Related papers: Genetic Paralog Analysis and Simulations
We introduce a population dynamics model, where individual genomes are represented by bit-strings. Selection is described by death probabilities which depend on these genomes, and new individuals continuously replace the ones that die,…
We reconsider the deterministic haploid mutation-selection equation with two types. This is an ordinary differential equation that describes the type distribution (forward in time) in a population of infinite size. This paper establishes…
Here we describe how some important scaling laws observed in the distribution of languages on Earth can emerge from a simple computer simulation. The proposed language dynamics includes processes of selective geographic colonization,…
We have simulated the evolution of age structured populations whose individuals represented by their diploid genomes were distributed on a square lattice. The environmental conditions on the whole territory changed simultaneously in the…
In observational studies, researchers must select a method to control for confounding. Options include propensity score methods and regression. It remains unclear how dataset characteristics (size, overlap in propensity scores, exposure…
We use large-scale Monte Carlo simulations to obtain comprehensive results for domain growth and aging in the random field XY model in dimensions $d=2,3$. After a deep quench from the paramagnetic phase, the system orders locally via…
We study the interplay of clumping at small scales with the collapse and relaxation of perturbations at larger scales using N-Body simulations. We quantify the effect of collapsed haloes on perturbations at larger scales using two point…
We perform atomistic Monte Carlo simulations of bending a Lennard-Jones single crystal in two dimensions. Dislocations nucleate only at the free surface as there are no sources in the interior of the sample. When dislocations reach…
{We study biasing as a physical phenomenon by analysing geometrical and clustering properties of density fields of matter and galaxies.} {Our goal is to determine the bias function using a combination of geometrical and power spectrum…
As it follows from the interrelation of Gamma and Poisson distributions the observed value of asymmetry for Poisson flows of events has the bias. The Monte Carlo experiment confirms the presence of this bias between the observed and initial…
Topologically constrained genome-like polymers often double-fold into tree-like configurations, which can be modelled on the level of folded (ring) polymers or on the level of the underlying random trees. For both descriptions, we have…
We consider two versions of stochastic population models with mutation and selection. The first approach relies on a multitype branching process; here, individuals reproduce and change type (i.e., mutate) independently of each other,…
In a multicellular organism different cell types express a gene in different amounts. Samples from which gene expression levels can be measured typically contain a mixture of different cell types, the resulting measurements thus give only…
We show that for any Cayley graph, the probability (at any $p$) that the cluster of the origin has size n decays at a well-defined exponential rate (possibly 0). For general graphs, we relate this rate being positive in the supercritical…
Phylogenetics has seen an steady increase in substitution model complexity, which requires increasing amounts of computational power to compute likelihoods. This model complexity motivates strategies to approximate the likelihood functions…
The quality of the inferences we make from pathogen sequence data is determined by the number and composition of pathogen sequences that make up the sample used to drive that inference. However, there remains limited guidance on how to best…
We present some results of simulations of population growth and evolution, using the standard asexual Penna model, with individuals characterized by a string of bits representing a genome containing some possible mutations. After about…
The probability that two randomly selected phylogenetic trees of the same size are isomorphic is found to be asymptotic to a decreasing exponential modulated by a polynomial factor. The number of symmetrical nodes in a random phylogenetic…
Time evolution of number of species (genera, families, and others), population of them, and size distribution of present ones and life times are studied in terms of a new model, where population of each genetic taxon increases by a (random)…
For random percolation at p_c, the probability distribution P(n) of the number of spanning clusters (n) has been studied in large scale simulations. The results are compatible with $P(n) \sim \exp(-an^2)$ for all dimensions. We also study…