Related papers: Random motility regulation drives the fragmentatio…
In this research, we study biological networks at different scales: a gene autoregulatory network at the single-cell level and the gut microbiota at the population level. Proteins are the main actors in cells, they are the building blocks,…
The colonisation of a soft passive material by motile cells such as bacteria is common in biology. The resulting colonies of the invading cells are often observed to exhibit intricate patterns whose morphology and dynamics can depend on a…
Bacteria commonly inhabit porous environments such as host tissues, soil, and marine sediments, where complex geometries constrain and redirect their motion. Although bacterial motility has been studied in porous media, the roles of cell…
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…
Our planet is roughly closed to matter, but open to energy input from the sun. However, to harness this energy, organisms must transform matter from one chemical (redox) state to another. For example, photosynthetic organisms can capture…
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…
Recent advances in microscopy techniques has uncovered unique aspects of flagella-driven motility in bacteria. A remarkable example is the discovery of flagellar wrapping, a phenomenon whereby a bacterium wraps its flagellum (or flagellar…
We propose a minimal off-lattice model of living organisms where just a very few dynamical rules of growth are assumed. The stable coexistence of many clusters is detected when we replace the global restriction rule by a locally applied…
The periodic swarming of bacteria is one of the simplest examples for pattern formation produced by the self-organized collective behavior of a large number of organisms. In the spectacular colonies of Proteus mirabilis (the most common…
Evolution occurs in populations of reproducing individuals. The structure of a biological population affects which traits evolve. Understanding evolutionary game dynamics in structured populations is difficult. Precise results have been…
During the past century, biologists and mathematicians investigated two mechanisms underlying bacteria motion: the run phase during which bacteria move in straight lines and the tumble phase in which they change their orientation. When…
The run-and-tumble dynamics of bacteria, as exhibited by \textit{E. coli}, offers a simple experimental realization of non-Brownian, yet diffusive, particles. Here we present some analytic and numerical results for models of the ideal…
What determines biodiversity in nature is a prominent issue in ecology, especially in biotic resource systems that are typically devoid of cross-feeding. Here, we show that by incorporating pairwise encounters among consumer individuals…
Soft surfaces, spanning vastly different environmental and biomedical settings, are frequently colonised by surface-associated bacteria. Yet, how soft surfaces govern bacterial dynamics and their self-organisation into colonies remains…
The human gut microbiome is a complex ecosystem, in which hundreds of microbial species and metabolites coexist, in part due to an extensive network of cross-feeding interactions. However, both the large-scale trophic organization of this…
Mutation rate is a key determinant of the pace as well as outcome of evolution, and variability in this rate has been shown in different scenarios to play a key role in evolutionary adaptation and resistance evolution under stress caused by…
Complex or hostile environments can sometimes inhibit the movement capabilities of diffusive particles or active swimmers, who may thus become stuck in fixed positions. This occurs, for example, in the adhesion of bacteria to surfaces at…
The dynamics of microbial communities is incredibly complex, determined by competition for metabolic substrates and cross-feeding of byproducts. Species in the community grow by harvesting energy from chemical reactions that transform…
We use dynamical generating functionals to study the stability and size of communities evolving in Lotka-Volterra systems with random interaction coefficients. The size of the eco-system is not set from the beginning. Instead, we start from…
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…