Related papers: A limiting rule for the variability of coding sequ…
The aim of this study is to compare the growth speed of different cell populations measured by their Malthus parameter. We focus on both the age-structured and size-structured equations. A first population (of reference) is composed of…
By introducing the notions of living and dead nodes a new model of random tree evolution with continuous time parameter has been constructed. It is assumed that two random variables, the lifetime and the offspring number of living nodes…
Herein it is shown that in order to study the statistical properties of DNA sequences in bacterial chromosomes it suffices to consider only one half of the chromosome because they are similar to its corresponding complementary sequence in…
Genetic information is stored in a linear sequence of base-pairs; however, thermal fluctuations and complex DNA conformations such as folds and loops make it challenging to order genomic material for in vitro analysis. In this work, we…
We rigorously prove a form of disorder-resistance for a class of one-dimensional cellular automaton rules, including some that arise as boundary dynamics of two-dimensional solidification rules. Specifically, when started from a random…
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…
In an evolutionary system in which the rules of mutation are local in nature, the number of possible outcomes after $m$ mutations is an exponential function of $m$ but with a rate that depends only on the set of rules and not the size of…
Colonies of rod-shaped bacteria constitute a system of colloidal active matter with nematic properties. As a single initial bacterium multiplies through repeated divisions, the resulting colony quickly loses long-range orientational order,…
Several orders of magnitude typically separate the contour length of eukaryotic chromosomes and the size of the nucleus where they are confined. The ensuing topological constraints can slow down the relaxation dynamics of genomic filaments…
Microbial communities are ubiquitous in nature and come in a multitude of forms, ranging from communities dominated by a handful of species to communities containing a wide variety of metabolically distinct organisms. This huge range in…
Growth-fragmentation processes model systems of cells that grow continuously over time and then fragment into smaller pieces. Typically, on average, the number of cells in the system exhibits asynchronous exponential growth and, upon…
The evolutionary reason for the increase in gene length from archaea to prokaryotes to eukaryotes observed in large scale genome sequencing efforts has been unclear. We propose here that the increasing complexity of protein-protein…
A gene expression compendium is a heterogeneous collection of gene expression experiments assembled from data collected for diverse purposes. The widely varied experimental conditions and genetic backgrounds across samples creates a…
The antibody repertoire of each individual is continuously updated by the evolutionary process of B cell receptor mutation and selection. It has recently become possible to gain detailed information concerning this process through…
It has been recently shown that the exponential growth rate of a population of bacterial cells starting from a single cell shows transient oscillations due to early synchronized bursts of division. These oscillations are enhanced by cell…
We have analysed the possibility of scaling the sexual Penna ageing model. Assuming that the number of genes expressed before the reproduction age grows linearly with the genome size and that the mutation rate per genome and generation is…
The relationship between the size of the whole and the size of the parts in language and music is known to follow Menzerath-Altmann law at many levels of description (morphemes, words, sentences...). Qualitatively, the law states that…
Organelles of optimum size are crucial for proper functioning of a living cell. The cell employs various mechanisms for actively sensing and controlling the size of its organelles. Recently Bauer et al have opened a new research frontier in…
A chord diagram consists of a circle, called the backbone, with line segments, called chords, whose endpoints are attached to distinct points on the circle. The genus of a chord diagram is the genus of the orientable surface obtained by…
Cell growth and gene expression, essential elements of all living systems, have long been the focus of biophysical interrogation. Advances in single-cell methods have invigorated theoretical studies into these processes. However, until…