Related papers: Genetic Code as a Harmonic System
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…
A plausible architecture of an ancient genetic code is derived from an extended base triplet vector space over the Galois field of the extended base alphabet {D, G, A, U, C}, where the letter D represents one or more hypothetical bases with…
We have presented the basic knowledge on the structure of molecules coding the genetic information, mechanisms of transfer of this information from DNA to proteins and phenomena connected with replication of DNA. In particular, we have…
The sequence of nucleotide bases occurring in an organism's DNA is often regarded as a codescript for its construction. However, information in a DNA sequence can only be regarded as a codescript relative to an operational biochemical…
The present work is devoted to describe a set of rules explaining the discriminating versus non-discriminating behavior of the di-basic stages and to characterize the role of each base in determining such a behavior. Bases are analyze as…
We investigate the possibility of encoding multiple solutions of a problem in a single chromosome. The best solution encoded in an individual will represent (will provide the fitness of) that individual. In order to obtain some benefits the…
The analysis of the three-dimensional structure of proteins is an important topic in molecular biochemistry. Structure plays a critical role in defining the function of proteins and is more strongly conserved than amino acid sequence over…
Modelising the translation errors by suitable mathematical operators in the crystal basis model of the genetic code and requiring that codons prone to be misread encode the same amino-acid, the main features of the organisation in…
The main statistical distributions applicable to the analysis of genome architecture and genome tracks are briefly discussed and critically assessed. Although the observed features in distributions of element lengths can be equally well…
Genetic algorithms are high-level heuristic optimization methods which enjoy great popularity thanks to their intuitive description, flexibility, and, of course, effectiveness. The optimization procedure is based on the evolution of…
Many modified genetic codes are found in specific genomes in which one or more codons have been reassigned to a different amino acid from that in the canonical code. We present a model that unifies four possible mechanisms for reassignment,…
Rich information on the prebiotic evolution is still stored in contemporary genomic data. The statistical mechanism at the sequence level may play a significant role in the prebiotic evolution. Based on statistical analysis of genome…
Although several synonymous codons can encode the same aminoacid, this symmetry is generally broken in natural genetic systems. In this article, we show that the symmetry breaking can result from selective pressures due to the violation of…
Musical chords, harmonies or melodies in Just Intonation have note frequencies which are described by a base frequency multiplied by rational numbers. For any local section, these notes can be converted to some base frequency multiplied by…
Formal methods apply algorithms based on mathematical principles to enhance the reliability of systems. It would only be natural to try to progress from verification, model checking or testing a system against its formal specification into…
Cyclic codes are among the most important families of codes in coding theory for both theoretical and practical reasons. Despite their prominence and intensive research on cyclic codes for over a half century, there are still open problems…
Protein structure prediction can be shown to be an NP-hard problem; the number of conformations grows exponentially with the number of residues. The native conformations of proteins occupy a very small subset of these, hence an exploratory,…
Using basic properties of p-adic numbers, we consider a simple new approach to describe main aspects of DNA sequence and genetic code. Central role in our investigation plays an ultrametric p-adic information space which basic elements are…
In genetic systems there is a non-trivial interface between the sequence of symbols which constitutes the chromosome, or ``genotype'', and the products which this sequence encodes --- the ``phenotype''. This interface can be thought of as a…
The standard genetic code is known to be robust to translation errors and point mutations. We studied how small modifications of the standard code affect its robustness. The robustness was assessed in terms of a proper stability function,…