Determination of the Shape of a Helix Particle Based on Small-Angle X-ray Scattering Data: Modification of the “Simulated Annealing” Algorithm

Capa

Citar

Texto integral

Acesso aberto Acesso aberto
Acesso é fechado Acesso está concedido
Acesso é fechado Somente assinantes

Resumo

The modified “simulated annealing” algorithm implemented in the DAMMINV software allows one to obtain 10 to 15 different nanoparticle models fitting small-angle X-ray scattering data. This method is based on the mode of intermittent weights of the objective function, which balances between minimization of the penalty coefficients, responsible for the model meaningfulness, and the discrepancy between the experimental and model scattering data. The effect of noise on the scattering curves on the quality of three-dimensional helix shape reconstruction has been investigated, and the results are compared with the data obtained using standard programs. The method has been verified on noise-free model data and data with superimposed Poisson noise by the example of a helix particle with a thickness of turns comparable to the characteristic size of the space between them. A comparative analysis of the reconstructed models and the three-dimensional shapes obtained using standard modes of the “simulated annealing” algorithm has been performed.

Sobre autores

V. Grigorev

Shubnikov Institute of Crystallography, Federal Scientific Research Centre “Crystallography and Photonics,” Russian Academy of Sciences, 119333, Moscow, Russia

Email: vasiliy.grigorev.1996@mail.ru
Россия, Москва

P. Konarev

Shubnikov Institute of Crystallography, Federal Scientific Research Centre “Crystallography and Photonics,” Russian Academy of Sciences, 119333, Moscow, Russia; National Research Centre “Kurchatov Institute”, 123182, Moscow, Russia

Email: peter_konarev@mail.ru
Россия, Москва; Россия, Москва

V. Volkov

Shubnikov Institute of Crystallography, Federal Scientific Research Centre “Crystallography and Photonics,” Russian Academy of Sciences, 119333, Moscow, Russia; National Research Centre “Kurchatov Institute,”, 123182, Moscow, Russia

Autor responsável pela correspondência
Email: vvo@crys.ras.ru
Россия, Москва; Россия, Москва

Bibliografia

  1. Свергун Д.И., Фейгин Л.А. Рентгеновское и малоугловое рассеяние. М.: Наука, 1986. 280 с.
  2. Petoukhov M.V., Franke D., Shkumatov A.V. et al. // J. Appl. Cryst. 2012. V. 45. P. 342.https://doi.org/10.1107/S0021889812007662
  3. Kirkpatrick S., Gelatt C.D., Vecchi M.P. // Science. 1983. V. 220. P. 671.https://doi.org/10.1126/science.220.4598.671
  4. Svergun D.I. // Biophys J. 1999. V. 78. P. 2879.https://doi.org/10.1016/S0006-3495(99)77443-6
  5. Franke D., Svergun D.I. // J. Appl. Cryst. 2009. V. 42. P. 342.https://doi.org/10.1107/S0021889809000338
  6. Svergun D.I., Stuhrmann H.B. // Acta Cryst. A. 1991. V. 47. P. 736. https://doi.org/10.1107/S0108767391006414
  7. Svergun D.I., Volkov V.V., Kozin M.B. et al. // Acta Cryst. A. 1996. V. 52. P. 419. https://doi.org/10.1107/S0108767396000177
  8. Shannon C.E., Weaver W. The Mathematical Theory of Communication. University of Illinois Press, 1949. 125 p.
  9. Grant T.D. // Nature Methods. 2018. V. 15. P. 191. https://doi.org/10.1038/nmeth.4581
  10. He H., Liu C., Liu H. // iScience. 2020. V. 23. 100906.
  11. Волков В.В. // Кристаллография. 2021. Т. 66. С. 793. https://doi.org/10.31857/S0023476121050234
  12. Григорьев В.А., Конарев П.В., Волков В.В. // Успехи в химии и химической технологии. 2022. Т. 36. С. 53.
  13. Marsaglia G., Tsang W.W. // SIAM J. Sci. Stat. Comput. 1984. V. 5. P. 349. https://doi.org/10.1137/0905026
  14. Devroye L. // Computing. 1981. V. 26. P. 197. https://doi.org/10.1007/BF02243478
  15. Durbin J., Watson G.S. // Biometrika. 1950. V. 37. P. 409. https://doi.org/10.1093/biomet/37.3-4.409
  16. Durbin J., Watson G.S. // Biometrika. 1951. V. 38. P. 159. https://doi.org/10.2307/2332325
  17. Kozin M., Svergun D. // J. Appl. Cryst. 2001. V. 34. P. 33. https://doi.org/10.1107/S0021889800014126

Arquivos suplementares

Arquivos suplementares
Ação
1. JATS XML
2.

Baixar (306KB)
3.

Baixar (64KB)
4.

Baixar (1MB)
5.

Baixar (325KB)

Declaração de direitos autorais © Russian Academy of Sciences, 2023