ARTICLE | doi:10.20944/preprints202211.0528.v3
Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: DNA strands; complementary replication; DNA alphabets; binary opposition; binary numbers; dichotomy; dichotomic tree; algebras; split-quaternions; root-complementarity
Online: 25 May 2023 (07:56:14 CEST)
This article is devoted to the results of in-depth analysis of the system of binary-oppositional structures in DNA n-plet alphabets and their algebraic-matrix representations. These results show that the molecular complementary replication of DNA strands is accompanied by the presence of an algebraic version of the principle "like begets like" in matrix representations of DNA alphabets having internal structures. This algebraic version is based on binary-oppositional structures in the genetic molecular system, which can be represented by binary numbers and corresponding matrices of DNA alphabets. The received results allow thinking that the phenomenon "like begets like" (or a complementary replication in a wide sense) is systemic in the genetic organization and is connected with algebraic features of biological organization. Correspondingly, the biological principle "like begets like" can be additionally modeled by algebraic-matrix methods and approaches. Such algebra-matrix modeling of the genetic coding system gives new ways for studying and understanding the key role of the named principle in genetic and other inherited physiological complexes. On this way, the author discovered general rules of stochastic organization of information binary sequences of genomic DNAs of eukaryotes and prokaryotes. The presented rules are connected with information dichotomies of probabilities and corresponding fractal-like trees of probabilities, which fundamentally differ from constructional dichotomies in biological bodies. The received phenomenological data and rules lead to new biological ideas.
ARTICLE | doi:10.20944/preprints202208.0435.v1
Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: genomic DNAs; stochastics; tensor-unitary transformation; quantum informatics; fractal; projection operators; gestalt phenomena; stochastic determinism
Online: 25 August 2022 (11:52:12 CEST)
The article is devoted to algebraic modeling of universal rules of stochastic organization of genomic DNA of higher and lower organisms, previously published by the author. The proposed algebraic apparatus, which uses formalisms of quantum mechanics and quantum informatics and which is based on the so-called tensor-unitary transformations of vectors that generate families of interrelated stochastic-deterministic vectors of increased dimensions. The features of the vectors' interconnections in these families model the stochastic-deterministic properties of the named phenomenological rules. There are new approaches to modeling of developing multi-parameter biosystems, whose number of parameters increases in the course of step-by-step development. In the light of the presented materials, the issues of fractal-like organization in genetically inherited biosystems are considered. The development of the theory of stochastic determinism as an antipode of deterministic chaos is discussed.
ARTICLE | doi:10.20944/preprints202203.0100.v2
Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: genomic DNA; probability; matrices; tensor product; Hadamard product; antenna arrays; photonic crystals; liquid crystals; biophotonics; quantum informatics
Online: 26 April 2022 (10:30:56 CEST)
The article continues the author's publications about the matrix-tensor study of universal rules of stochastic (probabilistic) organization of long single-stranded DNA sequences in eukaryotic and prokaryotic genomes. The author reveals that corresponding matrices of probabilities of n-plets in n-textual representations of each genomic DNA are numerically interrelated each with other in such algebraic form, which has analogies with formalisms of the known tensor-matrix theory of digital antenna arrays. These arrays combine many separate antennas into a single coordinated ensemble with unique emergent properties, due to which antenna arrays are widely used in devices of medicine, astrophysics, avionics, etc. The noted analogies allow putting forward the author's hypothesis that the stochastic organization of genomic DNAs is connected with bio-antenna arrays. From the point of view of this hypothesis, many known facts about using principles of antenna arrays in inherited physiological phenomena are collected in a single grouping with genomic DNAs. This new topic about the biological meaning of profitable properties of antenna arrays includes problems of biological evolution, the origin of the genetic code, regenerative medicine, and the development of algebraic biology. These issues are discussed jointly with the author's results of quantum information analysis of stochastic features of genomic DNAs.
ARTICLE | doi:10.20944/preprints202101.0360.v3
Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: DNA alphabets, genomes, percentages of n-plets, binary-oppositions, tensor family of matrices, tetra-groupings, quantum biology, algebraic holography.
