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Helix-coil transition in terms of Potts-like spins

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Abstract

In the spin model of a helix-coil transition in polypeptides a preferred value of spin has to be assigned to the helical conformation, in order to account for different symmetries of the helical vs. the coil states, leading thus to the Generalized Model of Polypeptide Chain (GMPC) Hamiltonian as opposed to the Potts model Hamiltonian, both with many-body interactions. Comparison of explicit transfer matrix secular equations of the Potts model and the GMPC model reveals that the largest eigenvalue of the Potts model with Δ many-body interactions coincides with the largest eigenvalue of the GMPC model with Δ − 1 many-body interactions, indicating the identity of both free energies. In distinction, the second largest eigenvalues in both models do not coincide, indicating a different behavior for the spatial correlation length that in its turn defines the width of the helix-coil transition interval. We explore in detail the thermodynamic consequences, resulting from spin models with and without the built-in spin anisotropy, that should indicate which model to favour as a more appropriate description of the equilibrium physical properties pertaining to the helix-coil transition.

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Author notes

  1. Artem Badasyan

    Present address: Materials Research Laboratory, University of Nova Gorica, Vipavska 13, SI-5000, Nova Gorica, Slovenia

Authors and Affiliations

  1. Department of Theoretical Physics, J. Stefan Institute, Jamova 39, SI-1000, Ljubljana, Slovenia

    Artem Badasyan & Rudolf Podgornik

  2. Dipartimento di Scienze Molecolari e Nanosistemi, Università Ca’ Foscari Venezia, Calle Larga S. Marta DD2137, I-30123, Venezia, Italy

    Achille Giacometti

  3. Department of Physics, Faculty of Mathematics and Physics, University of Ljubljana, SI-1000, Ljubljana, Slovenia

    Rudolf Podgornik

  4. Department of Molecular Physics, Yerevan State University, A. Manougian Str. 1, 375025, Yerevan, Armenia

    Yevgeni Mamasakhlisov & Vladimir Morozov

Authors
  1. Artem Badasyan
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  2. Achille Giacometti
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  3. Rudolf Podgornik
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  4. Yevgeni Mamasakhlisov
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  5. Vladimir Morozov
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Correspondence to Artem Badasyan.

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Badasyan, A., Giacometti, A., Podgornik, R. et al. Helix-coil transition in terms of Potts-like spins. Eur. Phys. J. E 36, 46 (2013). https://doi.org/10.1140/epje/i2013-13046-7

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  • DOI: https://doi.org/10.1140/epje/i2013-13046-7

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