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Baker's yeast (Saccharomyces cerevisiae) is a model organism for studying the morphology that emerges at the scale of multi-cell colonies. To look at how morphology develops, we collect a dataset of time-lapse photographs of the growth of…

In the growth of bacterial colonies, a great variety of complex patterns are observed in experiments, depending on external conditions and the bacterial species. Typically, existing models employ systems of reaction-diffusion equations or…

Despite the importance that fluid flow plays in transporting and organizing populations, few laboratory systems exist to systematically investigate the impact of advection on their spatial evolutionary dynamics. To address this problem, we…

Growth patterns generated by filamentous organisms (e.g. actinomycetes and fungi) involve spatial and temporal dynamics at different length scales. Several mathematical models have been proposed in the last thirty years to address these…

Bacteria are prolific at colonizing diverse surfaces under a widerange of environmental conditions, and exhibit fascinating examples of self-organization across scales. Though it has recently attracted considerable interest, the role of…

Yeasts exist in communities that expand over space and time to form complex structures and patterns. We developed a computational lattice-based framework to perform spatial-temporal simulations of budding yeast colonies exposed to different…

Cells coexist together in colonies or as tissues. Their behaviour is controlled by an interplay between intercellular forces and biochemical regulation. We develop a simple model of the cell cycle, the fundamental regulatory network…

Nutrient gradients and limitations play a pivotal role in the life of all microbes, both in their natural habitat as well as in artificial, microfluidic systems. Spatial concentration gradients of nutrients in densely packed cell…

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…

Cell colonies of bacteria, tumour cells and fungi, under nutrient limited growth conditions, exhibit complex branched growth patterns. In order to investigate this phenomenon we present a simple hybrid cellular automaton model of cell…

We investigate the dynamics of a colony of crawling, proliferating cells with a minimal, mechanical cell model. The cells consist of two disks, modelling the cell body and a pseudopod, connected by a finite extensible spring. The cells…

Bacterial conglomerates such as biofilms and microcolonies are ubiquitous in nature and play an important role in industry and medicine. In contrast to well-mixed, diluted cultures routinely used in microbial research, bacteria in a…

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…

Biological functions in living cells are controlled by protein interaction and genetic networks. These molecular networks should be dynamically stable against various fluctuations which are inevitable in the living world. In this paper, we…

A new model for biological growth is introduced that couples the geometry of an organism (or part of the organism) to the flow and deposition of material. The model has three dynamical variables (a) a Riemann metric tensor for the geometry,…

Bacterial colonies are abundant on living and nonliving surfaces and are known to mediate a broad range of processes in ecology, medicine, and industry. Although extensively researched, from single cells to demographic scales, a…

We propose a class of evolutionary models that involves an arbitrary exchangeable process as the breeding process and different selection schemes. In those models, a new genome is born according to the breeding process, and then a genome is…

We model an enclosed system of bacteria, whose motility-induced phase separation is coupled to slow population dynamics. Without noise, the system shows both static phase separation and a limit cycle, in which a rising global population…

We present a new kinetic equation for cell migration driven by mechanical interactions with the substrate, an effect not previously captured in kinetic models, and essential for explaining observed collective behaviors such as those in…

Understanding the behaviour of biological systems requires a complex setting of in vitro and in vivo experiments, which attracts high costs in terms of time and resources. The use of mathematical models allows researchers to perform…