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Volume 11   Issue 2   Year 2016
Bobkov S.A., Teslyuk A.B., Ilyin V.A., Vartanyants I.A.

Diffraction Images Classification for Biological Particles With Different Symmetry Types in Coherent X-Ray Diffraction Imaging Experiments

Mathematical Biology & Bioinformatics. 2016;11(2):299-310.

doi: 10.17537/2016.11.299.

References

 

  1. Schmahl G. X-ray microscopy. Nuclear Instruments and Methods in Physics Research. 1983;208(1):361-365. doi: 10.1016/0167-5087(83)91151-1
  2. Sayre D., Howells M., Kirz J., Rarback H. X-ray microscopy ii. Springer series in optical sciences. 1988;56(272).
  3. Kirz J., Jacobsen C., Howells M. Soft x-ray microscopes and their biological applications. Quarterly reviews of biophysics. 1995;28(1):33-130. doi: 10.1017/S0033583500003139
  4. Aoki S., Kikuta S. X-ray holographic microscopy. Japanese Journal of Applied Physics. 1974;13(9):1385. doi: 10.1143/JJAP.13.1385
  5. Eichert D., Gregoratti L., Kaulich B., Marcello A., Melpignano P., Quaroni L., Kiskinova M. Imaging with spectroscopic micro-analysis using synchrotron radiation. Analytical and bioanalytical chemistry. 2007;389(4):1121-1132. doi: 10.1007/s00216-007-1532-4
  6. Giacovazzo C., Monaco H.L., Artioli G., Vitebro D., Ferraris G., Gilli G., Zanotti G., Catti M. Fundamentals of crystallography. 2002.
  7. Henderson R. The potential and limitations of neutrons, electrons and x-rays for atomic resolution microscopy of unstained biological molecules. Quarterly Reviews of Biophysics. 1995;28:171-193. doi: 10.1017/S003358350000305X
  8. Howells M.R., Beets T., Chapman H.N., Cui C., Holton J.M., Jacobsen C.J., Kirz J., Lima E., Marchesini S., Miao H. et al. An assessment of the resolution limitation due to radiation-damage in {X-ray diffraction microscopy. Journal of Electron Spectroscopy and Related Phenomena. 2009;170(4). doi: 10.1016/j.elspec.2008.10.008
  9. Miao J., Ishikawa T., Johnson B., Anderson E.H., Lai B. θ Hodgson K. High resolution 3d x-ray diffraction microscopy. Physical review letters. 2002;89(8):088303. doi: 10.1103/PhysRevLett.89.088303
  10. Chapman H.N., Nugent K.A. Coherent lensless x-ray imaging. Nature Photonics. 2010;4(12):833-839. doi: 10.1038/nphoton.2010.240
  11. Chapman H.N., Barty A., Bogan M.J., Boutet S., Frank M., Hau-Riege S.P., Marchesini S., Woods B.W., Bajt S., Benner W.H et al. Femtosecond diffractive imaging with a soft-x-ray free-electron laser. Nat Phys. 2006;2(12):839-843. doi: 10.1038/nphys461
  12. Gaffney K.J., Chapman H.N. Imaging Atomic Structure and Dynamics with Ultrafast X-ray Scattering. Science. 2007;316:1444. doi: 10.1126/science.1135923
  13. Seibert M.M., Ekeberg T., Maia F., Svenda M., Andreasson J., Jonsson O., Odic D., Iwan B., Rocker A., Westphal D et al. Single mimivirus particles intercepted and imaged with an x-ray laser. Nature. 2011;470(7332):78-81. doi: 10.1038/nature09748
  14. Mancuso A.P., Yefanov O M., Vartanyants I.A. Coherent diffractive imaging of biological samples at synchrotron and free electron laser facilities. J. Biotechnology. 2010;149(229). doi: 10.1016/j.jbiotec.2010.01.024
  15. Robinson I.K., Vartanyants I.A., Williams G.J., Pfeifer M.A., Pitney J.A. Reconstruction of the shapes of gold nanocrystals using coherent x-ray diffraction. Physical Review Letters. 2001;87(19):195505. doi: 10.1103/PhysRevLett.87.195505
