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

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Coherent Single Particle Imaging(WBS 1.3)J. B.
Hastings
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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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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)
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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
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Wavefront sensor
1 micron KB system
0.1 micron KB system
Sample chamber
Detector
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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

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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

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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?

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1.3.2 X-ray Optics - focusing
Focusing optics
Pixel detector
Beam-stop
Sample handler
KB Mirrors 1 µm 0.1 µm
Be Lens
Offset mirror pair
Monochromator/ pulse-compressor
FEL source
Sample chamber diagnostics
f1 µm
zd
f0.1 µm
zs 400 m
Image reconstruction
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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 B4C as coating
• Damage resistant
• Good reflectivity

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

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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/a
pplets/crlcalc.html
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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

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1.3.2 X-ray Optics - compressor
476 µm
? (nm) d (nm) ? f b Sin ß H (mm) ??w/? ()
0.15 2.0 2.1º -90º 1 0.03 2600 0.5
Henry Chapman LLNL
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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

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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

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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
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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, d5.2 nm
zd
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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

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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

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System Specifications
Item Purpose Specification
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
Detector Measurement 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 length 20 fs pulse length
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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

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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

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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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