Related papers: Analysis of evolution through competitive selectio…
We introduce a new model of evolution on a fitness landscape possessing a tunable degree of neutrality. The model allows us to study the general properties of molecular species undergoing neutral evolution. We find that a number of…
We propose a general agent population learning system, and on this basis, we propose lineage evolution reinforcement learning algorithm. Lineage evolution reinforcement learning is a kind of derivative algorithm which accords with the…
Infinitely many distinct trait values may arise in populations bearing quantitative traits, and modeling their population dynamics is thus a formidable task. While classical models assume fixed or infinite population size, models in which…
Since protein mutations are the main driving force of evolution at the molecular level, a proper analysis of them (and the factors controlling them) will enable us to find a response to several crucial queries in evolutionary biology. Among…
Complex systems, such as life and languages, are governed by principles of evolution. The analogy and comparison between biology and linguistics\cite{alphafold2, RoseTTAFold, lang_virus, cell language, faculty1, language of gene, Protein…
We present an individual-based model of phenotypic trait evolution in two-sex populations, which includes semi-random mating of individuals of the opposite sex, natural death and intra-specific competition. By passing the number of…
We develop an theoretical approach for predicting biodiversity in multi-dimensional niche spaces, arising due to ecological drivers such as competitive exclusion. The novelty of our approach relies on the fact that ecological niches are…
The problem of the directionality of genome evolution is studied from the information-theoretic view. We propose that the function-coding information quantity of a genome always grows in the course of evolution through sequence duplication,…
Adaptive dynamics is a widely used framework for modeling long-term evolution of continuous phenotypes. It is based on invasion fitness functions, which determine selection gradients and the canonical equation of adaptive dynamics. Even…
Neutral evolution is the simplest model of molecular evolution and thus it is most amenable to a comprehensive theoretical investigation. In this paper, we characterize the statistical properties of neutral evolution of proteins under the…
We will study the relationship between two well-known theories, genetic evolution and random matrix theory in the context of many-body systems. It is suggested that genetic evolution can be described by a random matrix theory with…
A class of models for large-scale evolution and mass extinctions is presented. These models incorporate environmental changes on all scales, from influences on a single species to global effects. This is a step towards a unified picture of…
Evolution is a fundamental process that shapes the biological world we inhabit, and reinforcement learning is a powerful tool used in artificial intelligence to develop intelligent agents that learn from their environment. In recent years,…
The main topic of this thesis is the analysis of evolution equations reflecting issues in ecology and population dynamics. In mathematical modelling, the impact of environmental elements and the interaction between species is read into the…
We propose a mathematical framework for natural selection in finite populations. Traditionally, many of the selection-based processes used to describe cultural and genetic evolution (such as imitation and birth-death models) have been…
Proteins need to selectively interact with specific targets among a multitude of similar molecules in the cell. But despite a firm physical understanding of binding interactions, we lack a general theory of how proteins evolve high…
We study communities emerging from generalised random Lotka--Volterra dynamics with a large number of species with interactions determined by the degree of niche overlap. Each species is endowed with a number of traits, and competition…
Reaction-diffusion equations are widely used as the governing evolution equations for modeling many physical, chemical, and biological processes. Here we derive reaction-diffusion equations to model transport with reactions on a…
We present a quantitative model for the biological evolution of species body masses within large groups of related species, e.g., terrestrial mammals, in which body mass M evolves according to branching (speciation), multiplicative…
The regulation of a gene depends on the binding of transcription factors to specific sites located in the regulatory region of the gene. The generation of these binding sites and of cooperativity between them are essential building blocks…