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Electron crystallography: imaging and diffraction
GNM School – Bressanone February 2018
E. Mugnaioli ([email protected])
Istituto Italiano di Tecnologia
Center for Nanotechnology Innovation@NEST – Pisa (Italy)
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• Electron crystallography: why and when
• Transmission electron microscopy (TEM)
• Electron diffraction from oriented zones
• Electron diffraction tomography (EDT)
Outline
• An example of EDT analysis
• Three applications to mineralogy and petrography
• Strengths and limits of EDT
• Some perspectives (very beam sensitive samples)2
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Enrico Mugnaioli2007 PhD in Electron Crystallography at the University of Siena (geology)
●Siena
●Mainz
2007-2014 Post-Doc at the University of Mainz (physical-chemistry)
2014-2017 PI for the National Project “Exploring the Nanoworld” at the University of Siena (geology)
2017-ongoing senior researcher at IIT@NEST – Pisa (nanotechnology)
●Pisa
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Crystallography
Crystallography is the science that studies the atom arrangement in (crystalline) solids, i.e. how solid materials are essentially made
Macroscopic properties of materials largely depend on the atomic structure at the sub-nanometric scale
UN proclaimed 2014 as the International Year of Crystallography,celebrating the centenary of Max von Laue’s Nobel Prize in Physics
for the discovery of X-ray scattering
Visible light has a wavelength of 4000-7000 Å,atomic radius and bonds are about 1-3 Å
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Nano-crystalline materials
Calcite(CaCO3)
Aragonite(CaCO3)
Single-crystal X-raydiffraction
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Nano-crystalline materials
10 nm10 nm
Calcite(CaCO3)
Aragonite(CaCO3)
Vaterite (CaCO3)
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Vaterite (CaCO3)
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X-ray powder diffraction (XRPD)
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X-ray powder diffraction (XRPD)ഥ� = ഥ� �λ2sin θ= �λ2sin θ
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X-ray Powder DiffractionRietveld refinement
Inte
nsity
(co
unts
)
2θ (°)
Phase 1
Phase 3Phase 2
1D information
problematic in case of: • long cell parameters• pseudo-symmetries• polyphasic samples
• broadening of peaks for nanocrystalline materials
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One single nano-crystalPolyphasic materials
5 µm
Chondrite Welding fumes
Single sectors of an assemble
Isolated crystals
500 nm 10Intr
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SEM & TEM
Transmission electron microscope
(TEM)
Scanning electron microscope
(SEM)Scanning-transmission
electron microscopy
(STEM)
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Images
Spectral analysis
Diffractions
Transmission Electron Microscope (TEM)
Intr
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Accelerated electrons
• Short wavelength (~ 0.01-0.1 Å)- small scattering angle- almost flat Ewald sphere- many reflections excited contemporarily
• Strong (Coulomb) interaction with matter- 103-104 stronger interaction than X-rays- good signal/noise from nanovolumes- dynamical scattering
• Charged (e-)- easy to deflect and focus in a nanoprobe- scattered information can be recombined in imagesTEM
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Lens
X-rays Electrons
Sample
Incoming radiation
Scattering
Image
Sample
Incoming radiation
Scattering
Diffraction
Ruska & Knoll, 1932
X-rays vs. Electrons
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HRTEM on nanomaterials: local structure
CdSe
5 nm
Ag
5 nm
SnS2
10 nm
SnS2
10 nm
WS2
15 nm
NbS2
15 nm15
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HRTEM on crystal boundariesWO3@WO3
5 nm
(100)
(012)
5 nm2 nm
Au_d111 = 2.36 Å
MnO_d111 = 2.56 Å
Au@MnO
Fourier Transform
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5 nm
HRTEM on defects of polytypes
500 nm
Cha-96
Cha-96
Cha-90
5 nmCha-96
Cha-90
Charoite
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Polygonal SerpentinePolygonal Serpentine XRPD: 6 additional
reflections on lizardite
Brindley & von Knorring, 1954: “Orto-antigorite”Zussman & Brindley, 1957: “Lizardite 6-T”
PS30PS15
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Polygonal Serpentinec = 7.3 Å (O), 7.5 Å (R, L)
= 90° (O), 78° (R), 102° (L), i.e. ± b/6.
50 nm
L O R
[100]
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Polygonal Serpentinec = 7.3 Å (O), 7.5 Å (R, L)
= 90° (O), 78° (R), 102° (L), i.e. ± b/6.
