Related papers: p-Adic Modelling of the Genome and the Genetic Cod…
Exploring and understanding the protein-folding problem has been a long-standing challenge in molecular biology. Here, using molecular dynamics simulation, we reveal how parallel distributed adjacent planar peptide groups of unfolded…
The paper represents three supplements to the source paper, q-bio/0610044 [q-bio.OT], with three new series of harmonic structures of the genetic code, determined by Gauss arithmetical algorithm; by Table of Minimal Adding, as in…
Convolutional codes are error-correcting linear codes that utilize shift registers to encode. These codes have an arbitrary block size and they can incorporate both past and current information bits. DNA codes represent DNA sequences and…
The problem of the directionality of genome evolution is studied. Based on the analysis of C-value paradox and the evolution of genome size we propose that the function-coding information quantity of a genome always grows in the course of…
The mathematical basis of p-adic Higgs mechanism discussed in papers [email protected] 9410058-62 is considered in this paper. The basic properties of p-adic numbers, of their algebraic extensions and the so called canonical…
We propose a model that explains the hierarchical organization of proteins in fold families. The model, which is based on the evolutionary selection of proteins by their native state stability, reproduces patterns of amino acids conserved…
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…
Proteins are the fundamental macromolecules that play diverse and crucial roles in all living matter and have tremendous implications in healthcare, manufacturing, and biotechnology. Their functions are largely determined by the sequences…
We study the coupled dynamics of primary and secondary structure formation (i.e. slow genetic sequence selection and fast folding) in the context of a solvable microscopic model that includes both short-range steric forces and and…
This paper surveys foundation models for AI-enabled biological design, focusing on recent developments in applying large-scale, self-supervised models to tasks such as protein engineering, small molecule design, and genomic sequence design.…
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…
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…
Gene expression programming, a genotype/phenotype genetic algorithm (linear and ramified), is presented here for the first time as a new technique for the creation of computer programs. Gene expression programming uses character linear…
How robust is the natural genetic code with respect to mistranslation errors? It has long been known that the genetic code is very efficient in limiting the effect of point mutation. A misread codon will commonly code either for the same…
The sequence of nucleotide bases occurring in an organism's DNA is often regarded as a codescript for its construction. However, information in a DNA sequence can only be regarded as a codescript relative to an operational biochemical…
Genomes evolve as modules. In prokaryotes (and some eukaryotes), genetic material can be transferred between species and integrated into the genome via homologous or illegitimate recombination. There is little reason to imagine that the…
Protein sequences serve as a natural record of the evolutionary constraints that shape their functional structures. We show that it is possible to use only sequence information to go beyond predicting native structures and global stability…
In this review paper, we delve into the nascent field of molecular data storage, focusing on system implementations and code constructions. We start by providing an overview of basic concepts in synthetic and computational biology.…
Phylogenetic analysis of DNA or other data commonly gives rise to a collection or sample of inferred evolutionary trees. Principal Components Analysis (PCA) cannot be applied directly to collections of trees since the space of evolutionary…
The evolution of the full repertoire of proteins encoded in a given genome is mostly driven by gene duplications, deletions, and sequence modifications of existing proteins. Indirect information about relative rates and other intrinsic…