Related papers: Genetic code on the dyadic plane
A new n-dimensional vector space of the DNA sequences on the Galois field of the 64 codons (GF(64)) is proposed. In this vector space gene mutations can be considered linear transformations or translations of the wild type gene. In…
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…
Genetic Programming is an evolutionary algorithm that generates computer programs, or mathematical expressions, to solve complex problems. In this Guide, we demonstrate how to use Genetic Programming to develop surrogate models to mitigate…
DNA storage has emerged as an important area of research. The reliability of DNA storage system depends on designing the DNA strings (called DNA codes) that are sufficiently dissimilar. In this work, we introduce DNA codes that satisfy a…
In this paper we study in detail, both analytically and numerically, the dynamical properties of the triangle map, a piecewise parabolic automorphism of the two-dimensional torus, for different values of the two independent parameters…
The precise sequence of aminoacids plays a central role in the tertiary structure of proteins and their functional properties. The Hydrophobic-Polar lattice models have provided valuable insights regarding the energy landscape. We…
The standard genetic code multiplet structure as well as the correct degeneracies, class by class, are all extracted from the (unique) number 23, the order of the permutation group of 23 objects.
All known terrestrial proteins are coded as continuous strings of ~20 amino acids. The patterns formed by the repetitions of elements in groups of finite sequences describes the natural architectures of protein families. We present a method…
Coding information is the main source of heterogeneity (non-randomness) in the sequences of bacterial genomes. This information can be naturally modeled by analysing cluster structures in the "in-phase" triplet distributions of relatively…
We describe a general method of arithmetic coding of geodesics on the modular surface based on a two parameter family of continued fraction transformations studied previously by the authors. The finite rectangular structure of the…
A mathematical algorithm to describe DNA or RNA sequences of $N$ nucleotides by a string of $2N$ integers numbers is presented in the framework of the so called crystal basis model of the genetic code. The description allows to define a not…
Of the twenty amino acids used in proteins, ten were formed in Miller's atmospheric discharge experiments. The two other major proposed sources of prebiotic amino acid synthesis include formation in hydrothermal vents and delivery to Earth…
The coding space of protein sequences is shaped by evolutionary constraints set by requirements of function and stability. We show that the coding space of a given protein family--the total number of sequences in that family--can be…
There is an intrinsic relationship between the molecular evolution in primordial period and the properties of genomes and proteomes of contemporary species. The genomic data may help us understand the driving force of evolution of life at…
The string theory landscape may include a multitude of ultraviolet embeddings of the Standard Model, but identifying these has proven difficult due to the enormous number of available string compactifications. Genetic Algorithms (GAs)…
New analyses of the organization of the genetic code system together with their relation to the two classes of aminoacyl-tRNA synthetases are reported in this work. A closer inspection revealed how the enzymes and the 20 amino acids of the…
This paper is the second part of a two-part paper investigating the structure and properties of dyadic polygons. A dyadic polygon is the intersection of the dyadic subplane $D^2$ of the real plane $R^2$ and a real convex polygon with…
Evolution algebras were introduced into Genetics to deal with the mechanism of inheritance of asexual organisms. Their distribution into isotopism classes is uniquely related with the mutation of alleles in non-Mendelian Genetics. This…
We measure elastomechanical spectra for a family of thin shells. We show that these spectra can be described by a "semiclassical" trace formula comprising periodic orbits on geodesics, with the periods of these orbits consistent with those…
Gene finding is the task of identifying the locations of coding sequences within the vast amount of genetic code contained in the genome. With an ever increasing quantity of raw genome sequences, gene finding is an important avenue towards…