Related papers: The Genetic Code as a Periodic Table: Algebraic As…
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…
We address the question, related with the origin of the genetic code, of why are there three bases per codon in the translation to protein process. As a followup to our previous work, we approach this problem by considering the…
In this paper we have established relations of the genetic tables with magic and bimagic squares. Connections with Hamming distances, binomial coefficients are established. The idea of Gray code is applied. Shannon entropy of magic squares…
Using the shape space of codons and tRNAs we give a physical description of the genetic code evolution on the basis of the codon capture and ambiguous intermediate scenarios in a consistent manner. In the lowest dimensional version of our…
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,…
In evolutionary policy search, neural networks are usually represented using a direct mapping: each gene encodes one network weight. Indirect encoding methods, where each gene can encode for multiple weights, shorten the genome to reduce…
It has been conjectured that evolution exerted pressure to preserve amino acids bearing thermodynamic, kinetic, and functional roles. In this letter we show that the physical requirement to maintain protein stability gives rise to a…
Natural protein sequences somehow encode the structural forms that these molecules adopt. Recent developments in structure-prediction are agnostic to the mechanisms by which proteins fold and represent them as static objects. However, the…
Present day data allow significant reconsideration of ideas on mechanisms underlying the degeneracy in the genetic code. Here a hypothesis is presented which links the degeneracy to possible conformational alterations in the codon-anticodon…
A hypothesis of the evolution of the genetic code is proposed, the leading mechanism of which is the nucleotide spontaneous damage leading to AT-enrichment of the genome. The hypothesis accounts for stability of the genetic code towards…
A primordial genetic code is proposed, having only four codons assigned, GGC meaning glycine, GAC meaning aspartate/glutamate, GCC meaning alanine-like and GUC meaning valine-like. Pathways of ambiguity reduction enlarged the codon…
The dynamics of coupled intermittent maps is used to model the correlated structure of genomic sequences. The use of intermittent maps, as opposed to other simple chaotic maps, is particularly suited for the production of long range…
Perhaps the most significant, if not the most important, achievements in chemistry and physics are the Periodic Table of the Elements in Chemistry and the Standard Model of Elementary Particles in Physics. A comparable achievement in…
The genetic code underlying protein synthesis is a canonical example of a degenerate biological system. Degeneracies in physical and biological systems can be lifted by external perturbations thus allowing degenerate systems to exhibit a…
The protein folding problem must ultimately be solved on all length scales from the atomic up through a hierarchy of complicated structures. By analyzing the stability of the folding process using physics and mathematics, this paper shows…
Many modified genetic codes are found in specific genomes in which one or more codons have been reassigned to a different amino acid from that in the canonical code. We present a model that unifies four possible mechanisms for reassignment,…
This paper reports about an approach to the classification of proteins' primary structures taking advantage of the Self Organizing Maps algorithm and of a numerical coding of the aminoacids based upon their physico-chemical properties.…
The periodic transference of nucleotide strings in bacterial and archaeal complete genomes is investigated by using the metric representation and the recurrence plot method. The generated periodic correlation structures exhibit four kinds…
Although mechanical properties of DNA are well characterized at the kilo base-pair range, a number of recent experiments have suggested that DNA is more flexible at shorter length scales, which correspond to the regime that is crucial for…
We demonstrate, using examples from $2$ and $3$-dimensions, a systematic method of finding all possible periodic arrangements of a given molecule or molecules such that the arrangements have the symmetry of a given space group. The…