phasing of three dimensional diffraction patterns from finite-sized objects
DESCRIPTION
Phasing of Three Dimensional Diffraction Patterns from Finite-Sized Objects. Ian Robinson Ivan Vartanyants Mark Pfeifer John Pitney Garth Williams Sébastien Boutet. Department of Physics University of Illinois SSRL Imaging Workshop, October 2002. Outline. Coherence in Diffraction - PowerPoint PPT PresentationTRANSCRIPT
![Page 1: Phasing of Three Dimensional Diffraction Patterns from Finite-Sized Objects](https://reader033.vdocuments.us/reader033/viewer/2022051517/5681581d550346895dc58254/html5/thumbnails/1.jpg)
I. K. Robinson, SSRL Imaging Workshop, October 2002 1
Phasing of Three Dimensional Diffraction Patterns from Finite-Sized Objects
• Ian Robinson
• Ivan Vartanyants
• Mark Pfeifer
• John Pitney
• Garth Williams
• Sébastien Boutet
Department of Physics University of Illinois
SSRL Imaging Workshop, October 2002
![Page 2: Phasing of Three Dimensional Diffraction Patterns from Finite-Sized Objects](https://reader033.vdocuments.us/reader033/viewer/2022051517/5681581d550346895dc58254/html5/thumbnails/2.jpg)
I. K. Robinson, SSRL Imaging Workshop, October 2002 2
Outline
• Coherence in Diffraction
• The Phase Problem
• Nanocrystal Shapes
• Crystallization of Proteins
• Applications at LCLS
![Page 3: Phasing of Three Dimensional Diffraction Patterns from Finite-Sized Objects](https://reader033.vdocuments.us/reader033/viewer/2022051517/5681581d550346895dc58254/html5/thumbnails/3.jpg)
I. K. Robinson, SSRL Imaging Workshop, October 2002 3
Tomato Bushy Stunt Virus1980
![Page 4: Phasing of Three Dimensional Diffraction Patterns from Finite-Sized Objects](https://reader033.vdocuments.us/reader033/viewer/2022051517/5681581d550346895dc58254/html5/thumbnails/4.jpg)
I. K. Robinson, SSRL Imaging Workshop, October 2002 4
Goals of Coherent Diffraction
• Thermodynamic fluctuations– No ensemble average in CXD
• Probe of structure on nm scale– 1D, 2D and 3D– non-periodic object gives continuous F(q)
• Oversampling (in reciprocal space) permits solution of the phase problem
![Page 5: Phasing of Three Dimensional Diffraction Patterns from Finite-Sized Objects](https://reader033.vdocuments.us/reader033/viewer/2022051517/5681581d550346895dc58254/html5/thumbnails/5.jpg)
I. K. Robinson, SSRL Imaging Workshop, October 2002 5
Lensless X-ray Microscopebased on diffraction from crystal lattice
![Page 6: Phasing of Three Dimensional Diffraction Patterns from Finite-Sized Objects](https://reader033.vdocuments.us/reader033/viewer/2022051517/5681581d550346895dc58254/html5/thumbnails/6.jpg)
I. K. Robinson, SSRL Imaging Workshop, October 2002 6
Coherence at the APSTypical 3rd Generation (undulator) Synchrotron Source
LCLS coherence will be better
Coherence of VER HORIZ LONG Flux
Raw Undulator 35m 9m 0.004m 21012
Si(111) Monochromator 35m 9m 1m 11010
C(111) Monochromator 35m 9m 3m 3109
Coherent region defined by slits
![Page 7: Phasing of Three Dimensional Diffraction Patterns from Finite-Sized Objects](https://reader033.vdocuments.us/reader033/viewer/2022051517/5681581d550346895dc58254/html5/thumbnails/7.jpg)
I. K. Robinson, SSRL Imaging Workshop, October 2002 7
Diffuse Scattering acquires Structure using CXD
![Page 8: Phasing of Three Dimensional Diffraction Patterns from Finite-Sized Objects](https://reader033.vdocuments.us/reader033/viewer/2022051517/5681581d550346895dc58254/html5/thumbnails/8.jpg)
I. K. Robinson, SSRL Imaging Workshop, October 2002 8
Phase Problem: Finite-size Effect
![Page 9: Phasing of Three Dimensional Diffraction Patterns from Finite-Sized Objects](https://reader033.vdocuments.us/reader033/viewer/2022051517/5681581d550346895dc58254/html5/thumbnails/9.jpg)
I. K. Robinson, SSRL Imaging Workshop, October 2002 9
Generic “Error Reduction” method
J. R. Fienup Appl. Opt. 21 2758 (1982)R. W. Gerchberg and W. O. Saxton Optik 35 237 (1972)
![Page 10: Phasing of Three Dimensional Diffraction Patterns from Finite-Sized Objects](https://reader033.vdocuments.us/reader033/viewer/2022051517/5681581d550346895dc58254/html5/thumbnails/10.jpg)
I. K. Robinson, SSRL Imaging Workshop, October 2002 10
“ER” Methods in CrystallograhyR. P. Millane, J. Opt. Soc Am. A 13 725 (1996)
• ‘Positivity’ constraint
