Tuesday 30 August
Time Amphithéâtre Salle Bellecour 1,2,3 Salle Prestige Gratte Ciel Salle Gratte Ciel 1&2 Salle Tête d'or 1&2 Salon Tête d'Or Salle Gratte Ciel 3
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Plenary Lecture 3

Plenary Lecture 3

08:45 - 09:45 Plenary Lecture 3 - Can phase manipulation turn TEM into an even more versatile instrument? Johan VERBEECK (BELGIUM)

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The Skin Imaging Society meeting
SLOT III (posters)

The Skin Imaging Society meeting
SLOT III (posters)

08:45 - 09:45 Session 3. Posters – free visit, discussion with the presenters.

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IM2: Micro-Nano Lab and dynamic microscopy

IM2: Micro-Nano Lab and dynamic microscopy

Chairmen: Francisco José CADETE SANTOS AIRES (VILLEURBANNE CEDEX, FRANCE), Niels DE JONGE (Saarbrücken, GERMANY), Gerhard DEHM (Düsseldorf, GERMANY)
10:15 - 10:45 #8421 - IM02-S36 Scanning Probe Microscopy goes Live: seeing dynamic phenomena with STM.
Scanning Probe Microscopy goes Live: seeing dynamic phenomena with STM.

Scanning Tunneling Microscopy (STM) and other forms of Scanning Probe Microscopy (SPM), are traditionally applied mainly to static structures that are investigated mainly under relatively artificial conditions, such as ultrahigh vacuum (UHV). This is surprising in the light of the relative insensitivity of the operation mechanism of STM and that of most other types of SPM to such aspects as temperature or gas pressure or even the presence of liquids.

In this talk, I will demonstrate that it is possible to apply SPM techniques without compromising their atomic resolution even under harsh conditions [1-4]. Extra attention is required to construct the SPM instrumentation such that it avoids the complications that are introduced by these conditions, such as excessive thermal drift or damage to delicate components. This is, in principle, a straightforward engineering task, which leads typically to dedicated designs for specific classes of imaging conditions [1-4].

The examples provided in this talk are all live STM observations of relevant dynamic surface phenomena. They range from model catalysts under the conditions of high temperatures and high pressures at which they are being used in the chemical industry, to the chemical vapor deposition of graphene on metal substrates and the atom-by-atom deposition or erosion of surfaces under the influence of atom and ion beams.


1.  M.S. Hoogeman et al., Rev. Sci. Instrum. 69, 2072 (1998).

2.  M.J. Rost et al., Rev. Sci. Instrum. 76, 053710 (2005).

3.  C.T. Herbschleb et al., Rev. Sci. Instrum. 85, 083703 (2014).

4.  S.B. Roobol et al., Rev. Sci. Instrum. 86, 033706 (2015).

5.  G. Dong, D.W. van Baarle, M.J. Rost and J.W.M. Frenken, ACS Nano 7, 7028  (2013).

10:45 - 11:00 #5751 - IM02-OP058 Operando electron microscopy in heterogeneous catalysis.
Operando electron microscopy in heterogeneous catalysis.

Visualizing nanoparticles at atomic-resolution by transmission electron microscopy (TEM) is beneficial for the understanding of their physico-chemical properties. However, nanoparticles respond dynamically to changes in the surrounding gas or liquid environment, and such changes can have profound impact on their properties. It has therefore remained a long-standing challenge in heterogeneous catalysis and related chemical fields to functionalize TEM for operando studies in which the state and functionality of nanoparticles are simultaneously evaluated at the atomic-scale under catalytically meaningful reaction conditions [1].

Recent, we have developed a nanoreactor that enables atomic-resolution TEM of catalysts at ambient pressure conditions and elevated temperatures [2-5]. The nanoreactor is a micro-electro-mechanical system (MEMS) device that integrates a micrometer-sized and unidirectional gas-flow channel with a micro-heater and an array of electron-transparent SiNx windows (Fig. 1). This nanoreactor design also allows concurrent mass-spectrometry, calorimetry and electron energy loss spectroscopy of changes occuring in the gas phase during catalysis. Hereby, the nanoreactor enables operando TEM studies in heterogeneous catalysis [6].

Here, we showcase operando TEM movies that correlate the atomic-scale dynamics of Pt nanoparticles with their catalytic activity for the CO oxidation at relevant pressure and temperature conditions (Fig. 2) [6,7]. This reaction has long served as the prototypical example for oscillating chemical reactions. The movies surprisingly show that the catalytically active surface sites undergo periodic and reversible changes that are synchronous with the oscillations in the reaction rate. The atomic-resolution TEM was performed under low electron dose-rate conditions to surpress beam-induced alterations [6,8], and the observations were location-dependent due to the mass- and heat-distributions across the reaction zone [6,7]. In interplay with density functional theory, microkinetic and mass- and heat-transport calculations, the operando TEM observations unveiled a mechanism for the oscillatory behavior based on the difference in CO adsorption energy and oxidation rate on the prevalent Pt surface terminations. Thus, operando TEM can extend the description of dynamics and functionality in catalysis with atomic-scale information that is specific to the surface sites, and bridge simultaneously both the so-called materials and pressure gap in catalysis and surface science.


[1] S. Helveg, J. Catal. 328, 102 (2015)

[2] J.F. Creemer, S. Helveg, G.V. Hoveling, S. Ullmann, A.M. Molenbroek, P.M. Sarro, H.W. Zanbergen, Ultramicroscopy 108, 993 (2008)

[3 ] J.F. Creemer, S. Helveg, P.J. Kooyman, A.M. Molenbroek, H.W. Zandbergen, P.M. Sarro, J. Microelectromech. Systm. 19, 254 (2010)

[4] J.F. Creemer, F. Santagata, B. Morana, L. Mele, T. Alan, E. Lervolino, G. Pandraud, P.M. Sarro, Proc. 2011 IEEE  24th Int. Conf. MEMS 1103-1106  (2011)

[5] S.B. Vendelbo, P.J. Kooyman, J.F. Creemer, B. Morana, L. Mele, P. Dona, B.J. Nelissen, S. Helveg, Ultramicroscopy 13, 72 (2013)

[6] S.B. Vendelbo, C.F. Elkjær, I. Puspitasari, J.F. Creemer, P. Dona, L. Mele, B. Morana, B.J. Nelissen, R. van Rijn, P.J. Kooyman, S. Helveg, Nature Mater 13, 884 (2014)

[7] C.F. Elkjær, S.B. Vendelbo, P. Kooyman, S. Helveg, in preparation  (2016)

[8] S. Helveg, C.F. Kisielowski, J.R. Jinschek, P. Specht, G. Yuan, H. Frei, Micron 68, 176 (2014)

Christian F. ELKJÆR, Søren VENDELBO, Patricia J. KOOYMAN, Stig HELVEG (Kgs. Lyngby, DENMARK)
11:00 - 11:15 #7066 - IM02-OP078 High resolution environmental TEM investigation of the catalytic channeling of few-layer graphene.
High resolution environmental TEM investigation of the catalytic channeling of few-layer graphene.

As the 2D graphene flakes are zero-gap semiconductors, one strategy proposed for the fabrication of graphene structures with a finite bad gap was its patterning in quasi-one dimensional (1D) shapes called graphene nanoribbons (GNRs)1. Several methods have been developed to fabricate GNRs, such as direct chemical routes2, unzipping carbon nanotubes3 or graphene/FLG flakes nanopatterning4. The catalytic nanopatterning of FLG using metallic nanoparticles (MNPs) as “nanoscissors” is one of the most promising methods. Under well-controlled conditions, a number of MNPs supported on graphene-based structures act as mobile nanoreactors able to pattern the graphene support with a nanometer precision. At the origin of the nanoparticles’ “graphene cutting” lies their capacity to dissolve carbon and catalyze, at high temperatures, gas-carbon reactions. Transmission electron microscopy (TEM) plays an important role in the investigation of the metal-catalyzed gas-graphite reactions. However, ex-situ TEM approach offers a limited perspective over the dynamic behavior of the catalyzed reaction. Environmental TEM (ETEM) is a more appropriate technique for investigating dynamical processes, offering in real-time imaging and chemical analyses at atomic resolution.

            In this study we present a complete ETEM investigation of the catalytic nanopatterning of FLG by metallic iron nanoparticles (FeNPs) performed in a dedicated environmental Atmosphere (Protochips) cell.  At first the influence of a number of parameters, such as the structure of the initial magnetite nanoparticles on the channeling activity is carefully investigated. This analysis shows that incompletely reduced FeNPs cannot sustain a well-defined channeling activity that is specific only for pure metallic FeNPs for which a specific crystallographic orientation formed between the metallic nanoparticle and the graphene edge is controlling their motion. In the second part, the ETEM reaction setup is controlled at such an extent that it allows the real-time imaging of nanoparticles at high resolution. We show that the nanoparticles’ frontal facets, i.e. the facets sustaining the carbon dissolution from the graphene edges, presents a continuous nanometer-sized “waving” during the channeling activity as an effect of the constant carbon dissolution and its diffusion from the contact area to the rear facets of the nanoparticle. The real-time imaging of the rear facet of the nanoparticle shows an even more interesting phenomenon, e. g. the formation of graphitized nanosized carbon structure with a very short lifetime as well as of amorphous carbon tails. Their location together with their evolution during channeling reveals important aspects concerning catalytic channeling mechanism. The last part deals with a number of aspects related with the nanoparticles motion on the graphene subtracted such as the changes in the channeling direction or the channeling rates. As shown in Fig. 1, the changes in the cutting directions are a very complex phenomenon where the restructuration of the nanoparticle and especially the rearmament of the frontal faceting geometry play the most important role. The causes of the cutting directions changes can be separated in two categories, one related with a gradient of the carbon dissolved in the nanoparticle and one caused by “external” uncontrolled factors as the position fluctuations of the carbon tail.

1. Han, M., Özyilmaz, B., Zhang, Y. & Kim, P. Energy Band-Gap Engineering of Graphene Nanoribbons. Phys. Rev. Lett. 98, (2007).
2. Narita, A. et al. Synthesis of structurally well-defined and liquid-phase-processable graphene nanoribbons. Nat. Chem. 6, 126–132 (2014).
3. Jiao, L., Zhang, L., Wang, X., Diankov, G. & Dai, H. Narrow graphene nanoribbons from carbon nanotubes. Nature 458, 877–880 (2009).
4. G. Melinte, I. Florea, S. Moldovan, I. Janowska, W. Baaziz, R. Arenal, A. Wisnet, C. Scheu, S. Begin-Colin, D. Begin, C. Pham-Huu, O. Ersen, Nat Commun. 5, 2014.

11:15 - 11:30 #6344 - IM02-OP066 Using in situ environmental transmission microscopy and operando X-ray absorption spectroscopy to investigate ceria based diesel oxidation catalysts.
Using in situ environmental transmission microscopy and operando X-ray absorption spectroscopy to investigate ceria based diesel oxidation catalysts.

A knowledge-based design of catalysts requires the determination of so-called structure-activity-relationships. Such correlations between the catalytic activity and its properties on the microscopic and macroscopic scales help to identify new routes for improving state-of-the-art and to develop new generations of catalytic systems. However, in particular at the microscopic level, certain properties of the catalyst, like for example the oxidation state and the morphology of noble metal nanoparticles, can be influenced by the temperature and the atmosphere [1, 2]. As a consequence, it is mandatory to obtain such information under working conditions ("operando").

This accounts in particular for automotive exhaust gas catalysts [3-5]. In the present study, ceria supported catalysts were investigated for application as diesel oxidation catalysts. In contrast to catalysts not supported on ceria, their activity strongly depended on the pre-conditioning. As previously observed, the activity could be significantly enhanced with respect to low temperature CO and hydrocarbon oxidation, by short reducing pulses (lean/rich-treatment) at moderate temperatures [6]. Since such treatments could be exploited in a car from the technological point of view it is of high interest to understand the origin and the mechanism of this activation step. Hence, a comprehensive approach was applied appreciating especially the importance of a catalyst characterization in relevant conditions (pressure and temperature). In this regard in situ environmental transmission electron microscopy (ETEM) was applied together with operando quick-scanning X-ray absorption spectroscopy (QEXAFS).
According to the QEXAFS data obtained on Pt/CeO2/Al2O3 the low temperature activity of the catalyst was found to be improved (Figure 1), after the Pt oxidation state got reduced  effectively during a lean/rich treatment (Figure 2), e.g. by using CO as reductant. After activation, however, the catalyst got deactivated again during the subsequent light-off experiment, if treated at too high temperature, accompanied by Pt oxidation. Complementary  ETEM studies offered a closer look on the processes on the catalyst surface, e.g. of a reductively treated Pt/CeO2 catalyst in an oxidizing atmosphere at elevated temperatures (10 mbar O2, 400 °C). Prominent structural changes were found depending on the reaction atmosphere. Upon treatment similar to those where XAS evidenced deactivation of the catalyst and Pt oxidation, the disappearance of most of the smallest Pt particles was observed (Figure 3) and a lower number of larger particles were found to remain. The disapperance of small Pt particles could represent a possible deactivation pathway due to redispersion of Pt atoms at elevated temperatures. Hence, ETEM experiments confirmed the strong structural dynamics at the microscopic level of the catalyst, which probably represent the origin of the catalysts activation and deactivation and will be further exploited in future.

[1] Weckhuysen B M, In situ Spectroscopy of Catalysts, American Scientific Publishers (2004) 255-270
[2] Grunwaldt J-D, Wagner J B and Dunin-Borkowski R E, ChemCatChem 5 (2013) 62-80
[3] Deutschmann O and Grunwaldt J-D, Chem. Ing.Tech. 85 (2013) 595-617
[4] Doronkin D E, Casapu M, Günter T, Müller O, Frahm R and Grunwaldt J-D, J.Phys.Chem.C. 118 (2014) 10204-10212
[5] Gänzler A M, Casapu M, Boubnov A, Müller O, Conrad S, Lichtenberg H, Frahm R and Grunwaldt J-D, J. Catal. 328 (2015) 216-224
[6] Hoyer R, Schuler A, Franoschek S, Pauly T R and Jeske G, WO 2013/149881 A1, October 22, 2014

[7] The authors thank the BMBF-ANR project ORCA (Oxidation-Reduction-Catalyst, BMBF-19U15014B, ANR-14-CE22-0011-02) for financial support, the synchrotron beamlines SuperXAS (SLS, Villigen), ROCK (SOLEIL, Paris) and XAS (ANKA, Karlsruhe) for beamtime and the CLYM for access to the Ly-EtTEM.

