Related papers: Entropic contributions to the splicing process

In euryarchaeal methanogen M.kandleri and in Nanoarchaea N. equitans some of the missing tRNA genes are embedded in others. We argue from bioinformatic evidence that position specific intron splicing is the key behind co-location of these…

We study the statistical mechanics of RNA secondary structures designed to have an attraction between two different types of structures as a model system for heteropolymer aggregation. The competition between the branching entropy of the…

Solutes added to solutions often dramatically impact molecular processes ranging from the suspension or precipitation of colloids to biomolecular associations and protein folding. Here we revisit the origins of the effective attractive…

We study by simulation and theory how the addition of insulating spherical particles affects the conductivity of fluids of conducting rods, modeled by spherocylinders. The electrical connections are implemented as tunneling processes,…

With a view to connecting random mutation on the molecular level to punctuated equilibrium behavior on the phenotype level, we propose a new model for biological evolution, which incorporates random mutation and natural selection. In this…

The entropy loss due to the formation of one or multiple loops in circular and linear DNA chains is calculated from a scaling approach in the limit of long chain segments. The analytical results allow to obtain a fast estimate for the…

Grafting linkers with open ends of complementary single-stranded DNA makes a flexible tool to tune interactions between colloids,which facilitates the design of complex self-assembly structures. Recently, it has been proposed to coat…

Collective coordinate and direct numerical integration methods are applied to the analysis of a one-dimensional DNA model. A modification of the coupling constant in an extended region is found to be less selective towards the breather it…

Adhesion bonds between membranes and surfaces are attracted to each other via effective interactions whose origin the entropy loss due to the reduction in the amplitude of the membrane thermal fluctuations in the vicinity of the adhesion…

We show how active transport of ions can be interpreted as an entropy facilitated process. In this interpretation, the pore geometry through which substrates are transported can give rise to a driving force. This gives a direct link between…

Transcriptional repressor CTCF is an important regulator of chromatin 3D structure, facilitating the formation of topologically associating domains (TADs). However, its direct effects on gene regulation is less well understood. Here, we…

Both genomic stability and sustenance of day-to-day life rely on efficient and accurate readout of the genetic code. Single-molecule experiments show that transcription and replication are highly stochastic and irregular processes, with the…

We characterize different cell states, related to cancer and ageing phenotypes, by a measure of entropy of network ensembles, integrating gene expression values and protein interaction networks. The entropy measure estimates the parameter…

Eukaryote genomes contain excessively introns, inter-genic and other non-genic sequences that appear to have no vital functional role or phenotype manifestation. Their existence, a long-standing puzzle, is viewed from the principle of…

We develope a theoretical framework, based on exclusion process, that is motivated by a biological phenomenon called transcript slippage (TS). In this model a discrete lattice represents a DNA strand while each of the particles that hop on…

Using Brownian dynamics simulations, we study the migration of long charged chains in an electrophoretic microchannel device consisting of an array of microscopic entropic traps with alternating deep regions and narrow constrictions. Such a…

The concept of entropy in statistical physics is related to the existence of irreversible macroscopic processes. In this work, we explore a recently introduced entropy formula for a class of stochastic processes with more than one absorbing…

Internalization of particles by cells plays a crucial role for adsorbing nutrients and fighting infection. Endocytosis is one of the most important mechanisms of the particles uptake which encompass multiple pathways. Although endocytosis…

Induced pluripotent stem cells (iPSCs) provide a great model to study the process of reprogramming and differentiation of stem cells. Single-cell RNA sequencing (scRNA-seq) enables us to investigate the reprogramming process at single-cell…

Splicing sites provide unique statistics in human genome due to their large number and reasonably complete annotation. Analyses of the cumulative SNPs distribution in splicing sites reveal a few interesting observations. While a degree of…