1. J. B. Hastings jbh@slac.stanford.edu LCLS FAC April 17, 2007 Coherent X-Ray Imaging Coherent Single Particle Imaging (WBS 1.3) J. B. Hastings*

2. J. B. Hastings jbh@slac.stanford.edu LCLS FAC April 17, 2007 Coherent X-Ray Imaging Science Team Specifications and instrument concept developed with the science team. The team Janos Hajdu, Photon Science-SLAC, Upsala University (leader) Henry Chapman, LLNL John Miao, UCLA Specifications and instrument concept developed with the science team. The team Janos Hajdu, Photon Science-SLAC, Upsala University (leader) Henry Chapman, LLNL John Miao, UCLA

3. J. B. Hastings jbh@slac.stanford.edu LCLS FAC April 17, 2007 Coherent X-Ray Imaging A 3D dataset can be assembled from diffraction patterns in unknown orientations Diffraction from a single molecule: FEL pulse Noisy diffraction pattern Combine 10 5 to 10 7 measurements into 3D dataset: ClassifyAverageCombineReconstruct Miao, Hodgson, Sayre, PNAS 98 (2001) Unknown orientation Gösta Huldt, Abraham Szöke, Janos Hajdu (J.Struct Biol, 2003 02-ERD-047) The highest achievable resolution is limited by the ability to group patterns of similar orientation

4. J. B. Hastings jbh@slac.stanford.edu LCLS FAC April 17, 2007 Coherent X-Ray Imaging Particle injection XFEL beam (focussed, possibly Compressed) Optical and x- ray diagnostics Pixel detector Intelligent beam-stop To mass spectrometer PotentialParticle orientation beam The diffraction imaging interaction chamber and detector arrangement Readout and reconstruction Hartman Wavefront Mask

5. J. B. Hastings jbh@slac.stanford.edu LCLS FAC April 17, 2007 Coherent X-Ray Imaging Coherent X-ray Imaging Instrument 1 micron KB system 0.1 micron KB system Sample chamber Detector Wavefront sensor

6. J. B. Hastings jbh@slac.stanford.edu LCLS FAC April 17, 2007 Coherent X-Ray Imaging Detector geometry ‘Hole’ in detector to pass Incident beam Tiled detector, permits variable ‘hole’ size: Ideally the hole is ~ x2 bigger than incident beam at most Dead area at edges of detector tiles limits minimum ‘hole’ size Alternate approach: larger ‘hole’ and a single tile for forward direction Simulations required

7. J. B. Hastings jbh@slac.stanford.edu LCLS FAC April 17, 2007 Coherent X-Ray Imaging X-ray optics (1.3.2) Focusing K-B systems for 1 and 0.1 micron foci Be lens for 10 micron focus Slits, attenuators, ‘pulse picker’ Pulse compression optic X-ray optics (1.3.2) Focusing K-B systems for 1 and 0.1 micron foci Be lens for 10 micron focus Slits, attenuators, ‘pulse picker’ Pulse compression optic 1.3.2 X-ray Optics

8. J. B. Hastings jbh@slac.stanford.edu LCLS FAC April 17, 2007 Coherent X-Ray Imaging 1.3.2 X-ray Optics - focusing Two approaches: separate optical components for 10, 1, 0.1 micron focii or a single 0.1 micorn optic and work out of focus for ‘variable’ spot size Separate optics: Ideally wavefront is ‘flat’ Complicated motion for sample chamber-detector system Single optic: Simple ‘translation of sample varies focus’ Wavefront curavture when ‘out of focus, is this harmful? Two approaches: separate optical components for 10, 1, 0.1 micron focii or a single 0.1 micorn optic and work out of focus for ‘variable’ spot size Separate optics: Ideally wavefront is ‘flat’ Complicated motion for sample chamber-detector system Single optic: Simple ‘translation of sample varies focus’ Wavefront curavture when ‘out of focus, is this harmful?

9. J. B. Hastings jbh@slac.stanford.edu LCLS FAC April 17, 2007 Coherent X-Ray Imaging 1.3.2 X-ray Optics - focusing FEL source Offset mirror pair Monochromator/ pulse- compressor Sample chamber & diagnostics Focusing optics Pixel detector Sample handler Image reconstruction z s ≈ 400 m f 1 µm zdzd Beam- stop Be Lens KB Mirrors 1 µm 0.1 µm f 0.1 µm

10. J. B. Hastings jbh@slac.stanford.edu LCLS FAC April 17, 2007 Coherent X-Ray Imaging Kirkpatrick Baez (KB) focusing mirrors 1.3.2.2 Mirror system (1 µm and 0.1 µm KB) KB mirrors have produced 50 nm focuses of SR(Yamauchi et al., SRI 2006). Can use bent plane mirrors – plane mirrors most accurate polishing. Achromatic focusing. Use B 4 C as coating Damage resistant Good reflectivity 1.3.2.2 Mirror system (1 µm and 0.1 µm KB) KB mirrors have produced 50 nm focuses of SR(Yamauchi et al., SRI 2006). Can use bent plane mirrors – plane mirrors most accurate polishing. Achromatic focusing. Use B 4 C as coating Damage resistant Good reflectivity