Andreas M. GÄNZLER (Karlsruhe, GERMANY), Maria CASAPU, Géraldine FERRE, Francisco J. CADETE SANTOS AIRES, Mimoun AOUINE, Christophe GEANTET, Thierry EPICIER, Philippe VERNOUX, Jan-Dierk GRUNWALDT
11:30 - 11:45 #5261 - IM02-OP055 In-situ E(S)TEM Observations of Single Atom Dynamics in Catalytic Reactions.
In-situ E(S)TEM Observations of Single Atom Dynamics in Catalytic Reactions.

In heterogeneous catalysis gas (or liquid)-solid catalyst reactions take place at the atomic level at elevated temperatures. Understanding and control of complex catalytic reactions on the atomic scale are crucial for the rational development of improved catalysts and processes. The development of the first atomic resolution environmental (scanning) transmission electron microscope (E(S)TEM) is described (1-6) including for the direct visualisation of reacting individual atoms in gas-solid reactions in the working state in real time (3-6), opening up striking new opportunities for studies of catalysis at the atomic level.  Our development of the atomic resolution ETEM (2) is now used globally.  Benefits of the in-situ studies include new knowledge, improved and more environmentally beneficial technological processes for healthcare and renewable energy as well as better or replacement mainstream technologies in the chemical and energy industries.

Examples include heterogeneous catalysis of biomass conversion into bioenergy and water gas shift (WGS) reaction (employing carbon monoxide and water) which is the basis of heterogeneous catalysis important in the generation of clean hydrogen energy for fuel cells, transportation fuels and in ammonia manufacture (7). Potential supported noble metal catalysts are examined for low temperature WGS catalysis (Fig.1) and compared with reaction data and modelling. The in-situ observations in WGS have revealed the formation of clusters of only a few noble metal atoms resulting from single atom dynamics and the catalytic effect of low coordination surface sites.  The new insights have important implications for applications of nanoparticles in chemical process technologies including for transportation fuels and emission control.



1. P.L. Gai, et al: Science 267 (1995) 661.
2. E.D. Boyes and P.L. Gai, Ultramicroscopy  67 (1997)219.
3. P.L. Gai and E.D. Boyes, Microscopy Research and Tech. 72 (2009) 153.
4. E.D. Boyes, M. Ward, L. Lari and P.L. Gai, Ann. Phys. (Berlin) 525 (2013) 423.
5. P.L. Gai, L. Lari, M. Ward and E.D. Boyes, Chemical Physics Letters, 592 (2014) 355.
6. E.D. Boyes and P.L. Gai, Comptes Rendus Physique, 15 (2014) 200.
7. P.L. Gai, K. Yoshida, M R Ward, M Walsh, E D Boyes, et al : Catal. Sc. Tech.  2015:  DOI: 10.1039/c5cy01154j
8.Email :  pratibha.gai@york.ac.uk  


We thank the EPSRC (UK) for the strategic critical mass research grant EP/J018058/1.

Pratibha GAI (YORK, UK), Kenta YOSHIDA, Michael WARD, Edward BOYES
11:45 - 12:00 #5360 - IM02-OP056 Aberration corrected environmental STEM (AC ESTEM) for atom-by-atom analysis of nanoparticle catalyst activation and deactivation mechanisms.
Aberration corrected environmental STEM (AC ESTEM) for atom-by-atom analysis of nanoparticle catalyst activation and deactivation mechanisms.

The core design for the modern ETEM (1, 2), of which there are now some 20 replicates worldwide, has been modified to support full ESTEM functionality and to be compatible with a different basic instrument, in this case the JEOL 2200, with a series of differentially pumped column sections separated by fixed beamline apertures reconfigured for purpose in size and position.  Single atom resolved HAADF imaging and full analytical functionalities, including wide angle electron diffraction, CBDP, EDX and EELS, are enabled under controlled chemical reaction conditions of high temperatures in a continuously flowing gas atmosphere around the supported nanoparticle catalysts samples while retaining sub-Angstrom resolution and single atom sensitivity for atom-by-atom analysis of critical processes.  The novel AC ESTEM machine at York provides new insights into the processes of metal nanoparticle catalyst activation, operational state and deactivation (3) which have economic and other societal importance, including for scientifically informed environmental management.   At typical 2-20Pa gas pressures the gas supply covers the sample surface with multiple 1000s of monolayers of gas per second and generally fully adequate to continuously flood the surface with gas molecules.  They drive the chemistry under conditions defined in surface science as 'high pressure' (4) and minimise e-beam driven artefacts.  Catalysis is a massive industry with highly leveraged investments in processes and plants.  However, in many applications, including automotive emission controls (5), it is still relatively inefficient compared to what might be possible with a better informed knowledge base generating strategies to restrain deactivation processes.   The unique to York AC ESTEM supports quantitative atom-by-atom analysis of the underlying mechanisms of Ostwald Ripening (OR) through atom detachment, migration and re-attachment at lower temperatures around constant particle centres of gravity (6,).  This is compared with (and sometimes mixed with) higher temperature modes of particle migration and coalscence (PMC), with local nanostructure attributes in the round influencing local outcomes.  Neither process is found to be sensitive to gas pressure at 2-20Pa levels.   Both mechanisms have now been studied with new levels of precision using the novel capabilities at York; leading to a better informed understanding of the technical problems and options and helping to specify the enabling developments needed going forward.

1. E D Boyes and P L Gai, Ultramicroscopy, 67 (1997) 219
2. P L Gai et al, MRS Bulletin, 32 (2007) 1044
3. E D Boyes, M R Ward, L Lari and P L Gai, Ann Phys, 525 (2013) 423
4. G Somorjai et al, Phys Chem Chem Phys, 9 (2007) 3500
5. M R Ward et al Chem Cat Chem, 4 (2012) 1622
6. T E Martin et al Chem Cat Chem. 7 (2015) 3705

The EPSRC (UK) is supporting the AC ESTEM development and applications at York under strategic research grant EP/J018058/1 

Edward BOYES (York, UK), Michael WARD, Thomas MARTIN, Leonardo LARI, Robert MITCHELL, Alec LAGROW, David LLOYD, Ian WRIGHT, Pratibha GAI
12:00 - 12:15 #5825 - IM02-OP059 In-situ observations of nanoparticles of carbon supported copper electrocatalyst during electrochemical cycling.
In-situ observations of nanoparticles of carbon supported copper electrocatalyst during electrochemical cycling.

Microwave assisted synthesis of metallic nanoparticles is an attractive way for the elaboration of electrocatalysts using energy efficient processes. This method consists in the use of a weak reducing agent that acts as solvent with high boiling point at the same time. Among the possible solvents, diethylene glycol is one of the most suitable molecules for microwave absorption and heating. Since microwave energy leads to a more uniform heat-treatment than a conventional heating process, the overall activation energy for metal ion reduction decreases under microwave exposure. The carbon supported copper catalyst described herein is a good candidate for electrocatalytic processes due to the fact that copper is an abundant and effective transition metal for a number of reactions.

Observations were conducted in a Tecnai G2 fitted with a FEG, an EDX spectrometer and GIF Quantum. STEM-HAADF was the primary technique of image recording. Scan speed was kept high in order to follow the kinetic of the evolution of the system. In this experiment, we use a sealed TEM cell recently developed by Protochips , i.e. liquid/bias TEM specimen holder (Poseidon 510). This system permits to study materials under electrochemical environment in TEM instrument. The sample (Copper nanoparticles on carbon) that is inside the sealed TEM cell (liquid gap is from 500 nm to 3000 nm) is immersed in the liquid electrolyte introduced by micro-fluidic system (here aqueous electrolyte KCl/H2O at 0.01ML) and then electrochemically cycled using designed working electrode (glassy carbon) on transparent SixN1-x windows. For electrochemical measurement, the applied currents were between 100 nA and 500 nA. Voltammogram was taken to ensure the correct oxidation and reduction of the copper atoms during a cycle. A strong corrosion of the supporting carbon is then observed. Experiments at constant current (chronopotentiometry) show the coalescence of large Cu grains and their disappearance depending on the applied current (See figure 1 and 2). Gas bubble formation is also observed (Figure 3). In these specific liquid experiments, optimized conditions remain to be found for TEM observation and in-situ cycling, especially for electrocatalysis which is particularly demanding in terms of control of the experimental condition.



Jerome PACAUD (Chasseneuil), Arnaud DEMORTIERE, Walid DACHRAOUI, Niat Ege SAHIN, Aurelien HABRIOUX, Clément COMMINGES, Tekko NAPPORN, Boniface KOKOH, Stephane AGUY
12:15 - 12:30 #6539 - IM02-OP070 The Dynamics of Active Metal Catalysts Revealed by In-Situ Electron Microscopy.
The Dynamics of Active Metal Catalysts Revealed by In-Situ Electron Microscopy.

Conventional high-resolution imaging by electron microscopy plays an important role in the structural and compositional analysis of catalysts. However, since the observations are generally performed under vacuum and close to room temperature, the obtained atomistic details describe an equilibrium state that is of limited value when the active state of a catalyst is in the focus of the investigation. Since the early attempts of Ruska in 1942 [1], in situ microscopy has demonstrated its potential and, with the recent availability of commercial tools and instruments, led to a shift of the focus from ultimate spatial resolution towards observation of relevant dynamics. [2]

During the last couple of years we have implemented commercially available sample holders for in situ studies of catalysts in their reactive state inside a transmission electron microscope. In order to relate local processes that occur on the nanometer scale with collective processes that involve fast movement of a large number of atoms, we have furthermore adapted a commercial environmental scanning electron microscope (ESEM) for the investigation of surface dynamics on active catalysts. Using these two instruments, we are now able to cover a pressure range from 10-4 to 103 mbar and a spatial resolution ranging from the mm to the sub-nm scale by in situ electron microscopy.

Presently we are investigating the behavior of metal catalysts during hydrocarbon partial oxidation and decomposition reactions as well as structural dynamics during oscillatory red-ox reactions.
The observations are performed in real-time and under conditions in which the active state of the catalyst can be monitored by on-line mass spectroscopy. The latter is of upmost importance, since the key requirement is to observe relevant processes and dynamics that are related to catalytic function.

The ability to directly image the active catalyst and associated morphological changes at high spatial resolution enables us to refine the interpretation of spatially averaged spectroscopic data that was obtained under otherwise similar reaction conditions, for example during near-ambient-pressure in situ XPS measurements. [3]

It will be shown that the ability of observing the adaption of an active surface to changes in the chemical potential of the surrounding gas phase in real-time potentially offers new and direct ways of optimizing catalysts and applied reaction conditions. One of the examples that will be demonstrated is the dynamic state of copper, where the simultaneous and very dynamic formation of oxidized and reduced islands is observed during red-ox conditions in different atmospheres and on different length scales (Figure 1). Direct observation of active catalysts, such as shown in this contribution, will have a big impact on our understanding of their function. It is already clear that some of the assumptions that were published in the catalysis literature on the basis of TEM observations made in vacuum, have to be revised.



[1]   E. Ruska, Kolloid-Zeitschrift, 1942, 100, 2, 212-219

[2]   S. B. Vendelbo, et al., Nat. Mater. 2014, 13, 884–890

[3]   R. Blume, et al., PhysChemChemPhys, 2014, 16, 25989

Jing CAO, Ramzi FARRA, Zhu-Jun WANG, Ali RINALDI, Robert SCHLÖGL, Marc Georg WILLINGER (Berlin, GERMANY)

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MS6 : Oxide-based, Magnetic and other Functional materials

MS6 : Oxide-based, Magnetic and other Functional materials

Chairmen: Etienne SNOECK (Toulouse, FRANCE), Maria VARELA (Madrid, SPAIN)
10:15 - 10:45 #8639 - MS06-S80 Recent applications of high energy and spatial resolution STEM-EELS to energy harvesting materials.
Recent applications of high energy and spatial resolution STEM-EELS to energy harvesting materials.

A new generation of electron beam monochromators has recently pushed the energy resolution of (scanning) transmission electron microscopes deep into the sub 20meV range [1]. In addition to the obvious increase in resolution which has made exploring the phonon region of the EELS spectrum possible [1], the increased flexibility of these instruments is proving hugely advantageous for materials science investigations. The energy resolution, beam current and electron optics can be adjusted seamlessly and traded off each other as necessary within a greatly increased range, as will be illustrated on a number of systems studied using a Nion UltraSTEM100MC ‘Hermes’ instrument recently installed at the SuperSTEM Laboratory.

This added flexibility was essential in particular in studying the crystal structure of Li- and Mn-rich transition metal oxides, whose pristine state is not yet fully understood in spite of their great potential as high-capacity cathode materials for Li-ion batteries. Only through complementary electron microscopy and spectroscopy techniques at multi-length scale could the structural make-up of Li1.2(Ni0.13Mn0.54Co0.13)O2 crystals be described unambiguously. Systematically observing the entire primary particles along multiple zone axes (Fig. 1) reveals that they are consistently made up of a single phase, save for rare localized defects and a thin surface layer on certain crystallographic facets. More specifically, this careful STEM and EELS study at the atomic scale using revealed that the bulk of the oxides consists of randomly stacked domains that correspond to three variants of monoclinic structure. Crucially, it is also shown that only the very surface is composed of a different Co- and/or Ni-rich spinel with antisite defects [2].

Similarly, atomically-resolved monochromated EELS mapping and imaging were used to study the structure and chemistry of promising complex oxide thermoelectrics such as misfit layered cobaltates [3] or Ca-stabilized A-site deficient titanates [4]. For the latter, careful inspection of images and atomically resolved EELS chemical maps in two orthogonal directions suggests that in the Nd0.6Ca0.10.3TiO3 system, Ca predominantly occupies Nd vacancy shared sites, creating locally a higher occupation of the site and thus promotes short range vacancy-cation ordering in both a and b lattice directions. This in turn results in intricately modulated octahedral tilting distortions of the O sublattice, whose signature can be fingerprinted at the atomic scale through the near-edge fine structure of the Ti (and O) electron energy loss edges [5].

[1] O.L. Krivanek et al., Phil. Trans. Roy. Soc. 367 (2009), pp. 3683-3697; T.Miyata et al., Microscopy 5 (2014), pp. 377-382 ; O.L. Krivanek et al., Nature 514 (2014), pp. 209-212.

[2] A.K. Shukla, Q.M. Ramasse, C. Ophus, H. Duncan, F. Hage and G. Chen, Nature Communications 6 (2015), 8711.

