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Teoreticheskaya i Matematicheskaya Fizika, 2014, Volume 181, Number 1, Pages 121–154
DOI: https://doi.org/10.4213/tmf8756
(Mi tmf8756)
 

This article is cited in 15 scientific papers (total in 15 papers)

Gauge fields, strings, solitons, anomalies, and the speed of life

A. J. Niemiabc

a Department of Physics, Beijing Institute of Technology, Beijing, China
b Laboratoire de Mathématiques et Physique Théorique, CNRS UMR, Université de Tours, Tours, France
c Department of Physics and Astronomy, Uppsala University, Uppsala, Sweden
References:
Abstract: Joel Cohen proposed that ‘`mathematics is biology’s next microscope, only better; biology is mathematics' next physics, only better." Here, we aim for something even better. We try to combine mathematical physics and biology into a picoscope of life. For this, we merge techniques that were introduced and developed in modern mathematical physics, largely by Ludvig Faddeev, to describe objects such as solitons and Higgs and to explain phenomena such as anomalies in gauge fields. We propose a synthesis that can help to resolve the protein folding problem, one of the most important conundrums in all of science. We apply the concept of gauge invariance to scrutinize the extrinsic geometry of strings in three-dimensional space. We evoke general principles of symmetry in combination with Wilsonian universality and derive an essentially unique Landau–Ginzburg energy that describes the dynamics of a generic stringlike configuration in the far infrared. We observe that the energy supports topological solitons that relate to an anomaly similarly to how a string is framed around its inflection points. We explain how the solitons operate as modular building blocks from which folded proteins are composed. We describe crystallographic protein structures by multisolitons with experimental precision and investigate the nonequilibrium dynamics of proteins under temperature variations. We simulate the folding process of a protein at in vivo speed and with close to picoscale accuracy using a standard laptop computer. With picobiology as next pursuit of mathematical physics, things can only get better.
Keywords: physics of proteins, soliton, nonlinear Schrödinger equation, extrinsic string geometry.
Received: 28.06.2014
English version:
Theoretical and Mathematical Physics, 2014, Volume 181, Issue 1, Pages 1235–1262
DOI: https://doi.org/10.1007/s11232-014-0210-x
Bibliographic databases:
Document Type: Article
Language: Russian
Citation: A. J. Niemi, “Gauge fields, strings, solitons, anomalies, and the speed of life”, TMF, 181:1 (2014), 121–154; Theoret. and Math. Phys., 181:1 (2014), 1235–1262
Citation in format AMSBIB
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  • https://www.mathnet.ru/eng/tmf8756
  • https://doi.org/10.4213/tmf8756
  • https://www.mathnet.ru/eng/tmf/v181/i1/p121
  • This publication is cited in the following 15 articles:
    1. A. M. Begun, A. A. Korneev, A. V. Zorina, “Effect of a Knot on the Thermal Stability of Protein MJ0366: Insights into Molecular Dynamics and Monte Carlo Simulations”, J. Phys. Chem. B, 2025  crossref
    2. D. Bazeia, M. A. Liao, M. A. Marques, “Generalized Maxwell–Higgs vortices in models with enhanced symmetry”, Eur. Phys. J. C, 82:4 (2022)  crossref
    3. D. Melnikov, A. B. F. Neves, “Chern-Simons-Higgs model as a theory of protein molecules”, J. Appl. Phys., 126:24 (2019), 244701  crossref  isi
    4. A. Begun, N. Gerasimenyuk, A. Korneev, A. Molochkov, A. Niemi, “Gauge theory: protein topology and dynamics”, J. Bioenerg. Biomembr., 50:6 (2018), 500–501  isi
    5. Nevena Ilieva, Jiaojiao Liu, Xubiao Peng, Jianfeng He, Antti Niemi, Peicho Petkov, Leandar Litov, Lecture Notes in Computer Science, 10665, Large-Scale Scientific Computing, 2018, 507  crossref
    6. J. Liu, J. Dai, J. He, A. J. Niemi, N. Ilieva, “Multistage modeling of protein dynamics with monomeric Myc oncoprotein as an example”, Phys. Rev. E, 95:3 (2017), 032406  crossref  isi  scopus
    7. A. Molochkov, A. Begun, A. Niemi, “Gauge symmetries and structure of proteins”, XIIth Quark Confinement and the Hadron Spectrum, EPJ Web Conf., 137, eds. Y. Foka, N. Brambilla, V. Kovalenko, EDP Sciences, 2017, UNSP 04004  crossref  isi  scopus
    8. T. Ioannidou, A. J. Niemi, “Poisson hierarchy of discrete strings”, Phys. Lett. A, 380:3 (2016), 333–336  crossref  mathscinet  zmath  adsnasa  isi  scopus
    9. J. Dai, A. J. Niemi, J. He, “Conformational landscape of an amyloid intra-cellular domain and Landau–Ginzburg–Wilson paradigm in protein dynamics”, J. Chem. Phys., 145:4 (2016), 045103  crossref  isi  elib  scopus
    10. X. Peng, A. K. Sieradzan, A. J. Niemi, “Thermal unfolding of myoglobin in the Landau–Ginzburg–Wilson approach”, Phys. Rev. E, 94:6 (2016), 062405  crossref  mathscinet  isi  scopus
    11. N. Ilieva, J. Liu, R. Marinova, P. Petkov, L. Litov, J. He, A. J. Niemi, “Are there folding pathways in the functional stages of intrinsically disordered proteins?”, Application of Mathematics in Technical and Natural Sciences (AMITANS'16), AIP Conf. Proc., 1773, ed. M. Todorov, Amer. Inst. Phys., 2016, 110008  crossref  isi
    12. N. Ilieva, J. Liu, R. Marinova, P. Petkov, L. Litov, J. He, A. J. Niemi, AIP Conference Proceedings, 1773, 2016, 110008  crossref
    13. J. He, J. Dai, J. Li, X. Peng, A. J. Niemi, “Aspects of structural landscape of human islet amyloid polypeptide”, J. Chem. Phys., 142:4 (2015), 045102  crossref  adsnasa  isi  scopus
    14. X. Peng, J. He, A. J. Niemi, “Clustering and percolation in protein loop structures”, BMC Struct. Biol., 15 (2015), 22  crossref  isi  scopus
    15. A. Sinelnikova, A. J. Niemi, M. Ulybyshev, “Phase diagram and the pseudogap state in a linear chiral homopolymer model”, Phys. Rev. E, 92:3 (2015), 032602  crossref  adsnasa  isi  elib  scopus
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    Теоретическая и математическая физика Theoretical and Mathematical Physics
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