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Ecological systems are emergent features of ecological and adaptive dynamics of a community of interacting species. By natural selection through the abiotic environment and by co-adaptation within the community, species evolve, thereby…
What makes living things special is how they manage matter, energy, and entropy. A general theory of organismal metabolism should therefore be quantified in these three currencies while capturing the unique way they flow between individuals…
The metabolic processes complexity is at the heart of energy conversion in living organisms and forms a huge obstacle to develop tractable thermodynamic metabolism models. By raising our analysis to a higher level of abstraction, we develop…
Redox biology underpins signalling, metabolism, immunity, and adaptation, yet lacks a unifying theoretical framework capable of formalising structure, function, and dynamics. Current interpretations rely on descriptive catalogues of…
Ecosystems frequently display the coexistence of diverse species under resource competition, typically resulting in skewed distributions of rarity and abundance. A potential driver of such coexistence is environmental fluctuations that…
We propose a model of multispecies populations surviving on distributed resources. System dynamics are investigated under changes in abiotic factors such as the climate, as parameterized through environmental temperature. In particular, we…
Vegetation in semi-arid environments self-organizes into striking spatial patterns -- bands, spots, labyrinths, and gaps -- with characteristic wavelengths on the order of tens to hundreds of meters. Existing reaction-diffusion models…
In this and a companion paper we outline a general framework for the thermodynamic description of open chemical reaction networks, with special regard to metabolic networks regulating cellular physiology and biochemical functions. We first…
How diversity is maintained in natural ecosystems is a long-standing question in Theoretical Ecology. By studying a system that combines ecological dynamics, heterogeneous interactions and spatial structure, we uncover a new mechanism for…
Active matter constantly dissipates energy to power the self-propulsion of its microscopic constituents. This opens the door to designing innovative cyclic engines without any equilibrium equivalent. We offer a consistent thermodynamic…
We study the problem of how a ``living'' system complex in structure can respond perfectly to local changes in the environment. Such a system is assumed to consist of a distributed ``living'' medium and a hierarchical ``supplying'' network…
Planktonic active matter represents an emergent system spanning different scales: individual, population and community; and complexity arising from sub-cellular and cellular to collective and ecosystem scale dynamics. This cross-scale…
Self-organization is the autonomous assembly of a network of interacting components into a stable, organized pattern. This article shows that the process of self-assembly can be encoded in terms of evolutionary entropy, a statistical…
Consider a population of organisms that harvest free energy from their environment to reproduce. This paper shows that if the organisms' reproductive rates are proportional to the amount of physical free energy that they can convert into…
We investigate the thermodynamics as well as the population dynamics of ecosystems based on a stochastic approach in which the number of individuals of the several species of the ecosystem are treated as stochastic variables. The several…
The eco-evolutionary dynamics of species are fundamentally linked to the energetic constraints of its constituent individuals. Of particular importance is the interplay between reproduction and the dynamics of starvation and recovery. To…
Environmental science almost invariably proposes problems of extreme complexity, typically characterized by strongly nonlinear evolution dynamics. The systems under investigation have many degrees of freedom - which makes them complicated -…
Ecologists and conservation biologists need to identify the relative importance of species to make sound management decisions and effectively allocate scarce resources. We introduce a new method, termed environ centrality, to determine the…
The Late Pleistocene Antarctic temperature variation curve is decomposed into two parts: cyclic and stochastic. These two parts represent different but tightly interconnected processes and also represent two different types of…
The history of the Earth has been marked by major ecological transitions, driven by metabolic innovation, that radically reshaped the composition of the oceans and atmosphere. The nature and magnitude of the earliest transitions, hundreds…