities. Interest in population-level cellular behaviour is increasing, due to both our expanding knowledge of the underlying biological…
We propose a general parametrizable model to capture the dynamic interaction among bacteria in the formation of micro-colonies. micro-colonies represent the first social step towards the formation of structured multicellular communities…
Immotile microbes inhabit nearly every environment on Earth, from soils and sediments to food matrices -- yet how they disperse through these physically confining environments is poorly understood. Here, we show that immotile microbial…
Bacteria on surfaces exhibit collective behaviors, such as active turbulence and active stresses, which result from their motility, growth, and interactions with their local surroundings. However, interfacial deformations on soft surfaces…
Bacterial biofilms are usually assumed to originate from individual cells deposited on a surface. However, many biofilm-forming bacteria tend to aggregate in the planktonic phase so that it is possible that many natural and infectious…
Biological systems excel at building spatial structures on scales ranging from nanometers to kilometers and exhibit temporal patterning from milliseconds to years. One approach that nature has taken to accomplish this relies on the…
We propose a model of antibiotic diffusion through a bacterial biofilm when diffusion and/or absorption barriers develop in the biofilm. The idea of this model is: We deduce details of the diffusion process in a medium in which direct…
We consider biochemical reaction chains and investigate how random external fluctuations, as characterized by variance and coefficient of variation, propagate down the chains. We perform such a study under the assumption that the number of…
Recent studies have shown that packings of cells, both eukaryotic cellular tissues and growing or swarming bacterial colonies, can often be understood as active nematic fluids. A key property of volume-conserving active nematic model…