  16. Vartanyants I.A., Robinson I.K. Partial coherence effects on the imaging of small crystals using coherent x-ray diffraction. Journal of Physics: Condensed Matter. 2001;13(47):10593. doi: 10.1088/0953-8984/13/47/305
  17. Vartanyants I.A., Robinson I.K. Origins of decoherence in coherent x-ray diffraction experiments. Optics communications. 2003;222(1):29-50. doi: 10.1016/S0030-4018(03)01558-X
  18. Williams G.J., Quiney H.M., Peele A.G., Nugent K.A. Coherent diffractive imaging and partial coherence. Physical Review B. 2007;75(10):104102. doi: 10.1103/PhysRevB.75.104102
  19. Neutze R., Wouts R., van der Spoel D., Weckert E., Hajdu J. Potential for biomolecular imaging with femtosecond x-ray pulses. Nature. 2000;406(6797):752-757. doi: 10.1038/35021099
  20. Miao J., Sayre D., Chapman H.N. Phase retrieval from the magnitude of the fourier transforms of nonperiodic objects. Journal of the Optical Society of America A. 1998;15(6):1662-1669. doi: 10.1364/JOSAA.15.001662
  21. Fienup J.R. Reconstruction of an object from the modulus of its fourier transform. Optics letters. 1978;3(1):27-29. doi: 10.1364/OL.3.000027
  22. Fienup J.R. Phase retrieval algorithms: a comparison. Appl. Opt. 1982;21(15):2758. doi: 10.1364/AO.21.002758
  23. Chen C., Miao J., Wang C.W., Lee T.K. Application of optimization technique to noncrystalline x-ray diffraction microscopy: Guided hybrid input-output method. Physical Review B. 2007;76(6):064113. doi: 10.1103/PhysRevB.76.064113
  24. Marchesini S., He H., Chapman H.N., Hau-Riege S.P., Noy A., Howells M.R., Weierstall U., Spence J.C.H. X-ray image reconstruction from a diffraction pattern alone. Physical Review B. 2003;68(14):140101. doi: 10.1103/PhysRevB.68.140101
  25. Shen Q., Bazarov I., Thibault P. Diffractive imaging of nonperiodic materials with future coherent x-ray sources. Journal of synchrotron radiation. 2004;11(5):432-438. doi: 10.1107/S0909049504016772
  26. Bergh M., Huldt G., Timneanu N., Maia F., Hajdu J. Feasibility of imaging living cells at subnanometer resolutions by ultrafast x-ray diffraction. Quarterly reviews of biophysics. 2008;41(3-4):181-204. doi: 10.1017/S003358350800471X
  27. Huang X., Nelson J., Kirz J., Lima E., Marchesini S., Miao H., Neiman A.M., Shapiro D., Steinbrener J., Stewart A. et al. Soft x-ray diffraction microscopy of a frozen hydrated yeast cell. Physical review letters. 2009;103(19):198101. doi: 10.1103/PhysRevLett.103.198101
  28. Miao J., Hodgson K., Ishikawa T., Larabell C.A., LeGros M.A., Nishino Y. Imaging whole escherichia coli bacteria by using single-particle x-ray diffraction. Proceedings of the National Academy of Sciences. 2003;100(1):110-112. doi: 10.1073/pnas.232691299
  29. Shapiro D., Thibault P., Beetz T., Elser V., Howells M., Jacobsen C., Kirz J., Lima E., Miao H., Neiman A.M. et al. Biological imaging by soft x-ray diffraction microscopy. Proceedings of the National Academy of Sciences. 2005;102(43):15343-15346. doi: 10.1073/pnas.0503305102
  30. Song C., Jiang H., Mancuso A., Amirbekian B., Peng L., Sun R., Shah S.S., Zhou Z.H., Ishikawa T., Miao J. Quantitative imaging of single, unstained viruses with coherent x rays. Physical review letters. 2008;101(15):158101. doi: 10.1103/PhysRevLett.101.158101
  31. Nishino Y., Takahashi Y., Imamoto N., Ishikawa T., Maeshima K. Three-dimensional visualization of a human chromosome using coherent x-ray diffraction. Physical review letters. 2009;102(1):018101. doi: 10.1103/PhysRevLett.102.018101
