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The natural evolution of life seems to proceed through steps characterized by phases of relatively rapid changes, followed by longer, more stable periods. In the light of the string-theory derived physical scenario proposed in [1], we…
Genomic evolution can be viewed as string-editing processes driven by mutations. An understanding of the statistical properties resulting from these mutation processes is of value in a variety of tasks related to biological sequence data,…
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.…
We consider braids with repeating patterns inside arbitrary knots which provides a multi-parametric family of knots, depending on the "evolution" parameter, which controls the number of repetitions. The dependence of knot (super)polynomials…
We theoretically investigate the effect of multi-mode dynamics on the creation of macroscopic superposition states (spin-cat states) in Bose-Einstein condensates via one-axis twisting. A two-component Bose-Einstein condensate naturally…
Evolution is a dynamic process. The two classical forces of evolution are mutation and selection. Assuming small mutation rates, evolution can be predicted based solely on the fitness differences between phenotypes. Predicting an…
Dawkins' replicator-based conception of evolution has led to widespread mis-application selectionism across the social sciences because it does not address the paradox that inspired the theory of natural selection in the first place: how do…
A collection of thin structures buckle, bend, and bump into each-other when confined. This contact can lead to the formation of patterns: hair will self-organize in curls; DNA strands will layer into cell nuclei; paper, when crumpled, will…
Phenotypes of individuals in a population of organisms are not fixed. Phenotypic fluctuations, which describe temporal variation of the phenotype of an individual or individual-to-individual variation across a population, are present in…
We report on the exciton formation and relaxation dynamics following photocarrier injection in a single-layer two-dimensional lead-iodide perovskite. We probe the time evolution of four distinct exciton resonances by means of time-resolved…
Background: Gene duplication and exonization of intronic transposed elements are two mechanisms that enhance genomic diversity. We examined whether there is less selection against exonization of transposed elements in duplicated genes than…
Some genes can change their relative locations in a genome. Thus for different individuals of the same species, the orders of genes might be different. Such jumping genes are called transposons. A practical problem is to determine…
Considering the rheology of two-dimensional soft suspensions above the jamming density, we derive a tensorial constitutive model from the microscopic particle dynamics. Starting from the equation governing the $N$-particle distribution, we…
Motivated by diverse phenomena in cellular biophysics, including bacterial flagellar motion and DNA transcription and replication, we study the overdamped nonlinear dynamics of a rotationally forced filament with twist and bend elasticity.…
The evolution in coding DNA sequences brings new flexibility and freedom to the codon words, even as the underlying nucleotides get significantly ordered. These curious contra-rules of gene organisation are observed from the distribution of…
We investigate the evolution of Boolean networks subject to a selective pressure which favors robustness against noise, as a model of evolved genetic regulatory systems. By mapping the evolutionary process into a statistical ensemble and…
Genomic complexity is a growing field of evolution, with case studies for comparative evolutionary analyses in model and emerging non-model systems. Understanding complexity and the functional components of the genome is an untapped wealth…
Many physical, chemical and biological processes rely on intrinsic oscillations to employ resonance responses to external stimuli of certain frequency. Such resonance phenomena in biological systems are typically explained by one of two…
Recently, Pareto Set Learning (PSL) has been proposed for learning the entire Pareto set using a neural network. PSL employs preference vectors to scalarize multiple objectives, facilitating the learning of mappings from preference vectors…
The genes of eukaryotes are characterized by protein coding fragments, the exons, interrupted by introns, i.e. stretches of DNA which do not carry any useful information for the protein synthesis. We have analyzed the melting behavior of…