1. SSRL Workshop, 10/8-9/2002 1 STXM and diffraction-imaging - the view from Stony Brook Janos Kirz, Stony Brook University on leave for 2002-2003 at the ALS With special thanks to Chris Jacobsen

2. SSRL Workshop, 10/8-9/2002 2

3. 3 X-ray focusing: Fresnel zone plates Diffractive optics: radially varied grating spacing Largest diffraction angle is given by outermost (finest) zone width  rN as  = /(2  rN ) Rayleigh resolution is then  t =0.61 /(  ) =1.22  rN Zones must be positioned to ~1/3 width over diameter (10 nm in 100  m, or 1:10 4 ) Central stop and order sorting aperture (OSA) to isolate first order focus

4. SSRL Workshop, 10/8-9/2002 4 Zone plates by electron beam lithography A. Stein, B. Hornberger, M. Lu, S. Spector (PhD 1998), C. Jacobsen D. Tennant (Lucent) JEOL JBX-6000FS: 1 nA into 7 nm spot, 2.5 nm over 80  m, 50 keV JEOL JBX-9300FS: 1 nA into 4 nm spot, 1.2 nm over 500  m, 100 keV A. Stein and JBX-9300FS E-beam resistRIE of Ge maskRIE of polymerElectroplating 40 nm zones in 120 nm Ni

5. SSRL Workshop, 10/8-9/2002 5 STXM IV: the new room temperature microscope M. Feser et al., Stony Brook Two identical copies now in operation Sealed, helium-filled chamber: makes E>400 eV accessible Improved scanning stage: higher resolution Motorized detector platform Laser interferometer and fast scanning upgrade underway

6. SSRL Workshop, 10/8-9/2002 6 Why I like scanning? XANES spectroscopy Multi-channel detector Low dose, large area overview scans –Convenient correlation to visible light microscopy Wet, dry, or cryo specimens Minimizes radiation dose Quantitative

7. SSRL Workshop, 10/8-9/2002 7 Drawbacks Slower than full-field microscopy Hungry for coherent photons –(but note new STXM at ALS bending magnet!) Thickness restrictions in transmission mode

8. SSRL Workshop, 10/8-9/2002 8 Wet specimens One can get 50-80% transmission through 100 nm Si, Si 3 N 4 Place 1  l fluid droplet on 1 cm 2, sandwich between two thin windows: gives 10  m fluid thickness Let fluid wet one window (~1-2  m thickness by wetting), place another 1 mm away to preserve air hydration

9. SSRL Workshop, 10/8-9/2002 9 Imaging of wet specimens NIL 8 fibroblast (glutaraldehyde fixed): V. Oehler, J. Fu, C. Jacobsen Human sperm (unfixed): S. Wirick, C. Jacobsen, Y. Sheynkin

10. SSRL Workshop, 10/8-9/2002 10 Spectromicroscopy by image stacks Acquire sequence of images over XANES spectral region; automatically align using Fourier cross-correlations; extract spectra. C. Jacobsen et al., J. Microscopy 197, 173 (2000). Images at N =150 energies are common. IDL-based analysis tools are made available

11. SSRL Workshop, 10/8-9/2002 11 Analysis of stacks C. Jacobsen and students Singular Value Decomposition –(components and model spectra known) Principal Component Analysis; Cluster analysis –(components unknown)

12. SSRL Workshop, 10/8-9/2002 12 Detector development: segmented, current mode Silicon drift detector Simultaneous recording of bright field, dark field, differential phase and interference contrast (Polack & Joyeux) No significant upper limit to signal rate. Acceptable dark noise (~8 photons/msec equivalent; room temperature) High quantum efficiency (>90%) M. Feser, C. Jacobsen (Stony Brook); P. Rehak, G. de Geronimo (BNL Instrumentation); L. Strüder, P. Holl (MPI München) Assembly: 40 mm across Active area: 600  m

13. SSRL Workshop, 10/8-9/2002 13 Segmented silicon drift detector Corner of silicon nitride window: silicon at ~45° wall slope forms a prism Refraction of x-ray beam in opposite direction from visible light prisms X-ray refractive index: n=1-  -i  All channels acquired simultaneously

14. SSRL Workshop, 10/8-9/2002 14 Amplitude, phase contrast imaging in STXM Use segmented detector for phase reconstruction. Finest features ~30 nm. Beam noise is normalized out for free! Note organic “crud” M. Feser, PhD thesis 1  m

15. SSRL Workshop, 10/8-9/2002 15 Mapping protein and DNA in sperm X. Zhang et al., J. Struct. Bio. 116, 335 (1996) New project to study human sperm just beginning!

