Related papers: DNA coding and G\"odel numbering
We present a genetic algorithm which is distributed in two novel ways: along genotype and temporal axes. Our algorithm first distributes, for every member of the population, a subset of the genotype to each network node, rather than a…
In molecular phylogeny, relationships among organisms are reconstructed using DNA or protein sequences and are displayed as trees. A linear increase in the number of sequences results in an exponential increase of possible trees. Thus,…
Formation of random network of DNA strands is simulated on a two-dimensional triangular lattice. We investigate the size distribution of pores in the network. The results are interpreted within theory of percolation on Bethe lattice.
A mathematical algorithm to describe DNA or RNA sequences of $N$ nucleotides by a string of $2N$ integers numbers is presented in the framework of the so called crystal basis model of the genetic code. The description allows to define a not…
This article introduces a novel binary representation of the canonical genetic code based on both the structural similarities of the nucleotides, as well as the physicochemical properties of the encoded amino acids. Each of the four mRNA…
In this work it is shown that 20 canonical amino acids (AAs) within genetic code appear to be a whole system with strict AAs positions; more exactly, with AAs ordinal number in three variants; first variant 00-19, second 00-21 and third…
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…
We study a minimal model for genome evolution whose elementary processes are single site mutation, duplication and deletion of sequence regions and insertion of random segments. These processes are found to generate long-range correlations…
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 present work is devoted to describe a set of rules explaining the discriminating versus non-discriminating behavior of the di-basic stages and to characterize the role of each base in determining such a behavior. Bases are analyze as…
This work illustrates potentials for recognition within {\em ad hoc} sensor networks if their nodes possess individual inter-related biologically inspired genetic codes. The work takes ideas from natural immune systems protecting organisms…
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…
A self-organizing approach is proposed for gene finding based on the model of codon usage for coding regions and positional preference for noncoding regions. The symmetry between the direct and reverse coding regions is adopted for reducing…
In this paper we consider a physical system in which two DNA molecules braid about each other. The distance between the two molecular ends, on either side of the braid, is held at a distance much larger than supercoiling radius of the…
The genetic code is connection between 64 codons, which are building blocks of the genes, and 20 amino acids, which are building blocks of the proteins. In addition to coding amino acids, a few codons code stop signal, which is at the end…
We define the complexity of DNA sequences as the information content per nucleotide, calculated by means of some Lempel-Ziv data compression algorithm. It is possible to use the statistics of the complexity values of the functional regions…
We study the evolution of artificial learning systems by means of selection. Genetic programming is used to generate a sequence of populations of algorithms which can be used by neural networks for supervised learning of a rule that…
Given a set of species whose evolution is represented by a species tree, a gene family is a group of genes having evolved from a single ancestral gene. A gene family evolves along the branches of a species tree through various mechanisms,…
Functionalization of nanoparticles or colloids is increasingly being used to develop customizable "atoms". Functionalization by attaching single strands of DNA allows for direct control of the binding between nanoparticles, since…
Molecular phenotypes are important links between genomic information and organismic functions, fitness, and evolution. Complex phenotypes, which are also called quantitative traits, often depend on multiple genomic loci. Their evolution…