Related papers: The genetic code invariance: when Euler and Fibona…
Even--even nuclei in the $A\sim100$ mass region are investigated within the framework of the interacting boson model-1 ({IBM-1}). The study includes energy spectra and electric quadrupole transition properties of zirconium, molybdenum,…
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…
In the framework of the crystal basis model of the genetic code, where each codon is assigned to an irreducible representation of $U_{q \to 0}(sl(2) \oplus sl(2))$, single base mutation matrices are introduced. The strength of the mutation…
In the ball-stick model, interatomic cohesions are considered "sticks". But enormous details and features of the "sticks" are usually oversimplified as indexed quantities or equivocated as geometry characteristics. These indexed quantities…
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…
In this work it is shown that three pairs of the factors appear to be the key, i.e. main factors of a natural classification of protein (canonical) amino acids within the amino acid (genetic) code. First pair: the factors of the habit of an…
We analyze the effect of variation of fundamental couplings and mass scales on primordial nucleosynthesis in a systematic way. The first step establishes the response of primordial element abundances to the variation of a large number of…
The large values of the singlet and triplet scattering lengths locate the two-nucleon system close to the unitary limit, the limit in which these two values diverge. As a consequence, the system shows a continuous scale invariance which…
The Fibonacci polynomials are defined recursively as $f_{n}(x)=xf_{n-1}(x)+f_{n-2}(x)$, where $f_0(x) = 0$ and $f_1(x)= 1$. We generalize these polynomials to an arbitrary number of variables with the $r$-Fibonacci polynomial. We extend…
We consider the phylogenetic tree model in which every node of the tree is observed and binary and the transitions are given by the same matrix on each edge of the tree. We are able to compute the Grobner basis and Markov basis of the toric…
Using Barnes-Wall lattices and 1-cocycles on finite groups of monomial matrices, we give a procedure to construct tricosine spherical codes. This was inspired by a 14-dimensional code which Ballinger, Cohn, Giansiracusa and Morris…
A new version of DNA walks, where nucleotides are regarded unequal in their contribution to a walk is introduced, which allows us to study thoroughly the "fine structure" of nucleotide sequences. The approach is based on the assumption that…
A nucleotides sequence is identified, in the two (four) letters alphabet, by the the labels of a vector state of an irreducible representation of U_q(sl(2)) (U_q(sl(2) + sl(2))), in the limit q -> 0. A master equation for the distribution…
Evolutionally conserved quantity that specifies folding nuclei is pursued by a case study for a small protein (PDB code: 1ten). First it is demonstrated that the sequences of amino acids at folding nuclei are not conserved. Then 3D…
Background/ Objectives: Resolving the origin of the genetic code is fundamental to understanding how life began its journey out of the chemical world. Since its deciphering some 60 years ago, there is still no general theory of the…
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.…
Eukaryote genomes contain excessively introns, inter-genic and other non-genic sequences that appear to have no vital functional role or phenotype manifestation. Their existence, a long-standing puzzle, is viewed from the principle of…
Background: A partially random target selection method was developed to design and produce affinity reagents (target) to any protein query. It is based on the recent concept of Proteomic Code (for review see Biro, 2007 [1]) which suggests…
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…
Apart from being the gateway for all access to the eukaryotic genome, chromatin has in recent years been identified as carrying an epigenetic code regulating transcriptional activity. The detailed knowledge of this code contrasts the…