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

V. A. Grigorev; Григорьев В. А.; P. V. Konarev; Конарев П. В.; V. V. Volkov; Волков В. В.

doi:10.31857/S0023476123600295

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

Autores: Grigorev V.A.¹, Konarev P.V.¹^,2, Volkov V.V.¹^,3
Afiliações:
1. Shubnikov Institute of Crystallography, Federal Scientific Research Centre “Crystallography and Photonics,” Russian Academy of Sciences, 119333, Moscow, Russia
2. National Research Centre “Kurchatov Institute”, 123182, Moscow, Russia
3. National Research Centre “Kurchatov Institute,”, 123182, Moscow, Russia
Edição: Volume 68, Nº 6 (2023)
Páginas: 941-945
Seção: ДИФРАКЦИЯ И РАССЕЯНИЕ ИОНИЗИРУЮЩИХ ИЗЛУЧЕНИЙ
URL: https://rjdentistry.com/0023-4761/article/view/673301
DOI: https://doi.org/10.31857/S0023476123600295
EDN: https://elibrary.ru/FZZKKB
ID: 673301

Citar

Texto integral

Acesso aberto
Acesso é fechado

Acesso está concedido
Acesso é fechado

Somente assinantes

Resumo
Sobre autores
Bibliografia
Arquivos suplementares
Estatísticas

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.

Bibliografia

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