Related papers: Quasispecies Theory for Horizontal Gene Transfer a…
We introduce a new way to study molecular evolution within well-established Hamilton-Jacobi formalism, showing that for a broad class of fitness landscapes it is possible to derive dynamics analytically within the $1/N$-accuracy, where $N$…
We consider a fitness-structured population model with competition and migration between nearest neighbors. Under a combination of large population and rare migration limits we are particularly interested in the asymptotic behavior of the…
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…
We study the evolution of sexual and asexual populations in general fitness landscapes. We find deep relations between the mathematics of biological evolution and the formalism of quantum mechanics. We give the general structure of the…
This Letter studies the quasispecies dynamics of a population capable of genetic repair evolving on a time-dependent fitness landscape. We develop a model that considers an asexual population of single-stranded, conservatively replicating…
This paper extends the semiconservative quasispecies equations to account for arbitrary post-replication lesion repair efficiency. Such an extension could be an important tool for understanding processes such as cancer development and stem…
Cryptic genetic sequences have attenuated effects on phenotypes. In the classic view, relaxed selection allows cryptic genetic diversity to build up across individuals in a population, providing alleles that may later contribute to…
The fuel-driven process of replication in living systems generates distributions of copied entities with varying degrees of copying accuracy. Here we introduce a thermodynamically consistent ensemble for investigating universal population…
In this review some simple models of asexual populations evolving on smooth landscapes are studied. The basic model is based on a cellular automaton, which is analyzed here in the spatial mean-field limit. Firstly, the evolution on a fixed…
The Kimura equation is a degenerated partial differential equation of drift-diffusion type used in population genetics. Its solution is required to satisfy not only the equation but a series of conservation laws formulated as integral…
Maintaining tissue homeostasis requires appropriate regulation of stem cell differentiation. The Waddington landscape posits that gene circuits in a cell form a potential landscape of different cell types, wherein cells follow attractors of…
High-fidelity and robust coherent population transfer is a major challenge in coherent quantum control. Different from the well known adiabatic condition, we present a rigorous adiabatic condition that is inspired by the idea of the…
A general population evolution model is considered. Any individual of the population is characterized by its score. Certain general conditions are assumed concerning the number of the individuals and their scores. Asymptotic theorems are…
We consider evolution of a large population, where fitness of each organism is defined by many phenotypical traits. These traits result from expression of many genes. We propose a new model of gene regulation, where gene expression is…
The ongoing explosion of genome sequence data is transforming how we reconstruct and understand the histories of biological systems. Across biological scales, from individual cells to populations and species, trees-based models provide a…
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…
Designing a good transfer channel for arbitrary quantum states in spin chains implies optimizing a cost function, usually the averaged fidelity of transmission. The fidelity of transmission measures how much the transferred state resembles…
Genetic studies often involve quantitative traits. Identifying genetic features that influence quantitative traits can help to uncover the etiology of diseases. Quantile regression method considers the conditional quantiles of the response…
We examine the dynamics of an age-structured population model in which the life expectancy of an offspring may be mutated with respect to that of the parent. While the total population of the system always reaches a steady state, the…
An explosion of high-throughput DNA sequencing in the past decade has led to a surge of interest in population-scale inference with whole-genome data. Recent work in population genetics has centered on designing inference methods for…