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Tidjani Negadi

Publications and source records attributed to Tidjani Negadi.

11 recordsLinked to original sources
arXiv2016

Semi-phenomenological classification models of the genetic code(s) using q-deformed numbers

The mathematical concept of q-deformations, in particular the one of qnumbers, is used to study the genetic code(s). After considering two kinds of q-numbers, for comparison, a phenomenological classification scheme of the genetic code together with its numerous minor variants is, first, established. Next, numbers describing the presence of additional amino acids, such as Selenocysteine or/and Pyrrolysine, are also produced. Finally, a minimal number of amino acids, which could fit the small number of them which are thought to have been involved, at the origin of life on Earth, is found. All together, these results constitute our final semi-phenomenological model.

q-bio.OT↗
arXiv2015

A Mathematical Model for the Genetic Code(s) Based on Fibonacci Numbers and their q-Analogues

This work aims at showing the relevance and the applications possibilities of the Fibonacci sequence, and also its q-deformed or quantum extension, in the study of the genetic code(s). First, after the presentation of a new formula, an indexed double Fibonacci sequence, comprising the first six Fibonacci numbers, is shown to describe the 20 amino acids multiplets and their degeneracy as well as a characteristic pattern for the 61 meaningful codons. Next, the twenty amino acids, classified according to their increasing atom-number (carbon, nitrogen, oxygen and sulfur), exhibit several Fibonacci sequence patterns. Several mathematical relations are given, describing various atom-number patterns. Finally, a q-Fibonacci simple phenomenological model, with q a real deformation parameter, is used to describe, in a unified way, not only the standard genetic code, when q=1, but also all known slight variations of this latter, when q~1, as well as the case of the 21st amino acid (Selenocysteine) and the 22nd one (Pyrrolysine), also when q~1. As a by-product of this elementary model, we also show that, in the limit q=0, the number of amino acids reaches the value 6, in good agreement with old and still persistent claims stating that life, in its early development, could have used only a small number of amino acids.

q-bio.OT↗
arXiv2014

The genetic code invariance: when Euler and Fibonacci meet

The number of atoms in the four ribonucleotides uridine monophosphate, cytidine monophosphate, adenine monophosphate and guanine monophosphate is taken as a key parameter. A mathematical relation describing the condensation of the three basic subunits a nucleobase, a ribose and a phosphate group, to form a ribonucleotide, is first obtained from this parameter. Next, the use of the latter and Euler totient function is shown to lead to the atom number content of the 64 codons and also to Rakocevic pattern. Finally, selected finite sums of Fibonacci numbers are shown to lead to the nucleon number content of the amino acids in various degeneracy patterns, and also to the multiplet structure of the 20 amino acids as well as to the degeneracy.

q-bio.OT↗
arXiv2012

The multiplet structure of the genetic code, in one and small number

In this short paper, it is shown that the multiplet structure of the standard genetic code is derivable from the total number of nucleotides contained in 64 codons, 192, a small number. The degeneracy class-number is derived as the number of numbers coprime to the number of Family-Boxes involved for the quartets, the doublets and the singlets. Those for the triplet and the sextets are computed as simple linear combinations of the preceeding ones. Some interesting consequences are also presented.

q-bio.OT↗
arXiv2009

A taylor-made arithmetic model of the genetic code and applications

We present a completely new version of our arithmetic model of the standard genetic code and compute in a straightforward manner the exact numeric degeneracies of the five multiplets without any trick for the doublets and the sextets, as we have done previously. We give also some interesting applications.

q-bio.OT↗
arXiv2009

The genetic code degeneracy and the amino acids chemical composition are connected

We show that our recently published Arithmetic Model of the genetic code based on Godel Encoding is robust against symmetry transformations, specially Rumer s one U > G, A > C, and constitutes a link between the degeneracy structure and the chemical composition of the 20 canonical amino acids. As a result, several remarkable atomic patterns involving hydrogen, carbon, nucleon and atom numbers are derived. This study has no obvious practical application(s) but could, we hope, add some new knowledge concerning the physico-mathematical structrure of the genetic code.

q-bio.OT↗
arXiv2008

The genetic code Via Godel encoding

The genetic code structure into distinct multiplet-classes as well as the numeric degeneracies of the latter are revealed by a two-step process. First, an empirical inventory of the degeneracies (of the shuffled multiplets) in two specific equal moieties of the experimental genetic code table is made and transcribed in the form of a sequence of integers. Second, a Godel Encoding procedure is applied to the latter sequence delivering, as an output, a Godel Number the digits of which, from the decimal representation, could remarkably describe the amino acids and the stops and allow us also to compute the exact degeneracies, class by class. The standard and the vertebrate mitochondrial genetic codes are considered and their multiplet structure is fully established.

q-bio.OT↗
arXiv2004

A q-deformed Aufbau Prinzip

A building principle working for both atoms and monoatomic ions is proposed in this Letter. This principle relies on the q-deformed chain SO(4) > G where G = SO(3)_q.

quant-ph↗
arXiv2004

On the q-analogue of the hydrogen atom

The discrete spectrum of a q-analogue of the hydrogen atom is obtained from a deformation of the Pauli equations. As an alternative, the spectrum is derived from a deformation of the four-dimensional oscillator arising in the application of the Kustaanheimo-Stiefel transformation to the hydrogen atom. A model of the 2s-2p Dirac shift is proposed in the context of q-deformations.

quant-ph↗