coherent single particle imaging (wbs 1.3) j. b. hastings*
DESCRIPTION
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. - PowerPoint PPT PresentationTRANSCRIPT
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J. B. [email protected]
LCLS FAC April 17, 2007Coherent X-Ray Imaging
Coherent Single Particle Imaging(WBS 1.3)J. B. Hastings*
Coherent Single Particle Imaging(WBS 1.3)J. B. Hastings*
![Page 2: Coherent Single Particle Imaging (WBS 1.3) J. B. Hastings*](https://reader036.vdocuments.us/reader036/viewer/2022070419/56815b11550346895dc8bbdd/html5/thumbnails/2.jpg)
J. B. [email protected]
LCLS FAC April 17, 2007Coherent X-Ray Imaging
Science TeamScience Team
Specifications and instrument concept developed with the science team.
The teamJanos Hajdu, Photon Science-SLAC, Upsala University (leader)Henry Chapman, LLNLJohn Miao, UCLA
Specifications and instrument concept developed with the science team.
The teamJanos Hajdu, Photon Science-SLAC, Upsala University (leader)Henry Chapman, LLNLJohn Miao, UCLA
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J. B. [email protected]
LCLS FAC April 17, 2007Coherent X-Ray Imaging
A 3D dataset can be assembled from diffraction patterns in unknown orientations
A 3D dataset can be assembled from diffraction patterns in unknown orientations
Diffraction from a single molecule:
FEL pulse
Noisydiffractionpattern
Combine 105 to 107 measurements into 3D dataset:Classify Average Combine Reconstruct
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
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J. B. [email protected]
LCLS FAC April 17, 2007Coherent X-Ray Imaging
Particle injection
XFEL beam
(focussed, possiblyCompressed)
Optical and x-ray
diagnostics
Pixel detector
Intelligent beam-stop
To mass spectrometer
PotentialParticle orientation
beam
The diffraction imaging interaction chamber and detector arrangementThe diffraction imaging interaction chamber and detector arrangement
Readout and reconstructio
n
Hartman Wavefront
Mask
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J. B. [email protected]
LCLS FAC April 17, 2007Coherent X-Ray Imaging
Coherent X-ray Imaging Instrument
Coherent X-ray Imaging Instrument
1 micronKB system
0.1 micronKB system
Samplechamber
Detector
Wavefrontsensor
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J. B. [email protected]
LCLS FAC April 17, 2007Coherent X-Ray Imaging
Detector geometryDetector geometry
‘Hole’ in detector to passIncident 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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J. B. [email protected]
LCLS FAC April 17, 2007Coherent X-Ray Imaging
X-ray optics (1.3.2)Focusing
K-B systems for 1 and 0.1 micron fociBe 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 fociBe lens for 10 micron focus
Slits, attenuators, ‘pulse picker’Pulse compression optic
1.3.2 X-ray Optics1.3.2 X-ray Optics
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J. B. [email protected]
LCLS FAC April 17, 2007Coherent X-Ray Imaging
1.3.2 X-ray Optics - focusing1.3.2 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 sizeSeparate 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 sizeSeparate 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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J. B. [email protected]
LCLS FAC April 17, 2007Coherent X-Ray Imaging
1.3.2 X-ray Optics - focusing1.3.2 X-ray Optics - focusing
FEL source Offset mirror pair
Monochromator/ pulse-compressor
Sample chamber & diagnostics
Focusing optics Pixel
detectorSample handler
Image reconstruction
zs ≈ 400 m
f1 µm zd
Beam-stop
Be LensKB Mirrors1 µm 0.1 µm
f0.1 µm
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J. B. [email protected]
LCLS FAC April 17, 2007Coherent X-Ray Imaging
Kirkpatrick Baez (KB) focusing mirrorsKirkpatrick 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 resistantGood 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 B4C as coating
