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Transposons are small, self-replicating DNA sequences found in every branch of life. Often, one transposon will parasitize another, forming a tiny intracellular ecosystem. In some species these ecosystems thrive, while in others they go…
This study investigates the role of spatial segregation, prompted by competition avoidance, as a key mechanism for emergent coexistence within microbial communities. Recognizing these communities as complex adaptive systems, we challenge…
Cellular life requires the presence of a set of biochemical mechanisms in order to maintain a predictable process of growth and division. Several attempts have been made towards the building of minimal protocells from a top-down approach,…
Cellular actin structures are continuously turned over while keeping similar sizes. Since they all compete for a shared pool of actin monomers, the question arises how they can coexist in these dynamic steady states. Recently, the…
We present an algorithm for the stochastic simulation of gene expression and heterogeneous population dynamics. The algorithm combines an exact method to simulate molecular-level fluctuations in single cells and a constant-number Monte…
In complex ecological communities, species may self-organize into clusters or clumps where highly similar species can coexist. The emergence of such species clusters can be captured by the interplay between neutral and niche theories. Based…
How multicellular life forms evolved out from unicellular ones constitutes a major problem in our understanding of the evolution of our biosphere. A recent set of experiments involving yeast cell populations has shown that selection for…
The objective is to find a Cellular Automata rule that can form a 2D point pattern with a maximum number of points (1-cells). Points are not allowed to touch each other, they have to be separated by 0-cells, and every 0-cell can find at…
Nearly all cell models explicitly or implicitly deal with the biophysical constraints that must be respected for life to persist. Despite this, there is almost no systematicity in how these constraints are implemented, and we lack a…
We present a generic mechanism by which reproducing microorganisms, with a diffusivity that depends on the local population density, can form stable patterns. It is known that a decrease of swimming speed with density can promote separation…
Microbial populations generally evolve in volatile environments, under conditions fluctuating between harsh and mild, e.g. as the result of sudden changes in toxin concentration or nutrient abundance. Environmental variability thus shapes…
Bacteria and their bacteriophages are the most abundant, widespread and diverse groups of biological entities on the planet. In an attempt to understand how the interactions between bacteria, virulent phages and temperate phages might…
Cooperation is prevalent in nature, not only in the context of social interactions within the animal kingdom, but also on the cellular level. In cancer for example, tumour cells can cooperate by producing growth factors. The evolution of…
Recent work draws attention to community-community encounters ("coalescence") as likely an important factor shaping natural ecosystems. This work builds on MacArthur's classic model of competitive coexistence to investigate such…
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…
Motivated by experiments on cell segregation, we present a two-species model of interacting particles, aiming at a quantitative description of this phenomenon. Under precise scaling hypothesis, we derive from the microscopic model a…
A new model that describes adsorption and clustering of particles on a surface is introduced. A {\it clustering} transition is found which separates between a phase of weakly correlated particle distributions and a phase of strongly…
We present a conditional generative model to learn variation in cell and nuclear morphology and the location of subcellular structures from microscopy images. Our model generalizes to a wide range of subcellular localization and allows for…
A one dimensional stochastic exclusion process with two species of particles, $+$ and $-$, is studied where density of each species can fluctuate but the total particle density is conserved. From the exact stationary state weights we show…
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…