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

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*



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



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



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



Coherent X-ray Imaging Instrument

Coherent X-ray Imaging Instrument

1 micronKB system

0.1 micronKB system

Samplechamber

Detector

Wavefrontsensor



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



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



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?




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



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



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



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




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




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



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



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



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



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



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



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



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





1.3.3 Sample environment1.3.3 Sample environment



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



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





1.3.3 Sample environment – cryo-EM stage1.3.3 Sample environment – cryo-EM stage



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



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



Documents

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