Related papers: Modeling gene's length distribution in genomes
We investigate the selective forces that promote the emergence of modularity in nature. We demonstrate the spontaneous emergence of modularity in a population of individuals that evolve in a changing environment. We show that the level of…
In our paper selected linguistic features of genomes to study the statistics of the gene codes are considered. We present the information theory from which it follows that if the system is described by distributions of hyperbolic type it…
Network science provides an indispensable theoretical framework for studying the structure and function of real complex systems. Different network models are often used for finding the rules that govern their evolution, whereby the correct…
Much information is stored in amino acid composition of protein and base composition of DNA. We simulated the evolution of amino acid frequencies and genomic GC content by a linguistic model. It is showed that the evolution of genetic code…
We studied a relations between the triplet frequency composition of mitochondria genomes, and the phylogeny of their bearers. First, the clusters in 63dimensional space were developed due to $K$-means. Second, the clade composition of those…
This paper presents an analysis of building blocks propagation in Quantum-Inspired Genetic Algorithm, which belongs to a new class of metaheuristics drawing their inspiration from both biological evolution and unitary evolution of quantum…
The Bak--Sneppen model is a simple stochastic model of evolution that exhibits self-organized criticality and for which few analytical results have been established. In the original Bak-Sneppen model and many subsequent variants,…
We study the time dependence of the grain size distribution N(r,t) during crystallization of a d-dimensional solid. A partial differential equation including a source term for nuclei and a growth law for grains is solved analytically for…
We study the asymptotic behavior of the long cycles of a random permutation of $n$ objects with respect to multiplicative measures with polynomial growing cycle weights. We show that the longest cycle and the length differences between the…
Entropy plays a key role in statistical physics of complex systems, which in general exhibit diverse aspects of emergence on different scales. However, it still remains not fully resolved how entropy varies with the coarse-graining level…
Classical population genetics a priori assigns fitness to alleles without considering molecular or functional properties of proteins that these alleles encode. Here we study population dynamics in a model where fitness can be inferred from…
This paper describes the application of finite-size scaling concepts to domain growth in systems with a non-conserved order parameter. A finite-size scaling ansatz for the time-dependent order parameter distribution function is proposed,…
With the help of one-dimensional random Potts-like model we study the origins of fine structure observed on differential melting profiles of double-stranded DNA. We assess the effects of sequence arrangement on DNA melting curves through…
Gene expression is inherently noisy, posing a challenge to understanding how precise and reproducible patterns of gene expression emerge in mammals. We investigate this phenomenon using gastruloids, an in vitro model for early mammalian…
A punctuated equilibrium model of biological evolution with relative fitness between different species being the fundamental driving force of evolution is introduced. Mutation is modeled as a fitness updating cellular automaton process…
The nature of the quantitative distribution of the 64 DNA codons in the human genome has been an issue of debate for over a decade. Some groups have proposed that the quantitative distribution of the DNA codons ordered as a rank-frequency…
Gene expression is a central process to any form of life. It involves multiple temporal and functional scales that extend from specific protein-DNA interactions to the coordinated regulation of multiple genes in response to intracellular…
The innumerable shapes of plant leaves present a challenge to the explanatory power of biophysical theory. A model is needed that can produce these shapes with a small set of parameters. This paper presents a simple model of leaf shape…
Early literature on genome rearrangement modelling views the problem of computing evolutionary distances as an inherently combinatorial one. In particular, attention was given to estimating distances using the minimum number of events…
In this article, we study a model of random permutations, which we call random standardized permutations, based on a sequence of i.i.d. random variables. This model generalizes others, such as the riffle-shuffle and the major-index-biased…