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Empirical observations show that ecological communities can have a huge number of coexisting species, also with few or limited number of resources. These ecosystems are characterized by multiple type of interactions, in particular…
We present a modelling framework for the dynamics of cells structured by the concentration of a micromolecule they contain. We derive general equations for the evolution of the cell population and of the extra-cellular concentration of the…
We study the interplay of population growth and evolutionary dynamics using a stochastic model based on birth and death events. In contrast to the common assumption of an independent population size, evolution can be strongly affected by…
Evolution produces complex and structured networks of interacting components in chemical, biological, and social systems. We describe a simple mathematical model for the evolution of an idealized chemical system to study how a network of…
Cell-cell adhesion is one the most fundamental mechanisms regulating collective cell migration during tissue development, homeostasis and repair, allowing cell populations to self-organize and eventually form and maintain complex tissue…
In biology, the evolution of increasingly cooperative groups has shaped the history of life. Genes collaborate in the control of cells; cells efficiently divide tasks to produce cohesive multicellular individuals; individual members of…
In battery modeling, the electrode is discretized at the macroscopic scale with a single representative particle in each volume. This lacks the accurate physics to describe interparticle interactions in electrodes. To remedy this, we…
Microbes providing public goods are widespread in nature despite running the risk of being exploited by free-riders. However, the precise ecological factors supporting cooperation are still puzzling. Following recent experiments, we…
We introduce a mathematical model of symbiosis between different species by taking into account the influence of each species on the carrying capacities of the others. The modeled entities can pertain to biological and ecological societies…
To model the morphogenesis of rod-shaped bacterial micro-colony, several individual-based models have been proposed in the biophysical literature. When studying the shape of micro-colonies, most models present interaction forces such as…
Advances in synthetic biology allow us to engineer bacterial collectives with pre-specified characteristics. However, the behavior of these collectives is difficult to understand, as cellular growth and division as well as extra-cellular…
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…
Microbial ecosystems are commonly modeled by fixed interactions between species in steady exponential growth states. However, microbes often modify their environments so strongly that they are forced out of the exponential state into…
We propose a model of multispecies populations surviving on distributed resources. System dynamics are investigated under changes in abiotic factors such as the climate, as parameterized through environmental temperature. In particular, we…
We study the effect of discreteness on various models for patterning in bacterial colonies. In a bacterial colony with branching pattern, there are discrete entities - bacteria - which are only two orders of magnitude smaller than the…
A challenging simulation of evolutionary dynamics based on a three-state cellular automaton is used as a test of how cooperation can drive the evolution of complex traits. Building on the approach of Wolfram (2025), the fitness of a…
We explore the evolution of cooperation in the framework of the evolutionary game theory using the prisoner's dilemma as metaphor of the problem. We present a minimal model taking into account the growing process of the systems and…
The self-organization of microbial ecosystems involves a large variety of mechanisms, ranging from biochemical signaling to population dynamics. Among these, the role of motility regulation has been little studied, despite the importance of…
Most microorganisms regulate their cell size. We review here some of the mathematical formulations of the problem of cell size regulation. We focus on coarse-grained stochastic models and the statistics they generate. We review the…
This study explores the application of elongated particle interaction models, traditionally used in liquid crystal phase research, in the context of early bacterial biofilm development. Through computer simulations using an agent-based…