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We consider the accumulation of beneficial and deleterious mutations in large asexual populations. The rate of adaptation is affected by the total mutation rate, proportion of beneficial mutations and population size $N$. We show that…
Biological cells replicate their genomes in a well-planned manner. The DNA replication program of an organism determines the timing at which different genomic regions are replicated, with fundamental consequences for cell homeostasis and…
The size of mature oocytes is similar across mammalian species, yet the size of ovarian follicles increases with species size, with some ovarian follicles reaching diameters more than 1000-fold the size of the enclosed oocyte. Here we show…
Most living systems rely on double-stranded DNA (dsDNA) to store their genetic information and perpetuate themselves. This biological information has been considered the main target of evolution. However, here we show that symmetries and…
A general theoretical framework is put forth to organize and understand various observed phenomena and mathematical relationships in the field of molecular biology. By modeling each cell in eukaryotic organisms as a processor having a…
Classical population genetics a priori assigns fitness to alleles without considering molecular or functional properties of proteins that these alleles encode. Here we study population dynamics in a model where fitness can be inferred from…
In Escherichia coli the response to DNA damage shows strong cell-to-cell-heterogenity. This results in a random delay in cell division and asymmetrical binary fission of single cells, which can compromise the size homeostasis of the…
Research in quantitative evolutionary genomics and systems biology led to the discovery of several universal regularities connecting genomic and molecular phenomic variables. These universals include the log-normal distribution of the…
Nucleosomes organize the folding of DNA into chromatin and significantly influence transcription, replication, regulation and repair. All atom molecular dynamics simulations of a nucleosome and of its 146 basepairs of DNA free in solution…
The structural origin of the size of the 11 nm nucleosomal disc is addressed. On the nanometer length-scale the organization of DNA as chromatin in the chromosomes involves a coiling of DNA around the histone core of the nucleosome. We…
I propose to treat the biological evolution of genoms by means of quantum mechanical tools. We start with the concept of meta- gene, which specifies the "selfish gene" of R.Dawkins. Meta- gene encodes the abstract living unity, which can…
Although a vast amount of experimental information is available on the elongation, compression, and folding of proteins in biochemical processes, very little is known about the real structure and molecular dynamics of DNA at an atomic…
With the number of fully-sequenced genomes now well over a hundred it has become possible to start investigating if there are any quantitative regularities in the genetic make-up of genomes. In (physics/0307001), I originally showed that…
Genetic algorithms are heuristic optimization techniques inspired by Darwinian evolution. Quantum computation is a new computational paradigm which exploits quantum resources to speed up information processing tasks. Therefore, it is…
Inspired by recent experiments on DNA replication, we apply a one-dimensional nucleation-and-growth model to DNA-replication kinetics, focusing on how to extract the time-dependent nucleation rate I(t) and growth speed v from data. We…
Several recent studies show that companion cells in flowering plant gametophytes relax epigenetic control of transposable elements (TEs) to promote production of small RNA that presumably assist nearby reproductive cells in management of…
A review of the mechanisms of speciation is performed. The mechanisms of the evolution of species, taking into account the feedback of the state of the environment and mechanisms of the emergence of complexity, are considered. It is shown…
The problem of the directionality of genome evolution is studied. Based on the analysis of C-value paradox and the evolution of genome size we propose that the function-coding information quantity of a genome always grows in the course of…
Evolutionary algorithms have long been used for optimization problems where the appropriate size of solutions is unclear a priori. The applicability of this methodology is here investigated on the problem of designing a nano-particle (NP)…
A simple growth model for DNA evolution is introduced which is analytically solvable and reproduces the observed statistical behavior of real sequences.