Related papers: The naturally designed spherical symmetry in the g…
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…
Exploiting the symmetry of the regular icosahedron, Peter Doyle and Curt McMullen constructed a solution to the quintic equation. Their algorithm relied on the dynamics of a certain icosahedral equivariant map for which the icosahedron's…
In this paper we study a special type of quasi-cyclic (QC) codes called skew QC codes. This set of codes is constructed using a non-commutative ring called the skew polynomial rings $F[x;\theta ]$. After a brief description of the skew…
All known terrestrial proteins are coded as continuous strings of ~20 amino acids. The patterns formed by the repetitions of elements in groups of finite sequences describes the natural architectures of protein families. We present a method…
Polypolyhedra (after R. Lang) are compounds of edge-transitive 1-skeleta. There are 54 topologically different polypolyhedra, and each has icosidodecahedral, cuboctahedral, or tetrahedral symmetry, all are realizable as modular origami…
Background: Symmetries are a powerful way to characterize nuclear wave functions. A true dynamical symmetry, where the Hamiltonian is block-diagonal in subspaces defined by the group, is rare. More likely is a quasidynamical symmetry:…
The probability that two randomly selected phylogenetic trees of the same size are isomorphic is found to be asymptotic to a decreasing exponential modulated by a polynomial factor. The number of symmetrical nodes in a random phylogenetic…
We perform geometrization of genetics by representing genetic information by points of the 4-adic {\it information space.} By well known theorem of number theory this space can also be represented as the 2-adic space. The process of…
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 propose a physical model to describe the mechanisms of two major scenarios of the genetic code evolution, the codon capture and ambiguous intermediate scenarios, in a consistent manner. We sketch the lowest dimensional version of our…
In this paper we present the results of computer searches using a variation of an energy minimization algorithm used by Kottwitz for finding good spherical codes. We prove that exact codes exist by representing the inner products between…
We consider codes over the two semi-local non-unital rings of order six, \[ H_{23} = \langle a,b \mid 2a=0, 3b = 0, a^2=a, b^2 = 0, ab = 0 = ba \rangle,\] and \[H_{32} = \langle a,b \mid 2a=0, 3b = 0, a^2=0, b^2 = b, ab = 0 = ba \rangle. \]…
The Dissertation is focused on the studies of associations between functional elements in human genome and their nucleotide structure. The asymmetry in nucleotide content (skew, bias) was chosen as the main feature for nucleotide structure.…
The article continues an analysis of the genetic 8-dimensional Yin-Yang-algebra. This algebra was revealed in a course of matrix researches of structures of the genetic code and it was described in the author's articles arXiv:0803.3330 and…
This article is interested in the origin of the genetic code, it puts forward a scenario of a simultaneous selection of the bases and amino acids and setting up of a correlation between them. Each amino acid is associated with a pair of its…
We say that a Lie (super)algebra is ''symmetric'' if with every root (with respect to the maximal torus) it has the opposite root of the same multiplicity. Over algebraically closed fields of positive characteristics (up to 7 or 11, enough…
We systematically explore the self-assembly of semi-flexible polymers in deformable spherical confinement across a wide regime of chain stiffness, contour lengths and packing fractions by means of coarse-grained molecular dynamics…
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…
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…
DNA nanoparticles with three-fold coordination have been observed to self-assemble in experiment into a network equivalent to the hexagonal (6.6.6) tiling, and a network equivalent to the 4.8.8 Archimedean tiling. Both networks are built…