Related papers: An algebraic hypothesis about the primeval genetic…
The universal genetic code presents a fundamental paradox in molecular biology. Recent advances in synthetic biology have demonstrated that the code is remarkably flexible--organisms can survive with 61 codons instead of 64, natural…
Evolution of genetic code is studied as the change in the choice of enzymes that are used to synthesize amino acids from the genetic information of nucleic acids. We propose the following theory: the differentiation of physiological states…
Continuing our attempt to explain the degeneracy of the genetic code using basic classical Lie superalgebras, we present the branching schemes for the typical codon representations (typical 64-dimensional irreducible representations) of…
Genetic algorithms are heuristic optimization techniques inspired by Darwinian evolution, which are characterized by successfully finding robust solutions for optimization problems. Here, we propose a subroutine-based quantum genetic…
This letter reports complete sets of two-fold symmetries between partitions of the universal genetic code. By substituting bases at each position of the codons according to a fixed rule, it happens that properties of the degeneracy pattern…
DNA segments and sequences have been studied thoroughly during the past decades. One of the main problems in computational biology is the identification of exon-intron structures inside genes using mathematical techniques. Previous studies…
This paper characterizes the inherent power of evolutionary algorithms. This power depends on the computational properties of the genetic encoding. With some encodings, two parents recombined with a simple crossover operator can sample from…
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…
The structure of the genetic code is discussed in formal terms. A rectangular table of the code ("the code matrix"), whose properties reveal its arithmetical content tagged with the information symbols in several notations. New parameters…
A model of genome evolution is proposed. Based on three assumptions the evolutionary theory of a genome is formulated. The general law on the direction of genome evolution is given. Both the deterministic classical equation and the…
Composite DNA is a recent novel method to increase the information capacity of DNA-based data storage above the theoretical limit of 2 bits/symbol. In this method, every composite symbol does not store a single DNA nucleotide but a mixture…
One of the oldest problems in coding theory is to match the Gilbert-Varshamov bound with explicit binary codes. Over larger-yet still constant-sized-fields, algebraic-geometry codes are known to beat the GV bound. In this work, we leverage…
The genetic code refers to a rule that maps 64 codons to 20 amino acids. Nearly all organisms, with few exceptions, share the same genetic code, the standard genetic code (SGC). While it remains unclear why this universal code has arisen…
We wish to minimize the resources used for network coding while achieving the desired throughput in a multicast scenario. We employ evolutionary approaches, based on a genetic algorithm, that avoid the computational complexity that makes…
Given a gene tree and a species tree, ancestral configurations represent the combinatorially distinct sets of gene lineages that can reach a given node of the species tree. They have been introduced as a data structure for use in the…
In the crystal basis model of the genetic code, it is deduced that the sum of usage probabilities of the codons with C and A in the third position for the quartets and/or sextets is independent of the biological species for vertebrates. A…
Finding the minimum distance of linear codes is an NP-hard problem. Traditionally, this computation has been addressed by means of the design of algorithms that find, by a clever exhaustive search, a linear combination of some generating…
New families of unit memory as well as multi-memory convolutional codes are constructed algebraically in this paper. These convolutional codes are derived from the class of group character codes. The proposed codes have basic generator…
Evolutionary theorizing resembles building an aircraft while also piloting it; new results change the scaffold for older ideas, requiring revised strategy to remain airborne. A calculated kinetic pathway exists that, under explicit…
The Andrews-Curtis conjecture claims that every balanced presentation of the trivial group can be transformed into the trivial presentation by a finite sequence of "elementary transformations" which are Nielsen transformations together with…