Related papers: Exons, introns and DNA thermodynamics
The interconnected processes of protein folding, mutations, epistasis, and evolution have all been the subject of extensive analysis throughout the years due to their significance for structural and evolutionary biology. The origin…
Muons are a fascinating probe to study nuclear properties. Muonic atoms can easily be formed by stopping negative muons inside a material. The muon is subsequently captured by the nucleus and, due to its much higher mass compared to the…
Supernovae provide fascinating opportunities to study various particles and their interactions. Among these there are neutrinos, axions, and other light weakly interacting particles, which play a significant role in our understanding of…
The genetic material of a eukaryotic cell comprises both nuclear DNA (ncDNA) and mitochondrial DNA (mtDNA). These differ markedly in several aspects but nevertheless must encode proteins that are compatible with one another. Here we…
Knots (emission features in jets of active galactic nuclei) often show non-ballistic dynamics and variable emission/polarization properties. We model these features as emission pattern propagating in a jet that carries helical magnetic…
Three, interrelated biologically-relevant examples of biased random walks are presented: (1) A model for DNA melting, modelled as DNA unzipping, which provides a way to illustrate the role of the Boltzmann factor in a venue well-known to…
The force induced unzipping transition of a double stranded DNA is considered from a purely thermodynamic point of view. This analysis provides us with a set of relations that can be used to test microscopic theories and experiments. The…
{\bf Background}: Several features are known to correlate with the GC-content in the human genome, including recombination rate, gene density and distance to telomere. However, by testing for pairwise correlation only, it is impossible to…
A self-organizing approach is proposed for gene finding based on the model of codon usage for coding regions and positional preference for noncoding regions. The symmetry between the direct and reverse coding regions is adopted for reducing…
Behavior of some average characteristics of protons are studied in protons and deuterons induced interactions with carbon nuclei at 4.2 A GeV/c. The emitted particles are divided in two groups depending on their polar angle in the lab.…
Protein-DNA interactions are vital for many processes in living cells, especially transcriptional regulation and DNA modification. To further our understanding of these important processes on the microscopic level, it is necessary that…
Literature data on the properties of DNA open states are reviewed and analyzed. These states are formed as a result of strong DNA fluctuations and have a great impact on a number of biochemical processes; among them is charge transfer in…
Determining the full complement of protein-coding genes is a key goal of genome annotation. The most powerful approach for confirming protein coding potential is the detection of cellular protein expression through peptide mass spectrometry…
Despite numerous attempts, the understanding of the thermal denaturation of DNA is still a challenge due to the lack of structural data at the transition since standard experimental approaches to DNA melting are made in solution and do not…
The neutral mutation rate is known to vary widely along human chromosomes, leading to mutational hot and cold regions. We provide evidence that categories of functionally-related genes reside preferentially in mutationally hot or cold…
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 thermal evolution of properties of neutron rich asymmetric nuclear matter such as entropy density, internal energy density, free energy density and pressure are studied in the non-relativistic mean field theory using finite range…
The strongly repulsive core of the short-range nucleon-nucleon interaction leads to the existence of high-momentum nucleons in nuclei. Inclusive electron scattering can be used to probe these high-momentum nucleons and study the nature of…
The melting transition of deoxyribonucleic acid (DNA), whereby the strands of the double helix structure completely separate at a certain temperature, has been characterized using neutron scattering. A Bragg peak from B-form fibre DNA has…
Natural protein sequences that self-assemble to form globular structures are compact with high packing densities in the folded states. It is known that proteins unfold upon addition of denaturants, adopting random coil structures. The…