Related papers: A probabilistic analysis of a continuous-time evol…
Using a newly introduced connection between the local and non-local description of open quantum system dynamics, we investigate the relationship between these two characterisations in the case of quantum semi-Markov processes. This class of…
We introduce a Markov model for the evolution of a gene family along a phylogeny. The model includes parameters for the rates of horizontal gene transfer, gene duplication, and gene loss, in addition to branch lengths in the phylogeny. The…
Inspired by Fisher's geometric approach to study beneficial mutations, we analyse probabilities of beneficial mutation and crossover recombination of strings in a general Hamming space with arbitrary finite alphabet. Mutations and…
A well-established model for the genealogy of a large population in equilibrium is Kingman's coalescent. For the population together with its genealogy evolving in time, this gives rise to a time-stationary tree-valued process. We study the…
We analyse sequential Markov coalescent algorithms for populations with demographic structure: for a bottleneck model, a population-divergence model, and for a two-island model with migration. The sequential Markov coalescent method is an…
We investigate a continuous time, probability measure-valued dynamical system that describes the process of mutation-selection balance in a context where the population is infinite, there may be infinitely many loci, and there are weak…
An individual-based model of an infinite system of point particles in $\mathbb{R}^d$ is proposed and studied. In this model, each particle at random produces a finite number of new particles and disappears afterwards. The phase space for…
We study the stochastic dynamics of a system of interacting species in a stochastic environment by means of a continuous-time Markov chain with transition rates depending on the state of the environment. Models of gene regulation in systems…
We consider a Moran model with recombination in a haploid population of size $N$. At each birth event, with probability $1-\rho_N R$ the offspring copies one parent's chromosome, and with probability $\rho_N R$ she inherits a chromosome…
Biological systems are typically highly open, non-equilibrium systems that are very challenging to understand from a statistical mechanics perspective. While statistical treatments of evolutionary biological systems have a long and rich…
We study the evolution of the population genealogy in the classic neutral Moran Model of finite size and in discrete time. The stochastic transformations that shape a Moran population can be realized directly on its genealogy and give rise…
In this paper we study a class of stochastic individual-based models that describe the evolution of haploid populations where each individual is characterised by a phenotype and a genotype. The phenotype of an individual determines its…
We study the evolution of recombination using a microscopic model developed within the frame of the theory of quantitative traits. Two components of fitness are considered: a static one that describes adaptation to environmental factors not…
Phylogenetics uses alignments of molecular sequence data to learn about evolutionary trees relating species. Along branches, sequence evolution is modelled using a continuous-time Markov process characterised by an instantaneous rate…
It is well known that the classical recombination equation for two parent individuals is equivalent to the law of mass action of a strongly reversible chemical reaction network, and can thus be reformulated as a generalised gradient system.…
We model evolution according to an asymmetric game as occurring in multiple finite populations, one for each role in the game, and study the effect of subjecting individuals to stochastic strategy mutations. We show that, when these…
Markov branching systems form a fundamental class of stochastic models that are extensively applied in biology, physics, finance, and other domains. These systems are distinguished by their continuous-time evolution and inherent branching…
The stochastic growth-fragmentation model describes the temporal evolution of a structured cell population through a discrete-time and continuous-state Markov chain. The simulations of this stochastic process and its invariant measure are…
We explore the concept of a consistent exchangeable survival process - a joint distribution of survival times in which the risk set evolves as a continuous-time Markov process with homogeneous transition rates. We show a correspondence with…
A study of time homogeneous, real valued Markov processes with a special property and a non-atomic initial distribution is provided. The new notion of a function of evolution of distribution which determines the dependency between one…