[3] J.D. Baran, M. Molinari, N. Kulwongwit, F. Azough, R. Freer, D. Kepapstoglou, Q.M. Ramasse and S.C. Parker, J. Phys. Chem. C 119 (2015), pp. 21818-21827.

[4] F. Azough, D. Kepaptsoglou, Q.M. Ramasse, B. Schaffer and R. Freer, Chemistry of Materials 27 (2015), pp. 497-507.

[5] The SuperSTEM Laboratory is the U.K. National Facility for Aberration-Corrected STEM, supported by the Engineering and Physical Sciences Research Council (EPSRC). 

Quentin RAMASSE (Warrington, UK), Alpesh SHUKLA, Fredrik HAGE, Demie KEPAPTSOGLOU, Feridoon AZOUGH, Robert FREER
10:45 - 11:00 #6083 - MS06-OP285 Tracking Atoms, Vacancies and Electrons via Aberration-corrected Microscopy and First-Principles Theory.
Tracking Atoms, Vacancies and Electrons via Aberration-corrected Microscopy and First-Principles Theory.

The aberration-corrected scanning transmission electron microscope (STEM) can provide real space imaging and spectroscopy at atomic resolution with a new level of sensitivity to structure, bonding, elemental valence and even spin state [1]. Coupled with first-principles theory, this represents an unprecedented opportunity to probe the functionality of complex nanoscale systems. Two case studies will be presented utilizing the Nion UltraSTEM: first, determining the origin of the unexpected ferromagnetism in ultrathin, insulating LaCoO3-x (LCO) films, which is induced by the spontaneous ordering of oxygen vacancies to relieve misfit strain (see Fig. 1) [2]. Second, the origin of the colossal ionic conductivity in Y-stabilized ZrO2/SrTiO3 superlattices [3], which is due to spontaneous disordering of the oxygen sublattice in response to biaxial strain coupled with the incompatibility of the  oxygen sublattices at the interfaces (see Fig. 2) [4-6].

A JEOL ARM 200F has recently been installed in the National University of Singapore, equipped with UHR pole piece, ASCOR hexapole aberration corrector, Gatan Quantum ER and OneView camera and Oxford Aztec EDS system. It is installed within a JEOL isolated room with thermal radiation panels, vibration and magnetic field isolation systems. Fig. 3 shows a Ronchigram at 200 kV with near 70 mrad half angle flat phase region, and initial results from Si [110] show good splitting of the dumbbells with information transfer to sub-Angstrom levels, see Fig. 4. Results on oxides will be presented at the meeting [7].

  1. J. Gazquez, et al., Nano Lett, 11, 973 (2011).
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DOE BES Materials Science and Engineering Division, European Research Council Starting Investigator Award STEMOX # 239739, Fundación BBVA, DOE Grant No. DE-FG02- 09ER46554, National University of Singapore and JEOL Asia.

Stephen PENNYCOOK (Singapore, SINGAPORE), Maria VARELA, Jaume GAZQUEZ, Nevan BIŠKUP, Juan SALAFRANCA, Timothy PENNYCOOK, Yuyang ZHANG, Haijun WU, Tian FENG, Nagahata MASAHITO, Sokrates PANTELIDES, Thirumalai VENKATESAN
11:00 - 11:15 #4806 - MS06-OP278 Nanoscale Ordering in Oxygen Deficient Quintuple Perovskite Sm2 εBa3+εFe5O15-δ revealed by TEM.
Nanoscale Ordering in Oxygen Deficient Quintuple Perovskite Sm2 εBa3+εFe5O15-δ revealed by TEM.

The introduction of two sorts of cations with different valence and size, such as Ba2+ or Sr2+ and Ln3+, in the A-sites of transition metal perovskite oxides has generated numerous remarkable properties such as high Tc superconductivity,  oxygen storage in cobalt based oxides for the realization of solid oxide fuel cell (SOFC) cathodes , CMR in manganates .

The investigation of the system Sm-Ba-Fe-O in air has allowed an oxygen deficient perovskite Sm2-εBa3+εFe5O15-δ (δ=0.75, ε=0.125) to be synthesized. In contrast to the XRPD pattern which gives a cubic symmetry (ap= 3.934Å), the ED patterns of this phase (Fig.1a) show superstructure spots corresponding to c=5ap”. HRTEM study (Fig1b) revealed that this phase is nanoscale ordered with a quintuple tetragonal cell, “ap ´ ap ´ 5ap”. Bearing in mind that one cubic cell corresponds to the formula Sm0.375Ba0.625FeO2.85, these tetragonal nanostructures can be formulated as Sm2-εBa3+εFe5O15-δ (δ~0.75, ε~0.125). They consist of 5 SmO/BaO layers stacked alternately with 5 FeO2 layers along c. The HAADF-STEM image (Fig.1c) of the Sm2-εBa3+εFe5O15-δ structure along the [100] is clearly established from the contrast segregation that the Ba2+ and Sm3+ cations are ordered in (001) layers along the c-axis. One observes rows of bright dots perpendicular to c, which corresponds to three sorts of Sm or Ba cationic layers, judging from their intensity: pure Sm, mixed Ba/Sm and pure Ba layers. Thus the HAADF-STEM image can be interpreted by the following periodic stacking sequence of the A cationic layers along the c axis: “Sm-Ba-Sm/Ba-Sm/Ba-Ba-Sm”.

It appears from the ABF-STEM images along [100] (Fig.1d) and [110] orientations (Fig.1e) of a single Sm2‑εBa3+εFe5O15-δ domain, that the oxygen positions in all the layers are close to the ideal octahedral positions. However, a closer inspection of the images reveals that the oxygen columns in the equatorial positions close to the Sm layer deviate from their ideal octahedral position, and lie closer to the Sm3+ cations yielding a “zigzag” contrast along [100] and [110].

The “Sm-Ba-Sm/Ba-Sm/Ba-Ba-Sm” chemical ordering is also confirmed by elemental EELS mapping (Fig.2a,b). The spatially resolved EELS data show that the O-K edge spectra corresponding to the “FeO2” planes (labeled A,B,C) exhibit different intensity ratios of the two pre-peaks to the O-K edge, prepeak1/ prepeak2 at approximately 529/531 eV, depending on the nature of the surrounding “Sm,Ba” layers (Fig.2c). The O-K fine structure in the Sm plane is very similar to that of plane A, whereas those of the Ba and Ba/Sm planes are similar to B and C planes respectively. A first observation is that pre-peak 1 at ~529 eV is less intense for oxygen anions close to Sm cations (SmO layers as well as A layers). According to the literature, the height of this pre-peak is generally rather independent of the rare earth element and should be around the same height as pre-peak 2. Pre-peak 2, related to Fe3d eg – O2p hybridized states seems invariant in the structure, apart from the c plane where it is slightly subdued, accompanied by an increase of pre-peak 1 below 530eV. Pre-peak 1 can be attributed to a charge transfer from the eg to the t2g band of Fe (the eg band is usually empty for Fe3+). This increase of pre-peak 1 related to Fe3d t2g – O2p hybridized states is also visible in the Ba/Sm mixed layers, and can be linked to the presence of oxygen vacancies in those planes. This peak is stronger in the C plane suggesting the presence of more vacancies in this plane.The spatially resolved EELS spectra of the Fe-L2,3 edge are plotted in Fig. 2c. The Fe L3 and L2 “white lines” arise from transitions of 2p3/2 → 3d3/23d5/2 (L3) and 2p1/2 → 3d3/2 (L2) and are known to be sensitive to valency and coordination. Our data shows that the A and B FeO2 planes exhibit very similar Fe-L2,3 edges, with an L3 peak maximum at 709.5 eV, and a pre-peak to L3, even if faint at 708 eV. The energy position of the L3 maximum, together with the shape and positions of the L3 and L2 are then indicative of Fe3+ in an octahedral coordination. All the acquired Fe L3 edges are significantly broadened with respect to the plotted references for 6-fold, 5-fold and 4-fold coordinated Fe3+. This broadening can be explained by a change in coordination of the Fe atoms. Bearing in mind that the measured oxygen stoichiometry is 14.25, instead of 15, this suggests that the iron coordination is mainly 6, i.e. octahedral, but may also be mixed with the presence of some FeO5 pyramids in those layers.

The nanoscale ordering of this perovskite explains its peculiar magnetic properties on the basis of antiferromagnetic interactions with spin blockade at the boundary between the nanodomains. The variation of electrical conductivity and oxygen content of this oxide versus temperature suggest potential SOFC applications.

Oleg LEBEDEV (Caen), Stuart TURNER, Vladimir CHEREPANOV, Bernard RAVEAU
11:15 - 11:30 #6257 - MS06-OP289 Monochromated STEM-EELS Analysis of Interface-Induced Polarization in LaCrO3-SrTiO3 Superlattices.
Monochromated STEM-EELS Analysis of Interface-Induced Polarization in LaCrO3-SrTiO3 Superlattices.

Emergent phenomena at complex oxide interfaces continue to attract attention as the basis for a variety of next-generation devices, including photovoltaics and spintronics. Tremendous progress has been made toward understanding the role of interfacial defects, cation intermixing, and film stoichiometry in single heterojunction systems; however, the techniques commonly used to study these interfaces, such as X-ray photoelectron and absorption spectroscopies, are either sensitive only to near-surface regions or do not offer depth resolution to probe individual interfaces. Here we explore the induced polarization in superlattices of LaCrO3 (LCO) and SrTiO3 (STO) using a combination of aberration-corrected scanning transmission electron microscopy (STEM) and monochromated electron energy loss spectroscopy (STEM-EELS). We show that a correlative approach, utilizing an array of local and non-local probes, is necessary to fully understand the defect-mediated origin of the induced polarization in this system.


We have conducted detailed structural characterization of several LCO-STO superlattices, as shown in Figure 1. We employ high-angle annular dark field imaging (STEM-HAADF) to directly measure the induced ferroelectric polarization in the STO layers. We first acquire a relatively high-speed time series of multiple fast frames (0.4 µs px-1), which are then aligned using both rigid and non-rigid registration to remove both sample drift and scan distortion [1]. Using this procedure we directly measure the induced polarization with picometer precision, as we have demonstrated elsewhere [2]. Our results reveal that the built-in asymmetric potential across the LCO / STO interfaces is sufficient to induce a sizable polarization, on the order of 40-70 µC cm-2, in good agreement with ab initio calculations [3].


We next perform detailed characterization of chemical intermixing and local electronic fine structure changes to explore how defects affect the induced polarization. Figure 2 shows the result of monochromated EELS measurements of the Ti L23 edge fine structure, overlaid onto the integrated Ti L23 edge signal. An improved energy resolution of better than 0.120 eV allows us to observe significant Ti intermixing through the superlattice, as well as subtle fine structure changes in the vicinity of the LCO layers not apparent in earlier data. Mapping the Ti L3 t2geg crystal field splitting across the film, we find evidence consistent with a slight reduction in Ti valence from 4+ to 3+ in the vicinity of the LCO layers, possibly the consequence of La3+ substitution for Sr2+ or oxygen vacancies. Measurements of the Ti L3 t2g / eg ratio also point toward such a trend: moving from the STO toward the LCO layers the ratio begins to decrease within the intermixed region, indicating a redistribution of electrons from t2g to eg states, suggesting a reduction in valence. In light of these results, our experimental STEM-HAADF measurements and accompanying ab initio calculations indicate that the induced polarization is robust against even sizable chemical intermixing and defect formation.


[1] Jones, L. et al, “Smart Align – a new tool for robust non-rigid registration of scanning microscope data”, Advanced Structural & Chemical Imaging 1:8 (2015).

[2] Spurgeon, S. R. et al, “Polarization screening-induced magnetic phase gradients at complex oxide interfaces.” Nat. Commun. 6, 1–11 (2015).

[3] Comes, R.B. et al, “Interface-induced Polarization in SrTiO3-LaCrO3 Superlattices.” Adv. Mater. Int. (2016). DOI: 10.1002/admi.201500779

Steven SPURGEON, Despoina KEPAPTSOGLOU (Daresbury, UK), Lewys JONES, Ryan COMES, Quentin RAMASSE, Phuong-Vu ONG, Peter SUSHKO, Scott CHAMBERS
11:30 - 11:45 #6783 - MS06-OP293 Mapping cation-vacancy ordering and oxygen octahedral distortions in A-site deficient perovskites by monochromated core-loss EELS.
Mapping cation-vacancy ordering and oxygen octahedral distortions in A-site deficient perovskites by monochromated core-loss EELS.

A–site defficient perovskites are of particular interest for a range of engineering applications, such as ionic conductors, batteries and thermoelectric materials. The attraction of these systems lies in particular in their chemically stability over a wide range of compositions and operating conditions. Moreover, they can exhibit different degrees structural ordering, such as cation-vacancy or oxygen-octahedral-tilt-domain ordering [1,2] which can significantly affect their macroscopic physical properties.

In this work we combine state-of-the-art monochromated core loss electron energy loss spectroscopy (EELS) measurements with advanced image analysis to investigate the interplay between A-site cation-vacancy ordering and oxygen octahedral tilting domains in a series of Nd2/3xTiO3 double perovskites, exhibiting different degrees of structural ordering as a function of their heat treatment. [3,4] As a result they exhibit vastly different thermoelectric properties related to the presence of domain boundaries which  can suppress the thermal conductivity due to increased phonon scattering. [5,6]

 High-angle annular-dark-field (HAADF) imaging and large scale atomically-resolved EELS maps were used to investigate the chemical ordering of cations on the so-called A site of the perovskite structure (Figure 1), while pm-precision annular bright field (ABF) imaging of these compounds reveals the presence of TiO6 tilting domains, which we show can be correlated with variations in the A-site occupancy (Figure 2).   Furthermore, advanced image analysis of the electron micrographs was used to measure local distortions in the TiO6 lattice

These local distortions are further investigated using atomically-resolved monochromated EELS measurements with an energy resolution better than 0.1eV, in a Nion UltraSTEM 100MC. In particular, measurements of the of the Ti L2,3 edge (Figure 3), reveal local changes of the near-edge fine structure, usually not discernible with conventional EELS measurements. Changes in the Ti L2,3 pre-peak intensity, as well as subtle local variations in the Ti L3 eg/tg intensity ratios, clearly observable thanks the relatively high beam current still available at this energy resolution, are indicative of local distortions in the oxygen octahedral sublattice.


[1] D.M. Smyth, Annu. Rev. Mater. Sci. 15, 329 (1985).

[2] M. Labeau, I.E. Grey, J.C. Joubert, H. Vincent, and M.A. Alario-Franco, Acta Crystallogr. Sect. A 38, 753 (1982).

