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The Dissertation is focused on the studies of associations between functional elements in human genome and their nucleotide structure. The asymmetry in nucleotide content (skew, bias) was chosen as the main feature for nucleotide structure.…
Bioinformatics encompass storing, analyzing and interpreting the biological data. Most of the challenges for Machine Learning methods like Cellular Automata is to furnish the functional information with the corresponding biological…
We present an ab-initio study of Ru substitution in two different compounds, BaFe2As2 and LaFeAsO, pure and F-doped. Despite the many similarities among them, Ru substitution has very different effects on these compounds. By means of an…
Parts of DNA sequences known as exons and introns play very different role in coding and storage of genetic information. Here we show that their conducting properties are also very different. Taking into account long-range correlations…
We investigate the effects of crowding on the conformations and assembly of confined, highly charged, and thick polyelectrolyte brushes in the osmotic regime. Particle tracking experiments on increasingly dense suspensions of colloids…
In this paper we address the issue of pruning (i.e., shortening) a given interleaver via truncation of the transposition vector of the mother permutation and study its impact on the structural properties of the permutation. This method of…
The ability of double-stranded DNA or RNA to locally melt and form kinks leads to strong non-linear elasticity effects that qualitatively affect their packing in confined spaces. Using analytical theory and numerical simulation we show that…
DNA supercoiling plays an important role in a variety of cellular processes. The torsional stress related with supercoiling may be also involved in gene regulation through the local structure and dynamics of the double helix. To check this…
Recent work on atomic-precision dopant incorporation technologies has led to the creation of both boron and aluminum $\delta$-doped layers in silicon with densities above the solid solubility limit. We use density functional theory to…
RNA editing can be crucial for the expression of genetic information via inserting, deleting, or substituting a few nucleotides at specific positions in an RNA sequence. Within coding regions in an RNA sequence, editing usually occurs with…
Understanding the nature of the interface between a biomaterial implant and the biological fluid is an essential step towards creating improved implant materials. This study examined a diamond-like carbon coating biomaterial, the surface…
The non-relativistic spin-momentum locking in altermagnets gives rise to a time-reversal-odd spin Hall effect, known as the altermagnetic spin-splitting effect (ASSE). Although ASSE was first reported in RuO$_2$, subsequent experiments have…
Pre-mRNA splicing relies on the poorly understood dynamic interplay between >150 protein components of the spliceosome. The steps at which splicing can be regulated remain largely unknown. We systematically analyzed the effect of knocking…
The problem of RNA secondary structure design (also called inverse folding) is the following: given a target secondary structure, one aims to create a sequence that folds into, or is compatible with, a given structure. In several practical…
Transformers underpin modern large language models (LLMs) and are commonly assumed to be behaviorally unstructured at random initialization, with all meaningful preferences emerging only through large-scale training. We challenge this…
Gene duplications are one of major primary driving forces for evolutionary novelty. We took population genetics models of genes duplicate to study how evolutionary forces acting during the fixation of mutant allele at duplicate loci. We…
Reactive dopant atoms embedded in inert host metal surfaces define the active sites in single-atom alloys (SAAs), yet SAA synthesis remains challenging. To address this, we elucidate how dopant adatoms deposited on Cu and Ag surfaces become…
We precisely position a noncanonical intron in the odd second copy of tRNAAsp(GTC) gene in the newly sequenced crenarchaea S.acidocaldarius. The uniform assortment of some features from normal aspartate tDNA and some from those…
Organic spintronics is a promising emerging field, but the sign of the tunneling magnetoresistance (TMR) is highly sensitive to interface effects, a crucial hindrance to applications. A key breakthrough in molecular electronics was the…
A promising approach to deform metallic-intermetallic composite materials is the application of electric current pulses during the deformation process to achieve a lower yield strength and enhanced elongation to fracture. This is known as…