Online: 23 June 2021 (11:49:51 CEST)
The article presents the author's results of studying hidden rules of structural organizations of long DNA sequences in eukaryotic and prokaryotic genomes. The results concern some rules of percentages (or probabilities) of n-plets in genomes. To reveal such rules, the author considers genomic DNA nucleotide sequences as multilayers sequences of n-plets and studies the percentage contents of n-plets in different layers. Unexpected rules of invariance of total sums of percentages in certain tetra-groupings of n-plets in different layers of genomic DNA sequences are revealed. These discovered rules are candidates for the role of universal genomic rules. A tensor family of matrix representations of interrelated DNA-alphabets of 4 nucleotides, 16 doublets, 64 triplets, and 256 tetraplets is used in the study. This matrix approach allows revealing algebraic properties of the mentioned genetic rules of probabilities, which are useful for developing algebraic and quantum biology. Some analogies of the discovered genetic phenomena with phenomena of Gestalt psychology are noted and discussed. The author connects the received results about the genomic percentages rules with a supposition of P. Jordan, who is one of the creators of quantum mechanics and quantum biology, that life's missing laws are the rules of chance and probability of the quantum world. Additional attention is paid to the algebraic features of the system of structured DNA alphabets and their relationship with the methods of algebraic holography, known in the technique of processing discrete signals. The concept of algebraic-holographic genetics is being developed for the understanding of inherited holographic properties of organisms.
ARTICLE | doi:10.20944/preprints202005.0471.v2
Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: DNA oligomers; harmonic progression; hyperbolic rules; matrices; tensor product; quantum informatics; oligomer sums method; genomes; genes; viruses; proteins; long Russian texts; phonetic sequences
Online: 21 June 2020 (15:26:04 CEST)
The author's method of oligomer sums for analysis of oligomer compositions of eukaryotic and prokaryotic genomes is described. The use of this method revealed the existence of general rules for cooperative oligomeric organization of a wide list of genomes. These rules are called hyperbolic because they are associated with hyperbolic sequences including the harmonic progression 1, 1/2, 1/3, .., 1/n. These rules are demonstrated by examples of quantitative analysis of many genomes from the human genome to the genomes of archaea and bacteria. The hyperbolic (harmonic) rules, speaking about the existence of algebraic invariants in full genomic sequences, are considered as candidates for the role of universal rules for the cooperative organization of genomes. The described phenomenological results were obtained as consequences of the previously published author's quantum-information model of long DNA sequences. The oligomer sums method was also applied to the analysis of long genes and viruses including the COVID-19 virus; this revealed, in characteristics of many of them, the phenomenon of such rhythmically repeating deviations from model hyperbolic sequences, which are associated with DNA triplets. In addition, an application of the oligomer sums method are shown to the analysis of the following long sequences: 1) amino acid sequences in long proteins like the protein Titin; 2) phonetic sequences of long Russan literary texts (for checking of thoughts of many authors that phonetic organization of human languages is deeply connected with the genetic language). The topics of the algebraic harmony in living bodies and of the quantum-information approach in biology are discussed.
ARTICLE | doi:10.20944/preprints201908.0284.v4
Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: hyperbolic numbers; matrix; eigenvectors; genetics; Punnett squares; Fibonacci numbers; phyllotaxis; music harmony; literary texts; doubly stochastic matrices
Online: 13 April 2020 (11:04:05 CEST)
The article is devoted to applications of 2-dimensional hyperbolic numbers and their algebraic 2n-dimensional extensions in modeling some genetic and cultural phenomena. Mathematical properties of hyperbolic numbers and their bisymmetric matrix representations are described in a connection with their application to analyze the following structures: alphabets of DNA nucleobases; inherited phyllotaxis phenomena; Punnett squares in Mendelian genetics; the psychophysical Weber-Fechner law; long literary Russian texts (in their special binary representations). New methods of algebraic analysis of the harmony of musical works are proposed, taking into account the innate predisposition of people to music. The hypothesis is put forward that sets of eigenvectors of matrix representations of basis units of 2n-dimensional hyperbolic numbers play an important role in transmitting biological information. A general hyperbolic rule regarding the oligomer cooperative organization of different genomes is described jointly with its quantum-information model. Besides, the hypothesis about some analog of the Weber-Fechner law for sequences of spikes in single nerve fibers is formulated. The proposed algebraic approach is connected with the theme of the grammar of biology and applications of bisymmetric doubly stochastic matrices. Applications of hyperbolic numbers reveal hidden interrelations between structures of different biological and physical phenomena. They lead to new approaches in mathematical modeling genetic phenomena and innate biological structures.
