Related papers: Semi-phenomenological classification models of the…
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…
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…
In this note we outline the history of q-deformations; indicate their physical shortcomings; suggest their apparent resolution via an invariant formulation based on a new mathematics of genotopic type; and point out their expected physical…
The rules that specify how the information contained in DNA codes amino acids, is called "the genetic code". Using a simplified version of the Penna nodel, we are using computer simulations to investigate the importance of the genetic code…
The concept of $q$-deformation, or ``$q$-analogue'' arises in many areas of mathematics. In algebra and representation theory, it is the origin of quantum groups; $q$-deformations are important for knot invariants, combinatorial…
The quantum enveloping algebra U_q(sl(2) \oplus sl(2)) in the limit q \to 0 is proposed as a symmetry algebra for the genetic code. In this approach the triplets of nucleotids or codons in the DNA chain are classified in crystal bases,…
The systematics of indices of physico-chemical properties of codons and amino acids across the genetic code are examined. Using a simple numerical labelling scheme for nucleic acid bases, data can be fitted as low-order polynomials of the 6…
Why is the genetic code the way it is? The most successful theory states that the codon assignments minimise the effects of errors arising in primordial living systems. Here a transversion is reported that leaves invariant degeneracy in the…
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…
Replication of DNA and synthesis of proteins are studied from the view-point of quantum database search. Identification of a base-pairing with a quantum query gives a natural (and first ever) explanation of why living organisms have 4…
Using the crystal basis model of the genetic code, a set of relations between the physical-chemical properties of the amino acids are derived and compared with the experimental data. A prevision for the not yet measured thermodynamical…
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…
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.…
In the course of evolution, proteins undergo important changes in their amino acid sequences, while their three-dimensional folded structure and their biological function remain remarkably conserved. Thanks to modern sequencing techniques,…
We consider performance of a simple quantum convolutional code in a fault-tolerant regime using several syndrome measurement/decoding strategies and three different error models, including the circuit model.
We first observe a mysterious similarity between the braid arrangement and the arrangement of all hyperplanes in a vector space over the finite field $\mathbb{F}_q$. These two arrangements are defined by the determinants of the Vandermonde…
Examples are given of q-deformed systems that may be interpreted by the standard rules of quantum theory in terms of new degrees of freedom and supplementary quantum numbers.
New developments are presented in the framework of the model introduced by the authors in refs. [1,2] and in which nucleotides as well as codons are classified in crystal bases of the quantum group U_q(sl(2)+sl(2)) in the limit q -> 0. An…
Quantum and q-deformed algebras find their application not only in mathematical physics and field theoretical context, but also in phenomenology of particle properties. We describe (i) the use of quantum algebras U_q(su_n) corresponding to…
The genetic code is the set of rules by which information encoded in genetic material (DNA or RNA sequences) is translated into proteins (amino acid sequences) by living cells. The code defines a mapping between tri-nucleotide sequences,…