[3] S. Jackson, et al, J. Electron. Mater. 43 (2014) p.2331.

[4] F. Azough, et al, Chem. Mater 27 (2015) p.497.

[5] K. Koumoto, et al, Annu. Rev. Mater. Res. 40 (2010) p.363.

[6] D.J. Voneshen, et a,l Nat Mater 12 (2013) p.1028.

[7] SuperSTEM is the U.K’s national facility for Aberration Corrected STEM funded by EPSRC.  

11:45 - 12:00 #5344 - MS06-OP280 Determining the structure/property relation at oxide interfaces by means of advanced TEM spectroscopy and imaging.
Determining the structure/property relation at oxide interfaces by means of advanced TEM spectroscopy and imaging.

The study of novel physical properties appearing when two materials are interfaced has become one of the major fields of research in solid state physics over the last decade. For example, in the strive for novel non-silicon based electronics, the discovery of the formation of a conductive layer right at the interface region between 2 insulators (for example LaAlO3 and SrTiO3); a so-called two-dimensional electron gas (2DEG) or two dimensional electron liquid appears. Another important example of such emergent phenomena is the appearance of interface magnetism or superconductivity. As the materials involved in those new physical phenomena are often complex oxides, many factors such as strain, oxygen stoichiometry, cation intermixing, oxygen octahedral coupling.…[1,2] have to be considered when discussing their origin. The exact understanding of those phenomena is a key factor in order to turn these research ideas into working devices and in order to search for the most optimal materials.

In parallel, advances in electron microscopy instrumentation and techniques such as the introduction of aberration-correctors of the probe-forming lens have made it possible to achieve sub-angstrom spatial resolution allowing the study of materials on an atom column by atom column basis. High Angle Annular Dark Field (HAADF) combined with Annular Bright Field (ABF) imaging have made it possible to study and understand respectively the cationic and the oxygen sub-lattices in these materials.

As a first example, in the case of a (La,Sr)MnO3 (LSMO) film grown on a NdGaO3 (NGO) substrate, the magnetic easy axis of the LSMO film can be reversed by adding a SrTiO3 (STO) buffer layer between the substrate and the film. Using the statistical analysis of STEM ABF images, we could reveal that even one single STO layer is enough to remove the transferred octahedral tilt of NGO into the LSMO film reversing its magnetic easy axis from the a to the b axis(see ref 1 and figure 1).

In a second part, The appearance of superconductivity in a superlattice of (Sr,Ca)CuO2 (SCCO) and BaCuO2 (BCO) will be investigated. Comparing two different heterostructures where 8 layers of SCCO are sandwiched with STO (no superconductivity) and BCO (superconductivity) the effect of the structure of the different layers (orientation of the CuO2 in the form of planes or chains) on the appearance of superconductivity will be presented.

[1] Z. Liao, M. Huijben, Z. Zhong, N. Gauquelin, S. Macke, R. Green, S. van Aert, J. Verbeeck, G. Van Tendeloo, K. Held, G. A. Sawatzky, G. Koster & G. Rijnders, Nat. Mater. 15 (2016), p.425-431

[2] N. Gauquelin, E. Benckiser, M.K. Kinyanjui, M. Wu, Y. Lu, G. Christiani, G. Logvenov, H. –U. Habermeier, U. Kaiser, B. Keimer & G.A. Botton, Physical Review B 90 (2014), article 195140


J.V., G.V.T. and S.V.A. acknowledge funding from FWO projects G.0044.13N and G.0368.15N.  N.G. and J.V. acknowledge funding from the European Research Council under the 7th Framework Program (FP7), ERC Starting Grant 278510 VORTEX. All authors acknowledge financial support from the European Union under the Seventh Framework Program under a contract for an Integrated Infrastructure Initiative (Reference No. 312483-ESTEEM2).

Nicolas GAUQUELIN (Antwerpen, BELGIUM), Sandra VAN AERT, Johann VERBEECK, Gustaff VAN TENDELOO
12:00 - 12:15 #5052 - MS06-OP279 Point defect driven ferromagnetism in YBa2Cu3O7-x superconductor.
Point defect driven ferromagnetism in YBa2Cu3O7-x superconductor.

Although defects may be seen as detrimental, they play essential roles in many materials. In some complex oxides for instance, they present an opportunity to enhance particular properties, or even engineer new ones. An archetypal example is the high-Tc superconductor YBa2Cu3O7−δ (YBCO), where defects are indispensable to immobilize quantized vortices in the presence of magnetic fields. Therefore, determining the atomic structure of defects is critical to unravel and control their effect on the physical properties. In this talk, we will do precisely that with an unforeseen complex point-defect that leads to an unexpected formation of ferromagnetic clusters embedded within a superconductor. The commonest YBCO defect comprises the doubling of Cu-O chains between Ba-O planes, a ubiquitous intergrowth regardless of the deposition technique. Here, we will unclothe the true nature of this defect using a combination of experiments and theory to provide a complete picture of the structure and chemistry of these intergrowths at the atomic-scale and their effect on the electronic and magnetic properties of YBCO. First, we will show, by means of scanning transmission electron microscopy (STEM), how the system solves the local off-stoichiometry induced by the extra Cu-O chain, removing half of the Cu atoms in selected chains, and the distortions induced by the vacancies. Secondly, we will show using density functional theory (DFT) how the complex structure of these intergrowths affects the electronic properties, and yields a magnetization density that extends into the neighboring Cu-O planes. Finally, we will present X-ray magnetic circular dichroism (XMCD) spectroscopy results, which provide evidence of the theoretically predicted Cu magnetic moments and the presence of a dilute network of magnetic defects within the high-Tc superconducting state, see Figure 1. See for more details “Emerging dilute ferromagnetism in high-Tc superconductors driven by point defect clusters”, Adv. Sci. 2016, 1500295.

12:15 - 12:30 #5880 - MS06-OP281 Structural and Chemical Investigations of Superconducting Lanthanum Cuprate Bilayer Interfaces.
Structural and Chemical Investigations of Superconducting Lanthanum Cuprate Bilayer Interfaces.

Highly adaptable crystal structures of complex oxide materials enable changes in composition and provide the opportunity of fabricating them in different forms e.g., thin films and/or heterostructures. Complex oxide heterostructures show noteworthy electronic properties which are absent in bulk forms, and the phenomena occurring at their interfaces are intriguing. The interest attributed to these structures and interfaces is also related to the wide variety of the functionalities such as ferroelectricity, magnetism, superconductivity etc. [1]. One of the most exciting interface effects is high temperature interfacial superconductivity discovered in heterostructures consisting of non-superconducting layers of insulating La2CuO4 (LCO) and metallic La1.55Sr0.45CuO4 (LSCO). Moreover, cuprate bilayers are also attractive in which the critical temperature can be enhanced remarkably in comparison to single phase systems [2].

Atomic-layer-by-layer oxide molecular-beam epitaxy (ALL-oxide MBE) with its unique capabilities allowed us to synthesize bilayers consisting of 3 unit cells of metallic La1.6M0.4CuO4 layer and 3 unit cells of the undoped insulating (I) LCO layer neither of which is superconducting by its own, where M represents the dopant, namely Sr2+, Ca2+, and Ba2+ which have the same ionic charge but different ionic radii. The bilayers are superconducting with a critical temperature of ~17.0 K, ~37.0 K and ~38.5 K for Ca, Sr and Ba dopants, respectively.

For STEM investigations, a JEOL-ARM 200F STEM equipped with a cold field-emission electron source, a probe Cs corrector (DCOR, CEOS GmbH), a 100 mm2 JEOL Centurio SDD-type EDX detector, and a Gatan GIF Quantum ERS spectrometer was used. High-angle annular dark-field (HAADF) imaging and electron energy-loss spectroscopy (EELS) were performed at probe semi-convergence angles of 20 mrad and 28 mrad, respectively. Collection angles for HAADF and annular bright-field (ABF) images were 75-310 mrad and 11-24 mrad, respectively.

Atomically resolved ABF and HAADF images were simultaneously acquired. HAADF images unveil not only the perfect interfaces between substrate and the bilayers but also the high structural quality (Fig 1a-b). Atomic resolution EELS and energy-dispersive x-ray spectroscopy (EDXS) analyses were conducted to examine elemental distributions across the interfaces. EDXS analyses and EEL spectrum images (SI) reveal different cation redistribution behaviors and lengths depending on the cation size mismatch with respect to the La ionic radius. In Fig.1c the distribution of La and Sr across the interfaces of a Sr-doped bilayer sample is presented, which reveals relatively homogeneous distribution of Sr and also the redistribution of Sr near the interface.

Through ABF imaging, oxygen positions were determined, interatomic distortions (cation – cation and CuO6 octahedra) were measured and correlated with the dopant distributions obtained via chemical analyses. In Fig. 2a two of the quantitatively studied images (i.e. HAADF and ABF), are presented as an overlay and the arrows indicate the nominal interfaces. Figure 2b shows the measured interatomic distances which are indicated with arrows. Results for the different dopants will be presented and correlations with high-temperature interfacial superconductivity will be discussed [3].



[1] H. Y. Hwang et al., Nature Materials, 11 (2012) p.103.

[2] A. Gozar et al., Nature, 455 (2008) p.782.

[3] The research leading to these results has received funding from the European Union Seventh Framework Programme [FP7/2007-2013] under grant agreement n°312483 (ESTEEM2).

Y. Eren SUYOLCU (Stuttgart, GERMANY), Yi WANG, Wilfried SIGLE, Georg CRISTIANI, Gennady LOGVENOV, Peter A. VAN AKEN

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MS2: 1D and 2D materials

MS2: 1D and 2D materials

Chairmen: Raul ARENAL (Zaragoza, SPAIN), Ursel BANGERT (Limerick, IRELAND)
10:15 - 10:45 #7884 - MS02-S69 Electrical properties of atomic carbon chains measured by in-situ TEM.
Electrical properties of atomic carbon chains measured by in-situ TEM.

Carbon in the sp1 hybridization (carbyne) is able to form atomic chains that constitute the elementary one-dimensional phase of carbon [1]. Despite many efforts, the synthesis of carbon chains in appreciable quantities remains difficult and even the existence of bulk carbyne is subject of an ongoing controversy. However, the existence of individual carbon chains is undisputed since they have been observed in in-situ TEM studies. The present work allowed, for the first time, to measure the electrical properties of carbon chains by using a dedicated specimen stage for establishing electrical contacts in the TEM.

Carbon chains are unusual conductors that may occur either as metallic cumulene with double bonds or as semiconducting polyyne with alternating single and triple bonds. Now, as it became possible to characterize them electrically, these two electronic configurations can be distinguished. A piezo-driven tip (Nanofactory), integrated into the specimen holder of a TEM, allowed to establish contacts to graphenic material and, by controlled retraction of the electrodes, to unravel chains of carbon atoms (fig. 1a). At the same time, the electrical properties could be measured [2, 3]. By recording current-voltage curves of individual carbon chains, both cumulene and polyyne were identified (fig. 1b). It was found experimentally and by quantum conductance calculations (fig. 1c) that transport through narrow resonant states makes the conductivity much lower than predicted in previous theoretical work. At high applied bias, however, a sudden rise in current occurs, showing the absence of conduction channels at lower energy and their presence at higher energy.

When the 1D system is under strain, the chains exhibit a semiconducting behavior, corresponding to polyyne. Conversely, when the chain is unstrained, an ohmic behavior, corresponding to cumulene, is observed (fig. 1b) [4]. This confirms a recent theoretical prediction, namely that the Peierls distortion, which would stabilize polyyne, is suppressed by zero-point vibrations in an unstrained chain so that cumulene is the stable configuration. In the presence of strain, however, polyyne is favoured by the Peierls instability. Thus, a metal-insulator transition can be induced by adjusting the strain. Furthermore, it is shown that these atomic chains can act as rectifying diodes when they are in a non-symmetric contact configuration, i.e., between a carbon and a metal contact or between two carbon contacts of different type.



Financial support by the LABEX program "Nanostructures in Interaction with their Environment" (NIE) and different projects of the Agence Nationale de Recherche (ANR, France) is gratefully acknowledged.



1. F. Banhart, Beilstein J. Nanotech. 6, 559 (2015).

2. O. Cretu, A. R. Botello-Mendez, I. Janowska, C. Pham-Huu, J.-C. Charlier, F. Banhart, Nano Lett. 13, 3487 (2013).

3. A. La Torre, F. Ben Romdhane, W. Baaziz, I. Janowska, C. Pham-Huu, S. Begin-Colin, G. Pourroy, F. Banhart, Carbon 77, 906 (2014).

4. A. La Torre, A. Botello-Mendez, W. Baaziz, J.-C. Charlier, F. Banhart, Nature Comm. 6, 6636 (2015).

10:45 - 11:00 #4515 - MS02-OP217 Correlative Microscopy: Raman Imaging Meets AFM, SNOM, and SEM.
Correlative Microscopy: Raman Imaging Meets AFM, SNOM, and SEM.

The characterization of low-dimensional materials such as graphene or transition metal dichalogenides (TMDCs) often requires more than one technique to obtain a thorough understanding of their attributes for specific applications. Graphene and TMDCs both have layered structures and properties that vary significantly with thickness as compared to single layer conformations, making them very interesting for electronics design [1, 2]. Electronic device performance optimization can benefit greatly from knowledge of their crystalline structure and exciton dynamics. The aim of the following analysis is to show how several spectroscopy (Raman/Photoluminescence) and microscopy techniques (AFM/SEM) can, in correlation, provide a more detailed depiction of low-dimensional materials than the constituent measurements could offer in isolation.


Raman spectroscopy, and Raman imaging in particular, has proved to be of great value in differentiating spectra obtained from single, double and multi-layered low-dimensional materials. Raman imaging was also used to evaluate strain, doping, chirality and disorder in graphene and TMDCs [3, 4]. The information acquired with Raman spectroscopy and imaging can be complemented by data from highest resolution microscopy techniques such as Atomic Force Microscopy (AFM), Scanning Near-Field Microscopy (SNOM), or Scanning Electron Microscopy (SEM).


Fig. 1a shows a correlative Raman-SEM image of exfoliated graphene deposited on a non-conductive glass coverslip. The SEM image was acquired in the low vacuum mode using a BSE detector. Different graphene sheets can be clearly visualized. In the center of the SEM image a confocal Raman image was acquired, showing the presence of different number of graphene layers, from one (green) to ten (yellow). The high resolution confocal Raman image (Fig. 1b), acquired from the area marked in Fig. 1a shows the intensity distribution of the G band as a function of layers in the graphene sheet as indicated with 1, 2 and M (multy-) layers. By evaluating the intensity of the D-band, the chirality of the graphene crystal could be determined as highlighted in red color in Fig. 1b. The SNOM image from the same area (Fig. 1c) shows that the transparency of the graphene decreases with increase of number of layers providing direct access to the fine structure of graphene.