50 nm
L O R
[100]
OR
OLO
RL
L
R
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Polygonal Serpentine
OL R
R
LO
Single layer:
PS15: R-O-L
PS30: L-O-R
OR
OLO
RL
L
R
O O · 5 O + R + L21
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double layer polytypic stacking
Polygonal Serpentine
OL
R ORLO
RL
single layer
OR
O
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Polygonal Serpentine
single layerO, L, R
double layerO = RL, L = OL, R = OR
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Polygonal Serpentine[010]
Cell parameters of different polytypes
a b c α sciv. a sciv. b
O 5.3 9.2 14.7 90 97 90 no +a/3 no
L 5.3 9.2 15.0 102 97 90 no +a/3 -b/6
R 5.3 9.2 15.0 78 97 90 no +a/3 +b/6
RL 5.3 9.2 14.7 90 97 90 no +a/3 +b/6 -b/6
LO 5.3 9.2 14.8 96 97 90 no +a/3 -b/6 no
OR 5.3 9.2 14.8 84 97 90 no +a/3 no +b/624
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Polygonal SerpentineO020L-1-11
O-110L110
O-111L020
L-111 O111L-1-12 O022
L1-12O-112L111
Complexity in 15- and 30-sectors polygonal serpentine: Longitudinal sections, intrasector stacking faults and XRPD satellites. E. Mugnaioli, M. Logar, M. Mellini, C. Viti, Am Mineral 92, 603 (2007).
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Simulated HRTEMZnO
100
001
1600 Å 400 Å800 Å1200 Å
50 Å
150 Å
250 Å
350 Å
DEFOCUS
TH
ICK
NE
SS
[010] Programs for HRTEM simulation
NCEMSS free, not easy do handleJEMS commercialCALIDRIS commercialCERIUS commercial1 nm
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Filtered image
Simulated image
Projected structure
Experimental image
Antigorite m17 [001]
HRTEM evidence for 8-reversals in the m = 17 antigorite polysome. G.C. Capitani, M. Mellini, Am Mineral 90, 991 (2005).
Antigorite m16 [010]
Simulated HRTEM
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Corrected STEM imagingCu2-xTe [001]
[100]
Te
CuEDX nanomap
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� � =� � �� � �� −2�� � ∙ �
HRTEM for solving structures
Structure and catalytic properties of the most complex intergrown zeolite ITQ-39 determined by electron crystallography. T. Willhammar, J. Sun, W. Wan, P. Oleynikov, D. Zhang, X. Zou, M. Moliner, J. Gonzalez, C. Martínez, F. Rey, A. Corma, Nat Chem 4, 188 (2012).
ITQ-39
Transfer function of the TEM(focus, thickness, lens aberrations)
Resolution limit of about 2.0-1.5 Å for conventional TEMNecessity of an optimal orientation
Very complicate for structure with long cell parameters2D projections - Hard to build a 3D data set
Beam damage
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Beam damage
After 2 minutes100 nm
Who is beam sensitive?All organics, porous materials, water-containing materials,
many layered compounds… at a certain level everything but very conductive materials
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Electron imaging vs. Diffraction X-rays Electrons
Sample
Incoming radiation
Scattering
Sample
Incoming radiation
Scattering
Diffraction
Image
Diffraction
In diffraction we miss thecrystallographic phases,
but we need a much milder illumination,we achieve a better resolution
and it is more easy to get 3D data 31
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Accelerated electrons
• Short wavelength (~ 0.01-0.1 Å)- small scattering angle- almost flat Ewald sphere- many reflections excited contemporarily
• Strong (Coulomb) interaction with matter- 103-104 stronger interaction than X-rays- good signal/noise from nanovolumes- dynamical scattering
• Charged (e-)- easy to deflect and focus in a nanoprobe- scattered information can be recombined in imagesTEM
32
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dif
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Phase and orientation mapsPhase and orientation map through diffraction scanning
and template matching
… similar to EBSD but a smaller scale
Automated nanocrystal orientation and phase mapping in the transmission electron microscope on the basis of precession electron diffraction. E.F. Rauch, J. Portillo, S. Nicolopoulos, D. Bultreys, S. Rouvimov, P. Moeck, Z. Kristallogr. 225, 103 (2010).
Al2O3
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Convergent beam electron diffractionCBED
m
m
Direct observation of d-orbital holes and Cu-Cu bonding in Cu2O. J. M. Zuo, M. Kim, M. O'Keeffe, J. C. H. Spence, Nature 401, 49 (199).
Parallelbeam
Convergentbeam
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Double-tilt acquisition of in-zone ED
β = -11.6°
α = 0°β = 0°
α = -33.5°
β = 15.1°
β = 22.2°
α = 19.5°
α = 29.0°
α = -21.0°
β = 28.5°
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DT
-20°
[110]
-11°
[210]
0° [100]
10°
[2-10]
19°
[1-10]
36°
[1-20]
Conventional in-zone ED acquisition
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Data handling
ZOLZ
FOLZ
Vainshtein plot
Cell parameter determination
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DT
-20°
[110]
-11°
[210]
0° [100]
10°
[2-10]
19°
[1-10]
36°
[1-20]
Conventional in-zone ED acquisition
- crystal orientation: expertise, beam damage during orientation- limited number of zones: few reflections, data from different crystals - most of high index reflections are missing- in-zone patterns: maximum dynamical effects, difficult to merge
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Incoming radiation
Kinematic scatteringSingle scattering
Ihkl ~ (Fhkl)2
Always the case for X-rays
Dynamic scattering2-beam scatteringBlackman formula
Ihkl ~ Fhkl
Dynamic scatteringMulti-beam
?
