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Hadamard matrices of genetic code and trigonometric functions

Year 2024, Volume: 7 Issue: Special Issue: AT&A, 27 - 36, 16.12.2024
https://doi.org/10.33205/cma.1539666

Abstract

Algebraic theory of coding is one of the modern fields of applications of algebra. Genetic matrices and algebraic biology have been the latest advances in further understanding of the patterns and rules of genetic code. Genetics code is encoded in combinations of the four nucleotides (A, C, G, T) found in DNA and then RNA. DNA defines the structure and function of an organism and contains complete genetic information. DNA paired bases of (A, C, G, T) form a geometric curve of double helix, define the 64 standard genetic triplets, and further degenerate 64 genetic codons into 20 amino acids. In trigonometry, four basic trigonometric functions (sin x, tan x, cos x, cot x) provided bases for Fourier analysis to encode signal information. In this paper, we use these 4 paired bases of trigonometric functions (sin x, tan x, cos x, and cot x) to generate 64 trigonometric triplets similar to 64 standard genetic code, further exam these 64 trigonometric functions and obtained 20 trigonometric triplets similar to 20 amino acids. This parallel shows a similarity connection between universal genetic codes and the universality of trigonometric functions. This connection may provide a bridge to further uncover patterns of genetic code. This demonstrates that matrix algebra is one of promising instruments and of adequate languages in bioinformatics and algebraic biology.

References

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  • Y. A. Geadah, M. J. Corinthios: Natural, dyadic and sequency order algorithms and processors for the Walsh-Hadamard transform, IEEE Trans. Comput., C-26 (1977), 25–40.
  • A. V. Geramita: Orthogonal designs: quadratic forms and Hadamard matrices, London: Dekker (1979).
  • A. Gierer, K. W. Mundry: Production of mutants of tobacco mosaic virus by chemical alteration of its ribonucleic acid in vitro, Nature (London), 182 (1958), 1457–1458.
  • D. E. Goldberg: Genetic algorithms and Walsh functions, Complex Systems, 3 (2) (1989), 129–171.
  • S. Forrest, M. Mitchell: The performance of genetic algorithms on Walsh polynomials: Some anomalous results and their explanation, In R.K.Belew and L.B.Booker, (editors), Proceedings of the Fourth International Conference on Genetic Algorithms, p.182-189, San Mateo, CA: Morgan Kaufmann.
  • M. D. Frank-Kamenetskiy: The most principal molecule, Moscow: Nauka (1988).
  • M. He: Double helical sequences and doubly stochastic matrices, In S. Petoukhov (Ed.).Symmetry in genetic information, Symmetry: Culture and Science, Budapest, 307–330.
  • M. He: Symmetry in Structure of Genetic Code, Proceedings of the 3rd All-Russian Interdisciplinary Scientific Conference “Ethics and the Science of Future. Unity in Diversity”, Feb. 12-14, Moscow, 80–85.
  • M. He: Genetic Code, Attributive Mappings and Stochastic Matrices, Bulletin for Mathematical Biology, 66 (5) (2003), 965–973.
  • M. He, S. Petoukhov: Harmony of living nature, symmetries of genetic systems and matrix genetics, International journal of integrative medicine, 1 (1) (2007), 41–43.
  • M. He, S. V. Petoukhov and P. E. Ricci: Genetic code, Hamming distance and stochastic matrices, Bulletin for Mathematical Biology, 66 (5) (2004), 965–973.
  • H. Kargupta: A striking property of genetic code-like transformations, Complex systems, 11 (2001), 57–70.
  • M. H. Lee, M. Kaveh: Fast Hadamard transform based on a simple matrix factorization, IEEE Trans. Acoust., Speech, Signal Processing, ASSSP-34 (6) (1986), 1666–1667.
  • V. V. Lobzin, V. P. Chechetkin: The order and correlations in genome sequences of DNK, Achievements of physical sciences (Uspehi fizicheskih nauk), 170 (1) (2000), 57–81 (in Russian).
  • M. A. Nielsen, I. L. Chuang: Quantum computation and quantum information, Cambridge: Cambridge University Press (2001).
  • W. W. Peterson, E. J. Weldon: Error-correcting codes, Cambridge: MIT Press (1972).
  • S. V. Petoukhov: Genetic codes: binary sub-alphabets, bi-symmetric matrices and golden section; Genetic codes: numeric rules of degeneracy and the chronocyclic theory, Symmetry:Culture and Science, 12(1) (2001), 255–306.
  • S. V. Petoukhov: The rules of degeneracy and segregations in genetic codes. The chronocyclic conception and parallels with Mendel’s laws, In M.He, G.Narasimhan, S.Petoukhov (Ed.), Advances in Bioinformatics and its Applications, Series in Mathematical Biology&Medicine, Singapore: World Scientific, 8 (2005), (pp. 512-532).
  • S. V. Petoukhov: Hadamard matrices and quint matrices in matrix presentations of molecular genetic systems, Symmetry: Culture and Science, 16(3) (2005), 247–266.
  • S. V. Petoukhov: Matrix genetics, algebras of the genetic code, noise-immunity, Moscow: RCD (2008) (in Russian).
  • S. V. Peteukhov: Matrix genetics, part 2: the degeneracy of the genetic code and the octave algebra with two quasi-real units (the “Yin-Yang octave algebra”), 1-27, retrieved March, 08, from http://arXiv:0803.3330.
  • A. Shiozaki: A model of distributed type associated memory with quantized Hadamard transform, Biol. Cybern., 38 (1) (1980), 19–22.
  • P. E. Ricci, J. Gielis: From Pythagoras to Fourier and From Geometry to Nature, Athena, Publishing (2021).
  • B. Sklar: Digital communication. Fundamentals and applications, New-York: Prentice Hall (2001).
  • I. Stewart: Life’s other secret: The new mathematics of the living world, New-York: Penguin (1999).
  • A. Yu. Tolmachev: New optic spectrometers, Leningrad: Leningrad University (1976) (in Russian).
  • A. M. Trahtman, V. A. Trahtman: The foundations of the theory of discrete signals on finite intervals, Moscow: Sovetskoie Radio (1975) (in Russian).
  • M. Vose, A. Wright: The simple genetic algorithm and the Walsh transform: Part I, theory, Journal of Evolutionary Computation, 6 (3) (1998), 253–274.
  • M. S. Waterman (Ed.): Mathematical methods for DNA sequences, Florida: CRC Press, Inc (1999).
  • R. Yarlagadda, J. Hershey: Hadamard matrix analysis and synthesis with applications to communications and signal/image processing, . London: Kluwer Academic Publ (1997).
  • L. A. Zalmanzon: Fourier, Walsh and Haar transformations and their application in control, communication and other systems, Moscow: Nauka (1989) (in Russian).
Year 2024, Volume: 7 Issue: Special Issue: AT&A, 27 - 36, 16.12.2024
https://doi.org/10.33205/cma.1539666

