Related papers: Exons, introns and DNA thermodynamics
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…
We have presented the basic knowledge on the structure of molecules coding the genetic information, mechanisms of transfer of this information from DNA to proteins and phenomena connected with replication of DNA. In particular, we have…
We investigate melting transition of DNA sequences embedded in a Langevin fluctuation-dissipation thermal bath. Torsional effects are considered by a twist angle $\varphi$ between neighboring base pairs stacked along the molecule backbone.…
Unraveling the evolutionary forces shaping bacterial diversity can today be tackled using a growing amount of genomic data. While the genome of eukaryotes is highly stable, bacterial genomes from cells of the same species highly vary in…
The free energy of looping DNA by proteins and protein complexes determines to what extent distal DNA sites can affect each other. We inferred its in vivo value through a combined computational-experimental approach for different lengths of…
Strong influence of water molecules on the transport and magnetic properties of DNA, observed in this study, opens up real opportunities for application of DNA in molecular electronics. Interaction of the nucleobases with water molecules…
In this work, under the framework of vector meson dominance model, the trace anomaly contribution value inside neutrons are extracted for the first time based on vector meson photoproduction data. Furthermore, we systematically compare and…
A double-stranded DNA unravels thermally through intermediate denatured bubble segments. Intrinsically, fluctuations ensue at the bubble boundaries from non-equilibrium (NE) energy exchanges with the environment. However, such details gets…
Near the melting transition the bending elastic constant, $\kappa$, an emergent property of double-stranded DNA (dsDNA), is shown not to follow the rod-like scaling for small length $N$. The reduction in $\kappa$ with temperature is…
Complex systems with tightly coadapted parts frequently appear in living systems and are difficult to account for through Darwinian evolution, that is random variation and natural selection, if the constituent parts are independently coded…
Nowadays, due to the increasing amount of experimental data obtained by sequencing, the most interest is focused on determining the functions and characteristics of its individual parts of the genome instead of determining the nucleotide…
We calculate the frequencies of collective modes of neutrons, protons and electrons in the outer core of neutron stars. The neutrons and protons are treated in a hydrodynamic approximation and the electrons are regarded as collisionless.…
The presence of clusters of rare codons is known to negatively impact the efficiency and accuracy of protein production. In this paper, we demonstrate a statistical method of identifying such clusters in the coding sequence of a gene. Using…
Understanding the observed variability in the number of homologs of a gene is a very important, unsolved problem that has broad implications for research into co-evolution of structure and function, gene duplication, pseudogene formation…
Mechanical stretching of six proteins is studied through molecular dynamics simulations. The model is Go-like, with Lennard-Jones interactions at native contacts. Low temperature unfolding scenarios are remarkably complex and sensitive to…
Gene expression is a stochastic process governed by the presence of specific transcription factors. Here we study the dynamics of gene expression in the presence of feedback, where a gene regulates its own expression. The nonlinear coupling…
We examine the evolution of expression patterns and the organization of genetic information in populations of self-replicating digital organisms. Seeding the experiments with a linearly expressed ancestor, we witness the development of…
The biological effects of electromagnetic fields on proteins remain controversial beyond well-established thermal mechanisms, particularly with respect to frequency-dependent responses. Here, we propose that electromagnetic waves can…
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…
Motivated by the large number of jets detected by the Chandra X-ray Observatory, and by the inverse Compton X-ray emission model (IC/CMB) for relativistic jets, we revisit two basic questions: ``If the medium that carries the jet's energy…