  32. Huang X., Miao H., Steinbrener J., Nelson J., Shapiro D., Stewart A., Turner J., Jacobsen Ρ. Signal-to-noise and radiation exposure considerations in conventional and diffraction x-ray microscopy. Opt. Express. 2009;17(16):13541-13553. doi: 10.1364/OE.17.013541
  33. Bobkov S.A., Teslyuk A.B., Kurta R.P., Gorobtsov O.Y., Yefanov O.M., Ilyin V.A., Senin R.A., Vartanyants I.A. Sorting algorithms for single-particle imaging experiments at x-ray free-electron lasers. Journal of Synchrotron Radiation. 2015;22:1345-1352. doi: 10.1107/S1600577515017348
  34. Cortes C., Vapnik V. Support-vector networks. Machine Learning. 1995;20(3):273-297. doi: 10.1007/BF00994018
  35. Altarelli M., Kurta R.P., Vartanyants I.A. X-ray cross-correlation analysis and local symmetries of disordered systems: General theory. Physical Review B. 2010;82:104207. doi: 10.1103/PhysRevB.82.104207
  36. Kurta R.P., Altarelli M., Weckert E., Vartanyants I.A. X-ray cross-correlation analysis applied to disordered two-dimensional systems. Physical Review B. 2012;85(18):184204. doi: 10.1103/PhysRevB.85.184204
  37. Kurta R.P., Altarelli M., Vartanyants I.A. X-ray cross-correlation analysis of disordered ensembles of particles: Potentials and limitations. Adv. Cond. Matt. Phys.. 2013;2013:959835.
  38. Kurta R.P., Dronyak R., Altarelli M., Weckert E., Vartanyants I.A. Solution of the phase problem for coherent scattering from a disordered system of identical particles. New journal of physics. 2013;15(1):013059. doi: 10.1088/1367-2630/15/1/013059
  39. Van Molle I., Thomann A., Buckley D.L., So E.C., Lang S., Crews C.M., Ciulli A. Dissecting fragment-based lead discovery at the von hippel-lindau protein: hypoxia inducible factor 1$alpha$ protein-protein interface. Chemistry & biology. 2012;19(10):1300-1312. doi: 10.1016/j.chembiol.2012.08.015
  40. Forster A., Masters E.I., Whitby F.G., Robinson H., Hill Ρ.P. The 1.9 å structure of a proteasome-11s activator complex and implications for proteasome-pan/pa700 interactions. Molecular cell. 2005;18(5):589-599. doi: 10.1016/j.molcel.2005.04.016
  41. Bieger B., Essen L., Oesterhelt D. Crystal structure of halophilic dodecin: a novel, dodecameric flavin binding protein from halobacterium salinarum. Structure. 2003;11(4):375-385. doi: 10.1016/S0969-2126(03)00048-0
  42. Kim K.K., Kim R., Kim S. Crystal structure of a small heat-shock protein. Nature. 1998;394(6693):595-599. doi: 10.1038/29106
  43. Marvin D.A. Model-building studies of inovirus: genetic variations on a geometric theme. International journal of biological macromolecules. 1990;12(2):125-138. doi: 10.1016/0141-8130(90)90064-H
  44. Berman H.M., Westbrook J., Feng Z., Gilliland G., Bhat T.N., Weissig H., Shindyalov I.N., Bourne P.E. The protein data bank. Nucleic acids research. 2000;28(1):235-242. doi: 10.1093/nar/28.1.235
  45. Bobkov S.A., Teslyuk A.B., Ilyin V.A. Adaptation of spsim for simulation of diffraction images in xfel experiments. Procedia Computer Science. 2015;66:158-165. doi: 10.1016/j.procs.2015.11.019
Table of Contents
Original Article
Math. Biol. Bioinf.
2016;11(2):299-310
doi: 10.17537/2016.11.299
published in Russian

Abstract (rus.)
Abstract (eng.)
Full text (rus., pdf)
References

 
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