Related papers: The genetic code multiplet structure, in one numbe…
In answer to a question of Eggleton, we prove that the complete multigraph on 5 vertices with edge multiplicity 6, namely $K_{5}^{(6)}$, has a decomposition into 5 copies of the family of trees of order 5 and that $K_{7}^{(22)}$ has a…
The genetic code is profoundly shaped by an origin in ancient RNA-mediated interactions, needing an extended development to reach the Standard Genetic Code (SGC). That development can serially use RNA specificities, a ribonucleopeptide…
The present paper is devoted to the study of the combinatorics of 216 maximal $C^3$ circular codes --- a particular type of structure arising in the analysis of genomic sequences. Their circularity property is believed to be intimately…
Complex systems with tightly coadapted parts frequently appear in living systems and are difficult to account for through Darwinian evolution, that is random variation and natural selection, if the constituent parts are independently coded…
Degeneracy is a salient feature of genetic codes, because there are more codons than amino acids. The conventional table for genetic codes suffers from an inability of illustrating a symmetrical nature among genetic base codes. In fact,…
We prove that the number of permutations which avoid 132-patterns and have exactly one 123-pattern equals (n-2)2^(n-3). We then give a bijection onto the set of permutations which avoid 123-patterns and have exactly one 132-pattern.…
A permutation is (1-23-4)-avoiding if it contains no four entries, increasing left to right, with the middle two adjacent in the permutation. Here we give a 2-variable recurrence for the number of such permutations, improving on the…
The set of prime numbers has been analyzed, based on their algebraic and arithmetical structure. Here by obtaining a sort of linear formula for the set of prime numbers, they are redefined and identified; under a systematic procedure it has…
Different ways to describe a permutation, as a sequence of integers, or a product of Coxeter generators, or a tree, give different choices to define a simple permutation. We recollect few of them, define new types of simple permutations,…
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…
A representation of the genetic code as a six-dimensional Boolean hypercube is proposed. It is assumed here that this structure is the result of the hierarchical order of the interaction energies of the bases in codon-anticodon recognition.…
We enumerate the pattern class Av(2143,4231) and completely describe its permutations. The main tools are simple permutations and monotone grid classes.
Using concepts of physics of elementary particles concerning the breaking of symmetry and grannd unified theory we propose to study with the algebraic approximation the degeneracy finded in the genetic code with the incorporation of a…
Several technological applications require the translation of a protein into a nucleic acid that codes for it (``backtranslation''). The degeneracy of the genetic code makes this translation ambiguous; moreover, not every translation is…
A permutation-invariant code on m qubits is a subspace of the symmetric subspace of the m qubits. We derive permutation-invariant codes that can encode an increasing amount of quantum information while suppressing leading order spontaneous…
The genesis of the stand genetic code is considered as a result of a fusion of two AU- and GC-codes distributed in two dominant and two recessive domains. The fusion of these codes is described with simple empirical rules. This formal…
In this paper we describe a variation of the classical permutation decoding algorithm that can be applied to any affine-invariant code with respect to certain type of information sets. In particular, we can apply it to the family of…
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…
A system-level genetic code is a hypothetical genetic code that exclusively or preferentially codes systems of interacting coadapted parts. System-level genetic codes differ from part-level genetic codes in which each discrete part is coded…
Convolutional codes are constructed, designed and analysed using row and/or block structures of unit algebraic schemes. Infinite series of such codes and of codes with specific properties are derived. Properties are shown algebraically and…