Overview on Coherent Diffraction

Imaging and Its Applications

NSLS-II Workshop, Coherent Scattering Breakout Session
Brookhaven National Laboratory, 18 J uly 2007
Introduction
Why Coherent Diffraction Imaging
Applications suited for CDI
Qun Shen
X-ray Microscopy and Imaging Group
X-ray Science Division
Argonne National Laboratory
Current activities at APS
Future Prospects at NSLS-II
2
Coherent X-ray Diffraction Imaging (CDI)
Coherent diffraction imaging or microscopy is much
like crystallography but applied to noncrystalline
materials
First proposed by David Sayre in 1980, and
first experimental demonstration in 1999 using
soft x-rays [Miao, Charalambous, Kirz, Sayre
(1999) Nature 400, 342344]
Requires a fully coherent x-ray beam
and iterative phase retrieval
Analogous to crystallography
3
Coherent Diffraction Imaging Structures w/o 3D Crystals
Structural science today is mostly based on x-ray diffraction from 3D crystals.
However, not all materials can be crystallized.
In biology: examples include membrane proteins and larger macromolecular assemblies.
~85% structures by
SR x-ray crystallography
??
Shen et al.
Physics Today
(March 2006)
4
Coherent Diffraction Imaging Functional Structures
Imaging is the key to structural science, and structural imaging at functional levels
holds the key to knowledge on how things really work (or fail).
In biology, imaging at cellular and systems level is of critical importance in the post-
genomic era, for determinations of the functions of vast number of genes and gene
products identified as a result of modern molecular biology techniques.
In materials science, structural information at nm-scale on inhomogeneous and
heterogeneous specimens in their native environment (buried, nonperiodic) is needed
to fully understand and tailor nanoscale-materials properties
Size (m)
10

9
10

8
10
10
10

7
10

6
10

5
10

4
10

3
10

2
10

1
100 m
H
2
O
Reovirus
Ribosome
Ge/Si dots
Si pillars
microchip
cracks
ant
plants
onion cell
cheek cell
yeast
Cysteine
Si (111)7x7

C
60
Device/Medical Imaging Function/Cellular Imaging Molecular Imaging
grains
5
Coherent Diffraction vs. Lens-based X-ray Microscopy
Lens-based X-ray Microscopy:

Spatial resolution limited by x-ray
optics & aberrations
Even for perfect x-ray optics,
depth of focus is an issue for thicker
specimens (e.g. FZP with Ar
n
= 5nm
=> Az = 1m for = 1A)
Direct imaging in real space
Coherent Diffraction:

No fundamental limit on resolution other
than and S/N
Large depth of penetration limited only by
absorption (for 3D reconstruction)
Need phase retrieval to real space images
1.E-03
1.E-02
1.E-01
1.E+00
1.E+01
1.E+02
1.E+03
0.1 1 10 100
Outmost Zone Width (nm)
D
e
p
t
h

o
f

F
o
c
u
s

(
u
m
)
10 nm
1 nm
0.1 nm
120 keV
12
1.2
0.12
6
Coherent X-ray Diffraction Imaging at APS
Current Status:


Part-time APS beamlines:
2-ID-B (~30%)
8-ID-I (~15%)
34-ID-C (~40%)
R&D:
phasing algorithms
coherent optics,
limits due to damage

User science.

Design & build a dedicated
CDI beamline and facility

7
User Community Development at APS
Interested Groups

Physical Sciences:
Eric Isaacs (ANL) - nanoscience and nanomaterials
Ian Robinson & Ross Harder (UCL) -- strain in nanocrystals
Richard Weber (MDI) structures of amorphous solid
Subhash Risbud (UC Davis) nanoscience, quantum dots
Linda Young (ANL) imaging highly excited small molecules

Biological Sciences:
Chris Jacobsen (SBU) biological cells
Keith Nugent (U. Melbourne) red blood cells
Fuyu Tamanoi (UCLA) -- cellular membrane structure
Lila Graham (Harvard) -- 3D structure of mineral phases in bone
John Miao (UCLA) -- actin fibers, quantum dots