16. SSRL Workshop, 10/8-9/2002 16 Applications @ NSLS X1A Sperm morphology / infertility Jacobsen, USB Interplanetary dust, meteoritics Flynn, SUNY/Plattsburgh Organic geochemistry / wood, coal Cody, Carnegie Inst. Nuclear waste transport Schaefer, Karlsruhe Marine organic matter Brandes, U. Texas Bacteria and uranium chemistry Gillow, BNL Humic acid aggregates Rothe, Karsruhe Humic and fulvic acids Scheinost, Zurich Biofilms Thieme, Goettingen Emulsion stability Urquhart, Saskatchewan PMMA: damage as fn of temperature Jacobsen, USB ……

17. SSRL Workshop, 10/8-9/2002 17 Applications - elsewhere ALS 5.3.2 Polymer STXM (BM)*Ade, Hitchcock ALS 11.0.2 EMS STXM(EPU)#Shuh, Warwick BESSY II Soil, colloid STXM (U)#Thieme * New, 2002 # Under construction, 2002

18. SSRL Workshop, 10/8-9/2002 18 STXM – higher energy: 1-4 KeV APS 2ID-BMcNulty ESRF ID 21Susini Attractions: Na, Mg, Al, Si, P, S, Cl edges Challenges: High aspect ratio for zone plate Need for phase contrast or fluorescence

19. SSRL Workshop, 10/8-9/2002 19 Imaging using x-ray diffraction from non-periodic specimens Diffraction pattern can be recorded with no optics-imposed resolution limits Proposed by Sayre (in Schlenker, ed., Imaging and Coherence Properties in Physics, Springer-Verlag, 1980) Previous experiments by Sayre, Yun, Chapman, Miao, Kirz Reconstruction: iterate between real and Fourier space (Gerchberg-Saxton, Fienup, Elser) Real space: Finite support: object fills only part of the field Histogram Positivity? Fourier space: Re-impose the measured intensities while letting the phases evolve  FT 

20. SSRL Workshop, 10/8-9/2002 20 Diffraction imaging: present efforts New experimental chamber: rotate frozen hydrated specimen through  80° In-vacuum CCD, placement of optics/pinholes upstream and downstream of sample Diffraction tomography in biology: T. Beetz et al. Diffraction in biology: D. Shapiro, E. Lima et al. Magnetic speckle: T. Mentes, C. Sanchez-Hanke, C.-C. Kao (BNL)

21. SSRL Workshop, 10/8-9/2002 21 Diffraction patterns from yeast cells

22. SSRL Workshop, 10/8-9/2002 22 Damage! V. faba chromosomes fixed in 2% glutaraldehyde. S. Williams et al., J. Microscopy 170, 155 (1993) Previously unexposed: damage timescale longer than msec-range pixel time Repeated imaging of one chromosome shows mass loss, shrinkage Live bacteria

23. SSRL Workshop, 10/8-9/2002 23 Radiation damage resistance in cryo Left: frozen hydrated image after exposing several regions to ~10 10 Gray Right: after warmup in microscope (eventually freeze-dried): holes indicate irradiated regions! Maser et al., J. Microscopy 197, 68 (2000)

24. SSRL Workshop, 10/8-9/2002 24 PMMA at room, LN2 temperature T. Beetz, Stony Brook Repeated sequence: dose (small step size, long dwell time), spectrum (defocused beam) Images: dose region (small square) at end of sequence Room temperature: mass loss immediately visible LN2 temperature: no mass loss immediately visible After warm-up: mass loss becomes visible

25. SSRL Workshop, 10/8-9/2002 25 PMMA at LN2, room temperature: XANES spectra T. Beetz, SUNY Stony Brook Peak at 531.4 eV: C=0 bond Plateau at 540 eV: total mass (plus some emphasis on oxygen  * bonds) C=0 peak Plateau Room temperature Liquid nitrogen temperature

26. SSRL Workshop, 10/8-9/2002 26 Results from fitting spectra T. Beetz, SUNY Stony Brook LN2 temp: protection against mass loss, but not against breaking bonds (at least C=0 bond in PMMA) Plateau at 540 eV: total mass Peak at 531.4 eV: C=0 bond

27. SSRL Workshop, 10/8-9/2002 27 Group effort! Stony Brook group: –Faculty: Chris Jacobsen and Janos Kirz –Senior research support specialist: Sue Wirick –Postdoc: Michael Feser –Students: Tobias Beetz, Holger Fleckenstein, Benjamin Hornberger, Mirna Lerotic, Enju Lima, Ming Lu, David Shapiro, Aaron Stein –Guest scientist: David Sayre –Recent alumni: Sven Abend, Mary Carlucci-Dayton, Konstantin Kaznacheyev, Jianwei Miao, Ulrich Neuhäusler, Angelika Osanna, Thorsten Schäfer, Stefan Vogt, Steve Wang, Barry Winn… –Lucent: Don Tennant Many collaborators…