shen soft coherent
TRANSCRIPT
-
7/30/2019 Shen Soft Coherent
1/26
Overview on Coherent Diffraction
Imaging and Its Applications
NSLS-II Workshop, Coherent Scattering Breakout SessionBrookhaven National Laboratory, 18 J uly 2007
Introduction
Why Coherent Diffraction Imaging
Applications suited for CDI
Qun ShenX-ray Microscopy and Imaging Group
X-ray Science DivisionArgonne National Laboratory
Current activities at APS
Future Prospects at NSLS-II
-
7/30/2019 Shen Soft Coherent
2/26
2
Coherent X-ray Diffraction Imaging (CDI)
Coherent diffraction imaging or microscopy is much
like crystallography but applied to noncrystallinematerials
First proposed by David Sayre in 1980, andfirst experimental demonstration in 1999 usingsoft x-rays [Miao, Charalambous, Kirz, Sayre(1999) Nature 400, 342344]
Requires a fully coherent x-ray beamand iterative phase retrieval
Analogous to crystallography
-
7/30/2019 Shen Soft Coherent
3/26
3
Coherent Diffraction Imaging Structures w/o 3D CrystalsStructural 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)
-
7/30/2019 Shen Soft Coherent
4/26
4
Coherent Diffraction Imaging Functional StructuresImaging isthe key to structural science, and structural imaging at functional levelsholds the key to knowledge on how things really work (or fail).
In biology, imaging at cellularand systems level is of critical importance in the post-genomic era, for determinations of the functions of vast number of genes and geneproducts identified as a result of modern molecular biology techniques.
In materials science, structural information at nm-scale on inhomogeneous andheterogeneous specimens in their native environment (buried, nonperiodic) is neededto fully understand and tailor nanoscale-materials properties
Size (m)
10-910-8 10-1010-710-610-510-410-310-210-1
100 mm
H2O
Reovirus
Ribosome
Ge/Si dotsSi pillars
microchip
cracks
ant
plantsonion cell
cheek cell
yeast
Cysteine
Si (111)7x7
C60
Device/Medical Imaging Function/Cellular Imaging Molecular Imaging
grains
-
7/30/2019 Shen Soft Coherent
5/26
5
Coherent Diffraction vs. Lens-based X-ray Microscopy
Lens-based X-ray Microscopy:
Spatial resolution limited by x-rayoptics & aberrations
Even for perfect x-ray optics,depth of focus is an issue for thickerspecimens (e.g. FZP with Drn = 5nm=> Dz = 1mm forl = 1A)
Direct imaging in real space
Coherent Diffraction:
No fundamental limit on resolution otherthan l and S/N
Large depth of penetration limited only byabsorption (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
0.1110100
Outmost Zone Width (nm)
DepthofFocus(um)
10 nm
1 nm
0.1 nm
120 keV
12
1.2
0.12
-
7/30/2019 Shen Soft Coherent
6/26
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 algorithmscoherent optics,
limits due to damage
User science.
Design & build a dedicatedCDI beamline and facility
-
7/30/2019 Shen Soft Coherent
7/267
User Community Development at APS
Interested Groups
Physical Sciences:Eric Isaacs (ANL) - nanoscience and nanomaterialsIan Robinson & Ross Harder (UCL) -- strain in nanocrystalsRichard Weber (MDI) structures of amorphous solidSubhash Risbud (UC Davis) nanoscience, quantum dotsLinda Young (ANL) imaging highly excited small molecules
Biological Sciences:
Chris Jacobsen (SBU) biological cellsKeith Nugent (U. Melbourne) red blood cellsFuyu Tamanoi (UCLA) -- cellular membrane structureLila Graham (Harvard) -- 3D structure of mineral phases in boneJohn Miao (UCLA) -- actin fibers, quantum dots
New Methods:John Spence (ASU) - serial crystallography & prospects
Abbas Ourmazd (UW Milwaukee) molecular beamsAndrew Peele (LaTrobe) CDI with curved beamsIan McNulty (ANL) phasing, Fourier transform holographyXianghui Xiao & Qun Shen (ANL) Fresnel diffraction imagingDo Young Noh (GIST, Korea) generalized iterative phasing
Develop roadmap oncoherent x-ray diffractionimaging program at ANLand APS
Bring scientists andexperts together to
address uniqueapplication areas of CDI
Inform usercommunity about exciting
APS upgrade plans
Workshop on
Coherent X-ray Microscopy
May 8-9, 2007
-
7/30/2019 Shen Soft Coherent
8/268
User Science Examples
3D mapping of deformation fieldinside a nanocrystal
M.A. Pferferet al. Nature 442, 63 (2006)
Pb
34-ID-C
Fresnel Coherent Diffractive Imaging
G. Williams et al. PRL 97, 025506(2006)
-
7/30/2019 Shen Soft Coherent
9/269
Refraction-Phase Correction inCoherent Diffraction
Ross Harder & Ian Robinson(2007)
-
7/30/2019 Shen Soft Coherent
10/2610
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 incollagen protein matrix during mineralization2. Structural aspect of the mineral phase in bone is poorly understood
-
7/30/2019 Shen Soft Coherent
11/2611
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. Experimentdone at APS 8-ID-I.
