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The pedestrian flow is one of the most complex systems, involving large populations of interacting agents. Models at microscopic and macroscopic scales offer different advantages for studying related problems. In general, microscopic models…

Genome-scale metabolic models have become a fundamental tool for examining metabolic principles. However, metabolism is not solely characterized by the underlying biochemical reactions and catalyzing enzymes, but also affected by regulatory…

A central and long-standing issue in evolutionary theory is the origin of the biological variation upon which natural selection acts1. Some hypotheses suggest that evolutionary change represents an adaptation to the surrounding environment…

Biological systems are known to communicate by diffusing chemical signals in the surrounding medium. However, most of the recent literature has neglected the electron transfer mechanism occurring amongst living cells, and its role in…

Microbes are everywhere, including in and on our bodies, and have been shown to play key roles in a variety of prevalent human diseases. Consequently, there has been intense interest in the design of bacteriotherapies or "bugs as drugs,"…

The microbiome constitutes a complex microbial ecology of interacting components that regulates important pathways in the host. Measurements of microbial abundances are key to learning the intricate network of interactions amongst microbes.…

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…

Complex contagion models that involve contagion along higher-order structures, such as simplicial complexes and hypergraphs, yield new classes of mean-field models. Interestingly, the differential equations arising from many such models…

Recent advances in bioinformatics have made high-throughput microbiome data widely available, and new statistical tools are required to maximize the information gained from these data. For example, analysis of high-dimensional microbiome…

This paper concerns the modeling and numerical simulation of the process of speciation. In particular, given conditions for which one or more speciation events within an ecosystem occur, our aim is to develop the necessary modeling and…

Biological and social systems are structured at multiple scales, and the incentives of individuals who interact in a group may diverge from the collective incentive of the group as a whole. Mechanisms to resolve this tension are responsible…

Many of the chemical reactions that take place within a living cell are irreversible. Due to evolutionary pressures, the number of allowable reactions within these systems are highly constrained and thus the resulting metabolic networks…

Communication between cells is realized by exchange of biochemical substances. Due to internal organization of living systems and variability of external parameters, the exchange is heavily influenced by perturbations of various parameters…

We consider a simple model for the assembly of chiral molecules in two dimensions driven by maximization of the contact area. We derive a macroscopic model described by a parameter taking nine possible values corresponding to the possible…

We consider a three-level food chain in which an epidemics affects the intermediate population. Two models are presented, respectively either allowing for unlimited food supply for the bottom prey, or instead assuming for it a logistic…

Notable recent works have focused on the multi-layer properties of coevolving diseases. We point out that very similar systems play an important role in population ecology. Specifically we study a meta food-web model that was recently…

Social dilemmas are an integral part of social interactions. Cooperative actions, ranging from secreting extra-cellular products in microbial populations to donating blood in humans, are costly to the actor and hence create an incentive to…

A stochastic epidemic model is defined in which each individual belongs to a household, a secondary grouping (typically school or workplace) and also the community as a whole. Moreover, infectious contacts take place in these three settings…

Navigation of microorganisms is controlled by internal processes ultimately sensitive to mechanical or chemical signaling encountered along the path. In many natural environments, such as porous soils or physiological ducts, motile species…

Production of energy (metabolism) and its distribution is vital for living organisms, both at individual level - between different functions of an organism, as well as between species of communities at different organizational levels,…