Related papers: Lagerkvist versus Crick
The genetic code is the function from the set of codons to the set of amino acids by which a DNA sequence encodes proteins. Since the codons also influence the shape of the DNA molecule itself, the same sequence that encodes a protein also…
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…
Reconciling gene trees with a species tree is a fundamental problem to understand the evolution of gene families. Many existing approaches reconcile each gene tree independently. However, it is well-known that the evolution of gene families…
From the perfect radial symmetries of radiolarian mineral skeletons to the broken symmetry of homochirality, the logic of Nature's regularities has fascinated scientists for centuries. Some of Nature's symmetries are clearly visible in…
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…
Degeneracies in the energy spectra of physical systems are commonly considered to be either of accidental character or induced by symmetries of the Hamiltonian. We develop an approach to explain degeneracies by tracing them back to…
New developments are presented in the framework of the model introduced by the authors in refs. [1,2] and in which nucleotides as well as codons are classified in crystal bases of the quantum group U_q(sl(2)+sl(2)) in the limit q -> 0. An…
The nucleotide composition of human genes with a special emphasis on transcription-related strand asymmetries is analyzed. Such asymmetries may be associated with different mutational rates in two principal factors. The first one is…
In this paper, we generally analyze the $\mu - \tau$ reflection symmetry modified by small mixings of charged leptons and how will future experiments verify deviations from the predictions of the symmetry. As an approximation, the…
The present paper is devoted to foundations of p-adic modelling in genomics. Considering nucleotides, codons, DNA and RNA sequences, amino acids, and proteins as information systems, we have formulated the corresponding p-adic formalisms…
Major discrepancies have been noted for some time between fossil ages and molecular divergence dates for a variety of taxa. Recently, systematic trends within avian clades have been uncovered. The trends show that the disparity is much…
A non-Hermitian version of Rashba Hamiltonian has been introduced motivated from the Levy-leblond type linearisation of Schrodinger equation in a Galilean invariant frame-work. The said Hamiltonian is found to be pseudo-Hermitian under…
The previously published data are examined on the base of the hypothesis about existence of differential polyteny of chromosomes and excess chromatin diminution during the first stages of embryogenesis. It has been concluded that available…
Ultrametric approach to the genetic code and the genome is considered and developed. $p$-Adic degeneracy of the genetic code is pointed out. Ultrametric tree of the codon space is presented. It is shown that codons and amino acids can be…
When estimating a phylogeny from a multiple sequence alignment, researchers often assume the absence of recombination. However, if recombination is present, then tree estimation and all downstream analyses will be impacted, because…
A simple explanation for the symmetry of the genetic code has been suggested. An alternative to the wobble hypothesis has been proposed. The facts revealed in this study offer a new insight into physical mechanisms of the functioning of the…
A tuple (or subgroup) in a group is said to degenerate to another if the latter is an endomorphic image of the former. In a countable reduced abelian group, it is shown that if tuples (or finite subgroups) degenerate to each other, then…
Below the electroweak scale, new physics that violates lepton number in two units ($\Delta L = 2$) and is mediated by heavy particle exchange can be parameterized by a dimension-9 low-energy effective Lagrangian. Operators in this…
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…
We consider conformal field theories around points of large twist degeneracy. Examples of this are theories with weakly broken higher spin symmetry and perturbations around generalised free fields. At the degenerate point we introduce twist…