Abstract

References

  • N. Ahmed, K. Rao: Orthogonal transforms for digital signal processing, New-York: Springer-Verlag Inc (1975).
  • Y. A. Geadah, M. J. Corinthios: Natural, dyadic and sequency order algorithms and processors for the Walsh-Hadamard transform, IEEE Trans. Comput., C-26 (1977), 25–40.
  • A. V. Geramita: Orthogonal designs: quadratic forms and Hadamard matrices, London: Dekker (1979).
  • A. Gierer, K. W. Mundry: Production of mutants of tobacco mosaic virus by chemical alteration of its ribonucleic acid in vitro, Nature (London), 182 (1958), 1457–1458.
  • D. E. Goldberg: Genetic algorithms and Walsh functions, Complex Systems, 3 (2) (1989), 129–171.
  • S. Forrest, M. Mitchell: The performance of genetic algorithms on Walsh polynomials: Some anomalous results and their explanation, In R.K.Belew and L.B.Booker, (editors), Proceedings of the Fourth International Conference on Genetic Algorithms, p.182-189, San Mateo, CA: Morgan Kaufmann.
  • M. D. Frank-Kamenetskiy: The most principal molecule, Moscow: Nauka (1988).
  • M. He: Double helical sequences and doubly stochastic matrices, In S. Petoukhov (Ed.).Symmetry in genetic information, Symmetry: Culture and Science, Budapest, 307–330.
  • M. He: Symmetry in Structure of Genetic Code, Proceedings of the 3rd All-Russian Interdisciplinary Scientific Conference “Ethics and the Science of Future. Unity in Diversity”, Feb. 12-14, Moscow, 80–85.
  • M. He: Genetic Code, Attributive Mappings and Stochastic Matrices, Bulletin for Mathematical Biology, 66 (5) (2003), 965–973.
  • M. He, S. Petoukhov: Harmony of living nature, symmetries of genetic systems and matrix genetics, International journal of integrative medicine, 1 (1) (2007), 41–43.
  • M. He, S. V. Petoukhov and P. E. Ricci: Genetic code, Hamming distance and stochastic matrices, Bulletin for Mathematical Biology, 66 (5) (2004), 965–973.
  • H. Kargupta: A striking property of genetic code-like transformations, Complex systems, 11 (2001), 57–70.
  • M. H. Lee, M. Kaveh: Fast Hadamard transform based on a simple matrix factorization, IEEE Trans. Acoust., Speech, Signal Processing, ASSSP-34 (6) (1986), 1666–1667.
  • V. V. Lobzin, V. P. Chechetkin: The order and correlations in genome sequences of DNK, Achievements of physical sciences (Uspehi fizicheskih nauk), 170 (1) (2000), 57–81 (in Russian).
  • M. A. Nielsen, I. L. Chuang: Quantum computation and quantum information, Cambridge: Cambridge University Press (2001).
  • W. W. Peterson, E. J. Weldon: Error-correcting codes, Cambridge: MIT Press (1972).
  • S. V. Petoukhov: Genetic codes: binary sub-alphabets, bi-symmetric matrices and golden section; Genetic codes: numeric rules of degeneracy and the chronocyclic theory, Symmetry:Culture and Science, 12(1) (2001), 255–306.
  • S. V. Petoukhov: The rules of degeneracy and segregations in genetic codes. The chronocyclic conception and parallels with Mendel’s laws, In M.He, G.Narasimhan, S.Petoukhov (Ed.), Advances in Bioinformatics and its Applications, Series in Mathematical Biology&Medicine, Singapore: World Scientific, 8 (2005), (pp. 512-532).
  • S. V. Petoukhov: Hadamard matrices and quint matrices in matrix presentations of molecular genetic systems, Symmetry: Culture and Science, 16(3) (2005), 247–266.
  • S. V. Petoukhov: Matrix genetics, algebras of the genetic code, noise-immunity, Moscow: RCD (2008) (in Russian).
  • S. V. Peteukhov: Matrix genetics, part 2: the degeneracy of the genetic code and the octave algebra with two quasi-real units (the “Yin-Yang octave algebra”), 1-27, retrieved March, 08, from http://arXiv:0803.3330.
  • A. Shiozaki: A model of distributed type associated memory with quantized Hadamard transform, Biol. Cybern., 38 (1) (1980), 19–22.
  • P. E. Ricci, J. Gielis: From Pythagoras to Fourier and From Geometry to Nature, Athena, Publishing (2021).
  • B. Sklar: Digital communication. Fundamentals and applications, New-York: Prentice Hall (2001).
  • I. Stewart: Life’s other secret: The new mathematics of the living world, New-York: Penguin (1999).
  • A. Yu. Tolmachev: New optic spectrometers, Leningrad: Leningrad University (1976) (in Russian).
  • A. M. Trahtman, V. A. Trahtman: The foundations of the theory of discrete signals on finite intervals, Moscow: Sovetskoie Radio (1975) (in Russian).
  • M. Vose, A. Wright: The simple genetic algorithm and the Walsh transform: Part I, theory, Journal of Evolutionary Computation, 6 (3) (1998), 253–274.
  • M. S. Waterman (Ed.): Mathematical methods for DNA sequences, Florida: CRC Press, Inc (1999).
  • R. Yarlagadda, J. Hershey: Hadamard matrix analysis and synthesis with applications to communications and signal/image processing, . London: Kluwer Academic Publ (1997).
  • L. A. Zalmanzon: Fourier, Walsh and Haar transformations and their application in control, communication and other systems, Moscow: Nauka (1989) (in Russian).
There are 32 citations in total.