• Finite support, molecular envelope
• Solvent flattening
• Molecular replacement
• Non-crystallographic symmetry
• Basis of ‘direct methods’ (Sayre, Bricogne)
• Non-uniqueness is ‘pathologically rare’ (d>1)
![Page 11: Phasing of Three Dimensional Diffraction Patterns from Finite-Sized Objects](https://reader033.vdocuments.us/reader033/viewer/2022051517/5681581d550346895dc58254/html5/thumbnails/11.jpg)
I. K. Robinson, SSRL Imaging Workshop, October 2002 11
![Page 12: Phasing of Three Dimensional Diffraction Patterns from Finite-Sized Objects](https://reader033.vdocuments.us/reader033/viewer/2022051517/5681581d550346895dc58254/html5/thumbnails/12.jpg)
I. K. Robinson, SSRL Imaging Workshop, October 2002 12
Diffraction as a Surface Integral
Annalen der Physik [5] 26 55 (1936)
“Stacheln”
![Page 13: Phasing of Three Dimensional Diffraction Patterns from Finite-Sized Objects](https://reader033.vdocuments.us/reader033/viewer/2022051517/5681581d550346895dc58254/html5/thumbnails/13.jpg)
I. K. Robinson, SSRL Imaging Workshop, October 2002 13
![Page 14: Phasing of Three Dimensional Diffraction Patterns from Finite-Sized Objects](https://reader033.vdocuments.us/reader033/viewer/2022051517/5681581d550346895dc58254/html5/thumbnails/14.jpg)
I. K. Robinson, SSRL Imaging Workshop, October 2002 14
SEMS
• Au blanket film
• Quartz substrate
• Annealed at 950°C for 70 hrs.
![Page 15: Phasing of Three Dimensional Diffraction Patterns from Finite-Sized Objects](https://reader033.vdocuments.us/reader033/viewer/2022051517/5681581d550346895dc58254/html5/thumbnails/15.jpg)
I. K. Robinson, SSRL Imaging Workshop, October 2002 15
Micron-sized gold crystal:(111) Bragg reflection
![Page 16: Phasing of Three Dimensional Diffraction Patterns from Finite-Sized Objects](https://reader033.vdocuments.us/reader033/viewer/2022051517/5681581d550346895dc58254/html5/thumbnails/16.jpg)
I. K. Robinson, SSRL Imaging Workshop, October 2002 16
Symmetrized Data and two best fits
Chisq=0.0005
![Page 17: Phasing of Three Dimensional Diffraction Patterns from Finite-Sized Objects](https://reader033.vdocuments.us/reader033/viewer/2022051517/5681581d550346895dc58254/html5/thumbnails/17.jpg)
I. K. Robinson, SSRL Imaging Workshop, October 2002 17
2D Reconstructionschisquare = 0.0005
![Page 18: Phasing of Three Dimensional Diffraction Patterns from Finite-Sized Objects](https://reader033.vdocuments.us/reader033/viewer/2022051517/5681581d550346895dc58254/html5/thumbnails/18.jpg)
I. K. Robinson, SSRL Imaging Workshop, October 2002 18
3D Diffraction Method
kf
ki
Q=kf - ki
![Page 19: Phasing of Three Dimensional Diffraction Patterns from Finite-Sized Objects](https://reader033.vdocuments.us/reader033/viewer/2022051517/5681581d550346895dc58254/html5/thumbnails/19.jpg)
I. K. Robinson, SSRL Imaging Workshop, October 2002 19
In-situ Study of Crystallization
![Page 20: Phasing of Three Dimensional Diffraction Patterns from Finite-Sized Objects](https://reader033.vdocuments.us/reader033/viewer/2022051517/5681581d550346895dc58254/html5/thumbnails/20.jpg)
I. K. Robinson, SSRL Imaging Workshop, October 2002 20
Experiment at APS Sector 34
![Page 21: Phasing of Three Dimensional Diffraction Patterns from Finite-Sized Objects](https://reader033.vdocuments.us/reader033/viewer/2022051517/5681581d550346895dc58254/html5/thumbnails/21.jpg)
I. K. Robinson, SSRL Imaging Workshop, October 2002 21
“Pink beam” sees CTRs
![Page 22: Phasing of Three Dimensional Diffraction Patterns from Finite-Sized Objects](https://reader033.vdocuments.us/reader033/viewer/2022051517/5681581d550346895dc58254/html5/thumbnails/22.jpg)
I. K. Robinson, SSRL Imaging Workshop, October 2002 22
Ferritin (111) Powder Ring
•50 frames•30sec exposure•0.3sec playback•150x200 pixels of 22.5μm
![Page 23: Phasing of Three Dimensional Diffraction Patterns from Finite-Sized Objects](https://reader033.vdocuments.us/reader033/viewer/2022051517/5681581d550346895dc58254/html5/thumbnails/23.jpg)
I. K. Robinson, SSRL Imaging Workshop, October 2002 23
Conclusions and Outlook
• “Diffuse” scattering acquires fine structure
• Phase problem solved by oversampling
• Images of small particles in 3D
• Applications of CXD at LCLS– (physics) fluctuations at the atomic level– (biology) imaging of viruses and proteins