New Methods:
John Spence (ASU) - serial crystallography & prospects
Abbas Ourmazd (UW Milwaukee) molecular beams
Andrew Peele (LaTrobe) CDI with curved beams
Ian McNulty (ANL) phasing, Fourier transform holography
Xianghui Xiao & Qun Shen (ANL) Fresnel diffraction imaging
Do Young Noh (GIST, Korea) generalized iterative phasing
Develop roadmap on
coherent x-ray diffraction
imaging program at ANL
and APS
Bring scientists and
experts together to
address unique
application areas of CDI
Inform user
community about exciting
APS upgrade plans
Workshop on
Coherent X-ray Microscopy
May 8-9, 2007
8
User Science Examples
3D mapping of deformation field
inside a nanocrystal
M.A. Pferfer et al. Nature 442, 63 (2006)
Pb
34-ID-C
Fresnel Coherent Diffractive Imaging
G. Williams et al. PRL 97, 025506 (2006)
9
Refraction-Phase Correction in
Coherent Diffraction
Ross Harder & Ian Robinson
(2007)
10
User Science Examples
Low degree mineralized fish bone and its reconstructed image.
The scale bar corresponds to 500nm
Biominerals fishbone at different mineralization stages:
Miao et al. (UCLA) Work in progress at APS, 2-ID-B

Mineralized Bone (Fish bone particles at different mineralization stages):
1. Development and aggregation of calcium apatite nano-crystals in
collagen protein matrix during mineralization
2. Structural aspect of the mineral phase in bone is poorly understood
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Extended Object
Moving aperture lensless transmission microscopy [Rodenburg,
et al, PRL (2007)]: overlapped sampling regions provide
additional constraints in real space.
Generalized iterative phase retrieval by D.Y. Noh (GIST, Korea):
density outside specimen is not zero, but is known. Experiment
done at APS 8-ID-I.
Rodenburg, et al, PRL (2007)
ESRF
Noh et al.
(2007)
12
Improving S/N with Crystal Guard Aperture
Coherence
defining
aperture
Sample
CCD
Synchrotron
X-rays
Crystal
guard
aperture
Xiao et al. Opt. Lett. 31, 3194 (2006)
Si (111): polished surfaces, Z-cut design,
Macrander et al. Proc. SPIE 5537, 171 (2004)
13
Recent Experiment at 8-ID-I with Direct Detection CCD
X-ray energy: 7.35 keV
Highest angle signal ~20nm resolution,
limited by counting statistics and size of CCD
Parasitic scattering background < 0.1 ph/s
Phasing in progress .
SEM
14
Ray-tracing for Optimization of Experiment
$60k $540k $1.5M
10 nm
2 nm
3.3 nm
Better Detectors
15
Oversampling in Coherent Diffraction Imaging
L
L
t 2
=> Sampling at frequency 2t/L in
Fourier space is not fine enough to
resolve interference fringes!
=> Additional measurements in-
between 2t/L are necessary to tell
us some interference is going on.
Shen et al. J SR 11, 432 (2004)
L L
Q
t t
= = A
2
1 2
D 1
max
=> Minimum oversampling ratio is 2,
regardless whether it is 1D, 2D or 3D.
L L
Q
t t 2
2
1 2
D 2
max
= = A
3
D 3
max
2
1 2
= A
L
Q
t
u

u t

| u
cos 2 cos 2
) 2 (
2
2
2
L
Q Q
y x
=
A A
|
.
|

\
|
= A A = AO
AO =
2
2
0
) ( ) ( Q S N r I Q I
e
3 2
0
~ ) / 2 ( d t I d Q I t =
16
Angular Variation of
Scattered X-Rays

c
~ 3

c
~ 0.5
Dilano Saldin (UW-Milwaukee)
exp(Q
2
)
Q
4

WAXS peaks
Q
I (Q)
17
Radiation Dose vs. Resolution & Damage
(biomaterials)

Shen et al. J . Synch.
Rad. 11, 432 (2004)
V = (100nm)
3
Femtosecond
diffraction with XFEL
pulses [Hajdu 2000]

