Related papers: Genetic Paralog Analysis and Simulations
We explore the connection between evolution and large-deviation theory. To do so, we study evolutionary dynamics in which individuals experience mutations, reproduction, and selection using variants of the Moran model. We show that, in the…
We study a class of growth algorithms for directed graphs that are candidate models for the evolution of genetic regulatory networks. The algorithms involve partial duplication of nodes and their links, together with innovation of new…
Monte Carlo simulations are an important tool in statistical physics, complex systems science, and many other fields. An increasing number of these simulations is run on parallel systems ranging from multicore desktop computers to…
Bayesian design of experiments and sample size calculations usually rely on complex Monte Carlo simulations in practice. Obtaining bounds on Bayesian notions of the false-positive rate and power therefore often lack closed-form or…
In mathematical population genetics, it is well known that one can represent the genealogy of a population by a tree, which indicates how the ancestral lines of individuals in the population coalesce as they are traced back in time. As the…
A steady influx of a single deleterious multilocus genotype will impose genetic load on the resident population and leave multiple descendants carrying various numbers of the foreign alleles. Provided that the foreign types are rare at…
It has been proposed that the degeneracy of the genetic code,i.e., the phenomenon that different codons (base triplets) of DNA are transcribed into the same amino acid, may be interpreted as the result of a symmetry breaking process. In the…
We consider relaxation processes that exhibit a stretched exponential behavior. We find that in those systems, where the relaxation arises from two competing exponential processes, the size of the system may play a dominant role. Above a…
When the logarithmic slope of the galaxy counts is lower than 0.4 (this is the case in all filters at high magnitude), the magnification bias due to the lens makes the number density of objects decrease. Consequently, the radial…
We study the evolution of allele frequencies in a large population where random mating is violated in a particular way that is related to recent works on speciation. Specifically, we consider non-random encounters in haploid organisms…
We describe a general strategy for sampling configurations from a given distribution, NOT based on the standard Metropolis (Markov chain) strategy. It uses the fact that nontrivial problems in statistical physics are high dimensional and…
The far-from-equilibrium dynamics of glassy systems share important phenomenological traits. A transition is generally observed from a time-homogeneous dynamical regime to an aging regime where physical changes occur intermittently and, on…
Intragenomic recombination (crossover) is a very important evolutionary mechanism. The crossover events are not evenly distributed along the natural chromosomes. Monte Carlo simulations revealed that frequency of recombinations decides…
The characterization and reconstruction of heterogeneous materials, such as porous media and electrode materials, involve the application of image processing methods to data acquired by microscopy techniques. In this study, we present a…
We show how to incorporate fluctuations of the recombination rate along the chromosome into standard gene-genealogical models for the decorrelation of gene histories. This enables us to determine how small-scale fluctuations (Poissonian…
Following genetic ancestry in eukaryote populations poses several open problems due to sexual reproduction and recombination. The history of extant genetic material is usually modeled backwards in time, but tracking chromosomes at a large…
Research in quantitative evolutionary genomics and systems biology led to the discovery of several universal regularities connecting genomic and molecular phenomic variables. These universals include the log-normal distribution of the…
In Monte Carlo particle transport codes, it is often important to adjust reaction cross sections to reduce the variance of calculations of relatively rare events, in a technique known as non-analogous Monte Carlo. We present the theory and…
We discuss two different ways of chromosomes' and genomes' evolution. Purifying selection dominates in large panmictic populations, where Mendelian law of independent gene assortment is valid. If the populations are small, recombination…
We study the statistical properties of the generation of random graphs according the configuration model, where one assigns randomly degrees to nodes. This model is often used, e.g., for the scale-free degree distribution ~d^gamma. For the…