Damage resistantGood reflectivity
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J. B. [email protected]
LCLS FAC April 17, 2007Coherent X-Ray Imaging
KB Pair for 1 μm focusGrazing angle 0.2 DegB4C coatingHorz. Mirror 20 cmVert. Mirror 10 cmFocal spot size (FWHM in microns)
Horz: 0.6Vert: 0.9
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J. B. [email protected]
LCLS FAC April 17, 2007Coherent X-Ray Imaging
KB Pair for 0.1 μm focusGrazing angle 0.2 DegB4C coatingHorz. Mirror 20 cmVert. Mirror 10 cmFocal spot size (FWHM in microns)
Horz: 0.097Vert: 0.083
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J. B. [email protected]
LCLS FAC April 17, 2007Coherent X-Ray Imaging
1.3.2 X-ray Optics - focusing1.3.2 X-ray Optics - focusing
FEL source Offset mirror pair
Monochromator/ pulse-compressor
Sample chamber & diagnostics
Focusing optics Pixel
detectorSample handler
Image reconstruction
zs ≈ 400 m
fBe lens zd
Beam-stop
Be LensKB Mirrors1 µm 0.1 µm
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J. B. [email protected]
LCLS FAC April 17, 2007Coherent X-Ray Imaging
1.3.2 X-ray Optics - focusing1.3.2 X-ray Optics - focusing
1.3.2.2 – Beryllium lens focusing optic~ 10µm FWHM focal spot sizePositioning resolution and repeatability to 1 µm
1.3.2.2 – Beryllium lens focusing optic~ 10µm FWHM focal spot sizePositioning resolution and repeatability to 1 µm
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J. B. [email protected]
LCLS FAC April 17, 2007Coherent X-Ray Imaging
http://www.institut2b.physik.rwth-aachen.de/xray/applets/crlcalc.html
Be lens calculation for 10 micron focusFocal spot size including diffraction and roughnessFWHM in microns:
Horiz: 12.0Vert: 10.1
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J. B. [email protected]
LCLS FAC April 17, 2007Coherent X-Ray Imaging
1.3.2 X-ray Optics – pulse picker1.3.2 X-ray Optics – pulse picker
1.3.2.1.2 – Pulse pickerPermit LCLS operation at 120 hzSingle pulses. Useful for samples supported on substratesReduced rate ex. 10 hz operationHigh damage thresholdUse rotating discs, concept already in use at ESRF
1.3.2.1.2 – Pulse pickerPermit LCLS operation at 120 hzSingle pulses. Useful for samples supported on substratesReduced rate ex. 10 hz operationHigh damage thresholdUse rotating discs, concept already in use at ESRF
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J. B. [email protected]
LCLS FAC April 17, 2007Coherent X-Ray Imaging
1.3.2 X-ray Optics - compressor1.3.2 X-ray Optics - compressor
Henry Chapman LLNL
λ
(nm)
d
(nm)
θ φ b Sin β H*
(mm)
Δλw/λ
(%)
0.15 2.0 2.1º -90º +1 0.03 2600 0.5%
476 µm
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J. B. [email protected]
LCLS FAC April 17, 2007Coherent X-Ray Imaging
1.3.3 Sample environment - Vacuum requirements1.3.3 Sample environment - Vacuum requirements
Assumptions:‘unshielded’ beam path of 10 cm for 1 µm2 beambio-molecule ~ 500kDa ~ 5 x 104 atomsBackground scatter 1% 500 atoms in pathAtoms in background gas same z as in the molecule
p ≤ 1 x10-7 torr
Assumptions:‘unshielded’ beam path of 10 cm for 1 µm2 beambio-molecule ~ 500kDa ~ 5 x 104 atomsBackground scatter 1% 500 atoms in pathAtoms in background gas same z as in the molecule
p ≤ 1 x10-7 torr
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J. B. [email protected]
LCLS FAC April 17, 2007Coherent X-Ray Imaging
Sample environment (1.3.3)Sample chamber (vacuum better than 10-7 torr)Detector positioning 50-4000 mm from sampleSample diagnostics - ion and electron ToFCryo-EM stage
Sample environment (1.3.3)Sample chamber (vacuum better than 10-7 torr)Detector positioning 50-4000 mm from sampleSample diagnostics - ion and electron ToFCryo-EM stage
1.3.3 Sample environment – detector position1.3.3 Sample environment – detector position
