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We study the stochastic evolution of four species in cyclic competition in a well mixed environment. In systems composed of a finite number $N$ of particles these simple interaction rules result in a rich variety of extinction scenarios,…
We introduce an automatic machine learning (AutoML) modeling architecture called Autostacker, which combines an innovative hierarchical stacking architecture and an Evolutionary Algorithm (EA) to perform efficient parameter search. Neither…
Recently, we proposed a self-propelled particle model with competing alignment interactions: nearby particles tend to align their velocities whereas they anti-align their direction of motion with particles which are further away [R.…
Evolutionary and ecosystem dynamics are often treated as different processes --operating at separate timescales-- even if evidence reveals that rapid evolutionary changes can feed back into ecological interactions. A recent long-term field…
The persistence of biodiversity of species is a challenging proposition in ecological communities in the face of Darwinian selection. The present article investigates beyond the pairwise competitive interactions and provides a novel…
We study a model for the evolution of chemical species under a combination of population dynamics on a short time scale and a selection mechanism on a longer time scale. Least fit nodes are replaced by new nodes whose links are attached to…
Spontaneous self-assembly in molecular systems is a fundamental route to both biological and engineered soft matter. Simple micellisation, emulsion formation, and polymer mixing principles are well understood. However, the principles behind…
The biological requirements for an ecosystem to develop and maintain species diversity are in general unknown. Here we consider a model ecosystem of sessile and mutually excluding organisms competing for space [Mathiesen et al. Phys. Rev.…
A model of $s$ interacting species is considered with two types of dynamical variables. The fast variables are the populations of the species and slow variables the links of a directed graph that defines the catalytic interactions among…
We provide evidence of an extreme form of sensitivity to initial conditions in a family of one-dimensional self-ruling dynamical systems. We prove that some hyperchaotic sequences are closed-form expressions of the orbits of these…
We review models of biological evolution in which the population frequency changes deterministically with time. If the population is self-replicating, although the equations for simple prototypes can be linearised, nonlinear equations arise…
Particles that are catalytically-active and chemotactic can interact through the concentration fields upon which they act, which in turn may lead to wide-scale spatial self-organization. When these active particles interact through several…
We propose a class of evolutionary models that involves an arbitrary exchangeable process as the breeding process and different selection schemes. In those models, a new genome is born according to the breeding process, and then a genome is…
Species-rich communities, such as the microbiota or microbial ecosystems, provide key functions for human health and climatic resilience. Increasing effort is being dedicated to design experimental protocols for selecting community-level…
The concept of evolutionary development of structures constituted a \emph{real} revolution in biology: it was possible to understand how the very complex structures of life can arise in an out-of-equilibrium system. The investigation of…
Self-assembly is a ubiquitous process in synthetic and biological systems, broadly defined as the spontaneous organization of multiple subunits (e.g. macromolecules, particles) into ordered multi-unit structures. The vast majority of…
With a view to connecting random mutation on the molecular level to punctuated equilibrium behavior on the phenotype level, we propose a new model for biological evolution, which incorporates random mutation and natural selection. In this…
Self-assembling, semi-flexible polymers are ubiquitous in biology and technology. However, there remain conflicting accounts of the equilibrium kinetics for such an important system. Here, by focusing on a dynamical description of a minimal…
Ecological systems comprise an astonishing diversity of species that cooperate or compete with each other forming complex mutual dependencies. The minimum requirements to maintain a large species diversity on long time scales are in general…
Mathematical models play an increasingly important role in the interpretation of biological experiments. Studies often present a model that generates the observations, connecting hypothesized process to an observed pattern. Such generative…