Weak interaction Strong interaction
Dynamic effects
Sample Sample Sample
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Dynamical effects Kinematic scattering
Kinematic scatteringSingle scattering
Ihkl ~ (Fhkl)2
Always the case for X-rays
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Intr
oduc
tion
Dynamic scattering
Dynamic scattering2-beam scatteringBlackman formula
Ihkl ~ Fhkl
Dynamic scatteringMulti-beam
?
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Scan
De-scan
Specimen
Courtesy of Northwestern
University, USA (C.S. Own, L. Marks)
Precession electron diffraction
Double conical beam-rocking system for measurement of integrated electron diffraction intensities. R. Vincent, P.A. Midgley, Ultramicroscopy 53, 271 (1994).
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DigiStar by NanoMEGAS
Beam is rotating very fast avoiding full orientation of
the zone
Double conical beam-rocking system for measurement of integrated electron diffraction intensities. R. Vincent, P.A. Midgley, Ultramicroscopy 53, 271 (1994).
Precession Electron Diffraction
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SAED PED
Cinematico
Uvarovite [001]
Ca3Cr2(SiO4)3
Ia3d
Structure solution with three-dimensional sets of precessed electron diffraction intensities. M. Gemmi, S. Nicolopoulos, Ultramicroscopy 107, 483 (2007).
Precession Electron Diffraction
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Structure solution of the new titanate Li4Ti8Ni3O21 using precession electron diffraction. M. Gemmi, H. Klein, A. Rageau, P. Strobelb, F. Le Cras, Acta Crystallogr B 66, 60 (2010).
Li4Ti8Ni3O21 LiBH4
Crystal Structure of a Lightweight Borohydride from Submicrometer Crystallites by Precession Electron Diffraction. J. Hadermann, A. Abakumov, S. Van Rompaey, T. Perkisas, Y. Filinchuk, G. Van Tendeloo, Chem Mater 24, 3401 (2012).
Structure solution by in-zone ED
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Structure solution of the new titanate Li4Ti8Ni3O21 using precession electron diffraction. M. Gemmi, H. Klein, A. Rageau, P. Strobelb, F. Le Cras, Acta Crystallogr B 66, 60 (2010).
Li4Ti8Ni3O21 LiBH4
Crystal Structure of a Lightweight Borohydride from Submicrometer Crystallites by Precession Electron Diffraction. J. Hadermann, A. Abakumov, S. Van Rompaey, T. Perkisas, Y. Filinchuk, G. Van Tendeloo, Chem Mater 24, 3401 (2012).
Structure solution by in-zone ED
Ihkl ≠ c Fhkl2
Negative thermal factorMissing light atoms
Difficulties in sorting the correct solution
Direct elctron crystallographic determination of zeolite zonal structures.D.L. Dorset, C.J. Gilmore, J.L. Jorda, S. Nicolopoulos, Ultramicroscopy 107, 462 (2007).
46
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DT
-20°
[110]
-11°
[210]
0° [100]
10°
[2-10]
19°
[1-10]
36°
[1-20]
Can we use the TEM as a (primitive) single-crystal diffractometer?
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- no need for crystal orientation: fast and easy acquisition- off-zone patterns: reduction of dynamical effects- use of the full tilt range of the microscope: improved completeness
and collection of high index reflections
Automated electron Diffraction Tomography (ADT or EDT):
acquisition of not oriented diffraction patterns in fixed steps of 1°
Towards automated diffraction tomography. Part I - Data Acquisition.U. Kolb, T. Gorelik, C. Kübel, M.T. Otten, D. Hubert, Ultramicroscopy 107, 507 (2007).
Tomographic acquisition strategy
48ED
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Tomographic acquisition strategy
Towards automated diffraction tomography. Part I - Data Acquisition.U. Kolb, T. Gorelik, C. Kübel, M.T. Otten, D. Hubert, Ultramicroscopy 107, 507 (2007).49E
DT
ADT is easy, fast and highly reproducible
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Zonal vs. Tomographic ED acquisition
Tomographic acquisition:sampling the full accessible reciprocal space
in steady stepsaround an arbitrary (non-crystallographic) axis
Conventional ED acquisition:
collection of oriented crystallographic zones
50ED
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ADT data analysis
Towards automated diffraction tomography. Part II – Cell parameter determination. U. Kolb, T. Gorelik and M.T. Otten, Ultramicroscopy, 108, 763-772 (2008).
