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In this paper, we study convolutional codes with a specific cyclic structure. By definition, these codes are left ideals in a certain skew polynomial ring. Using that the skew polynomial ring is isomorphic to a matrix ring we can describe…
An RNA sequence is a word over an alphabet on four elements $\{A,C,G,U\}$ called bases. RNA sequences fold into secondary structures where some bases match one another while others remain unpaired. Pseudoknot-free secondary structures can…
We investigate the fine structure of the sp3 hybridized covalent bond geometry that governs the tetrahedral architecture around the central C$_\alpha$ carbon of a protein backbone, and for this we develop new visualization techniques to…
The concepts of symmetry and symmetry groups are at the heart of several developments in modern theoretical and mathematical physics. The present paper is devoted to a number of selected topics within this framework: Euclidean and rotation…
The quantum spin $1/2$ XXZ chain with anisotropy parameter $\Delta=-1/2$ possesses a dynamic supersymmetry on the lattice. This supersymmetry and a generalisation to higher spin are investigated in the case of open spin chains. A family of…
The genetic code markup is the assignment of stop codons. The standard genetic code markup ensures the maximum possible stability of genetic information with respect to two fault classes: frameshift and nonsense mutations. There are only…
Most amino acids are encoded by multiple synonymous codons. For an amino acid, some of its synonymous codons are used much more rarely than others. Analyses of positions of such rare codons in protein sequences revealed that rare codons can…
The tendencies described in this work were revealed in the course of examination of adenine and uracil distribution in the mRNA encoding sequence. The study also discusses the usage of codons occupied by the amino acid arginine in the table…
Using theoretical results about the homogeneous weights for Frobenius rings, we describe the homogeneous weight for the ring family $R_k$, a recently introduced family of Frobenius rings which have been used extensively in coding theory. We…
The shape of crystalline nanoparticles (NP) can often be described by polyhedra with flat facet surfaces. Thus, structural studies of polyhedral bodies can help to describe geometric details of NPs. Here we consider compact polyhedra of…
Quantum spin rings represent fundamental model systems that exhibit distinctive quantum phenomena-such as quantum critical behavior and quasiparticle excitations-arising from their periodic boundary conditions and enhanced quantum…
A quaternionic representation of the genetic code, previously reported by the authors, is updated in order to incorporate chirality of nucleotide bases and amino acids. The original representation assigns to each nucleotide base a prime…
Ultrametric approach to the genetic code and the genome is considered and developed. $p$-Adic degeneracy of the genetic code is pointed out. Ultrametric tree of the codon space is presented. It is shown that codons and amino acids can be…
An infinite family of quasi-maximally superintegrable Hamiltonians with a common set of (2N-3) integrals of the motion is introduced. The integrability properties of all these Hamiltonians are shown to be a consequence of a hidden…
A novel scheme is introduced to capture the spatial correlations of consecutive amino acids in naturally occurring proteins. This knowledge-based strategy is able to carry out optimally automated subdivisions of protein fragments into…
Several interesting astrophysical phenomena are symmetric with respect to the rotation axis, like the head-on collision of compact bodies, the collapse and/or accretion of fields with a large variety of geometries, or some forms of…
The macromolecules that encode and translate information in living systems, DNA and RNA, exhibit distinctive structural asymmetries, including homochirality or mirror image asymmetry and $3' - 5'$ directionality, that are invariant across…
Protein-fragment seqlets typically feature about 10 amino acid residue positions that are fixed to within conservative substitutions but usually separated by a number of prescribed gaps with arbitrary residue content. By quantifying a…
Evolutionary theorizing resembles building an aircraft while also piloting it; new results change the scaffold for older ideas, requiring revised strategy to remain airborne. A calculated kinetic pathway exists that, under explicit…
We investigate the ``generalized Heron polynomial'' that relates the squared area of an n-gon inscribed in a circle to the squares of its side lengths. For a (2m+1)-gon or (2m+2)-gon, we express it as the defining polynomial of a certain…