相关论文: Symmetries by base substitutions in the genetic co…

A new set of DNA base-nucleic acid codes and their hypercomplex number representation have been introduced for taking the probability of each nucleotide into full account. A new scoring system has been proposed to suit the hypercomplex…

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…

We present an effective theory for the Bloch functions of a two-dimensional square lattice near a quadratic degeneracy point. The degeneracy is protected by the symmetries of the crystal, and breaking these symmetries can either open a…

We study theoretically the denaturation of single RNA molecules by mechanical stretching, focusing on signatures of the (un)folding pathway in molecular fluctuations. Our model describes the interactions between nucleotides by incorporating…

Foundation models for biology and physics optimize predictive accuracy, but their internal representations systematically fail to preserve the continuous geometry of the systems they model. We identify the root cause: the Geometric…

Transfer RNAs (tRNAs) are essential components of the translational machinery. Their abundance and diversity shape decoding capacity and protein synthesis efficiency and accuracy. Because tRNA abundance is encoded in the genome through tDNA…

So far mutations analysis was performed in terms of transitions and trasversions, so on the basis of the molecule, or in terms of GC-content and isochors, through the quantification of GC->AT mutations over AT->GC mutations. We tried a…

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…

We consider Abelian topological quantum field theories (TQFTs) in 3d and show that gaugings of invertible global symmetries naturally give rise to additive codes. These codes emerge as nonanomalous subgroups of the 1-form symmetry group,…

RNA's diversity of structures and functions impacts all life forms since primordia. We use calorimetric force spectroscopy to investigate RNA folding landscapes in previously unexplored low-temperature conditions. We find that Watson-Crick…

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 standard genetic code multiplet structure as well as the correct degeneracies, class by class, are all extracted from the (unique) number 23, the order of the permutation group of 23 objects.

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…

Biologists have long sought a way to explain how statistical properties of genetic sequences emerged and are maintained through evolution. On the one hand, non-random structures at different scales indicate a complex genome organisation. On…

We provide a detailed study of the general structure of two-dimensional topological stabilizer quantum error correcting codes, including subsystem codes. Under the sole assumption of translational invariance, we show that all such codes can…

Tilings and point sets arising from substitutions are classical mathematical models of quasicrystals. Their hierarchical structure allows one to obtain concrete answers regarding spectral questions tied to the underlying measures and…

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…

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…

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…

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…