Related papers: Statistics of DNA sequences: a low frequency analy…
A scaling analysis is presented of the statistics of long DNA confined in nanochannels and nanoslits. It is argued that there are several regimes in between the de Gennes and Odijk limits introduced long ago. The DNA chain folds back on…
We study the statistics of quantum transmission through a one-dimensional disordered system modelled by a sequence of independent scattering units. Each unit is characterized by its length and by its action, which is proportional to the…
The sequence-dependent elasticity of double-helical DNA on a nm length scale can be captured by the rigid base-pair model, whose strains are the relative position and orientation of adjacent base-pairs. Corresponding elastic potentials have…
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…
A number of signal processing and statistical methods can be used in analyzing either pieces of text or DNA sequences. These techniques can be used in a number of ways, such as determining authorship of documents, finding genes in DNA, and…
The complexity of the primary structure of human DNA is explored using methods from nonequilibrium statistical mechanics, dynamical systems theory and information theory. The use of chi-square tests shows that DNA cannot be described as a…
The probability distributions for bending angles in double helical DNA obtained in all-atom molecular dynamics simulations are compared with theoretical predictions. The computed distributions remarkably agree with the worm-like chain…
Recent studies of DNA sequence of letters A, C, G and T exhibit the inverse power law form. Inverse power-law form of the power spectra of fractal space-time fluctuations is generic to the dynamical systems in nature and is identified as…
Flexibility of short DNA helices is important for the biological functions such as nucleosome formation and DNA-protein recognition. Recent experiments suggest that short DNAs of tens of base pairs (bps) may have apparently higher…
The formation of DNA loops by proteins and protein complexes is ubiquitous to many fundamental cellular processes, including transcription, recombination, and replication. Here we review recent advances in understanding the properties of…
The radio continuum spectra of 14 star-forming galaxies are investigated by fitting nonthermal (synchrotron) and thermal (free-free) radiation laws. The underlying radio continuum measurements cover a frequency range of ~325 MHz to 24.5 GHz…
DNA stretching experiments are usually interpreted using the worm-like chain model; the persistence length A appearing in the model is then interpreted as the elastic stiffness of the double helix. In fact the persistence length obtained by…
The propensity of short DNA sequences to convert to the circular form is studied by a mesoscopic Hamiltonian method which incorporates both the bending of the molecule axis and the intrinsic twist of the DNA strands. The base pair…
We derive scaling relations for the extension statistics and the confinement free energy for a semi-flexible polymer confined to a channel with a rectangular cross-section. Our motivation are recent numerical results [Gupta {\em et al.},…
The fractal dimension provides a statistical index of object complexity by studying how the pattern changes with the measuring scale. Although useful in several classification tasks, the fractal dimension is under-explored in deep learning…
We present a study on the role of defects on the stability of short DNA molecules. We consider short DNA molecules (16 base pairs) and investigate the thermal as well as mechanical denaturation of these molecules in the presence of defects…
DNA microarrays are a relatively new technology that can simultaneously measure the expression level of thousands of genes. They have become an important tool for a wide variety of biological experiments. One of the most common goals of DNA…
The spectral dimension has been widely used to understand transport properties on regular and fractal lattices. Nevertheless, it has been little studied for complex networks such as scale-free and small world networks. Here we study the…
One-nucleon emission electron scattering experiments are studied with a model that considers short--range correlations up to the first order in the number of correlation lines. The proper normalization of the many-body wave functions…
Some bacterial and viral DNA sequences have been found to induce low frequency electromagnetic waves in high aqueous dilutions. This phenomenon appears to be triggered by the ambient electromagnetic background of very low frequency. We…