Related papers: Stability domains of actin genes and genomic evolu…
Genes are connected in complex networks of interactions where often the product of one gene is a transcription factor that alters the expression of another. Many of these networks are based on a few fundamental motifs leading to switches…
Successive whole genome duplications have recently been firmly established in all major eukaryote kingdoms. It is not clear, however, how such dramatic evolutionary process has contributed to shape the large scale topology of…
Protein dynamics form a critical bridge between protein structure and function, yet the impact of evolution on ultrafast processes inside proteins remains enigmatic. This study delves deep into nanosecond-scale protein dynamics of a…
Complex evolving systems such as the biosphere, ecosystems and societies exhibit sudden collapses, for reasons that are only partially understood. Here we study this phenomenon using a mathematical model of a system that evolves under…
Background: Transposable elements (TEs) have played an important role in the diversification and enrichment of mammalian transcriptomes through various mechanisms such as exonization and intronization (the birth of new exons/introns from…
Biological functions rely on ordered structures and intricately controlled collective dynamics. In contrast to systems in thermodynamic equilibrium, order is typically established and sustained in stationary states by continuous dissipation…
Evolving biomolecular networks have to combine the stability against perturbations with flexibility allowing their constituents to assume new roles in the cell. Gene duplication followed by functional divergence of associated proteins is a…
Most amino acids are encoded by multiple synonymous codons. For an amino acid, some of its synonymous codons are used much more rarely than others. Analyses of positions of such rare codons in protein sequences revealed that rare codons can…
Studies of coevolution of amino acids within and between proteins have revealed two types of coevolving units: coevolving contacts, which are pairs of amino acids distant along the sequence but in contact in the three-dimensional structure,…
The subject of this report is the dynamics of elastic system in conjunction with hydrogen bonds of the DNA. We draw attention to the draw-back of the familiar rod model of the DNA, and make a case of constructing models that could…
We perform theoretical studies of stretching of 20 proteins with knots within a coarse grained model. The knot's ends are found to jump to well defined sequential locations that are associated with sharp turns whereas in homopolymers they…
The primary aim of this work is to explore how proteins point mutations impact their marginal stability and, hence, their evolvability. With this purpose, we show that the use of four classic notions, namely, those from Leibniz & Kant…
Genome length varies widely among organisms, from compact genomes of prokaryotes to vast and complex genomes of eukaryotes. In this study, we theoretically identify the evolutionary pressures that may have driven this divergence in genome…
A eukaryotic gene consists of multiple exons (protein coding regions) and introns (non-coding regions), and a splice junction refers to the boundary between a pair of exon and intron. Precise identification of spice junctions on a gene is…
Actin is a globular protein which forms long polar filaments in eukaryotic. The actin filaments play roles of cytoskeleton, motility units , information processing and learning. We model actin filament as a double chain of finite state…
We perform an exhaustive analysis of genome statistics for organisms, particularly extremophiles, growing in a wide range of physicochemical conditions. Specifically, we demonstrate how the correlation between the frequency of amino acids…
The role of post-translational modification of histones in eukaryotic gene regulation is well recognized. Epigenetic silencing of genes via heritable chromatin modifications plays a major role in cell fate specification in higher organisms.…
Plectonemes are intertwined helically looped domains which form when a DNA molecule is supercoiled, i.e. over- or under-wounded. They are ubiquitous in cellular DNA and their physical properties have attracted significant interest both from…
Proteins are only moderately stable. It has long been debated whether this narrow range of stabilities is solely a result of neutral drift towards lower stability or purifying selection against excess stability is also at work - for which…
The composition of a protoplanetary disk is set by a combination of interstellar inheritance and gas and grain surface chemical reactions within the disk. The survival of inherited molecules, as well as the disk in situ chemistry depends on…