11. J. B. Hastings jbh@slac.stanford.edu LCLS FAC April 17, 2007 Coherent X-Ray Imaging KB Pair for 1 μ m focus Grazing angle 0.2 Deg B 4 C coating Horz. Mirror 20 cm Vert. Mirror 10 cm Focal spot size (FWHM in microns) Horz: 0.6 Vert: 0.9

12. J. B. Hastings jbh@slac.stanford.edu LCLS FAC April 17, 2007 Coherent X-Ray Imaging KB Pair for 0.1 μ m focus Grazing angle 0.2 Deg B 4 C coating Horz. Mirror 20 cm Vert. Mirror 10 cm Focal spot size (FWHM in microns) Horz: 0.097 Vert: 0.083

13. J. B. Hastings jbh@slac.stanford.edu LCLS FAC April 17, 2007 Coherent X-Ray Imaging 1.3.2 X-ray Optics - focusing FEL source Offset mirror pair Monochromator/ pulse- compressor Sample chamber & diagnostics Focusing optics Pixel detector Sample handler Image reconstruction z s ≈ 400 m f Be lens zdzd Beam- stop Be Lens KB Mirrors 1 µm 0.1 µm

14. J. B. Hastings jbh@slac.stanford.edu LCLS FAC April 17, 2007 Coherent X-Ray Imaging 1.3.2 X-ray Optics - focusing 1.3.2.2 – Beryllium lens focusing optic ~ 10µm FWHM focal spot size Positioning resolution and repeatability to 1 µm 1.3.2.2 – Beryllium lens focusing optic ~ 10µm FWHM focal spot size Positioning resolution and repeatability to 1 µm

15. J. B. Hastings jbh@slac.stanford.edu LCLS FAC April 17, 2007 Coherent X-Ray Imaging http://www.institut2b.physik.rwth-aachen.de/xray/applets/crlcalc.html Be lens calculation for 10 micron focus Focal spot size including diffraction and roughness FWHM in microns: Horiz: 12.0 Vert: 10.1

16. J. B. Hastings jbh@slac.stanford.edu LCLS FAC April 17, 2007 Coherent X-Ray Imaging 1.3.2 X-ray Optics – pulse picker 1.3.2.1.2 – Pulse picker Permit LCLS operation at 120 hz Single pulses. Useful for samples supported on substrates Reduced rate ex. 10 hz operation High damage threshold Use rotating discs, concept already in use at ESRF 1.3.2.1.2 – Pulse picker Permit LCLS operation at 120 hz Single pulses. Useful for samples supported on substrates Reduced rate ex. 10 hz operation High damage threshold Use rotating discs, concept already in use at ESRF

17. J. B. Hastings jbh@slac.stanford.edu LCLS FAC April 17, 2007 Coherent X-Ray Imaging 1.3.2 X-ray Optics - compressor Henry Chapman LLNL λ (nm) d (nm) θφbSin βH * (mm) Δλ w /λ (%) 0.152.02.1º-90º+10.0326000.5% 476 µm

18. J. B. Hastings jbh@slac.stanford.edu LCLS FAC April 17, 2007 Coherent X-Ray Imaging 1.3.3 Sample environment - Vacuum requirements Assumptions: ‘unshielded’ beam path of 10 cm for 1 µm 2 beam bio-molecule ~ 500kDa ~ 5 x 10 4 atoms Background scatter 1% 500 atoms in path Atoms in background gas same z as in the molecule p ≤ 1 x10 -7 torr Assumptions: ‘unshielded’ beam path of 10 cm for 1 µm 2 beam bio-molecule ~ 500kDa ~ 5 x 10 4 atoms Background scatter 1% 500 atoms in path Atoms in background gas same z as in the molecule p ≤ 1 x10 -7 torr

19. J. B. Hastings jbh@slac.stanford.edu LCLS FAC April 17, 2007 Coherent X-Ray Imaging Sample environment (1.3.3) Sample chamber (vacuum better than 10 -7 torr) Detector positioning 50-4000 mm from sample Sample diagnostics - ion and electron ToF Cryo-EM stage Sample environment (1.3.3) Sample chamber (vacuum better than 10 -7 torr) Detector positioning 50-4000 mm from sample Sample diagnostics - ion and electron ToF Cryo-EM stage 1.3.3 Sample environment – detector position