ADT data are less dynamical
51ED
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3D reconstructed diffraction volume visualization
52ED
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Cell parameters & Orientation
Cell parameters
manual selection or clustering in difference vector space
Orientation matrix
correlation with crystal shape for determination of direction of
growth and facets
300 nm
c*b*
a*
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Disorder & Symmetry
Disorder
0kl : k = 2n+1
Extinctions
hk0 : h = 2n
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Set an appropriate integration area
Determination of the reflection position
“Ab initio” structure solution from electron diffraction data obtained by a combination of automated diffraction tomography and precession technique. E. Mugnaioli, T. Gorelik, U. Kolb, Ultramicroscopy 109, 758 (2009).
Intensity integration
55ED
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Set an appropriate integration area
Determination of the reflection position
“Ab initio” structure solution from electron diffraction data obtained by a combination of automated diffraction tomography and precession technique. E. Mugnaioli, T. Gorelik, U. Kolb, Ultramicroscopy 109, 758 (2009).
Intensity integration
56ED
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Spots do have a volume (spike)
The Ewald sphere cuts each spot in a different way (excitation error)
NED Expected
Laue Zone
Excitation errorE
DT
dat
a ac
quis
itio
n &
ana
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DigiStar by NanoMEGAS
Beam is rotating very fast avoiding full orientation of
the zone
Double conical beam-rocking system for measurement of integrated electron diffraction intensities. R. Vincent, P.A. Midgley, Ultramicroscopy 53, 271 (1994).
Precession Electron Diffraction
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DT
Dat
a A
cqui
sitio
n
NED PEDExpected
θθ
θ = 1° PED makes Ewaldsphere to integrate reflection volume
Laue Zone
ADT + Precession
Spots do have a volume (spike)
The Ewald sphere cuts each spot in a different way (excitation error)
ED
T d
ata
acqu
isit
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& a
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Test structuresSpace group
N° indep. reflections
N° indep. atoms
Volume (Å3)
Resolution (Å)
Completeness
Inorganic materials
Calcite CaCO3 R-3c 106 3 120 0.8 97%
Semiconductor 6H-SiC P6mm 52 6 130 0.9 100%
Na2W4O13 P-1 738 10 262 0.8 69%
Barite BaSO4 Pnma 355 5 350 0.8 82%
ZnSb Pbca 106 2 440 1.2 70%
Layered Na2Ti6O13 C2/m 517 11 510 0.8 72%
Li26Ti8Ni4O21 P-3c1 187 15 720 1.0 91%
Na2W2O7 Cmce 454 9 1264 0.9 91%
Zeolites
Natrolite Fdd2 719 10 2250 0.8 92%
ZSM-5 Pnma 2288 39 5490 1.0 79%
IM-5 Cmcm 2170 71 16380 1.2 68%
Organics and Hybrids
10-CNBA C29NH17 P21/c 1871 30 2000 1.0 90%
Basolite C6H4CuO5 Fm-3m 384 7 18640 1.2 99%
Ihkl ~ Fhkl2
kinematical (1-scatter) approximation…like in X-ray
60ED
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~ 200 structures solved by ADT in 6 years
Intermetallic phasesBirkel CS et al (2010)
J Am Chem Soc 132, 9881
MineralsRozhdestvenskaya I et al
(2011) Mineral Mag 75, 2833
OrganicsKolb U et al (2010)Polym Rev 50, 385
PhosphatesMugnaioli E et al (2012)Eur J Inorg Chem, 121
Metal Organic Frameworks (MOF)
Denysenko D et al (2011)Chem-Eur J 17, 1837
Hybridscalcium-silicates
Bellussi G et al (2012)Angew Chem Int Ed 51, 666
Layered titanatesAndrusenko I et al (2011)
Acta Crystallogr B 67, 218
Ca-compoundsMugnaioli E et al (2012)
Angew Chem Int Ed 51, 7041
High pressure phasesGemmi M et al (2011)
Earth Planet Sc Lett 310, 422
ZeolitesJiang J et al (2011)Science 333,1131
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ED
T a
naly
sis
Tomographic acquisition strategy
Towards automated diffraction tomography. Part I - Data Acquisition.U. Kolb, T. Gorelik, C. Kübel, M.T. Otten, D. Hubert, Ultramicroscopy 107, 507 (2007).62
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Data analysis
Reconstruction of 3D diffraction space
We need:- accurate centring- accurate tilt axis determination
Towards automated diffraction tomography. Part II – Cell parameter determination. U. Kolb, T. Gorelik and M.T. Otten, Ultramicroscopy 108, 763 (2008).