In a second example a high resolution SEM image of CVD grown MoS2 is pesented (Fig. 2a). The Raman-SEM image (RISE image)  presented in Fig. 2b shows a correlation of changes in the Raman spectrum at the defects of the crystals.


[1] A. K. Geim , I. V. Grigorieva, Nature 499 (2013), p. 419.

[2] F. H. L. Koppens, T. Nueller, P. Avouris, A.C. Ferrari, M. S. Vitiello, M. Polini, M. Nat. Nano  9 (2014) p. 780.

[3] Y. You, Z. Ni, T.Yu, Z. Shen, Appl. Phys. Letters 39 (2008) p.13112.

[4]  P.K. Chow, R.J. Gedrim, J. Gao, T. M. Lu, B. Yu, H. Terrones, N. Koratka, ACS Nano (in press)

11:00 - 11:15 #5068 - MS02-OP218 Localized electrical resistance measurements of supported reduced graphene oxide using in-situ STM-TEM.
Localized electrical resistance measurements of supported reduced graphene oxide using in-situ STM-TEM.

The tunable electrical properties of reduced graphene oxide (RGO) make it an ideal candidate for many applications including energy storage.1 However, in order to utilize the material in industrially applied systems it is essential to understand the behavior of the material on the nanoscale, especially how naturally occurring phenomenon like wrinkling effects the electronic transport. While there have been many theoretical investigations on the transport behavior, there are much fewer experimental measurements.2, 3, 4 Here we used a transmission electron microscope (TEM) with scanning tunneling microscope (STM) probe in-situ holder is used to perform localized electrical measurements on wrinkled, supported RGO flakes. The RGO flakes are deposited onto pre-patterned Au electrodes on SiN membranes. The flakes are 1-3 layers thick and have lateral dimensions on the order of single micrometers. They are deposited through an ammonium laurate (AL) aqueous surfactant. The TEM allows for observation of the local wrinkling structure of the RGO and simultaneously a Nanofactory STM-TEM holder is used to perform localized resistance measurements. The holder allows for manipulation with and positioning of Au STM probes, with diameters less than 100 nm, with sub-nanometer precision. The results show that the overall resistance is low, on the order of single kΩ, if the contact between the probe and the RGO is optimized.  Wrinkles reduce the contact resistance between RGO and the probe. The overall trend for more than 70 measurements is that the total resistance decreases with increasing amount of wrinkles and that the contact resistance dominates the resistance when the probe makes contact with wrinkle free RGO. The sheet resistance and maximal contact resistance for our measurements range from 5-20 kΩ/☐ and 6-20E-7Ω cm2, respectively, which falls in line with other scanning probe measurements for graphene and metal contacts.5, 6  Here we use a bottom metal contact for the gold electrodes which eliminates the risk of resist contamination and metal doping of the graphene.7 These measurements give evidence that RGO with large amounts of wrinkling on a substrate can transport electrons well and that it is thus not necessary to produce suspended, pristine graphene in order to benefit from its electrical transport properties.


(1) Novoselov, K. S.; Fal'ko, V. I.; Colombo, L.; Gellert, P. R.; Schwab, M. G.; Kim, K. A roadmap for graphene. Nature 2012, 490, 192-200.

(2) Guinea, F.; Horovitz, B.; Le Doussal, P. Gauge fields, ripples and wrinkles in graphene layers. Solid State Communications 2009, 149, 1140-1143.

(3) Guo, Y.; Guo, W. Electronic and Field Emission Properties of Wrinkled Graphene. Journal of Physical Chemistry C 2013, 117, 692-696.

(4) Ladak, S.; Ball, J. M.; Moseley, D.; Eda, G.; Branford, W. R.; Chhowalla, M.; Anthopoulos, T. D.; Cohen, L. F. Observation of wrinkle induced potential drops in biased chemically derived graphene thin film networks. Carbon 2013, 64, 35-44.

(5) Yan, L.; Punckt, C.; Aksay, I. A.; Mertin, W.; Bacher, G. Local Voltage Drop in a Single Functionalized Graphene Sheet Characterized by Kelvin Probe Force Microscopy. Nano Letters 2011, 11, 3543-3549.

(6) Robinson, J. A.; LaBella, M.; Zhu, M.; Hollander, M.; Kasarda, R.; Hughes, Z.; Trumbull, K.; Cavalero, R.; Snyder, D. Contacting graphene. Applied Physics Letters 2011, 98.

(7) Babichev, A. V.; Gasumyants, V. E.; Egorov, A. Y.; Vitusevich, S.; Tchernycheva, M. Contact properties to CVD-graphene on GaAs substrates for optoelectronic applications. Nanotechnology 2014, 25.


Hanna NILSSON (Gothenburg, SWEDEN), Ludvig DE KNOOP, John CUMINGS, Eva OLSSON
11:15 - 11:30 #6189 - MS02-OP223 In-situ electrical measurements of Graphene Nanoribbons fabricated through Scanning Transmission Electron Microscopy.
In-situ electrical measurements of Graphene Nanoribbons fabricated through Scanning Transmission Electron Microscopy.

We recently demonstrated a controllable and reproducible method to obtain suspended monolayer graphene nanoribbons with atomically defined edge shape [1]. Our method exploits the electron-beam of a Scanning Transmission Electron Microscope (accelerated at 300 kV) to create vacancies in the lattice by knock-on damage and pattern graphene in any designed shape. The small beam spot size (0.1 nm) enables close-to-atomic cutting precision, while heating graphene at 900 K during the patterning process avoids formation of beam-induced Carbon deposition and allows self-repair of the graphene lattice.  Self-repair mechanism is essential to obtain well-defined (zig-zag or armchair) edge shape and, if the electron beam dose is lowered, to perform non-destructive imaging of the graphene nanoribbons.

Drawing the electron-beam path with a software script, we were able to obtain reproducible graphene nanoribbons with sub 10 nm width. Using an in-house built microscopy holder equipped with electrical feedthroughs, we performed 2 and 4 wire measurements on several graphene nanoribbons, with different number of layers. Wide nanoribbons (width> 50 nm) exhibited ohmic behaviour, with conductivity linearly proportional to the width. Narrower ribbons (10 nm < width < 50 nm) displayed non-linear current-voltage (IV) relationship at low temperature (4 K, ex-situ), possibly indicating the opening of a band gap. The narrowest ribbon was 1.5 nm wide, with strong non-linear IV also at room temperature.

Electrical measurements were also performed in the high temperature range (300 K – 900 K), from which we concluded that thermal generated carriers give the main contribution to  electrical conductivity above room temperature.

Ackwnoledgements: This work was supported by ERC funding,  project 267922 - NEMinTEM 


[1]        Q.Xu, M. Wu, G. F. Schneider, L. Houben, S.K. Malladi, C. Dekker, E. Yucelen, R.E. Dunin-Borkowski, and H.W. Zandbergen, ACS Nano  7 (2), 1566-1572, 2013

11:30 - 11:45 #6684 - MS02-OP227 In situ cyclic telescoping of multi-walled carbon nanotubes.
In situ cyclic telescoping of multi-walled carbon nanotubes.

        In this work, we perform an in-depth study of the cyclic telescoping of multi-walled carbon nanotubes (MWCNTs) inside a transmission electron microscope. The nanotubes are observed in real time, while simultaneously measuring their electrical properties. To date, examples of in situ TEM nanotube telescoping have remained few in number due to the highly specialized equipment and technical expertise required.

        Experiments were conducted by first ‘sharpening’ a MWCNT by approaching it with a piezo-controlled tungsten tip and applying a voltage pulse. This results in controlled and localized peeling of the outer walls, giving rise to a telescope structure. The exposed core is then contacted with the tungsten tip and reproducibly pulled out then re-inserted, while measuring conductance behavior at each movement step. Figure 1 shows an example of in situ telescoping of a MWCNT in real time.

        Results demonstrate that an electrical current can be maintained for multiple in-and-out cycles (up to 11 cycles have been tested to date), and for telescoping distances of up to 650 nm. This is exemplified in Figure 2. The systems display complex conductance behavior, with of some MWCNT telescopes demonstrating improved conduction (and current) as a function of the number of cycles, while for most these properties diminish.

        Control experiments have been conducted to investigate the effect of the electron beam on the behavior of the MWCNTs, and have indicated that changes in conductance behavior are not strongly influenced by the imaging process under normal beam conditions.

        One potential application for these structures is use as flexible electrical contacts, which allow for relative motion of the two electrodes, while maintaining electrical conduction.

        The authors would like to acknowledge funding as provided by the National Institute for Materials Science (NIMS), through the International Center for Materials Nanoarchitectonics (MANA).

Katherine MOORE, Ovidiu CRETU (Tsukuba, JAPAN), Dmitri GOLBERG
11:45 - 12:00 #6706 - MS02-OP228 Ion implantation into two-dimensional materials for electronic tailoring – observing the behaviour of individual implanted atoms.
Ion implantation into two-dimensional materials for electronic tailoring – observing the behaviour of individual implanted atoms.

Controlled manipulation of materials on the atomic scale is a continuing challenge in physics and material science. Doping of two-dimensional (2D) materials via low energy ion implantation could open possibilities for fabrication of nanometre-scale patterned devices, as well as for functionalization compatible with large-scale integrated semiconductor technology. High resolution imaging and spectroscopic analysis of these electronic dopants at the atomic scale is fundamental for understanding sites, retention, bonding and resulting effects on Fermi level shifts. This has been made achievable with the advent of aberration corrected transmission electron microscopy (TEM) and scanning TEM, as well as low-loss electron energy loss spectroscopy (EELS).


We show for the first time directly that 2Ds can be doped via ion implantation. Retention is in good agreement with predictions from calculation-based literature values [1], as are initial results of the sites of dopants and their influence on the band structure of surrounding atoms. We present results of N- and B-implantation in graphene [2,3] as well as current progress with ion-implantation in TMDCs.


  1. Ahlgren, E. H.; Kotakovski, J.; Krasheninnikov, A. V. Phys. Rev. B, 2011, 83, 115424
  2. U. Bangert, W. Pierce D. M. Kepaptsoglou, Q. Ramasse, R. Zan, M. H. Gass, J. A. Van den Berg, C. B. Boothroyd, J. Amani and H. Hofsäss, Nano Letters, 2013, 13, 4902-4907
  3. Demie Kepaptsoglou, Trevor P. Hardcastle, Che R. Seabourne, Ursel Bangert, Recep Zan, Julian Alexander Amani, Hans Hofsaess, Rebecca J. Nicholls, Rik M. D. Brydson,  Andrew J. Scott, and Quentin M. Ramasse, A.C.S., 2015, 9, 11398–11407
Eoghan O'CONNELL (Limerick, IRELAND), Beata KARDYNAL, Jhih-Sian TU , Florian WINKLER, Hans HOFSAESS, Demie KEPAPTSOGLOU, Quentin M. RAMASSE, Julian Alexander AMANI, Recep ZAN, Ursel BANGERT
12:00 - 12:15 #6717 - MS02-OP230 Effects of electron-beam-generated anion point defects on the long range order of charge density waves in 1T-TaSe2, 1T-TaS2.
Effects of electron-beam-generated anion point defects on the long range order of charge density waves in 1T-TaSe2, 1T-TaS2.

Charge density waves (CDW) are periodic modulations of charge density in low-dimensional metals observed as a function of temperature, doping and pressure. Due to electron-phonon coupling CDWs, are also accompanied by a periodic lattice distortion (PLD).1 Quasi two-dimensional (2D) transition metal dichalcogenides metals like 1T/2H-TaSe2, 1T/2H-TaS2, 2H-NbSe2 are some of the materials that exhibit strong CDW distortions. While CDW can be directly probed using Scanning Tunnelling Microscopy (STM), diffraction and imaging techniques such as High Resolution Transmission electron Microscopy (HRTEM) and selected area electron diffraction (SAED) are sensitive to the structural distortions (PLD) accompanying CDW. In an electric field, and in the absence of crystalline impurities and defects, sliding incommensurate CDW show transport properties similar to a superconducting state.1,2 It is therefore important to understand the effects of commensuration, defects, and impurities on the static and dynamic properties of the CDW state.2,3 On a transmission electron microscope (TEM), investigating the effects of  defects on the CDW/PLD state can be done in-situ by generating point defects through electron beam irradiation and at the same time monitoring the structure of the CDW/PLD through electron diffraction and atomic resolved HRTEM imaging. 

Here we report on the interaction of commensurate CDW/PLD with point defects generated by the electron beam in 1T-TaSe2 and 1T-TaS2. Due to the CDW/PLD, bulk 1T-TaS2 and 1T-TaSe2 are characterized by a commensurate √13 a×√13 a0 (a0= 3.447) superlattice at 180 K and 300 K respectively.Figure 1(a) displays a HRTEM image of 1T-TaSe2 obtained at 100 K. The HRTEM image was obtained at region consisting of upto 10-15 layers of 1T-TaSe2 and shows Ta atomic columns. The HRTEM image is also characterized by a bright, dark contrast modulation due to the PLD/CDW. A Fast Fourier Transform (FFT) of the HRTEM image shown in fig 1(b) has spots from the main structure (solid red circles) surrounded by six satellite spots (dotted circle) from the PLD/CDW. HRTEM image analysis involving masking of the satellite spots from the CDW/PLD with a circular mask, followed by inverse FFT helps to visualize the structure of the lattice arising from the commensurate PLD/CDW. The resulting image, shown in fig. 1(c), then displays an intensity image showing a √13 a×√13 a lattice of the CDW/PLD maxima.

To investigate the effects of electron-beam generated defects on the CDW/PLD, succesive HRTEM images  were obtained from the same sample region over time and at a constant electron dose. Images showing the evolution of PLD/CDW maxima with electron beam irradiation were then obtained from respective HRTEM images using the image analysis procedure elucidated above. Figures 1(d)-(f) show successive HRTEM images obtained over time. The HRTEM images were obtained from a region of upto 15 layers of 1T-TaSe2 and only show the Ta atomic columns. The PLD/CDW lattices shown in fig.1(g), 1(h), 1(i) correspond to the HRTEM images in figs. 1(d), 1(e), and 1(f) respectively. A radial distribution function (RDF) showing the nearest-neighbor and next-nearest-neighbor periodicities between the CDW maxima can also be calculated. The RDF in figs.1(j), 1(k), 1(l) have been calculated from the CDW/PLD lattices in figs. (g), (h), (i) respectively. The peak with the asterix shows the main periodicity due to the CDW/PLD wave-vector |qi =1…6| =  √13 a0. Loss of long-range order with increased exposure to the electron beam is characterized by broadening of RDF peaks (see regions marked with dotted rectangle in fig. 1(k) and fig.1 (l)). Based on the characterization of 1T-TaSe2, and 1T-TaS2 thin/single layers we show that this loss of long range order is due to interaction of CDW/PLD with S and Se anionic point defects generated by the electron beam.

