Related papers: A limiting rule for the variability of coding sequ…
The paper presents a method by which the mean field dynamics of a population of dynamical systems with parameter diversity and global coupling can be described in terms of a few macroscopic degrees of freedom. The method applies to…
Heterogeneous systems of active matter exhibit a range of complex emergent dynamical patterns. In particular, it is difficult to predict the properties of the mixed system based on its constituents. These considerations are particularly…
The mean size of exponentially dividing E. coli cells cultured in different nutrient conditions is known to depend on the mean growth rate only. However, the joint fluctuations relating cell size, doubling time and individual growth rate…
In a letter published in Molecular Biology Evolution [10], Chen and Zhang argue that the variation of the mutation rate along the Escherichia coli genome that we recently reported [3] cannot be evolutionarily optimised. To support this…
Previous investigation of coding sequence lengths (CDS) in the bacterial circular chromosome revealed short range correlation in the series of these data. We have further analyzed the averaged periodograms of these series and we found that…
A measure called Physical Complexity is established and calculated for a population of sequences, based on statistical physics, automata theory, and information theory. It is a measure of the quantity of information in an organism's genome.…
It is shown that metric representation of DNA sequences is one-to-one. By using the metric representation method, suppression of nucleotide strings in the DNA sequences is determined. For a DNA sequence, an optimal string length to display…
Background: There is a 3-fold redundancy in the Genetic Code; most amino acids are encoded by more than one codon. These synonymous codons are not used equally; there is a Codon Usage Bias (CUB). This article will provide novel information…
In exponentially proliferating populations of microbes, the population typically doubles at a rate less than the average doubling time of a single-cell due to variability at the single-cell level. It is known that the distribution of…
Motivated by recent experiments probing shape, size and dynamics of bacterial chromosomes in growing cells, we consider a polymer model consisting of a circular backbone to which side-loops are attached, confined to a cylindrical cell. Such…
In this work, the dynamics of fluctuations in gene expression time series is investigated. By using collected data of gene expression from yeast and human organisms, we found that the fluctuations of gene expression level and its average…
The evolution of wide shear zones (or shear bands) was investigated experimentally and numerically for quasistatic dry granular flows in split bottom shear cells. We compare the behavior of materials consisting of beads, irregular grains…
Quantitative methods for studying biodiversity have been traditionally rooted in the classical theory of finite frequency tables analysis. However, with the help of modern experimental tools, like high throughput sequencing, we now begin to…
Scientists have long sought to understand how vascular networks supply blood and oxygen to cells throughout the body. Recent work focuses on principles that constrain how vessel size changes through branching generations from the aorta to…
Recent advances in high-throughput genomics technologies have resulted in the sequencing of large numbers of (near) complete genomes. These genome sequences are being mined for important functional elements, such as genes. They are also…
Using a population dynamics inspired by an ensemble of growing cells, a set of fluctuation theorems linking observables measured at the lineage and population levels are derived. One of these relations implies specific inequalities…
We present a model of the evolution of control systems in a genome under environmental constraints. The model conceptually follows the Jacob and Monod model of gene control. Genes contain control elements which respond to the internal state…
It has been reported that the number of transcription factors encoded in prokaryotic genomes scales approximately quadratically with their total number of genes. We propose a conceptual explanation of this finding and illustrate it using a…
It is pointed out that the mystery of how biological systems measure their lengths vanishes away if one premises that they have discovered a way to generate linear waves analogous to compressional sound. These can be used to detect length…
Coding information is the main source of heterogeneity (non-randomness) in the sequences of bacterial genomes. This information can be naturally modeled by analysing cluster structures in the "in-phase" triplet distributions of relatively…