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J. B. [email protected]
LCLS FAC April 17, 2007Coherent X-Ray Imaging
The number and solid angle of the detector elements are dependent on particle size and resolution
The number and solid angle of the detector elements are dependent on particle size and resolution
N x
x
D = N x / s
fmaxf
Real space samples: xSmallest period sampled: 2x = d or fmax = 1/dOversampling (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
f 2 fmax /N
1/(Ds)
pix f
/(Ds)
Henry Chapman LLNL
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J. B. [email protected]
LCLS FAC April 17, 2007Coherent X-Ray Imaging
Detector size fixes resolutionDetector size fixes resolution
E.g., d = 0.3 nm, s = 2 , = 0.15 nm, N = 760 D ≈57 nmE.g., d = 0.3 nm, s = 2 , = 0.15 nm, N = 760 D ≈57 nm
2 = 30º
zd =1450 mm, 760 pixelsD = 1000 nm, d=5.2 nm
zd = 83.6 mm, 760 pixelsD = 57 nm zd
110 m pixels
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J. B. [email protected]
LCLS FAC April 17, 2007Coherent X-Ray Imaging
Sample environment (1.3.3)Sample chamber (vacuum better than 10-7 torr)Detector positioning 50-4000 mm from sampleSample diagnostics - ion and electron ToFCryo-EM stage
Sample environment (1.3.3)Sample chamber (vacuum better than 10-7 torr)Detector positioning 50-4000 mm from sampleSample diagnostics - ion and electron ToFCryo-EM stage
1.3.3 Sample environment1.3.3 Sample environment
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J. B. [email protected]
LCLS FAC April 17, 2007Coherent X-Ray Imaging
1.3.3 Sample environment - Sample diagnostics1.3.3 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
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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J. B. [email protected]
LCLS FAC April 17, 2007Coherent X-Ray Imaging
System SpecificationsSystem 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,110110 µm pixel size, with central hole (shared LCLS
det.)
Samplediagnostic
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
OpticalCompressor
Reduce pulse length 20 fs pulse length
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J. B. [email protected]
LCLS FAC April 17, 2007Coherent X-Ray Imaging
Sample environment (1.3.3)Sample chamber (vacuum better than 10-7 torr)Detector positioning 50-4000 mm from sampleSample diagnostics - ion and electron ToFCryo-EM stage
Sample environment (1.3.3)Sample chamber (vacuum better than 10-7 torr)Detector positioning 50-4000 mm from sampleSample diagnostics - ion and electron ToFCryo-EM stage
1.3.3 Sample environment – cryo-EM stage1.3.3 Sample environment – cryo-EM stage
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J. B. [email protected]
LCLS FAC April 17, 2007Coherent X-Ray Imaging
1.3.3 Sample environment - Cryo-EM stage1.3.3 Sample environment - Cryo-EM stage
Cryo-EM GoniometerAll motion drives outside vacuumIn use on SR sources for STXMProvides full angular-spatial degrees of freedom to collect 3D data
Cryo-EM GoniometerAll motion drives outside vacuumIn use on SR sources for STXMProvides full angular-spatial degrees of freedom to collect 3D data
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J. B. [email protected]
LCLS FAC April 17, 2007Coherent X-Ray Imaging
SummarySummary
Instrument concept advancing wellNear term issues: detector hole, single versus multiple optics
Sample chamber: design should accommodateRaster system (samples on substrate)Particle injectorCryo-EM stage
Data acquisition-storage-analysis are challengingDiagnostics-wavefront in particular are challenging
Instrument concept advancing wellNear term issues: detector hole, single versus multiple optics
Sample chamber: design should accommodateRaster system (samples on substrate)Particle injectorCryo-EM stage
Data acquisition-storage-analysis are challengingDiagnostics-wavefront in particular are challenging