Rodenburg, et al, PRL (2007)
ESRF
Noh et al.
(2007)
-
7/30/2019 Shen Soft Coherent
12/2612
Improving S/N with Crystal Guard Aperture
Coherencedefiningaperture Sample
CCD
SynchrotronX-rays
Crystalguard
aperture
Xiao et al. Opt. Lett. 31, 3194 (2006)
Si (111): polished surfaces, Z-cut design,Macrander et al. Proc. SPIE 5537, 171 (2004)
-
7/30/2019 Shen Soft Coherent
13/2613
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
-
7/30/2019 Shen Soft Coherent
14/2614
Ray-tracing for Optimization of Experiment
$60k $540k $1.5M
10 nm
2 nm
3.3 nm
Better Detectors
-
7/30/2019 Shen Soft Coherent
15/2615
Oversampling in Coherent Diffraction Imaging
LL
2
=> Sampling at frequency 2/L in
Fourier space is not fine enough toresolve interference fringes!
=> Additional measurements in-between 2/L are necessary to tellus some interference is going on.
Shen et al. J SR 11, 432 (2004)
LL
Q
D
2
12D1
max
=> Minimum oversampling ratio is 2,regardless whether it is 1D, 2D or 3D.
LLQ
2
2
12D2
max D
3D3
max2
12D
LQ
l
l
cos2cos2)2(
2
22
L
QQ yx
DD
DDD
D22
0 )()( QSNrIQI e
32
0~)/2( dtIdQI l
-
7/30/2019 Shen Soft Coherent
16/2616
Angular Variation of
Scattered X-Rays
c~ 3 c~ 0.5
Dilano Saldin (UW-Milwaukee)
exp(-Q2)
Q-4WAXS peaks
Q
I(Q)
-
7/30/2019 Shen Soft Coherent
17/26
17
Radiation Dose vs. Resolution & Damage(biomaterials)
Shen et al. J . Synch.Rad. 11, 432 (2004)
V = (100nm)3
Femtoseconddiffraction with XFELpulses [Hajdu 2000]
Self-assembledmacromolecule array
To go beyonddamage limit:
Continuous streamof molecules orientedby laser [Spence 2004]
See also: Marchesini et al.
Opt. Express (2003)
Small specimenlimits [Hajdu 2004]
-
7/30/2019 Shen Soft Coherent
18/26
18
X-ray Microscopy vs. Electron Microscopy
For electrons, multiple & inelasticscattering become more significant when
specimen thickness > 0.5um (left panel).
X-rays become superior thanelectrons when specimen thickness >few microns (right panel).
Jacobsen, Medenwaldt, & Williams, in X-ray Microscopy & Spectromicroscopy(Springer, 1998).
Compared to electrons, x-rays arebetter suited for studying thickerbiological specimens such as cells,which are in the range of ~10um.
-
7/30/2019 Shen Soft Coherent
19/26
19
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)
-
7/30/2019 Shen Soft Coherent
20/26
20
Amorphous Silicon (a-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)
-
7/30/2019 Shen Soft Coherent
21/26
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
-
7/30/2019 Shen Soft Coherent
22/26
22
Few Unit-Cell Crystallography
Illustration of a coherent diffractionimaging experiment on few unit-cell
protein crystals (flash frozen), byscanning a spin-coated thin plate ofcrystal powder on a SiN window.
Sol Gruner (Cornell)
Overlapping Braggreflections may providephase information(if crystallite is smallenough).
-
7/30/2019 Shen Soft Coherent
23/26
23
Molecular Beams
J ohn Spence, APS Workshop, Lake Geneva, WI. (2004)
Spence and Doak, Phys Rev Lett. 92, 198102 (2004).
CoherentElectron orX-ray Beam
Laser Beam
Larsen, J. Chem Phys 111, 7774 (1999).
Nanoscience:
complex
nanoparticle beams
by electro-spray?
-
7/30/2019 Shen Soft Coherent
24/26
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)
-
7/30/2019 Shen Soft Coherent
25/26
25
Conclusions
Coherent X-ray Diffraction Imagingis an exciting research field with
many potential applications. It has the potential to extend structural
science from mostly crystal-based today to studies ofnonperiodic
structures, limited only by radiation damage
Considerable worldwide effortson methodology and optimization of
experimental and theoretical configurations for coherent diffraction
imaging experiments. Example: crystal guard aperture to improve S/N
Emerging Application Areasinclude(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-IIwill be one of the best sources for continuous-wave coherent
diffraction imaging experiments
-
7/30/2019 Shen Soft Coherent
26/26
Thank You !