Related papers: Gene Algebra from a Genetic Code Algebraic Structu…
Using concepts of physics of elementary particles concerning the breaking of symmetry and grannd unified theory we propose to study with the algebraic approximation the degeneracy finded in the genetic code with the incorporation of a…
We consider endomorphism algebras of $n$-term silting complexes in derived categories of hereditary algebras, and we show that the module category of such an endomorphism algebra has a separated $n$-section. For $n=3$ we obtain a trisection…
Motivation: Analysis of relationships of drug structure to biological response is key to understanding off-target and unexpected drug effects, and for developing hypotheses on how to tailor drug thera-pies. New methods are required for…
A method to construct and count all the linear codes (of arbitrary length) in $\mathbb{F}_{4}$ that are invariant under reverse permutation and that contain the repetition code is presented. These codes are suitable for constructing DNA…
The number of atoms in the four ribonucleotides uridine monophosphate, cytidine monophosphate, adenine monophosphate and guanine monophosphate is taken as a key parameter. A mathematical relation describing the condensation of the three…
We investigate the large-scale geometry of the DNA-protein complex of chromatin using a generalized optimality principle, which requires that not only should all sub-parts of a natural process be optimal but also the unfolding of higher…
We study the dynamics of genetic code evolution. The model of Vetsigian et al. [1] and Vetsigian [2] uses the mechanism of horizontal gene transfer to demonstrate convergence of the genetic code to a near universal solution. We reproduce…
A haplotype block, or simply a block, is a chromosomal segment, DNA base sequence or string that occurs in only a few variants or types in the genomes of a population of interest, and that has an encapsulated or 'private' frequency…
In this paper, we present a novel design strategy of DNA codes with length $3n$ over the non-chain ring $R=\mathbb{Z}_4+u\mathbb{Z}_4+u^2\mathbb{Z}_4$ with $64$ elements and $u^3=1$, where $n$ denotes the length of a code over $R$. We first…
The genetic code maps the sixty-four nucleotide triplets (codons) to twenty amino-acids. Some argue that the specific form of the code with its twenty amino-acids might be a 'frozen accident' because of the overwhelming effects of any…
An important aspect in the theory of algebras with polynomial identities is the study of the asymptotic behavior of the codimension sequence $c_n(A),\, n\geq 1,$ which measures the growth of polynomial identities of a given algebra $A$. In…
The genetic code is nearly universal, and the arrangement of the codons in the standard codon table is highly non-random. The three main concepts on origin and evolution of the code are the stereochemical theory; the coevolution theory; and…
This paper proposes a new mathematical approach to characterize native protein structures based on the discrete differential geometry of tetrahedron tiles. In the approach, local structure of proteins is classified into finite types…
The post-genomic era has brought opportunities to bridge traditionally separate fields of early history of life and brought new insight into origin and evolution of biodiversity. According to distributions of codons in genome sequences, I…
An involution of a real commutative algebra $A$ is a real-linear homomorphism $f : A \rightarrow A$ such that $f^2 = \mathrm{Id}$. We show that there are six involutions of the algebra of bicomplex numbers, contrary to the actual number of…
Genotype networks are a method used in systems biology to study the "innovability" of a set of genotypes having the same phenotype. In the past they have been applied to determine the genetic heterogeneity, and stability to mutations, of…
When biological foundation models such as scGPT and Geneformer process single-cell gene expression, what geometric and topological structure forms in their internal representations? Is that structure biologically meaningful or a training…
The main result of [FG20] classifies the 92 geometric endomorphism algebras of geometrically split abelian surfaces defined over Q. We show that 54 of them arise as geometric endomorphism algebras of Jacobians of genus 2 curves defined over…
The phenotype of any organism on earth is, in large part, the consequence of interplay between numerous gene products encoded in the genome, and such interplay between gene products affects the evolutionary fate of the genome itself through…
Drug resistance to HIV-1 Protease involves accumulation of multiple mutations in the protein. Here we investigate the role of these mutations by using molecular dynamics simulations which exploit the influence of the native-state topology…