Related papers: Supplementary information for "Selective sweeps in…

With the development of next generation sequencing technology, researchers have now been able to study the microbiome composition using direct sequencing, whose output are bacterial taxa counts for each microbiome sample. One goal of…

Mixed microbial communities, usually composed of various bacterial and fungal species, are fundamental in a plethora of environments, from soil to human gut and skin. Their evolution is a paradigmatic example of intertwined dynamics, where…

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…

The distribution of chemical abundances and their variation in time are important tools to understand the chemical evolution of galaxies: in particular, the study of chemical evolution models can improve our understanding of the basic…

We investigate spatial evolutionary games with death-birth updating in large finite populations. Within growing spatial structures subject to appropriate conditions, the density processes of a fixed type are proven to converge to the…

Here, we study the evolution of specialization using realistic computer simulations of bacteria that secrete two public goods in a dynamic fluid. Through this first principles approach, we find physical factors such as diffusion, flow…

Bacterial colonies can form a wide variety of shapes and structures based on ambient and internal conditions. To help understand the mechanisms that determine the structure of and the diversity within these colonies, various numerical…

We study the evolution of recombination using a microscopic model developed within the frame of the theory of quantitative traits. Two components of fitness are considered: a static one that describes adaptation to environmental factors not…

Bacteria can form a great variety of spatially heterogeneous cell density patterns, ranging from simple concentric rings to dynamical spiral waves appearing in growing colonies. These pattern formation phenomena are important as they…

A robotic swarm that is required to operate for long periods in a potentially unknown environment can use both evolution and individual learning methods in order to adapt. However, the role played by the environment in influencing the…

A binary mixture of two-different-sizes proliferating motile disks is studied. As growth is space-limited, we focus on the conditions such that there is coexistence of both large and small disks, or dominance of the larger disks. The study…

Innovation is to organizations what evolution is to organisms: it is how organisations adapt to changes in the environment and improve. Governments, institutions and firms that innovate are more likely to prosper and stand the test of time;…

A contemporary procedure to grow artificial tissue is to seed cells onto a porous biomaterial scaffold and culture it within a perfusion bioreactor to facilitate the transport of nutrients to growing cells. Typical models of cell growth for…

Bacteria build multicellular communities termed biofilms, which are often encased in a self-secreted extracellular matrix that gives the community mechanical strength and protection against harsh chemicals. How bacteria assemble distinct…

Mechanical stresses stemming from environmental factors are a key determinant of cellular behavior and physiology. Yet, the role of self-induced biomechanical stresses in growing bacterial colonies has remained largely unexplored. Here, we…

The field of active matter explores the behaviors of self propelled agents out of equilibrium, with active suspensions, such as swimming bacteria in solutions, serving as impactful models. These systems exhibit spatio-temporal patterns akin…

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…

Ecological modelling of increasingly more complex microbial populations is necessary to reflect the highly functional and diverse behaviour inherent to many systems found in reality. Anaerobic digestion is one such process that has…

An organism that is newly introduced into an existing population has a survival probability that is dependent on both the population density of its environment and the competition it experiences with the members of that population.…

During their evolution, proteins explore sequence space via an interplay between random mutations and phenotypic selection. Here we build upon recent progress in reconstructing data-driven fitness landscapes for families of homologous…