Related papers: Quantum patterns of genome size variation in angio…
In this paper we analyze the evolution of the time averaged energy densities associated with a family of solutions to a Schr{\"o}dinger equation on a Lie group of Heisenberg type. We use a semi-classical approach adapted to the stratified…
Understanding the inherent timescales of large bubbles in DNA is critical to a thorough comprehension of its physicochemical characteristics, as well as their potential role on helix opening and biological function. In this work we employ…
Various rod-shaped bacteria such as the canonical gram negative Escherichia coli or the well-studied gram positive Bacillus subtilis divide symmetrically after they approximately double their volume. Their size at division is not constant,…
Background: The length of a protein sequence is largely determined by its function, i.e. each functional group is associated with an optimal size. However, comparative genomics revealed that proteins length may be affected by additional…
We present some results of simulations of population growth and evolution, using the standard asexual Penna model, with individuals characterized by a string of bits representing a genome containing some possible mutations. After about…
Mitochondrial and nuclear genomes must be co-adapted to ensure proper cellular respiration and energy production. Mito-nuclear incompatibility reduces individual fitness and induces hybrid infertility, suggesting a possible role in…
Real time, or quantitative, PCR typically starts from a very low concentration of initial DNA strands. During iterations the numbers increase, first essentially by doubling, later predominantly in a linear way. Observation of the number of…
Adsorption of monovalent and multivalent cat- and anions on a deoxyribose nucleic acid (DNA) molecule from a salt solution is investigated by computer simulation. The ions are modelled as charged hard spheres, the DNA molecule as a point…
The control over DNA elongation in nanofluidic devices holds great potential for large-scale genomic analysis. So far, the manipulation of DNA in nanochannels has been mostly carried out with electrophoresis and seldom with hydrodynamics,…
Among several quantitative invariants found in evolutionary genomics, one of the most striking is the scaling of the overall abundance of proteins, or protein domains, sharing a specific functional annotation across genomes of given size.…
In this article we present a new p-adic generalization of the Eigen-Schuster model where the genomes (sequences) are represented by words written in the alphabet 0,1,,p-1, where p is a prime number, with a time variable length. The time…
Large scale databases are available that contain homologous gene families constructed from hundreds of complete genome sequences from across the three domains of Life. Here we discuss approches of increasing complexity aimed at extracting…
We investigate the equilibrium state of the model of Peng, \textit{et al.} for molecular breeding. In the model, a population of DNA sequences is successively culled by removing the sequences with the lowest binding affinity to a particular…
The self-alignment concentrations, $c(x)$, as functions of the length, $x$, of the identically matching maximal segments in the genomes of a variety of species, typically present power-law tails extending to the largest scales, i.e., $c(x)…
DNA oligomers with properly designed sequences self-assemble into well defined constructs. Here, we exploit this methodology to produce bulk quantities of tetravalent DNA nanostars (each one composed by 196 nucleotides) and to explore the…
Motivated by landscape models in string theory, cosmic nuclear evolution is analyzed allowing the Standard Model Higgs expectation value w to take values different from that in our world (w=1), while holding the Yukawa couplings fixed.…
The simplest possible informational heteropolymer requires only a two-letter alphabet to be able to store information. The evolutionary choice of four monomers in the informational biomolecules RNA/DNA or their progenitors is intriguing,…
We show that operator dynamics in U(1) symmetric systems are constrained by two independent conserved charges and construct a non-Abelian operator size basis that respects both, enabling a symmetry-resolved characterization of operator…
We study the genetic behaviour of a population formed by haploid individuals which reproduce asexually. The genetic information for each individual is stored along a bit-string (or chromosome) with L bits, where 0-bits represent the…
The yearly global production of data is growing exponentially, outpacing the capacity of existing storage media, such as tape and disk, and surpassing our ability to store it. DNA storage - the representation of arbitrary information as…