137 research outputs found
p-Adic Modelling of the Genome and the Genetic Code
The present paper is devoted to foundations of p-adic modelling in genomics.
Considering nucleotides, codons, DNA and RNA sequences, amino acids, and
proteins as information systems, we have formulated the corresponding p-adic
formalisms for their investigations. Each of these systems has its
characteristic prime number used for construction of the related information
space. Relevance of this approach is illustrated by some examples. In
particular, it is shown that degeneration of the genetic code is a p-adic
phenomenon. We have also put forward a hypothesis on evolution of the genetic
code assuming that primitive code was based on single nucleotides and
chronologically first four amino acids. This formalism of p-adic genomic
information systems can be implemented in computer programs and applied to
various concrete cases.Comment: 26 pages. Submitted to the Computer Journal for a special issu
Genetic Code and Number Theory
Living organisms are the most complex, interesting and significant objects
regarding all substructures of the universe. Life science is regarded as a
science of the 21st century and one can expect great new discoveries in the
near futures. This article contains an introductory brief review of genetic
information, its coding and translation of genes to proteins through the
genetic code. Some theoretical approaches to the modelling of the genetic code
are presented. In particular, connection of the genetic code with number theory
is considered and the role of -adic numbers is underlined.Comment: 15 pages. To apper in "Modern Topics in Science", a book of invited
papers (Eds. R. Constantinescu, G. Djordjevic, Lj. Nesic
Genetic code on the dyadic plane
We introduce the simple parametrization for the space of codons (triples of
nucleotides) by 8\times 8 table. This table (which we call the dyadic plane)
possesses the natural 2-adic ultrametric. We show that after this
parametrization the genetic code will be a locally constant map of the simple
form. The local constancy of this map will describe degeneracy of the genetic
code.
The map of the genetic code defines 2-adic ultrametric on the space of amino
acids. We show that hydrophobic amino acids will be clustered in two balls with
respect to this ultrametric. Therefore the introduced parametrization of space
of codons exhibits the hidden regularity of the genetic code.Comment: Some gap in the construction was fixe
Standard genetic code: p-adic modelling, nucleon balances and selfsimilarity
This paper represents the preliminary results and conclusions on the one of fundamental questions of the genetic code related to the underlying selective mechanisms involved in its origin and evolution, in particular their hypothetical different nature, originally considered in [1,2,3]. A novel approach is introduced, based on known arithmetic regularities inside the genetic code, determined by the nucleon balances of amino acids and their divisibility by the decimal number 37 [4]. As a parameter of the genetic code systematization is introduced an aggregate nucleon number of amino acid and cognate codon, while divisibility test is carried out not only by the number 37, but also by 13.7, the selfsimilarity constant of decimal scaling [5]. Relevant nucleon sums were obtained for the most prominent divisions of the standard genetic code (SGC) according to p-adic model of the vertebrate mitochondrial code (VMC) in [6]. The nucleon number divisibility pattern of 37 and 13.7 for the RNA and DNA codon space, as well as for the amino acid space is also analyzed. The obtained results, particularly a general higher divisibility of the nucleon sums by the numbers 37 and 13.7 in SGC than in VMC, as well as a correspondence between the nucleon number divisibility pattern of both the RNA codon space and the amino acid space of SGC, how separately so conjointly, with the code degeneracy pattern, suggest some conclusions: support the hypothesis [1,2,3,7] that the selective driving forces acting during an emergence (an ancient phase) and an evolution (a modern phase) of the genetic code are different, imply the existence of an environmental-dependent stereochemical mechanism throughout the entire period of the genetic code emergence and support a mineral-mediated origin of the genetic code [7,8]
p-Adic Mathematical Physics
A brief review of some selected topics in p-adic mathematical physics is
presented.Comment: 36 page
- …