Related papers: Gene Algebra from a Genetic Code Algebraic Structu…
The automorphism groups of various linear codes are extensively studied yielding insights into the respective code structure. This knowledge is used in, e.g., theoretical analysis and in improving decoding performance, motivating the…
Electronic properties of DNA are believed to play a crucial role in many phenomena in living organisms, for example the location of DNA lesions by base excision repair (BER) glycosylases and the regulation of tumor-suppressor genes such as…
There is an intrinsic relationship between the molecular evolution in primordial period and the properties of genomes and proteomes of contemporary species. The genomic data may help us understand the driving force of evolution of life at…
How DNA is mapped to functional proteins is a basic question of living matter. We introduce and study a physical model of protein evolution which suggests a mechanical basis for this map. Many proteins rely on large-scale motion to…
Complex systems with tightly coadapted parts frequently appear in living systems and are difficult to account for through Darwinian evolution, that is random variation and natural selection, if the constituent parts are independently coded…
A plausible architecture of an ancient genetic code is derived from an extended base triplet vector space over the Galois field of the extended base alphabet {D, G, A, U, C}, where the letter D represents one or more hypothetical bases with…
A codon table is a useful tool for mapping codons to amino acids as they have been assigned by nature. It has become a scientific icon because of the way it embodies our understanding of this natural process and the way it immediately…
Background The theoretical requirements for a genetic code were well defined and modeled by George Gamow and Francis Crick in the 50-es. Their models failed. However the valid Genetic Code, provided by Nirenberg and Matthaei in 1961,…
How does the genome encode the form of the organism? What is the nature of this genomic code? Inspired by recent work in machine learning and neuroscience, we propose that the genome encodes a generative model of the organism. In this…
The mean length and the variability of coding sequences for 48 genomes of bacteria and archaea were analyzed. It was found that the plotted data can be described by an angular area. This suggests the followings: a) The variability of a…
Despite the thousands of genes implicated in age-related phenotypes, effective interventions for aging remain elusive, a lack of advance rooted in the multifactorial nature of longevity and the functional interconnectedness of the molecular…
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 holographic bound in physics constrains the complexity of life. The finite storage capability of information in the observable universe requires the protein linguistics in the evolution of life. We find that the evolution of genetic…
Proteins are responsible for the most diverse set of functions in biology. The ability to extract information from protein sequences and to predict the effects of mutations is extremely valuable in many domains of biology and medicine.…
Genetic and evolution algebras arise naturally from applied probability and stochastic processes. Gibbs measures describe interacting systems commonly studied in thermodynamics and statistical mechanics with applications in several fields.…
The main statistical distributions applicable to the analysis of genome architecture and genome tracks are briefly discussed and critically assessed. Although the observed features in distributions of element lengths can be equally well…
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…
Let $A$ be a finite dimensional algebra over an algebraically closed field $k$. We investigate the structure properties of the endomorphism algebras of semi-tilting $A$-modules, and prove that the endomorphism algebras arising from the…
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…
The mathematical concept of q-deformations, in particular the one of qnumbers, is used to study the genetic code(s). After considering two kinds of q-numbers, for comparison, a phenomenological classification scheme of the genetic code…