Related papers: A simple regulatory architecture allows learning t…
Gut microbial composition has been linked to multiple health outcomes. Yet, temporal analysis of this composition had been limited to deterministic models. In this paper, we introduce a probabilistic model for the dynamics of intestinal…
Recurrent neural policies are widely used in partially observable control and meta-RL tasks. Their abilities to maintain internal memory and adapt quickly to unseen scenarios have offered them unparalleled performance when compared to…
We show that the simplest stochastic epidemiological models with spatial correlations exhibit two types of oscillatory behaviour in the endemic phase. In a large parameter range, the oscillations are due to resonant amplification of…
We present a model for a biological reactor in which bacteria tend to aggregate in flocs, as encountered in wastewater treatment plants. The influence of this flocculation on the growth dynamics of the bacteria is studied. We argue that a…
Ecosystems, which are intricate amalgams of biological communities and their surrounding environments, continually evolve under the influence of their myriad interactions. The world is currently facing intensifying environmental…
The competition for resources is a defining feature of microbial communities. In many contexts, from soils to host-associated communities, highly diverse microbes are organized into metabolic groups or guilds with similar resource…
Environmental variations can significantly influence how populations compete for resources, and hence shape their evolution. Here, we study population dynamics subject to a fluctuating environment modeled by a varying carrying capacity…
Biological systems are modular, and this modularity evolves over time and in different environments. A number of observations have been made of increased modularity in biological systems under increased environmental pressure. We here…
Gene regulatory networks play a crucial role in controlling an organism's biological processes, which is why there is significant interest in developing computational methods that are able to extract their structure from high-throughput…
The galactose network is a complex system responsible for galactose metabolism. It has been extensively studied experimentally and mathematically at the unicellular level to broaden our understanding of its regulatory mechanisms at higher…
Statistical mechanics determines the abundance of different arrangements of matter depending on cost-benefit balances. Its formalism and phenomenology percolate throughout biological processes and set limits to effective computation. Under…
Many cellular components are present in such low numbers that individual stochastic production and degradation events lead to significant fluctuations in molecular abundances. Although feedback control can, in principle, suppress such…
Bacteria regulate their motility through a variety of mechanisms, including quorum sensing (QS) and other density-dependent responses mediated by diffusible signals. While nonlinear density-dependent motility is well known in active-matter…
Bacterial growth models are commonly used for the prediction of microbial safety and the shelf life of perishable foods. Growth is affected by several environmental factors such as temperature, acidity level and salt concentration. In this…
In this work we study the interplay between the dynamics of a model of diffusion governed by a mechanism of imitation and its underlying structure. The dynamics of the model can be quantified by a macroscopic observable which permits the…
We study the evolution of asexual microorganisms with small mutation rate in fluctuating environments, and develop techniques that allow us to expand the formal solution of the evolution equations to first order in the mutation rate. Our…
Mathematical modelling of the evolution of the size-spectrum dynamics in aquatic ecosystems was discovered to be a powerful tool to have a deeper insight into impacts of human- and environmental driven changes on the marine ecosystem. In…
In multicellular organisms, several cell states coexist. For determining each cell type, cell-cell interactions are often essential, in addition to intracellular gene expression dynamics. Based on dynamical systems theory, we propose a…
Bacteria can spontaneously develop collective motions by aligning their motions in dense systems. Here, we show that bacteria can also respond collectively to an alternating electrical field and form dynamic clusters oscillating at the same…
Single-cell experiments revealed substantial variability in generation times, growth rates but also in birth and division sizes between genetically identical cells. Understanding how these fluctuations determine the fitness of the…