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DT
Dat
a A
naly
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Centre of the central beam or Friedel pair
x
x
Accurate diffraction centering
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φX
Y
φ X
Y
The tilt axis azimuth changes for different camera lengths and for different diffraction focus
Tilt axis azimuth
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Correct tilt axis Incorrect tilt axis
If the tilt axis is wrong, in the reconstructed
volume reflection rows are “bananas”
Stereographic projection of difference
vectors
Tilt axis determination
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Diffraction volume reconstruction
reconstruction of 3D diffraction space
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3D reconstructed diffraction volume visualization
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The three not-coplanar difference vectors closer to the centre define the primitive cell
(Niggli cell)
Cell determination – clusteringAutomatic clusteringHand cell picking
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Reflection indexing
Reflection indexing
cell superimposed to the 3D reconstructed diffraction volume
along a* along b*
along c*
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Extinctions & Space group
Extinctions
hk0 : h = 2N
0kl : k+l = 2N } Pn-a71
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SIR
JANA
Space group determination
Automated determination of the extinction symbol via electrondiffraction data. M. Camalli, B. Carrozzini, G. L. Cascarano,C. Giacovazzo, J Appl Crystallogr 45, 351 (2012).
Crystallographic Computing System JANA2006:General features. V. Petříček, M. Dušek, L. Palatinus,Z Kristallogr 229, 345 (2014).
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Set an appropriate integration area
Determination of the reflection position
“Ab initio” structure solution from electron diffraction data obtained by a combination of automated diffraction tomography and precession technique. E. Mugnaioli, T. Gorelik, U. Kolb, Ultramicroscopy 109, 758 (2009).
Intensity integration
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Software for data analysis
ADT3D
In-house made Matlab routines
PETS – by Lukas Palatinus
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*.hkl file
h k l I σ(I)
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Software for structure analysis
SIR direct methods and simulated annealing
JANA charge flipping & dynamical refinement
SHELX suite direct methods & refinement
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SIR input
or ‘Fobs’
you can omit
1) Wilson Statistic2) Phase Search (Direct Methods)3) Interpretation of the Potential Map
!
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The result: a Potential Map
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hh rhr iF
Vcell
2exp1
)(The Potential Map is automatically interpreted
in terms of atom positionsED
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Atom positions and final model
The atom position list has to be interpreted
H2O
O
Na
Helps: Composition, interatomic distances and coordination 79ED
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Structure solved!!E
DT
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SEM
Polyphasic samples: HAPyE
DT
Exa
mpl
es
A new phase was detected at
5.2 Gpa, 700ºC,
Conventional ED: C-centred monoclinic cell
a=9.9Å, b=11.8 Å, c=5.1Å, β=110°
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1 μm86% completeness, 1.0 Å resolution
Polyphasic samples: HAPy
A new hydrous Al-bearing pyroxene as a water carrier in subduction zones.M. Gemmi, J. Fischer, M. Merlini, S. Poli, P. Fumagalli, E. Mugnaioli, U. Kolb,Earth Planet Sc Lett 310, 422 (2011).
Mg2Al(OH)2AlSiO6
Hydrous Al-bearing Pyroxene (HAPy)
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Charoite
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EDT Examples
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Charoite1978. Rogova et al., Zapiski
Vsesoyuznogo Mineralogischeskogo
Obshchetva: charoite is recognized as a new mineral1985. Nikishova et al., Crystal
Chemistry and Strucutre of Minerals: on the basis of XRPD charoite is assigned to spacegroup P2/m ( = 94.3°)2009. Rozhdestvenskaya et al., Mineral. Mag.: on the basis of XRPD and HRTEM a tentative charoite strucutre is proposed in spacegroup P21/m ( = 96.3°)2009. Rozhdestvenskaya et al., Z.
Kristallogr.: SAED and HRTEM reveal the presence of different polytypes 84
ED
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Charoite1978. Rogova et al., Zapiski
Vsesoyuznogo Mineralogischeskogo
Obshchetva: charoite is recognized as a new mineral1985. Nikishova et al., Crystal
Chemistry and Strucutre of Minerals: on the basis of XRPD charoite is assigned to spacegroup P2/m ( = 94.3°)2009. Rozhdestvenskaya et al., Mineral. Mag.: on the basis of XRPD and HRTEM a tentative charoite strucutre is proposed in spacegroup P21/m ( = 96.3°)2009. Rozhdestvenskaya et al., Z.
