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The coupling between evolutionary and ecological changes (eco-evolutionary dynamics) has been shown to be relevant among diverse species, and is also of interest outside of ecology, i.e. in cancer evolution. These dynamics play an important…
The response of ecosystems to perturbations is considered from a thermodynamic perspective by acknowledging that, as for all macroscopic systems and processes, the dynamics and stability of ecosystems is subject to definite thermodynamic…
We consider a dynamical system consisting of subsystems indexed by a lattice. Each subsystem has one conserved degree of freedom ("energy") the rest being uniformly hyperbolic. The subsystems are weakly coupled together so that the sum of…
Disordered systems subject to a fluctuating environment can self-organize into a complex history-dependent response, retaining a memory of the driving. In sheared amorphous solids, self-organization is established by the emergence of a…
We introduce the idea of weakly coherent collisional models, where the elements of an environment interacting with a system of interest are prepared in states that are approximately thermal, but have an amount of coherence proportional to a…
Ecological patterns arise from the interplay of many different processes, and yet the emergence of consistent phenomena across a diverse range of ecological systems suggests that many patterns may in part be determined by statistical or…
We demonstrate that active carpets of bacteria or self-propelled colloids generate coherent flows towards the substrate, and propose that these currents provide efficient pathways to replenish nutrients that feed back into activity. A full…
The dynamics of molecular collisions in a macroscopic body are encoded by the parameter Thermodynamic entropy - a statistical measure of the number of molecular configurations that correspond to a given macrostate. Directionality in the…
Many mechanisms, functions and structures of life have been unraveled. However, the fundamental driving force that propelled chemical evolution and led to life has remained obscure. The 2nd law of thermodynamics, written as an equation of…
It is shown that an ecosystem in equilibrium is generally organized in a state which is poised in the vicinity of a novel phase transition.
Self-organized spatial patterns of vegetation are frequent in drylands and, because pattern shape correlates with water availability, they have been suggested as important indicators of ecosystem health. However, the mechanisms underlying…
The high energy transfer efficiency of photosynthetic complexes has been a topic of research across many disciplines. Several attempts have been made in order to explain this energy transfer enhancement in terms of quantum mechanical…
Organisms shape their own environment, which in turn affects their survival. This feedback becomes especially important for communities containing a large number of species; however, few existing approaches allow studying this regime,…
Dormancy is an essential strategy for microorganisms to cope with environmental stress. However, global ecosystem models typically ignore microbial dormancy, resulting in major model uncertainties. To facilitate the consideration of…
We present an individual based model of evolutionary ecology. The reproduction rate of individuals characterized by their genome depends on the composition of the population in genotype space. Ecological features such as the taxonomy and…
Microbial communities display extreme diversity. A variety of strains or species coexist even when limited by a single resource. It has been argued that metabolite secretion creates new niches and facilitates such diversity. Nonetheless, it…
Cell cultures exhibit rich and complex behaviors driven by dynamic metabolic interactions among cells. In this work, we present a model that captures these interactions through a framework inspired by statistical mechanics. Using Monte…
We introduce various models for cellulose bio-degradation by micro-organisms. Those models rely on complex chemical mechanisms, involve the structure of the cellulose chains and are allowed to depend on the phenotypical traits of the…
These lecture notes are designed to provide a brief introduction into the phenomenology of active matter and to present some of the analytical tools used to rationalize the emergent behavior of active systems. Such systems are made of…
With the use of the appropriate technology, such as photovoltaics and seawater desalination, humans have the ability to sustainably increase their production of food and energy while minimising detrimental impacts on the Earth system.