Related papers: Statistics of DNA sequences: a low frequency analy…
Genetic sequences are known to possess non-trivial composition together with symmetries in the frequencies of their components. Recently, it has been shown that symmetry and structure are hierarchically intertwined in DNA, suggesting a…
The classification of DNA sequences is a key research area in bioinformatics as it enables researchers to conduct genomic analysis and detect possible diseases. In this paper, three state-of-the-art algorithms, namely Convolutional Neural…
Proteins have regular tertiary structures but irregular amino acid sequences. This made it very difficult to decode the structural information in the protein sequences. Here we demonstrate that many small alpha protein domains have hidden…
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…
We study the behaviour of the power spectrum (PS) in the case of fractal structures. We show that in this case the main observational features of the PS, the large scale flattening and the scaling of the amplitude with sample depth, are…
High impedance connecting links and cables are modeled at low frequency in terms of their impedance to ground and to neigbouring connecting links. The impedance is usually considered to be the parallel combination of a resistance and a…
We present experimental studies of the power spectrum and other fluctuation properties in the spectra of microwave networks simulating chaotic quantum graphs with violated time reversal in- variance. On the basis of our data sets we…
We discuss a model of protein conformations where the conformations are combinations of short fragments from some small set. For these fragments we consider a distribution of frequencies of occurrence of pairs (sequence of amino acids,…
We study the noise characteristics of stochastic oscillations in protein number dynamics of simple genetic oscillatory systems. Using the three-component negative feedback transcription regulatory system called the repressilator as a…
The fractal nature of complex networks has received a great deal of research interest in the last two decades. Similarly to geometric fractals, the fractality of networks can also be defined with the so-called box-covering method. A network…
When an individual's DNA is sequenced, sensitive medical information becomes available to the sequencing laboratory. A recently proposed way to hide an individual's genetic information is to mix in DNA samples of other individuals. We…
The high linear charge density of 20-base-pair oligomers of DNA is shown to lead to a striking non-monotonic dependence of the long-time self-diffusion on the concentration of the DNA in low-salt conditions. This generic non-monotonic…
In the course of evolution, proteins undergo important changes in their amino acid sequences, while their three-dimensional folded structure and their biological function remain remarkably conserved. Thanks to modern sequencing techniques,…
The tight-binding model for a chain, where the hopping constants follow a Fibonacci sequence, predicts multifractality in the spectrum and wavefunctions. Experimentally, we realize this model by chains of small dielectric resonators with…
Background: Trace quantities of contaminating DNA are widespread in the laboratory environment, but their presence has received little attention in the context of high throughput sequencing. This issue is highlighted by recent works that…
We have analyzed DNA sequences of known genes from 16 yeast chromosomes (Saccharomyces cerevisiae) in terms of oligonucleotides. We have noticed that the relative abundances of oligonucleotide usage in the genome follow a long-tail…
We study the time evolution of a chain of nonlinear oscillators. We focus on the fractal features of the spectral entropy and analyze its characteristic intermediate timescales as a function of the nonlinear coupling. A Brownian motion is…
Recent developments in extracting and processing biological and clinical data are allowing quantitative approaches to studying living systems. High-throughput sequencing, expression profiles, proteomics, and electronic health records are…
Non protein coding regions of the human genome contain many complex patterns which regulate the cellular activity. Studying the human genome is limited by the lack of understanding of its features and their complex interactions. However,…
In this letter, the possible dynamic scaling properties of protein molecules in folding are investigated theoretically by assuming that the protein molecules are percolated networks. It is shown that the fractal character and the fractal…