ARTICLE | doi:10.20944/preprints201904.0011.v2
Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: DNA sequence; helix; nucleotide frequencies; DNA epi-chains; helical antennas; Fröhlich's theory; long-range coherence; epigenetics; quantum biology; binary representation
Online: 14 May 2019 (06:22:48 CEST)
One of creators of quantum mechanics P. Jordan in his work on quantum biology claimed that life's missing laws were the rules of chance and probability of the quantum world. The article presents author’s results of studying frequencies (or probabilities) of nucleotides on so-called epi-chains of long DNA sequences of various eukaryotic and prokaryotic genomes. DNA epi-chains are algorithmically constructed subsequencies of DNA nucleotide sequences. According to the algorithm of construction of any epi-chain of the order n, the epi-chain is such nucleotide subsequence, in which the numerations of adjacent nucleotides differ by natural number n (n = 1, 2, 3, 4,…). Correspondingly each epi-chain of order n ≥ 2 contains n times less nucleotides than the original DNA sequence. The presented results unexpectedly discover that in long single-stranded and double-stranded DNA of any tested genome its DNA epi-chains of different orders n (values n are not too large) have practically identical frequencies (or probabilities) of each kind of nucleotides. These data allow considering DNA as a regular rich set of epi-chains, which can play a certain role in genetic and epigenetic phenomena as the author belives. Appropriate rules of nucleotide frequencies on epi-chains of long DNA sequences are formulated for further their tests on a wider set of genomes. These results testify on existence of long-range coherence in long DNA and remind the Fröhlich's theory of long-range coherence in biological systems. The phenomenological data are discussed from different standpoints: the DNA double helices and helical antennas with circular polarizations of electromagnetic waves; relations with the Fröhlich's theory; numerical analysis of DNA epi-chains under binary representations of nucleotides. Results are useful for developing quantum and algebraic biology.
ARTICLE | doi:10.20944/preprints201812.0142.v2
Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: DNA sequences, literary texts, probability, binary opposition, alphabet, tensor product, quantum informatics
Online: 18 February 2019 (17:22:56 CET)
Impressing discoveries in the field of the genetic code have been described by its researchers by means of the terminology borrowed from linguistics and the theory of communications. Leading experts on structural linguistics believe for a long time already that languages of human dialogue were formed not from an empty place, but they are continuation of genetic language or, anyhow, are closely connected with it, confirming the idea of information commonality of organisms. The aticle continues the theme about a connection of linquistic languages with the genetic language. It describes results of comparative study of long Russian literary texts (novels by L.Tolstoy, F.Dostoevsky, A.Pushkin, etc.) and long sequences of hydrogen bonds in double helixes of DNA of different organisms. Formalisms of quantum informatics are used in modeling some of these results taking into account thoughts of many researches about possible using principles of quantum informatics in organisation of living bodies.
ARTICLE | doi:10.20944/preprints201804.0131.v2
Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: genetic code, alphabet, unitary matrix, dyadic shift, decomposition, spectral presentation, fractal, tensor product, quantum informatics
Online: 27 September 2018 (13:36:53 CEST)
Information molecules of DNA and RNA should obey principles of quantum mechanics where unitary operators in form of unitary matrices have key meanings. Unitary matrices are the basis of calculations in quantum computers. This article presents some author's results, which show that matrix forms of the representation of structured systems of molecular-genetic alphabets can be considered as sets of sparse unitary matrices related with phenomenologic features of the degeneracy of the genetic code. These sparse unitary matrices have orthogonal systems of functions in their rows and columns. A complementarity exists among some unitary genetic matrices in relation each other. Decompositions of numeric genetic matrices into sets of sparse unitary matrices are connected with the logical operation of modulo-2 addition used in quantum computers as well. Tensor (or Kronecker) families of unitary genetic matrices with their fractal-like properties are also considered. The described results are discussed in the frame of development of quantum-information approaches for modeling genetic systems.