Related papers: Degeneracy in the genetic code and its symmetries …
Many cases of non-standard genetic codes are known in mitochondrial genomes. We carry out analysis of phylogeny and codon usage of organisms for which the complete mitochondrial genome is available, and we determine the most likely…
At any moment in time, evolution is faced with a formidable challenge: refining the already highly optimised design of biological species, a feat accomplished through all preceding generations. In such a scenario, the impact of random…
The degeneracy of central configurations in the planar $N$-body problem makes their enumeration problem hard and the related dynamics appealing. To truly understand the bifurcations of central configurations, we should work in the FULL…
Mutations can arise from the chance misincorporation of nucleotides during DNA replication or from DNA lesions that are not repaired correctly. We introduce a model that relates the source of mutations to their accumulation with cell…
We describe a quantum error correction scheme aimed at protecting a flow of quantum information over long distance communication. It is largely inspired by the theory of classical convolutional codes which are used in similar circumstances…
Most of the DNA that composes a complex organism is non-coding and defined as junk. Even the coding part is composed of genes that affect the phenotype differently. Therefore, a random mutation has an effect on the specimen fitness that…
The matrix form of the presentation of the genetic code is described as the cognitive form to analyze structures of the genetic code. A similar matrix form is utilized in the theory of signal processing. The Kronecker family of the genetic…
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…
We investigated the error-minimization properties of putative primordial codes that consisted of 16 supercodons, with the third base being completely redundant, using a previously derived cost function and the error minimization percentage…
Background: There is a 3-fold redundancy in the Genetic Code; most amino acids are encoded by more than one codon. These synonymous codons are not used equally; there is a Codon Usage Bias (CUB). This article will provide novel information…
Some genes can change their relative locations in a genome. Thus for different individuals of the same species, the orders of genes might be different. Such jumping genes are called transposons. A practical problem is to determine…
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 idea of the evolution of the genetic code from the CG to the CGUA alphabet has been developed further. The assumption of the originally triplet structure of the genetic code has been substantiated. The hypothesis of the emergence of…
Rich information on the prebiotic evolution is still stored in contemporary genomic data. The statistical mechanism at the sequence level may play a significant role in the prebiotic evolution. Based on statistical analysis of genome…
The question of why we age is a fundamental one. It is about who we are, and it also might have critical practical aspects as we try to find ways to age slower. Or to not age at all. Different reasons point at distinct strategies for the…
A simple explanation for the symmetry and degeneracy of the genetic code has been suggested. An alternative to the wobble hypothesis has been proposed. This hypothesis offers explanations for: i) the difference between thymine and uracil,…
Essential genes constitute the core of genes which cannot be mutated too much nor lost along the evolutionary history of a species. Natural selection is expected to be stricter on essential genes and on conserved (highly shared) genes, than…
We perform geometrization of genetics by representing genetic information by points of the 4-adic {\it information space.} By well known theorem of number theory this space can also be represented as the 2-adic space. The process of…
Genetic sequences are known to possess non-trivial composition together with symmetries in the frequencies of their components. Recently, it has been shown that symmetry and structure are hierarchically intertwined in DNA, suggesting a…
A coding of functions that allows a genetic algorithm to minimize functionals without analytic trial functions is presented and implemented for solving numerically some instances of variational problems from physics.