References and acknowledgments:

1. J. Wilson, F. D. Salvo, and S. Mahajan, Adv. Phys. 24, 117 (1975).

2.H. Dai, and C. Lieber, J. Phys. Chem. 97, 2362 (1993)

3. H. Mutka, Phase Transitions 11, 221 (1988).

12:15 - 12:30 #6908 - MS02-OP234 TEM Characterization of Indium Phosphide Nano-Flags Growth.
TEM Characterization of Indium Phosphide Nano-Flags Growth.

Quasi two-dimensional (2D) semiconductor materials are desirable for electronic, photonic, and energy conversion applications and have stimulated extensive research on their synthesis1-3 and applications4-6.  One such example is the growth of indium phosphide flag-like nanostructures (Fig. 1) by epitaxial growth on a nanowire template7. By the intentional incorporation of defects, control of the nano-flag location along the nanowire was achieved. Long InP nanowires with inherent high defect density in the top area of the flagpole, which pins the catalyst, resulted in top flag geometry (Fig. 1a). Intentional defect creation in the middle section of the flagpole produced middle nanoflags (Fig. 1b). Bottom flags were created by growing defect free primary nanowires under high phosphine flow (Fig. 1c).


Detailed investigation, using aberration corrected high resolution TEM (FEI Titan 80-300), high angle annular dark field STEM and electron diffraction, of the flag-like nano-structures at different stages of the growth provided valuable details about the growth mechanism and the resulting morphology of such nano-structures.


The main conclusion from the TEM observations is that the growth process involves a few stages. The first stage consists of asymmetrical dissolution of the nanowire (NW) tip into the catalyst (Fig. 2a), followed by the Au catalyst unpinning from the top of the nanowire, and its induced migration along the nanowire sidewall. The final position of the catalyst is determined by the position of structural defects (such as stacking faults - Fig. 2b) along the NW (i.e. the "flagpole"). The next stage involves the epitaxial growth of a pure Wurtzite nano-flag on one of the facets of the "flagpole" resulting in a two dimensional nano-membrane on a one dimensional NW sidewall template (Fig. 2c-d).


The comprehensive understanding of the growth process may help improve the synthesis of similar nano-structures. It may allow for better control on the growth process of more complex structures and also help achieving similar nanostructures in a variety of III-V semiconductor material systems with potential applications such as active nanophotonics.



  1. Gudiksen, M. S.; Lauhon, L. J.; Wang, J.; Smith, D. C.; Lieber, C. M. Nature 2002, 415 (February), 617–620.
  2. Algra, R. E.; Verheijen, M. a; Borgström, M. T.; Feiner, L.-F.; Immink, G.; van Enckevort, W. J. P.; Vlieg, E.; Bakkers, E. P. a M. Nature 2008, 456 (7220), 369–372.
  3. Gorji Ghalamestani, S.; Ek, M.; Ganjipour, B.; Thelander, C.; Johansson, J.; Caroff, P.; Dick, K. a. Nano Letters 2012, 12 (111), 4914–4919.
  4. Tomioka, K.; Tanaka, T.; Hara, S.; Hiruma, K.; Fukui, T. IEEE J. Sel. Top. Quantum Electron. 2011, 17 (4), 1112–1129.
  5. Nakayama, Y.; Pauzauskie, P. J.; Radenovic, A.; Onorato, R. M.; Saykally, R. J.; Liphardt, J.; Yang, P. Nature 2007, 447 (June), 1098–1101.
  6. Mourik, V.; Zuo, K.; Frolov, S. M.; Plissard, S. R.; Bakkers, E. P. a. M.; Kouwenhoven, L. P. Science (80-. ). 2012, 336, 1003.
  7. A. Kelrich, O. Sorias, Y. Calahorra, Y. Kauffmann, R. Gladstone, S. Cohen, M. Orenstein and D. Ritter, Nano Letters 2016, 10.1021/acs.nanolett.6b00648.

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IM1: Tomography and Multidimensional microscopy

IM1: Tomography and Multidimensional microscopy

Chairmen: Sara BALS (Antwerpen, BELGIUM), Wolfgang LUDWIG (Lyon, FRANCE), Sergio MARCO (Paris, FRANCE)
10:15 - 10:45 #8320 - IM01-S32 Electron Tomography at the Frontiers of Materials Chemistry.
Electron Tomography at the Frontiers of Materials Chemistry.

This presentation will follow two themes. The first considers recent contributions of electron tomography in materials chemistry, with particular focus on rationally designed multi-scale and multi-component systems. Second, developments and future prospects in electron tomographic methodology will be discussed.


Summarised in Figures 1 and 2, for example, is a recent study of Au nanorpisms decorated with Pt nanoparticles of size relevant for catalysis [1]. The tomographic analyses disclosed otherwise ambiguous details of the multi-component architecture, revealing that both pseudospherical protrusions and dendritic Pt nanoparticles grow on all faces of the nanoprisms, the faceted or occasionally twisted morphologies of which were also revealed, and shedding light on alignment of the Pt nanoparticles. Complementary electron energy-loss spectrum imaging showed that the Au nanoprisms support multiple localized surface plasmon resonances despite the presence of pendant Pt nanoparticles. These insights suggest potential applications in plasmon-enhanced catalysis and in situ monitoring of chemical processes via surface-enhanced spectroscopy, and pave the way toward comprehensive engineering of such multi-functional nanostructures.


With the widespread adoption of scanning transmission electron microscopy and high-angle annular-dark field imaging, structural electron tomographic studies have reached a consistently high standard. The fidelity of such studies has also been raised significantly by the development of advanced reconstruction algorithms, such as those based on compressed sensing [2]. These are undergoing continual evolution to address the range of contexts and challenges faced in contemporary nanoscale investigations, including quantitative, low-dose and analytical electron tomography.


Significant advances in hardware, such as fast and efficient X-ray and electron energy-loss spectrometers, and new camera technologies, have opened the flood gates to analytical electron tomography [3]. New ‘big data’ challenges are faced in the processing and analysis of multi-dimensional tomography data sets. In this regard, post facto ‘computational microscopy’ is becoming increasingly important; and versatile computational approaches can yield rich rewards. Indeed, computational analysis combined with advanced reconstruction can enable capture of the salient information content in a powerful and efficient manner. Computational modelling also offers the opportunity to utilise signals that have traditionally been thought unsuitable for tomography. Combined, hardware and computational advances are enabling a new era of analytical electron tomography, providing sophisticated 3D mapping at the nanoscale, spanning composition, crystallography, chemical, optical and electronic properties.



[1] R.K. Leary et al. J. Phys. Chem. C DOI: 10.1021/acs.jpcc.6b02103

[2] R.K. Leary et al. Ultramicroscopy 131 (2013) 70-91

[3] R.K. Leary & P.A. Midgley MRS Bulletin (in press)



I am grateful for a Junior Research Fellowship at Clare College, and for financial support from Emilie Ringe and Paul Midgley.

Rowan LEARY (Cambridge, UK)
10:45 - 11:15 Multimodal and multidimensional tomography with a hard X-ray nanoprobe. Peter CLOETENS (GRENOBLE CEDEX 9, FRANCE)
11:15 - 11:30 #5776 - IM01-OP039 Nanoparticles quantification inside cells by near-edge absorption soft X-ray nanotomography.
Nanoparticles quantification inside cells by near-edge absorption soft X-ray nanotomography.

Recent advances in superparamagnetic iron oxide nanoparticles (SPION) design have generated new possibilities for nano-biotechnology and nano-medicine.  Achieving the full potential of SPION will nonetheless require precise quantitative analysis at sufficient resolution to model the interactions between nanoparticles and the cell environment.  The results from this analysis will determine the dose for either drug-delivery or hyperthermia treatments as well as its feasibility.  To get an insight into this problem we incubated 15 nm SPION functionalized with dimercaptosuccinic acid with MCF-7 breast cancer cells [1] as a model system to be analyzed exploiting the iron differential absorption contrast in the L2-edge.  Near-edge absorption soft X-ray nanotomography (NEASXT) combines whole-cell 3D structure determination at 50 nm resolution, with 3D elemental mapping and high throughput.  We solved three-dimensional distribution of SPIONs within cells with sensitivity sufficient for detecting the density corresponding to a single nanoparticle (Fig. 1)[2].


[1] Chiappi M, Conesa JJ, Pereiro E, Sorzano CO, Rodríguez MJ, Henzler K, Schneider G, Chichón FJ, Carrascosa JL.  Cryo-soft X-ray tomography as a quantitative three-dimensional tool to model nanoparticle:cell interaction.  J Nanobiotechnology. 2016 Mar 3;14(1):15. doi: 10.1186/s12951-016-0170-4.

[2] Conesa JJ, Otón J, Chiappi M, Carazo JM, Pereiro E, Francisco Javier Chichón FJ, Carrascosa JL.  Intracellular nanoparticles mass quantification by near-edge absorption soft X-ray nanotomography.  Scientific Reports 6, Article number: 22354 (2016) doi:10.1038/srep22354.

Jose Javier CONESA (Madrid, SPAIN), Joaquin OTON, Michele CHIAPPI, Eva PEREIRO, José María CARAZO, Francisco Javier CHICHON, Jose L. CARRASCOSA
11:30 - 11:45 #5929 - IM01-OP041 Utilising correlative 3D imaging to understand creep cavitation in stainless steel.
Utilising correlative 3D imaging to understand creep cavitation in stainless steel.

The role of grain boundary orientation and secondary phase precipitation on creep cavitation in a stainless steel sample has been investigated using a correlative tomography1 approach. A number of different 3D imaging techniques are combined on the same sample in order to understand the initiation and progression of cavitation.

Correlative imaging has become an important tool in both biology2,3 and materials science4, where it provides 2D information of the same sample area at multiple length scales. Correlative tomography describes the extension of  correlative imaging to three dimensions via a range of techniques, which also provides the opportunity to probe sub-surface volumes1.

The position, size and morphology of cavities on three grain boundaries in a stainless steel sample taken from a power station steam header were examined using X-ray computed tomography (CT) 5. X-ray CT demonstrates that the presence of cavities, as well as their size and shape, varies for each of the grain boundaries examined in this study (Figure 1). Subsequently, FIB-SEM slice and view provides a higher-resolution analysis of the same sample to resolve and identify the precipitates decorating the cavitated grain boundaries. Additionally, 3D electron backscatter diffraction (EBSD) mapping reveals the misorientation at grain boundaries and thus offers some insight in to why certain boundaries may possess cavities and whether grain boundary misorientation affects the size and shape of cavities.

Furthermore, a 200 nm diameter pillar was sectioned from one of the cavitated boundaries in order to perform scanning transmission electron microscope (STEM) – energy dispersive X-ray (EDX) tomography 6,7. STEM-EDX tomography reveals the distribution of elements at nanometre scale in three dimensions (Figure 2). This high-resolution chemical information aids understanding of precipitate formation and provides accurate characterisation of precipitate morphology.

The correlative 3D imaging approach applied here gives unprecedented insight in to cavitation in stainless steels and is also applicable to a wide range of other materials that display characteristic features at a number of different length scales.


1              Burnett, T. L. et al. Correlative Tomography. Scientific Reports 4, (2014).

2              Caplan, J., Niethammer, M., Taylor Ii, R. M. & Czymmek, K. J. The power of correlative microscopy: multi-modal, multi-scale, multi-dimensional. Carbohydrates and glycoconjugates/Biophysical methods 21, 686-693 (2011).

3              Sengle, G., Tufa, S. F., Sakai, L. Y., Zulliger, M. A. & Keene, D. R. A Correlative Method for Imaging Identical Regions of Samples by Micro-CT, Light Microscopy, and Electron Microscopy: Imaging Adipose Tissue in a Model System. Journal of Histochemistry & Cytochemistry 61, 263-271 (2013).

4              Dumpala, S. a. O. A. A. a. P. S. a. B. S. R. a. L. J. M. a. R. K. Correlative Imaging of Stacking Faults using Atom Probe Tomography (APT) and Scanning Transmission Electron Microscopy (STEM). Microscopy and Microanalysis 20, 996-997, (2014).

5              Maire, E. & Withers, P. J. Quantitative X-ray tomography. International Materials Reviews 59, 1-43, (2014).

6              Lepinay, K., Lorut, F., Pantel, R. & Epicier, T. Chemical 3D tomography of 28 nm high K metal gate transistor: STEM XEDS experimental method and results. Micron 47, 43-49, (2013).

7              Slater, T. J. A. et al. Correlating Catalytic Activity of Ag-Au Nanoparticles with 3D Compositional Variations. Nano Letters 14, 1921-1926, (2014).

Thomas SLATER (Manchester, UK), Robert BRADLEY, Remco GEURTS, Giacomo BERTALI, Grace BURKE, Sarah HAIGH, Philip WITHERS, Timothy BURNETT
11:45 - 12:00 #6464 - IM01-OP048 Understanding the degradation of Pt nanoparticles in a fuel cell electrode via identical location electron tomography.
Understanding the degradation of Pt nanoparticles in a fuel cell electrode via identical location electron tomography.

The degradation and high cost of electrodes materials used in proton exchange membrane fuel cells (PEMFCs) are major barriers limiting their commercialization in automotive vehicles [1]. The search for more affordable electrode materials has focused on controlling the surface structure and composition of novel multi-metallic catalytic nanoparticles on high surface area support membrane [2]. During fuel cell operation, the catalyst nanoparticles can dissolve, re-deposit and agglomerate, resulting in electrochemical surface area losses, and an associated decrease in catalyst activity [3]. It is therefore critical to understand the degradation mechanism of the nanoparticle catalysts during electrochemical aging in a fuel cell electrodes in order to improve the performance and lifetime of PEMFCs. Here we characterize a newly proposed fuel cell cathode material, comprised of nano-particulate platinum on a NbOx-carbon hybrid support, using identical location electron tomography. A full HAADF-STEM tomographic tilt series of several representative clusters were obtained before and after acclerated stress tests (30,000 cycles from 0.6 to 1.0 V in an electrochemical cell).

