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Coherent Single Particle Imaging (WBS 1.3) J. B. Hastings*

Coherent Single Particle Imaging (WBS 1.3) J. B. Hastings*. 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.

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Coherent Single Particle Imaging (WBS 1.3) J. B. Hastings*

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  1. Coherent Single Particle Imaging(WBS 1.3)J. B. Hastings*

  2. 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

  3. A 3D dataset can be assembled from diffraction patterns in unknown orientations Diffraction from a single molecule: Noisy diffraction pattern FEL pulse Unknown orientation Combine 105 to 107 measurements into 3D dataset: Classify Average Combine Reconstruct The highest achievable resolution is limited by the ability to group patterns of similar orientation Miao, Hodgson, Sayre, PNAS 98 (2001) Gösta Huldt, Abraham Szöke, Janos Hajdu (J.Struct Biol, 2003 02-ERD-047)

  4. The diffraction imaging interaction chamber and detector arrangement Particle injection Pixel detector Intelligent beam-stop Hartman Wavefront Mask XFEL beam (focussed, possibly Compressed) PotentialParticle orientation beam Optical and x-ray diagnostics Readout and reconstruction To mass spectrometer

  5. Coherent X-ray Imaging Instrument Coherent X-ray Imaging Instrument Wavefront sensor 1 micron KB system 0.1 micron KB system Sample chamber Detector

  6. 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. 1.3.2 X-ray Optics • 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

  8. 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?

  9. 1.3.2 X-ray Optics - focusing Focusing optics Pixel detector Beam-stop Sample handler KB Mirrors 1 µm 0.1 µm Be Lens Monochromator/ pulse-compressor Offset mirror pair FEL source Sample chamber & diagnostics f1 µm f0.1 µm zd zs ≈ 400 m Image reconstruction

  10. Kirkpatrick Baez (KB) focusing mirrors • 1.3.2.2 Mirror system (1 µm and 0.1µm 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 B4C as coating • Damage resistant • Good reflectivity

  11. KB Pair for 1 μm focus Grazing angle 0.2 Deg B4C coating Horz. Mirror 20 cm Vert. Mirror 10 cm Focal spot size (FWHM in microns) Horz: 0.6 Vert: 0.9

  12. KB Pair for 0.1 μm focus Grazing angle 0.2 Deg B4C coating Horz. Mirror 20 cm Vert. Mirror 10 cm Focal spot size (FWHM in microns) Horz: 0.097 Vert: 0.083

  13. 1.3.2 X-ray Optics - focusing Focusing optics Pixel detector Beam-stop Sample handler KB Mirrors 1 µm 0.1 µm Be Lens Monochromator/ pulse-compressor Offset mirror pair FEL source Sample chamber & diagnostics fBe lens zd zs ≈ 400 m Image reconstruction

  14. 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

  15. Be lens calculation for 10 micron focus Focal spot size including diffraction and roughness FWHM in microns: Horiz: 12.0 Vert: 10.1 http://www.institut2b.physik.rwth-aachen.de/xray/applets/crlcalc.html

  16. 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

  17. 1.3.2 X-ray Optics - compressor 476 µm Henry Chapman LLNL

  18. 1.3.3 Sample environment - Vacuum requirements • Assumptions: • ‘unshielded’ beam path of 10 cm for 1 µm2 beam • bio-molecule ~ 500kDa ~ 5 x 104 atoms • Background scatter 1% 500 atoms in path • Atoms in background gas same z as in the molecule p ≤ 1 x10-7 torr

  19. 1.3.3 Sample environment – detector position • 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

  20. The number and solid angle of the detector elements are dependent on particle size and resolution N x fmax f x D = N x / s Real space samples:x Smallest period sampled: 2x = d or fmax = 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. Detector size fixes resolution E.g., d = 0.3 nm, s = 2 , = 0.15 nm, N = 760 D ≈57 nm 110 m pixels 2= 30º zd= 83.6 mm, 760 pixels D = 57 nm zd =1450 mm, 760 pixels D = 1000 nm, d=5.2 nm zd

  22. 1.3.3 Sample environment • 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

  23. 1.3.3 Sample environment - Sample diagnostics • 3 x1012 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. System Specifications

  25. 1.3.3 Sample environment – 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

  26. 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

  27. 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

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