20. J. B. Hastings jbh@slac.stanford.edu LCLS FAC April 17, 2007 Coherent X-Ray Imaging The number and solid angle of the detector elements are dependent on particle size and resolution N  x xx D = N  x / s f max ff Real space samples:  x Smallest period sampled: 2  x = d or f max = 1/d Oversampling (per dimension): s Array size: N = D s /  x = 2 D s / d E.g. D = 57 nm, d = 0.3 nm, s = 2  N = 760 = 0.15 nm  pix = 1.3 mrad Henry Chapman LLNL

21. J. B. Hastings jbh@slac.stanford.edu LCLS FAC April 17, 2007 Coherent X-Ray Imaging Detector size fixes resolution E.g., d = 0.3 nm, s = 2, = 0.15 nm, N = 760  D ≈57 nm 2 = 30º z d = 1450 mm, 760 pixels D = 1000 nm, d=5.2 nm z d = 83.6 mm, 760 pixels D = 57 nm zdzd 110  m pixels

22. J. B. Hastings jbh@slac.stanford.edu LCLS FAC April 17, 2007 Coherent X-Ray Imaging Sample environment (1.3.3) Sample chamber (vacuum better than 10 -7 torr) Detector positioning 50-4000 mm from sample Sample diagnostics - ion and electron ToF Cryo-EM stage Sample environment (1.3.3) Sample chamber (vacuum better than 10 -7 torr) Detector positioning 50-4000 mm from sample Sample diagnostics - ion and electron ToF Cryo-EM stage 1.3.3 Sample environment

23. J. B. Hastings jbh@slac.stanford.edu LCLS FAC April 17, 2007 Coherent X-Ray Imaging 1.3.3 Sample environment - Sample diagnostics 3 x10 12 photons in 100 nm spot (a) 2 fs pulse (b) 10 fs pulse (c) 50 fs pulse Provide diagnostics to understand the ‘explosion’ Electron and Ion ToF detectors able to resolve single atom fragments (1 AMU) 1/1000 in electron energy 3 x10 12 photons in 100 nm spot (a) 2 fs pulse (b) 10 fs pulse (c) 50 fs pulse Provide diagnostics to understand the ‘explosion’ Electron and Ion ToF detectors able to resolve single atom fragments (1 AMU) 1/1000 in electron energy

24. J. B. Hastings jbh@slac.stanford.edu LCLS FAC April 17, 2007 Coherent X-Ray Imaging System Specifications ItemPurposeSpecification Focusing optics Produce required flux.Focal spot sizes of 10,1, 0.1 micron Sample chamber Vacuum sample env., reduced background Vacuum below 10 -7 torr DetectorMeasurement of diffraction pattern 2-D, 760 x 760 pixels, 110  110 µm pixel size, with central hole (shared LCLS det.) Sample diagnostic Ion TOF analysis of sample fragments Resolution of one mass unit up to 100 AMU Sample diagnostic Electron TOF analysis of sample fragments Resolution of 10 -3 Optical Compressor Reduce pulse length20 fs pulse length

25. J. B. Hastings jbh@slac.stanford.edu LCLS FAC April 17, 2007 Coherent X-Ray Imaging Sample environment (1.3.3) Sample chamber (vacuum better than 10 -7 torr) Detector positioning 50-4000 mm from sample Sample diagnostics - ion and electron ToF Cryo-EM stage Sample environment (1.3.3) Sample chamber (vacuum better than 10 -7 torr) Detector positioning 50-4000 mm from sample Sample diagnostics - ion and electron ToF Cryo-EM stage 1.3.3 Sample environment – cryo-EM stage

26. J. B. Hastings jbh@slac.stanford.edu LCLS FAC April 17, 2007 Coherent X-Ray Imaging 1.3.3 Sample environment - Cryo-EM stage Cryo-EM Goniometer All motion drives outside vacuum In use on SR sources for STXM Provides full angular- spatial degrees of freedom to collect 3D data Cryo-EM Goniometer All motion drives outside vacuum In use on SR sources for STXM Provides full angular- spatial degrees of freedom to collect 3D data

27. J. B. Hastings jbh@slac.stanford.edu LCLS FAC April 17, 2007 Coherent X-Ray Imaging Summary Instrument concept advancing well Near term issues: detector hole, single versus multiple optics Sample chamber: design should accommodate Raster system (samples on substrate) Particle injector Cryo-EM stage Data acquisition-storage-analysis are challenging Diagnostics-wavefront in particular are challenging Instrument concept advancing well Near term issues: detector hole, single versus multiple optics Sample chamber: design should accommodate Raster system (samples on substrate) Particle injector Cryo-EM stage Data acquisition-storage-analysis are challenging Diagnostics-wavefront in particular are challenging

28. J. B. Hastings jbh@slac.stanford.edu LCLS FAC April 17, 2007 Coherent X-Ray Imaging