Preliminary results are summarized in Figure 1. A three dimensional (3D) schematic of a simple PEMFC shows the overall structure and location of the cathode electrode catalyst material used in this study. Pt nanoparticles, a few nanometers in diameter, decorate the complex, 3D NbOx-carbon hybrid support structure, imaged by HAADF STEM under identical conditions in (b) before and after electrochemical cycling and at two tilts separated by 400. The 3D tomographic reconstructions of the structure are aligned and compared in (c). The high fidelity of the reconstructions and the relatively small overall changes observed in the structure enabled the semi-automated matching of over 500 individual Pt nanoparticles before and after cycling (d). The semi-automatized approach was accomplished with the aid of quantitative image analysis techniques including histogram normalization and maximum entropy thresholding, and alignment of the before and after reconstructions via a singular valued decomposition of the reconstructed Pt centroids matrix.  Preliminary results suggest that a net leaching of the Pt into solution has occurred during cycling, indicated by the overall reduction in size of a vast majority of Pt nanoparticles (e). Analysis of 3D reconstructions obtained from Pt-NbOx-carbon hybrid structures differing in their Pt/NbOx ratio are underway to better elucidate the role of NbOx in the degradation of Pt.

Identical location electron tomography before and after electrochemical cycling has provided valuable insight into the degradation mechanism of the PEMFC electrode during cycling, enabling more informed decisions for the design of high-performance durable electrode materials.



[1] M. K. Debe, Nature, vol. 486, no. 7401, pp. 43–51, 2012.

[2] Y. Wang, K. S. Chen, J. Mishler, S. C. Cho, and X. C. Adroher, Appl. Energy, vol. 88, no. 4, pp. 981–1007, 2011.

[3] D. Banham, S. Ye, K. Pei, J. Ozaki, T. Kishimoto, and Y. Imashiro, J. Power Sources, vol. 285, pp. 334–348, 2015.



GAB is grateful for funding from NSERC under the CaRPE-FC network and to AFCC for partially supporting this work.

12:00 - 12:15 #5119 - IM01-OP036 Multi scale tomography of materials for Li-ion battery electrodes.
Multi scale tomography of materials for Li-ion battery electrodes.

Increasing energy capacity, power density and cycle life of Li-ion batteries requires optimizing the composite electrodes microstructure. 3D simulation analysis and modeling have shown that the amount, the size, the shape, the tortuosity and the specific surface area of pores and particles are all key parameters for the improvement of electrode performance.

Recently, the 3D morphologies of various anodes and cathodes for Li-ion batteries have been evaluated by FIB/SEM and X-Ray Computed Tomography (XRCT). In addition, 3D imaging softwares allow automatic processing and quantifying measurements by finite element calculations or other numerical models. XRCT is non destructive but routine procedures are limited to rather poor spatial resolution. Combined Focused Ion Beam (FIB) and Scanning Electron Microscopy (SEM) is destructive but has recently emerged as an established technique for the three-dimensional imaging at high spatial resolution, inaccessible with laboratory X-ray tomography. Electron TEM tomography is finally an option to improve the spatial resolution down to several nanometers.

This paper will give examples of different materials used for Li-ion  battery electrodes, analyzed at different scales with all these different 3D tomography techniques. It will be shown that static characterisation of the prestine materials gives the initial morphology of the electrodes.

Samples can then be analysed after electrical cycling and this shows the degradation mechanisms. Some methods even allow to do the observation in operado.

12:15 - 12:30 #6483 - IM01-OP049 3-D EM exploration of the hepatic microarchitecture – lessons learned for large-volume in situ serial sectioning.
3-D EM exploration of the hepatic microarchitecture – lessons learned for large-volume in situ serial sectioning.

To-date serial block-face scanning electron microscopy (SBF-SEM) dominates as the premier technique for generating three-dimensional (3-D) data of resin-embedded biological samples at an unprecedented resolution and depth volume. Given the relative infancy of the technique, limited literature is currently available regarding the applicability of SBF-SEM for the ultrastructural investigation of tissues that are inherently low in contrast, including hepatic tissue. Such tissues, relative to neural tissue – which has been extensively investigated by means of SBF-SEM – require dedicated SBF-SEM specimen preparation protocols combined with optimised imaging conditions in order to collect large-volume 3-D image data, at appropriate resolution which is devoid of imaging artefacts that are inherent to SEM investigations of uncoated samples.

          Therefore, in this study, we provide a comprehensive and rigorous appraisal of different tissue preparation protocols for the large-volume exploration of hepatic architecture at an unparalleled XY and Z resolution. In so doing, we qualitatively and quantitatively validate the use of a novel and time-saving SBF-SEM tissue preparation protocol, which involves the concomitant application of heavy metal fixatives, stains and mordanting agents for the subsequent imaging of contrast-rich SBF-SEM data, 3-D reconstruction and modelling of the hepatic architecture. We further extrapolate large-volume morphometric data relating to key tissue features of the murine liver, including hepatocytes, the hepatic sinusoids and bile canaliculi network (Fig. 1).

         Furthermore, we combine our validated SBF-SEM specimen preparation protocol with a correlative light and electron microscopy approach, to combine the respective advantages of confocal scanning laser microscopy and SBF-SEM in order to selectively picture particular subcellular hepatic details in a novel manner. We propose that this correlated multidimensional light and electron imaging approach will allow the study of different liver diseases under relevant experimental tissue models.

Gerald SHAMI (Sydney, AUSTRALIA), Delfine CHENG, Minh HUYNH, Celien VREULS, Eddie WISSE, Filip BRAET

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LS1: Macromolecular assemblies, supra molecular assemblies

LS1: Macromolecular assemblies, supra molecular assemblies

Chairmen: Bettina BOETTCHER (Edinburgh, UK), Karen DAVIES (Staff Scientist) (Berkeley, USA), Guy SCHOEHN (Grenoble, FRANCE)
10:15 - 10:45 #8354 - LS01-S03 High resolution cryo-EM of eukaryotic proteasomes: an emerging tool for therapeutic drug development.
High resolution cryo-EM of eukaryotic proteasomes: an emerging tool for therapeutic drug development.

Recently the field of biological structural electron microscopy has seen an enormous transformation, primarily triggered by the availability of improved electron microscopes and direct electron detectors. It is now possible to use electron cryo-microscopy (cryo-EM) and single particle analysis to determine the structure of proteins to resolutions that used to be achievable only by crystallography or NMR methods. The structural information attainable by such methodologies can in principle be used to infer into the detailed molecular mechanisms of proteins and protein complexes. We explored their application to study protein/ligand interactions using the eukaryotic 20S proteasome core.

The proteasome is a highly regulated protease complex essential in all eukaryotes for its role in cell homeostasis and regulation of fundamental mechanisms such as cell cycle progression. The proteasome proteolytic active sites are enclosed within its 20S core. In eukaryotes, the 20S proteasome is a ~750 kDa complex formed by 7 individual α and 7 individual β subunits, arranged in a barrel shaped two-fold symmetric α7β7β7α7 assembly. While the 20S proteasome core is a well-established target for cancer therapy, its inhibition is being further explored for an increasing range of varied therapeutic usages, including inflammatory disorders, viral infections and tuberculosis. We used cryo-EM and single particle analysis to determine the structure of the human 20S proteasome core bound to a substrate analogue inhibitor molecule, at a resolution of around 3.5Å. The resulting map allowed the building of protein coordinates as well as defining the location and conformation of the inhibitor at the different active sites. These results serve as proof of principle that cryo-EM is emerging as a realistic approach for more general structural studies of protein/ligand interactions, with its own advantages compared with other methods of protein structure determination. Cryo-EM has the potential benefits of extending such studies to complexes unsuitable for other methods of structure determination, namely by requiring significantly less amounts of sample, and allowing closer to physiological conditions, preserving ligand specificity. Within this context, we extended our studies to assist in the development of new highly specific inhibitors targeting the Plasmodium falciparum proteasome. Plasmodium falciparum is the parasite responsible for the most severe form of malaria, against which artemisinin is currently the forefront medication. The spreading of artemisinin resistant parasites, first identified in the Southeast Asia, represents a major threat to human health and to the current programs aiming at controlling and eventually eradicating malaria and urges the development of new antimalarials. We determined the structure of the Plasmodium falciparum 20S proteasome core bond to a new specific inhibitor, developed by our collaborator Matt Bogyo, Stanford University, at a resolution of around 3.6Å (figure 1). Our structure, and its comparison with that of the human 20S proteasome core, revealed the molecular basis for the inhibitor specificity for the parasite complex and for the improvement of this ligand into a more potent anti-malaria drug prototype, with demonstrated low toxicity to in vivo model hosts. The cryo-EM structure of the Plasmodium falciparum 20S proteasome can assist in the development of such inhibitors as ligands with potential as new-generation antimalarials.

Paula DA FONSECA (Cambridge, UK)
10:45 - 11:15 #8368 - LS01-S04 Our muscle at near-atomic resolution - Cryo-EM structure of the F-actin-tropomyosin complex.
Our muscle at near-atomic resolution - Cryo-EM structure of the F-actin-tropomyosin complex.

Muscular movement plays an essential role not only in our lives but also describes a fundamental mechanism of force production. Filamentous actin (F-actin) is the major protein of muscle thin filaments, and actin microfilaments are the main component of the eukaryotic cytoskeleton. The interaction of myosin with actin filaments is the central feature of muscle contraction and cargo movement along actin filaments. In striated muscle fibres, this interplay is mainly regulated by tropomyosin and troponin. Although crystal structures for monomeric actin are available, the difficulty of obtaining diffracting crystals, however, has prevented structure determination by crystallography of F-actin. High-resolution structures of F-actin in complex are still missing, hampering our understanding of how disease-causing mutations affect the function of thin muscle filaments and affecting skeletal and cardiac muscles.

We solved the three-dimensional structure of F-actin in complex with tropomyosin at a resolution of 3.7 Å (von der Ecken et al., 2015). We used cutting edge transmission electron cryomicroscopy and direct electron detectors and implemented new methods for processing of the data. The structure reveals insights in the inner interaction of the F-actin subunits and the interplay of F-actin and tropomyosin at near-atomic resolution.


von der Ecken J., Müller M., Lehman W., Manstein D.J., Penczek P.A., Raunser S. (2015): Structure of the F-actin-tropomyosin complex. Nature 519, 114-117.

Julian VON DER ECKEN (Dortmund, GERMANY), Mirco MÜLLER, William LEHMAN, Dietmar J. MANSTEIN, Pawel A. PENCZEK, Stefan RAUNSER
11:15 - 11:30 #6230 - LS01-OP003 Near atomic structure of flexible filamentous pepino mosaic virus by high resolution cryo-EM.
Near atomic structure of flexible filamentous pepino mosaic virus by high resolution cryo-EM.

Flexible filamentous viruses belonging to the Alphaflexiviridae family cause from severe to mild diseases in agricultural crops, often reducing yield and crop quality. Viral particles from the Alphaflexiviridae group are formed by a (+)ssRNA molecule encapsidated by single capsid protein (CP) monomers arranged in helical fashion. Pepino mosaic virus (PepMV) is a flexible filamentous plant virus belonging to the genus Potexvirus included in the family Alphaflexiviridae which genome consists of a ~6.4 kb (+)ssRNA and encodes five proteins. 


We report here the structure of intact PepMV virions by cryoEM at 3.9 Å resolution (Agirrezabala et al., 2015). The results and the resolution achieved (Figure 1) allowed the modeling of the CP, the (+)ssRNA and their relative interactions. The CP was modeled starting with the CP from PapMV (Yang et al., 2012), clearly showing a similar folding of the α-helical domain for the Alphaflexiviridae family. The ssRNA is allocated and protected in a continuous groove of high electropositive potential built up by the CP in helical arrangement. The CP polymerize through a flexible N-terminal arm providing the structural basis for the flexibility of the virus, in similar organization as the observed for BaMV (DiMaio et al., 2015).


Interestingly, the overall structure and organization of CP from PepMV is similar to the organization of nucleoproteins from the Bunyaviridae family, a group of enveloped (-)ssRNA viruses. Common features include: the folding and arrangement of the α-helical main domain; the groove for the ssRNA; the N-terminal arm for polymerization; and the relative position between all these elements. Although structural homology between viruses revealed by their atomic structures is common, in the current case, the different nature of capsid protein and nucleoprotein might have profound evolutionary implications.





-Agirrezabala, X., Mendez-Lopez, E., Lasso, G., Sanchez-Pina, M.A., Aranda, M., and Valle, M. (2015). The near-atomic cryoEM structure of a flexible filamentous plant virus shows homology of its coat protein with nucleoproteins of animal viruses. Elife 4.


-DiMaio, F., Chen, C.C., Yu, X., Frenz, B., Hsu, Y.H., Lin, N.S., and Egelman, E.H. (2015). The molecular basis for flexibility in the flexible filamentous plant viruses. Nat Struct Mol Biol 22, 642-644.


-Yang, S., Wang, T., Bohon, J., Gagne, M.E., Bolduc, M., Leclerc, D., and Li, H. (2012). Crystal structure of the coat protein of the flexible filamentous papaya mosaic virus. Journal of molecular biology 422, 263-273.

Xabier AGIRREZABALA, Francisco MENDEZ, Maria Amelia SANCHEZ-PIÑA, Miguel Angel ARANDA, Mikel VALLE (Derio, SPAIN)
11:30 - 11:45 #6941 - LS01-OP009 Structure of filamentous alternanthera mosaic virus and mechanism of its activation.
Structure of filamentous alternanthera mosaic virus and mechanism of its activation.

Alternanthera mosaic virus (AltMV) is a filamentous plant virus belonging to the genus Potexvirus. The virus contains a single-strand RNA and coat protein (CP) that self-assembles around RNA into a flexible helical sheath. In contrast to rich information on the rigid rod plant viruses, structural information for flexible plant viruses has been lacking. High-resolution structures are available only for papaya mosaic virus (Yang et al., 2012) and bamboo mosaic virus (DiMaio et al., 2015), and for some other Potexviruses low-resolution structures exist.

The aim of this work is to determine the structure of AltMV using cryo-EM and image processing and to propose a mechanism of uncoating of viral RNA during infection.

The virus particles were purified as described by Mukhamedzhanova et al. (2009) and quickly frozen in liquid ethane. The high resolution data were collected on Titan Krios electron microscope (FEI) at 300 kV acceleration voltage, using low dose condition. Images were captured using Falcon direct detector and image processing has been accomplished using software packages IMAGIC and Spider. All images (2000 single particles) were corrected for the CTF.