Details

Primary Language English
Subjects Approximation Theory and Asymptotic Methods
Journal Section Articles
Authors

Matthew He 0000-0002-7918-621X

Sergey Petoukhov

Early Pub Date December 16, 2024
Publication Date December 16, 2024
Submission Date August 27, 2024
Acceptance Date October 4, 2024
Published in Issue Year 2024 Volume: 7 Issue: Special Issue: AT&A

Cite

APA He, M., & Petoukhov, S. (2024). Hadamard matrices of genetic code and trigonometric functions. Constructive Mathematical Analysis, 7(Special Issue: AT&A), 27-36. https://doi.org/10.33205/cma.1539666
AMA He M, Petoukhov S. Hadamard matrices of genetic code and trigonometric functions. CMA. December 2024;7(Special Issue: AT&A):27-36. doi:10.33205/cma.1539666
Chicago He, Matthew, and Sergey Petoukhov. “Hadamard Matrices of Genetic Code and Trigonometric Functions”. Constructive Mathematical Analysis 7, no. Special Issue: AT&A (December 2024): 27-36. https://doi.org/10.33205/cma.1539666.
EndNote He M, Petoukhov S (December 1, 2024) Hadamard matrices of genetic code and trigonometric functions. Constructive Mathematical Analysis 7 Special Issue: AT&A 27–36.
IEEE M. He and S. Petoukhov, “Hadamard matrices of genetic code and trigonometric functions”, CMA, vol. 7, no. Special Issue: AT&A, pp. 27–36, 2024, doi: 10.33205/cma.1539666.
ISNAD He, Matthew - Petoukhov, Sergey. “Hadamard Matrices of Genetic Code and Trigonometric Functions”. Constructive Mathematical Analysis 7/Special Issue: AT&A (December 2024), 27-36. https://doi.org/10.33205/cma.1539666.
JAMA He M, Petoukhov S. Hadamard matrices of genetic code and trigonometric functions. CMA. 2024;7:27–36.
MLA He, Matthew and Sergey Petoukhov. “Hadamard Matrices of Genetic Code and Trigonometric Functions”. Constructive Mathematical Analysis, vol. 7, no. Special Issue: AT&A, 2024, pp. 27-36, doi:10.33205/cma.1539666.
Vancouver He M, Petoukhov S. Hadamard matrices of genetic code and trigonometric functions. CMA. 2024;7(Special Issue: AT&A):27-36.