Kristallogr.: SAED and HRTEM reveal the presence of different polytypes
QtzPtc
Ptc
Qtz
PtcApo PtcQtz
[010]
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EDT confirms two ordered polytypes and allows to measure their cell parameters (in 3D)
Charoite-90: a=31.96Å, b=19.64Å, c= 7.09Å, α=90.0°, β=90.0°, =90.0°
Charoite-96: a=32.11Å, b=19.77Å, c= 7.23Å, α=90.0°, β=95.9°, =90.0°
Charoite
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200 nm
cha-90 -60° to +60°
-45° to +60°
8495 total reflections 2878 independent ones
97% completeness1.18 Å resolution
P2/mPmmm
Space group: P21/m
Charoite
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Charoite
Ihkl ~ Fhkl2
kinematical (1-scatter) approximation…like in X-ray
quadrupole chain
[Si17O43]18-
The structure of charoite, (K,Sr,Ba,Mn)15-16(Ca,Na)32[(Si70(O,OH)180)](OH,F)4.0 * nH2O, solved by conventional and automated electron diffraction.I. Rozhdestvenskaya, E. Mugnaioli, M. Czank, W. Depmeier, U. Kolb, A. Reinholdt, T. Weirich, Mineral Mag 74, 159 (2010).
double chain [Si6O17]10-
triple chain [Si12O30]12-
Na
Ca
K+
Sr+ H2O
[001]
b
a
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Charoite
Charoite as OD layers shifted by ¼ c or -¼ c Possible sequences with the maximum degree of order (MDO): MDO1 (cha-90): ¼,-¼,¼,-¼… & MDO2 (cha-96): -¼,-¼,-¼,-¼…
2-½ 2-½2½
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Charoite
500 nm
cha-96cha-90
-50° to +60°
-60° to +60°
10271 total reflections 3353 independent reflections
97% completeness 1.15 Å resolution
Rsym = 22%
Space group: P21/m 90
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Charoite
Essential features of the polytypic charoite-96 structure compared to charoite-90. I. Rozhdestvenskaya, E. Mugnaioli, M. Czank, W. Depmeier, U. Kolb, S. Merlino, Mineral Mag 75, 2833 (2011).
-½ c*
[001]
b
a
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Charoite
Essential features of the polytypic charoite-96 structure compared to charoite-90. I. Rozhdestvenskaya, E. Mugnaioli, M. Czank, W. Depmeier, U. Kolb, S. Merlino, Mineral Mag 75, 2833 (2011).
-½ c*
[001]
b
a
Charoite-96
Charoite-90
[010]
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Garnet Codera dike pegmatite
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Metamict minerals
Matamict phase from Garnet Codera dike pegmatite
(Central-Western Italian Alps)
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Metamict minerals
Metamict processthe structure of minerals containing
radioactive elements is progressively destroyed by radiations produced by
radioactive decay
Sometimes, iso-oriented more crystalline areas of few tens of nanometers are preserved in the
mostly amorphous matrix
100 nm 10 nm
10 nm95
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Samarskite-(Y)
Samarskite is normally associated with formula:
(Y,REE,Fe,U,Th,Ca)4(Nb,Ta,Ti)4O16
(Y,REE,Fe,U,Th,Ca)3(Nb,Ta,Ti)5O16
WDS:
Nb2O5 36%
Ta2O5 15%
UO2 14%
YO3 9%
FeO 5%
Fe2O3 4%
TiO2 4%
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Samarskite-(Y)Ixiolite
Columbite
When samarskite is recrystallized in atmosphere,
several compounds form
When samarskite is recrystallized in reducing
conditions (H2), an ixiolite or columbite structure is obtained
Preservation of the samarskite structure in a metamict ABO4 mineral: a key to crystal structure identification. N. Tomašić, A. Gajović, M.R. Linarić, D. Su, R. Škoda, Eur. J. Mineral. 22, 435 (2010).
Polymorphism of samarskite and its relationship to other structural related Nb-Ta oxides with α-PbO2 structure. Y. Sugitani, Y. Suzuki, K. Nagashima, Am. Mineral. 70,
856 (1985).
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For X-ray diffraction, sample annealing and
recrystallization are necessary
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EDT on samarskite-(Y) crystalline relicts
view c*
view a* view b*
view 011
1661 reflections up to 0.8Å resolution (86% completeness)
Rsym = 21.3%
Cell parameters: a=10.9Å, b=7.5Å, c=5.1Å
Extinction symbol:Pn‒a
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EDT on samarskite-(Y) crystalline relicts
Ab-initio determination by direct methods:
Nioboaeschynite-(Y)
(Y,U,Fe2+)2(Nb,Ta,Ti,Fe3+,Fe2+)4O12
Ixiolite
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(Y,REE,Fe,U,Th,Ca)3(Nb,Ta,Ti)5O16
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How small? Zn1+xSb7
Cu2-xTe
150 nm
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Space group: P-1a~b=15Å, c=7.8Å30 independent atomsBirkel et al., JACS 132, 9881 (2010)
Space group: P2221
a=7.5Å, b=22.8ÅÅ, c=29.6Å58 independent atoms
100
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Intergrown phases
Synthesis and structural characterization of Cr-bearing magnesian h-magnetite recoverable to ambient conditions. M. Koch-Müller, E. Mugnaioli, D. Rhede, S. Speziale, U. Kolb, R. Wirth, Am Mineral 99, 2405 (2014).
