Related papers: Evolutionary Shaping of Low-Dimensional Path Facil…
Both evolution and ecology have long been concerned with the impact of variable environmental conditions on observed levels of genetic diversity within and between species. We model the evolution of a quantitative trait under selection that…
Recently described stochastic models of protein evolution have demonstrated that the inclusion of structural information in addition to amino acid sequences leads to a more reliable estimation of evolutionary parameters. We present a…
We study the coevolutionary dynamics of the diversity of phenotype expression and the evolution of cooperation in the Prisoner's Dilemma game. Rather than pre-assigning zero-or-one interaction rate, we diversify the rate of interaction by…
This work presents a new modeling approach to macroscopic, polycrystalline elasto-plasticity starting from first principles and a few well-defined structural assumptions, incorporating the mildly rate-dependent (viscous) nature of plastic…
In complex ecosystems such as microbial communities, there is constant ecological and evolutionary feedback between the residing species and the environment occurring on concurrent timescales. Species respond and adapt to their surroundings…
We analyze a nonlocal PDE model describing the dynamics of adaptation of a phenotypically structured population, under the effects of mutation and selection, in a changing environment. Previous studies have analyzed the large-time behavior…
The fitness landscape defines the relationship between genotypes and fitness in a given environment, and underlies fundamental quantities such as the distribution of selection coefficient, or the magnitude and type of epistasis. A better…
Genotypic fitness landscapes are constructed by assessing the fitness of all possible combinations of a given number of mutations. In the last years, several experimental fitness landscapes have been completely resolved. As fitness…
Darwinian evolution is driven by random mutations, genetic recombination (gene shuffling) and selection that favors genotypes with high fitness. For systems where each genotype can be represented as a bitstring of length $L$, an overview of…
We study metanetworks arising in genotype and phenotype spaces, in the context of a model population of Boolean graphs evolved under selection for short dynamical attractors. We define the adjacency matrix of a graph as its genotype, which…
Evolutionary adaptation is often likened to climbing a hill or peak. While this process is simple for fitness landscapes where mutations are independent, the interaction between mutations (epistasis) as well as mutations at loci that affect…
Evolutionary success depends on the capacity to adapt: organisms must respond to environmental challenges through both genetic innovation and lifetime learning. The gene-centric paradigm attributes evolutionary causality exclusively to…
We numerically examine a binary system of particles with repulsive interactions, where one species is driven by a rotating drive and the other is subjected either to a constant drive in a fixed direction or to a rotating drive that is out…
A microscopic agent dynamical model for diploid age-structured populations is used to study evolution of polymorphism and sympatric speciation. The underlying ecology is represented by a unimodal distribution of resources of some width.…
We consider the evolutionary trajectories traced out by an infinite population undergoing mutation-selection dynamics in static, uncorrelated random fitness landscapes. Starting from the population that consists of a single genotype, the…
The tempo and mode of an adaptive process is strongly determined by the structure of the fitness landscape that underlies it. In order to be able to predict evolutionary outcomes (even on the short term), we must know more about the nature…
In this work we develop a microscopic physical model of early evolution, where phenotype,organism life expectancy, is directly related to genotype, the stability of its proteins in their native conformations which can be determined exactly…
Regulatory networks consist of interacting molecules with a high degree of mutual chemical specificity. How can these molecules evolve when their function depends on maintenance of interactions with cognate partners and simultaneous…
In this review we summarize our recent efforts in trying to understand the role of heterogeneity in cancer progression by using neural networks to characterise different aspects of the mapping from a cancer cells genotype and environment to…
We are interested in the impact of natural selection in a prey-predator community. We introduce an individual-based model of the community that takes into account both prey and predator phenotypes. Our aim is to understand the phenotypic…