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In recent times whole-genome gene expression analysis has turned out to be a highly important tool to study the coordinated function of a very large number of genes within their corresponding cellular environment, especially in relation to…
We show how concepts from statistical physics, such as order parameter, thermodynamic limit, and quantum phase transition, translate into biological concepts in mutation-selection models for sequence evolution and can be used there. The…
The nonequilibrium dynamic phase transition, in the kinetic Ising model in presence of an oscillating magnetic field, has been studied by Monte Carlo simulation. The fluctuation of dynamic order parameter has been studied as a function of…
We introduce a statistical method that can reconstruct nonlinear genetic models (i.e., including epistasis, or gene-gene interactions) from phenotype-genotype (GWAS) data. The computational and data resource requirements are similar to…
In statistical genetics an important task involves building predictive models for the genotype-phenotype relationships and thus attribute a proportion of the total phenotypic variance to the variation in genotypes. Numerous models have been…
The linear response to temperature changes is derived for systems with overdamped stochastic dynamics. Holding both in transient and steady state conditions, the results allow to compute nonequilibrium thermal susceptibilities from…
The difference diffusion model with two equilibrium states is given by a stochastic equation with two components: the predicted one, which is determined by the regression function of increments with two equilibriums, and the stochastic one,…
Modern biomedicine is challenged to predict the effects of genetic variation. Systematic functional assays of point mutants of proteins have provided valuable empirical information, but vast regions of sequence space remain unexplored.…
The adaptive evolution of large asexual populations is generally characterized by competition between clones carrying different beneficial mutations. This interference phenomenon slows down the adaptation speed and makes the theoretical…
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…
The evolutionary dynamics of molecular populations are strongly dependent on the structure of genotype spaces. The map between genotype and phenotype determines how easily genotype spaces can be navigated and the accessibility of…
Molecular phenotypes are important links between genomic information and organismic functions, fitness, and evolution. Complex phenotypes, which are also called quantitative traits, often depend on multiple genomic loci. Their evolution…
We present the complete phase diagram for one-dimensional binary mixtures of bosonic ultracold atomic gases in a harmonic trap. We obtain exact results with direct numerical diagonalization for small number of atoms, which permits us to…
Epistasis refers to the phenomenon in which phenotypic consequences caused by mutation of one gene depend on one or more mutations at another gene. Epistasis is critical for understanding many genetic and evolutionary processes, including…
The statistical equilibrium properties of the linear sigma model are studied, with a view towards characterizing the field configurations employed as initial conditions for numerical simulations of the formation of disoriented chiral…
Fisher's geometric model was originally introduced to argue that complex adaptations must occur in small steps because of pleiotropic constraints. When supplemented with the assumption of additivity of mutational effects on phenotypic…
Multivariate elliptically-contoured distributions are widely used for modeling correlated and non-Gaussian data. In this work, we study the kurtosis of the elliptical model, which is an important parameter in many statistical analysis.…
I discuss the so-called stochastic individual based model of adaptive dynamics and in particular how different scaling limits can be obtained by taking limits of large populations, small mutation rate, and small effect of single mutations…
The evolution of high-dimensional phenotypes is investigated using a statistical physics model consists of interacting spins, in which genotypes, phenotypes, and environments are represented by spin configurations, interaction matrices, and…
A variety of selection-mutation models for DNA (or RNA) sequences, well known in molecular evolution, can be translated into a model of coupled Ising quantum chains. This correspondence is used to investigate the genetic variability and…