500 nn
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Intergrown phases
Synthesis and structural characterization of Cr-bearing magnesian h-magnetite recoverable to ambient conditions. M. Koch-Müller, E. Mugnaioli, D. Rhede, S. Speziale, U. Kolb, R. Wirth, Am Mineral 99, 2405 (2014).
HP Magnetite – Fe3O4
Goethite – FeO(OH)
500 nn
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How complex?Quasicrystal approximant Al77Rh15Ru8Space group: Pbma
a=23.4Å, b=16.2Å, c=20.0Å19 independent Rh/Ru, 59 independent AlSamuha et al., Acta Cryst B 70, 999 (2014)
Charoite-90Space group: P21/m
a=32.0Å, b=19.6Å, c=7.1Å, β=90.0°36 independent Si/Ca/Na/K/Sr
54 independent ORozhdestvenskaya et al.,
Mineral Mag 74, 159 (2010)103
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IM-17Space group: Amm2a=12.7Å, b=22.2Å, c=39.1Å24 independent Si, 60 independent OLorgouilloux et al., RSC Adv 4, 19440 (2014)
Inorganic zeolitesZSM-5Space group: Pnma
a=20.1Å, b=19.9Å, c=13.4Å12 independent Si/Al, 27 independent OMugnaioli & Kolb, Microp Mesop Mat 166, 93 (2013)
ITQ-43Space group: Cmmm
a=26.1Å, b=41.9Å, c=12.8Å11 independent Si/Ge, 28 independent O
Jiang et al., Science 333, 1131 (2011)
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IM-17Space group: Amm2a=12.7Å, b=22.2Å, c=39.1Å24 independent Si, 60 independent OLorgouilloux et al., RSC Adv 4, 19440 (2014)
Inorganic zeolitesZSM-5Space group: Pnma
a=20.1Å, b=19.9Å, c=13.4Å12 independent Si/Al, 27 independent OMugnaioli & Kolb, Microp Mesop Mat 166, 93 (2013)
ITQ-43Space group: Cmmm
a=26.1Å, b=41.9Å, c=12.8Å11 independent Si/Ge, 28 independent O
Jiang et al., Science 333, 1131 (2011)
Solved ab-initio withkinematical (1-scatter) approximation
Ihkl ~ Fhkl2
by direct methods
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Space group: C2/mCompleteness (0.8Å): 74%
Rsym(I): 13.5%
How accurate?(Na,□)5[MnO2]13
S-XRPD Rietveld
EDT Kinematical
EDT Dynamical
<Mn1-O> 191 185 191<Mn2-O> 194 196 194<Mn3-O> 191 190 190<Mn4-O> 201 193 194<Mn5-O> 192 189 192<Mn6-O> 188 191 191<Mn7-O> 195 195 198
R1: 17.1%
Structure refinement from precession electron diffraction data. L. Palatinus, D. Jacob, P. Cuvillier, M. Klementová, W. Sinkler, L.D. Marks, Acta Crystallogr A 69, 171 (2013).106
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Dynamical refinement
R(obs) = 0.0698 wR(obs) = 0.0767 R(all) = 0.2411 wR(all) = 0.0899 GOF(obs) = 2.23 GOF(all) = 1.56
Mn2– Mn4– Mn7–O2 200 O6 208 O3 218O4 197 O8 197O1 x2 194 O7 x2 193 O5 x2 192O3 x2 188 O9 x2 187 O12 x2 193
(Na,□)5[MnO2]13 nanorods: a new tunnel structure for electrode materials determinedab initio and refined through a combination of electron and synchrotron diffraction data.E. Mugnaioli, M. Gemmi, M. Merlini, M. Gregorkiewitz, Acta Crystallogr B 72, 893 (2016).
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Dynamical refinement
Hydrogen positions in single nanocrystals revealed by electron diffraction. L. Palatinus, P. Brázda, P. Boullay, O. Perez, M. Klementová, S. Petit, V. Eigner, M. Zaarour, S. Mintova,Science 355, 166 (2017).
H
H
H
H H
HH
Paracetamol
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Beam-sensitive porous materials – Zeolites
H2ONa+
Complete solution ab-initio
by charge flipping, Owater and Na+ included
Dynamical refinement
Space group: Fdd2
a=18.3Å, b=18.6Å, c=6.6Å
10 independent atoms
V = 2250 Å3
1 μm
Natrolite
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O-H distances: 1.1-1.3 Å
The water molecule plane is orthogonal to the Na-Na axis
Detection of hydrogen atoms of H2O molecule trapped into natrolitechannel
Maxima in the difference Fourier map after dynamical
refinement
R(obs) = 15.05%
Dynamical refinement
Single-crystal analysis of nanodomains by electron diffraction tomography: mineralogy at the order-disorder borderline. E. Mugnaioli, M. Gemmi,Z Kristallogr, doi: 10.1515/zkri-2014-1805.
