Shen Soft Coherent

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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


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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


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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)


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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


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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


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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


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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


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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)


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Refraction-Phase Correction inCoherent Diffraction

Ross Harder & Ian Robinson(2007)


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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


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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. Experimentdone at APS 8-ID-I.

Rodenburg, et al, PRL (2007)

ESRF

Noh et al.

(2007)


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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)


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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


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Ray-tracing for Optimization of Experiment

$60k $540k $1.5M

10 nm

2 nm

3.3 nm

Better Detectors


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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


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Angular Variation of

Scattered X-Rays

c~ 3 c~ 0.5

Dilano Saldin (UW-Milwaukee)

exp(-Q2)

Q-4WAXS peaks

Q

I(Q)


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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]


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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.


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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)


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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)


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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


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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).


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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?


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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)


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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


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Thank You !

Shen Soft Coherent

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