Self-assembled
macromolecule array

To go beyond
damage limit:

Continuous stream
of molecules oriented
by laser [Spence 2004]

See also: Marchesini et al.
Opt. Express (2003)
Small specimen
limits [Hajdu 2004]

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X-ray Microscopy vs. Electron Microscopy
For electrons, multiple & inelastic
scattering become more significant when
specimen thickness > 0.5um (left panel).
X-rays become superior than
electrons when specimen thickness >
few microns (right panel).
Jacobsen, Medenwaldt, & Williams, in X-ray Microscopy & Spectromicroscopy (Springer, 1998).
Compared to electrons, x-rays are
better suited for studying thicker
biological specimens such as cells,
which are in the range of ~10um.
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Potential Applications of Coherent Diffraction Imaging
Materials Science:

-- nanostructures in their native environment
-- bio-organic-inorganic hybrid structures
-- atomic structure of amorphous materials

Structural Cell & Systems Biology:

-- subcellular organelle structures in cells
-- groups of biological cells during development
-- biological tissues

Structural Molecular Biology:

-- 2D crystals, e.g. membrane proteins
-- few unit-cell crystals
-- laser-oriented biomolecules
Yan et al.
Science
(2003)
20
Amorphous Silicon (o-Si):
- atomic resolution structure data still lacking
- one of grand challenges in solid state physics
Structures of Amorphous Nanoparticles
Veit Elser (Cornell)
PRB 58, 4579 (1998)
Nature 418, 62 (2002)
21
Structural Cell &
Systems Biology
Shapiro et al. PNAS (2005)
ALS 750eV
Freeze-dried yeast cell:
reconstructed to ~30nm
Myocyte
thick specimens
extended object
nondestructive studies
~10 nm resolution
Group of dormant cells spores (Tamanoi, UCLA)
S. Vogt
(APS)
Ascus
22
Few Unit-Cell Crystallography
Illustration of a coherent diffraction
imaging experiment on few unit-cell
protein crystals (flash frozen), by
scanning a spin-coated thin plate of
crystal powder on a SiN window.
Sol Gruner (Cornell)
Overlapping Bragg
reflections may provide
phase information
(if crystallite is small
enough).
23
Molecular Beams
J ohn Spence, APS Workshop, Lake Geneva, WI. (2004)
Spence and Doak, Phys Rev Lett. 92, 198102 (2004).
Coherent
Electron or
X-ray Beam
Laser Beam
Larsen, J. Chem Phys 111, 7774 (1999).

Nanoscience:
complex
nanoparticle beams
by electro-spray?
24
Coherent Diffraction
Imaging at NSLS-II
NSLS-II will be the most coherent x-ray
source in 4-10 keV range
ideal for coherent diffraction imaging
NSLS-II CDR
(2006)
25
Conclusions
Coherent X-ray Diffraction Imaging is an exciting research field with
many potential applications. It has the potential to extend structural
science from mostly crystal-based today to studies of nonperiodic
structures, limited only by radiation damage
Considerable worldwide efforts on methodology and optimization of
experimental and theoretical configurations for coherent diffraction
imaging experiments. Example: crystal guard aperture to improve S/N
Emerging Application Areas include (a) nanocrystalline and nanoparticle
structures, (b) atomic structure of amorphous nanomaterials, (c) 2D crystals
and few unit-cell crystals, (d) subcellular organelle structures in cell &
systems biology, and (e) single nanoparticle imaging
Acknowledgments:
Crystal guard aperture: Xianghui Xiao, Martin de J onge, Yong Chu, Hanfei Yan
Radiation damage: Ivan Bazarov, Pierre Thibault, Veit Elser, Dilano Saldin
User science: Keith Nugent, J ohn Miao, Ross Harder, Ian Robinson, Stefan Vogt

APS is supported by the U.S. DOE, BES, under Contract No. DE-AC02-06CH11357.
NSLS-II will be one of the best sources for continuous-wave coherent
diffraction imaging experiments
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Thank You !