110
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Structure intrinsically disordered
Denisovite
Vaterite
Rozhdestvenskaya et al., IUCrJ 4, 223 (2017)
R1: 31.7%
111
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Mugnaioli et al., Angew Chem Int Ed 51, 7041 (2012)
R1: 37.6%
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Non-homogeneous intensity degradation during the acquisition
Structural Characterization of Organics Using Manual and Automated Electron Diffraction. U. Kolb, T.E. Gorelik, E. Mugnaioli, A. Stewart, Polym Rev 50, 385 (2010).
Low resolution data
The real limit: Beam sensitivityB
eam
sen
sibl
e sa
mpl
es
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O O
CC C
CCC
NN
NZn
Cl
0
10
20
30
40
50
60
Zn Cl O N Cl H
electrons
x-rays
Due to the Coulomb interaction, in theory electrons can detect more easily light atoms, down to H+
Theoretical data
Organics and ED
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Acquisition area shift
200 nm
Nanodiffraction
30-50 nm/Ø
300 nm C2 aperture
Automatic routine for crystal tracking in
STEM
Liquid N2 temperature
Beam damage reduction
Electron dose rate ~ 15 e/Å2s 114
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Single electron detector (MEDIPIX)
Ab initio structure determination of nanocrystals of organic pharmaceutical compounds by electron diffraction at room temperature using a Timepix quantum area direct electron detector. E. van Genderen, M.T.B. Clabbers, P.P. Das, A. Stewart, I. Nederlof, K.C. Barentsen, Q. Portillo, N.S. Pannu, S. Nicolopoulos, T. Gruene, J.P. Abrahams, Acta Crystallogr A 72, 236 (2016).
115
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Continuous (fast) acquisition
Dhexp
Dhdead
Dhexp = 0.14°
Dhdead = 0.29°
Dhtot = 0.43°
Standard CCD camerabinning 4 (512x512 px)
Exposure: 0.5 s
Fast electron diffraction tomography. M. Gemmi, M.G.I. La Placa, A.S. Galanis, E.F. Rauch, S. Nicolopoulos, J Appl Crystallogr 48, 718 (2015).
116
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Continuous (fast) acquisition
Dhexp
Dhdead
Dhexp = 0.14°
Dhdead = 0.29°
Dhtot = 0.43°
Standard CCD camerabinning 4 (512x512 px)
Exposure: 0.5 s
Dhexp = 0.83°
Dhdead = 0.08°
Dhtot = 0.91°
Timepix detector512x512 px
Exposure: 0.45 s
Fast electron diffraction tomography. M. Gemmi, M.G.I. La Placa, A.S. Galanis, E.F. Rauch, S. Nicolopoulos, J Appl Crystallogr 48, 718 (2015).
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MEDIPIX detector
Liquid N2
cryo-transfer sample holder
DigiSTAR for precession electron diffraction and
ASTAR for orientation mapping
TEM at CNI@NEST – Pisa
in-column Ω energy filter
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Very beam sensitive porous materials
Zeolite – ITQ-57MOF – NP164
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Pharmaceutics
200 nm
120
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Proteins
Electron crystallography of ultrathin 3D protein crystals: Atomic model with charges.K. Yonekura, K. Kato, M. Ogasawara, M. Tomita, C. Toyoshima, PNAS 112, 3368 (2015).
Three-dimensional electron crystallography of protein microcrystals. D. Shi, B.L. Nannenga, M. G Iadanza, T. Gonen, eLife 2, e01345 (2013).
1 μm
Lysozyme
Resolution 2.0 Å
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Proteins
Data acquisition
V Sample preparation
• SAED continuous• NB continuous• Step + precession
V
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Proteins
Cell parameters
Space group
Intensity integration
Phasing
VV
X123
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Concluding remarks• Electron crystallography (both imaging and diffraction) deliver
valuable support for the characterization of nanocrystallinematerials
• … and sometimes, it is the only option!
• Imaging deliver information on the ‘local structure’ of thematerial and on grain boundary relations and disorder features
• Electron diffraction (tomography) delivers more complete andhigher resolution 3D structural data and often allows todetermine the atomic structure of the phases present in the sample
• The current challenge is the possibility to work with more andmore beam sensitive materials: porous materials, very hydratedmaterials, organics, macromolecules
• A TEM, an expensive machine, but that can be afforded by asingle University, or actually by a single Research Institute 124
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Acknowledgements
Thank you for your attention!
Ute Kolb, Tatiana Gorelik – Johannes Gutenberg University of Mainz
Mauro Gemmi, Arianna Lanza, Valentina Capello – Istituto Italiano di Tecnologia@NEST Pisa
Stavros Nicolopoulos – NanoMEGAS
125