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Explaining biodiversity in nature is a fundamental problem in ecology. An outstanding challenge is embodied in the so-called Competitive Exclusion Principle: two species competing for one limiting resource cannot coexist at constant…
An ecosystem made of nutrients, plants, detritus and dissolved oxygen is presented. Its equilibria are established. Sufficient conditions for the existence of the coexistence equilibrium are derived and its feasibility is discussed in every…
Bacteria possess diverse mechanisms to regulate their motility in response to environmental and physiological signals, enabling them to navigate complex habitats and adapt their behavior. Among these mechanisms, interspecies recognition…
Understanding the emergent behavior of chemical reaction networks (CRNs) is a fundamental aspect of biology and its origin from inanimate matter. A closed CRN monotonically tends to thermal equilibrium, but when it is opened to external…
An autocatalytic pattern matching polymer system is studied as an abstract model for chemical ecosystem evolution. Highly ordered populations with particular sequence patterns appear spontaneously out of a vast number of possible states.…
Very recently we have developed a dynamic network model for eco-systems that achieved ``unification'' of ``micro'' and ``macro''-evolution. We now propose an extension of our model so as to stabilize the eco-system and describe {\it…
Disordered systems theory provides powerful tools to analyze the generic behaviors of highdimensional systems, such as species-rich ecological communities or neural networks. By assuming randomness in their interactions, universality…
Ecosystems often undergo abrupt regime shifts in response to gradual external changes. These shifts are theoretically understood as a regime switch between alternative stable states of the ecosystem dynamical response to smooth changes in…
Life is a complex biological phenomenon represented by numerous chemical, physical and biological processes performed by a biothermodynamic system/cell/organism. Both living organisms and inanimate objects are subject to aging, a biological…
Regardless of a system's complexity or scale, its growth can be considered to be a spontaneous thermodynamic response to a local convergence of down-gradient material flows. Here it is shown how growth can be constrained to a few distinct…
In this paper we consider a microscopic model of a simple ecosystem. The basic ingredients of this model are individuals, and both the phenotypic and genotypic levels are taken in account. The model is based on a long range cellular…
On the one hand, the dissipated heat of a thermodynamic work extraction process upper bounds the non-predictive information, which the associated system encodes about its environment. Thus, emergent information processing capabilities can…
Based on laboratory based growth of plant-like structures from inorganic materials, we present new theory for the emergence of plant structure at a range of scales dictated by levels of ionization (charge density), which can be traced…
Self-organization of active matter as well as driven granular matter in non-equilibrium dynamical states has attracted considerable attention not only from the fundamental and application viewpoints but also as a model to understand the…
We investigate the formation of stable ecological networks where many species share the same resource. We show that such stable ecosystem naturally occurs as a result of extinctions. We obtain an analytical relation for the number of…
The increasing volume of ecologically and biologically relevant data has revealed a wide collection of emergent patterns in living systems. Analyzing different datasets, ranging from metabolic gene-regulatory to species interaction…
The chemical composition of the earths atmosphere far from equilibrium is unique in the solar system and has been attributed to the presence of widespread life. Here I show that this perspective can be quantified using non-equilibrium…
Living systems self-organize in ways that conventional physical frameworks-based on forces, energies, and continuous fields-cannot fully capture. Processes like gene regulation and cellular decision-making involve rule-based logic and…
The human gut microbiome is a complex ecosystem, in which hundreds of microbial species and metabolites coexist, in part due to an extensive network of cross-feeding interactions. However, both the large-scale trophic organization of this…
Chemically active droplets provide simple models for cell-like systems that can grow and divide. Such active droplet systems are driven away from thermodynamic equilibrium and turn over chemically, which corresponds to a simple metabolism.…