Related papers: Co-evolution is Incompatible with the Markov Assum…
Joint species distribution models are popular in ecology for modeling covariate effects on species occurrence, while characterizing cross-species dependence. Data consist of multivariate binary indicators of the occurrences of different…
Generative models derived from large protein sequence alignments define complex fitness landscapes, but their utility for accurately modeling non-equilibrium evolutionary dynamics remains unclear. In this work, we perform a rigorous…
Phylogenetic comparative methods are well established tools for using inter-species variation to analyse phenotypic evolution and adaptation. They are generally hampered, however, by predominantly univariate approaches and failure to…
Machine learning techniques not only offer efficient tools for modelling dynamical systems from data, but can also be employed as frontline investigative instruments for the underlying physics. Nontrivial information about the original…
We address the problem of quantifying the non-Markovian character of quantum time-evolutions of general systems in contact with an environment. We introduce two different measures of non-Markovianity that exploit the specific traits of…
Relationships between sediment flux and geomorphic processes are combined with statements of mass conservation, in order to create continuum models of hillslope evolution. These models have parameters which can be calibrated using available…
Clonal interference, competition between multiple co-occurring beneficial mutations, has a major role in adaptation of asexual populations. We provide a simple individual based stochastic model of clonal interference taking into account a…
It is shown that a convex combination of two non-Markovian evolutions may lead to Markovian semigroup. This shows that convex combination of quantum evolutions displaying nontrivial memory effects may result in a perfectly memoryless…
Functional protein-protein interactions are crucial in most cellular processes. They enable multi-protein complexes to assemble and to remain stable, and they allow signal transduction in various pathways. Functional interactions between…
We consider the evolution of populations under the joint action of mutation and differential reproduction, or selection. The population is modelled as a finite-type Markov branching process in continuous time, and the associated…
Measuring gene expression simultaneously in both hosts and symbionts offers a powerful approach to explore the biology underlying species interactions. Such dual or simultaneous RNAseq approaches have primarily been used to gain insight…
Social dilemmas are an integral part of social interactions. Cooperative actions, ranging from secreting extra-cellular products in microbial populations to donating blood in humans, are costly to the actor and hence create an incentive to…
Biases in molecular evolution can significantly influence evolutionary trajectories. They have been described in a variety of contexts such as development and mutation, but not for acquiring new functions (i.e. emergence). Here, we…
Eco-evolutionary game dynamics which characterizes the mutual interactions and the coupled evolutions of strategies and environments has been of growing interests in very recent years. Since such feedback loops widely exist in a range of…
It has been argued that any evolution law taking pure states to mixed states in quantum field theory necessarily gives rise to violations of either causality or energy-momentum conservation, in such a way as to have unacceptable…
A Markov evolution of a system of point particles in $\mathbb{R}^d$ is described at micro-and mesoscopic levels. The particles reproduce themselves at distant points (dispersal) and die, independently and under the influence of each other…
In this paper we extend the framework of evolutionary inspection game put forward recently by the author and coworkers to a large class of conflict interactions dealing with the pressure executed by the major player (or principal) on the…
Markovian population models are suitable abstractions to describe well-mixed interacting particle systems in situation where stochastic fluctuations are significant due to the involvement of low copy particles. In molecular biology,…
This work proposes an extension to Structured Grammatical Evolution (SGE) called Co-evolutionary Probabilistic Structured Grammatical Evolution (Co-PSGE). In Co-PSGE each individual in the population is composed by a grammar and a genotype,…
Recently, computational modelling became a very important research tool that enables us to study problems that for decades evaded scientific analysis. Evolutionary systems are certainly examples of such problems: they are composed of many…