The helical parameters were estimated and the obtained 3D map of viral particle had a resolution of 7Å which allowed to reveal the orientation of alpha helixes. The high radius region of AltMV was quite similar to that of PapMV and this could be explained by high (79.8%) homology of CPs of these viruses (Geering, 1999). The electron density revealed a central channel with ~18Å in diameter. The viral RNA may be positioned at 36Å radius of the particle.

As crystal structure of AltMV is not known the homology modelling of AltMV coat protein was carried out. In order to interpret the obtained structure the homology model was fitted into 3D electron density map (Fig. 1). Like in other Potexviruses with known structure (Yang et al., 2012; DiMaio et al., 2015)N terminus of AltMV CP contacts with adjacent protein subunit. This contact likely plays a key role in maintaining of virion stability.

Previously it was shown that encapsidated AltMV RNA is nontranslatable in vitro, but can be converted into a translatable form after phosphorylation of coat protein (Mukhamedzhanova et al., 2011).

In order to understand the mechanism of uncoating of AltMV RNA after such phosphorylation a series of umbrella sampling simulations was carried out. We measured binding free energy of two AltMV CP subunits with all serine and threonine residues exposed on outer surface of a virion phosphorylated and compared it with binding free energy of AltMV CP subunits without phosphorylation. Our results indicate that phosphorylation considerably reduces binding energy of the complex and promotes its disassembly. The minimum on the energy profile of the non-phosphorylated complex corresponded to a conformation where N terminus of one subunit was in a close contact with the adjacent protein subunit. For the phosphorylated complex the minimum was reached when N terminus moved 1 nm away from the neighboring protein subunit (Fig. 2).

Thus the new evidence that the mechanism of AltMV activation during infection may include phosphorylation of CPs has been obtained. The phosphorylation causes destruction of the contact between N terminus of a CP and adjacent protein subunit. As a result, AltMV virion becomes unstable without the contact and uncoating of RNA starts.

Acknowledgements: The reported study was funded by RFBR according to the research project No. 16-34-00658 мол_a.

11:45 - 12:00 #5807 - LS01-OP002 Structural basis of Nanobody-mediated plant virus resistance and vector transmission revealed by cryo-EM.
Structural basis of Nanobody-mediated plant virus resistance and vector transmission revealed by cryo-EM.

Since their discovery, single-domain antigen-binding fragments of camelid-derived heavy chain-only antibodies, also known as Nanobodies (Nbs), have proven to be of outstanding interest as therapeutics against human diseases and pathogens including viruses, but their use against phytopathogens remains limited. Many plant viruses including Grapevine fanleaf virus (GFLV), a vector-transmitted icosahedral virus related to animal picornaviruses, have worldwide distribution and huge burden on crop yields representing billions of US dollars of losses annually, yet solutions to combat these viruses are often limited or inefficient. Here we show that a Nb specific to GFLV confers strong resistance to GFLV upon stable expression in plants due to virus neutralization at an early step of the virus life cycle, prior to cell-to-cell movement. To address the involved molecular mechanisms, we determined the cryo- electron microscopy (cryo-EM) structure of the Nb-virus complex at 2.8 Å resolution revealing the stoichiometric 1:1 complex formed with the viral capsid protein (CP). Remarkably, the conformational surface epitope recognized by the Nb covers a cavity analogous to the canyon of picornaviruses implicated in receptor binding. By showing that this cavity is also involved in nematode transmission of GFLV, our results suggest a structural conservation driving vector specificity and receptor binding among plant and animal Picornavirales. Our findings will not only be instrumental to confer resistance to GFLV in grapevine but more generally they pave the way for the generation of novel antiviral strategies in plants based on Nbs.

12:00 - 12:15 #6899 - LS01-OP008 Cryo-EM Structural characterization of the M. tuberculosis ESX-1 secreted virulence factor EspB.
Cryo-EM Structural characterization of the M. tuberculosis ESX-1 secreted virulence factor EspB.

Mycobacterium tuberculosis (Mtb) is the top infectious disease killer worldwide. The threat posed by this bacterium is higher than ever, with the recent discovery of multi and extended-drug resistant (MDR, XDR) strains with improved virulence.

Virulent mycobacteria infect their host cells through a Trojan Horse strategy: they get ingested by the normal phagocytosis route but instead of being digested through acidification and maturation of the phagosome to phagolysosome, these bacteria enter the host’s cell cytosol where they replicate freely. Controlled death of the host cell will allow the spreading of the descendants in the infected organism.

A key step in the infectious life cycle of the virulent mycobacteria is their escape from the phagosome compartment [1]. This phenomenon is mediated by the release of different proteins (EsxA, EsxB, EspB) with cytolytic activities, that will perforate the phagosome membrane. These factors are secreted by the specialized machinery ESX-1 of the recently discovered Type 7 Secretion System family [2].

The ESX-1 machinery is a multi-protein complex thought to span the entire mycobacterial cell envelope. It is constituted by a core of structural proteins (EccACabBDE1) and the assembly and/or functioning of the machinery seems to require the recruitment of additional proteins, including substrates.

Among the different ESX-1 substrates, the 48 kDa protein EspB seems to carry multiple roles: this secreted protein carries cytolytic activity on its own; it is co-secreted with EsxA (the main virulence factor) and this secretion is mutually dependent; EspB may also play a structural role suggested by its ability to oligomerize as well as its proteolytic maturation by MycP1 during the translocation process.

Recently, the structure of the N-terminus of EspB was published [3] showing the N-terminal be composed of a bundle of α-helices, similar to other ESX substrates; the C-terminal is predicted to be unfolded. A heptameric structure was modelled computationally based on the monomeric X-ray data in combination with negative-stain electron microscopy 2D classes.

Here, we report structural characterization of EspB using transmission electron microscopy data. We determined the structure of the N-terminal helix bundle, the mature form as well as the pre-protein EspB at sub-nanometer resolution. Moreover, we were able to identify several discrete oligomeric states of the proteins that were not previously observed: these data will aid to a better understanding of ESX-specific substrates.


[1] van der Wel, N., D. Hava, D. Houben, D. Fluitsma, M. van Zon, et al. 2007. M. tuberculosis and M. leprae Translocate from the Phagolysosome to the Cytosol in Myeloid Cells. Cell. 129: 1287.

[2] S.A. Stanley, S. Raghavan, W.W. Hwang, J.S. Cox. 2003. Acute infection and macrophage subversion by Mycobacterium tuberculosis require a specialized secretion system Proc. Natl. Acad. Sci. U. S. A., 100 (2003), pp. 13001–13006

[3] Solomonson M., Setiaputra D., Makepeace K.A., et al. 2015 . Structure of EspB from the ESX-1 type VII secretion system and insights into its export mechanism. Structure. 2015 Mar 3;23(3):571-83.

Giancarlo TRIA, Giancarlo TRIA (Maastricht, THE NETHERLANDS), Axel SIROY, Chen DELEI, Nino IAKOBACHVILI, Hirotoshi FURUSHO, Carmen LÓPEZ-IGLESIAS, Raimond B. G. RAVELLI, Peter J. PETERS
12:15 - 12:30 #6565 - LS01-OP005 Can DNA Organization in the Full Bacteriophage Capsid be modified by changes in Temperature or Ionic Conditions?
Can DNA Organization in the Full Bacteriophage Capsid be modified by changes in Temperature or Ionic Conditions?

    As revealed initially by X-ray diffraction and visualized later on by cryoEM in several bacteriophages, the DNA chain confined in the capsid is densely packed and organized locally in such a way that DNA segments form an hexagonal lattice with an average inter-helix spacing aH close to 26 – 27 Å. The 3D organization of DNA in the capsid or the path followed by the chain remains unknown. DNA is kinetically constrained and undergoes out-of-equilibrium conformational dynamics during packaging in the capsid. The structural analysis of full capsids also indicates that there is not a unique deterministic DNA packaging pathway. All consequences of this high confinement on DNA ordering and mobility are not yet well understood.

    Our aim is here to explore how confinement determines DNA organization in the full capsid and to what extent spermine and temperature may affect this ordering. CryoEM has been used to visualize DNA patterns in individual capsids, Circular Dichroism (CD) to detect possible changes of the conformation of DNA and of its supramolecular chiral organization and Small Angle X-ray Scattering (SAXS) to detect possible variations of inter-helix distances, while controlling the conformation of the full capsids. We have compared T5, λ, T7, and Φ29 bacteriophages. This selection let us explore the effect of extreme confinement and compare capsids of different shape (prolate or isometric icosahedron) and size, with or without an internal core. We also compared T5 strains containing the full-length genome to the mutant T5st0 containing a shorter DNA chain, to detect whether possible effects may be increased or reduced at lower densities.

    Selected CryoEM views show the overall shape of the phages (Figure 1A) and highlight the local hexagonal DNA lattice seen in top view (domains framed in red in Figure 1B). In the direction normal to the capsid faces, up to 5-6 layers define the thickness of the domain. Figure 1C presents structure factors recorded for all phages.

    - First, we did not detect any change of DNA organization as a function of temperature between 20 to 40°C, as opposed to previous results (1, 2).

    - Second, the presence of spermine (4+) enlarges the size of the hexagonal domains determined by the width of the diffraction peak: from 139 to 156 Å in T5, from 111 to 123 Å in λ, from 111 to 128 Å in T7, and from 96 to 110 Å in Φ29 when 100 mM sp is added in HS buffer (10 mM Tris-HCl, 100 mM NaCl, 1 mM MgCl2, and 1 mM CaCl2). 4 mM spermine is enough to produce this effect. We interpret this increase of the domain size detected for all phages as an increase of the DNA ordering upon spermine addition in agreement with (3). The addition of spermine, by reducing the repulsive interactions between DNA strands would help the local hexagonal order to expand and slightly move the defects further apart. In this hypothesis, DNA reorganization would require very minor sliding of the DNA chain inside the capsid. The enlargement of the DNA hexagonal domains by spermine does not modify the CD spectrum of the encapsidated DNA that stays close to the typical B-type spectrum. Our estimations of the DNA concentrations based on SAXS measurements (540 ± 20 mg/ml in T5, 525 ± 20 mg/ml in λ, 575 ± 20 in T7 and 615 ± 50 in Φ29) seem to indicate that the smallest phages (T7 and Φ29) are the most densely packed. The comparison between  λ and T7 (both icosahedral, with dimensions and DNA length in the same range) suggest that the presence of an internal core in T7 facilitate DNA organization by wounding part of the chain around it in a toroidal organization, thus reducing the defect lattice required to solve the frustration arising from the confinement of the hexagonal lattice in an icosahedral capsid (4).

(1) Liu, T. et al, Proc Natl Acad Sci U S A 2014, 111, 14675–14680 (2) Li, D.et al,  A. Nucleic Acids Res 2015, 43, 6348–6358 (3) Lander, G. C. et al, Nucleic Acids Res 2013, 41, 4518–4524 (4) De Frutos et al, JPhysChemB in press.


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LS8: Human health and disease

LS8: Human health and disease

Chairmen: Peter PETERS (University Professor and Director) (Maastricht, THE NETHERLANDS), Danijela VIGNJEVIC (Paris, FRANCE)
10:15 - 10:45 #8629 - LS08-S25 Real-time subcellular imaging of cancer cell behavior in living mice.
Real-time subcellular imaging of cancer cell behavior in living mice.

Although histological techniques have provided important information on epithelial stem cells and cancer, they draw static images of dynamic processes. To study dynamic processes, we have developed various imaging windows to image intestinal, liver and breast tissue, and visualize the behavior of individual cells at subcellular resolution for several weeks with two-photon intravital microscropy (IVM). Our IVM experiments illustrate that cellular properties and fate of cells are highly dynamic and change over time. For example, we show in healthy and tumorigenic tissues, that cells can acquire and lose stem cell properties, illustrating that stemness is a state as opposed to an intrinsic property of a cell. Moreover, we show that mammary tumor cells that are surrounded by T cells acquire migration properties. An additional aspect that complicates tumor heterogeneity is that cells may exchange active biomolecules through the release and uptake of extracellular vesicles (EVs). Our data shows, in living mice, that malignant tumor cells, through transfer of EVs, enhance the migratory behavior and metastatic capacity of more benign cells. Taken together, these data exemplify that tumor heterogeneity is far more complex than currently anticipated, which has profound consequences for our ideas on the mechanisms of tumor progression and for designing optimal treatment strategies.

10:45 - 11:15 #8363 - LS08-S26 Insights into mitochondrial protein import studied by cryoET.
Insights into mitochondrial protein import studied by cryoET.

As the primary cellular source of ATP, mitochondria form a vital bioenergetic, metabolic and signaling hub. Despite the presence of mitochondrial DNA, almost all mitochondrial proteins (99%) are nuclear encoded and are imported from the cytosol. Protein translocases in mitochondrial membranes are therefore essential for correct protein targeting and localisation. Mitochondrial dysfunction is implicated in ageing, as well as a growing number of human pathologies, including certain cancers, genetically inherited syndromes and neurodegenerative disorders such as Alzheimer’s disease. The biogenesis of mitochondrial proteins and import sites are therefore important factors that determine organelle functionality.


The broad aim of this research is to understand how protein import is correctly orchestrated and regulated by innovative approaches focussed on state-of-the-art electron cryo-tomography (cryoET). This technique is the method of choice for the study of proteins or complexes in situ (Figure 1). Samples are preserved by cryo-fixation, imaged in the electron microscope, and protein structures can be determined by subtomogram averaging (StA).


The majority of precursor proteins (preproteins) are actively imported into mitochondria from the cytosol through the Translocase of the Outer Membrane (TOM) complex, which forms a common entry gate for proteins that are subsequently targeted to various locations. For decades, it has been known that proteins can be imported into mitochondria post-translationally, after synthesis on ribosomes in the cytosol or in vitro. However, information regarding the organisation and distribution of mitochondrial protein import sites was sparse. To image active post-translational protein import in situ, we previously devised a new labelling strategy in which mitochondrial-targeted preproteins were arrested as two-membrane-spanning intermediates through both the TOM complex and the Translocase of the Inner Membrane (TIM23) complex concurrently (Gold, V. A. M. et al. (2014) Nat Commun 5, 4129). This work provided the first views of mitochondrial proteins in the act of import and enabled direct visualization of the number and location of active complexes for the first time (Figure 1). However, information regarding the cytosolic stage of mitochondrial precursor protein import and targeting was still lacking.


Most recently, we have developed a new method to investigate the cytosolic stage of mitochondrial protein targeting and import by biochemical techniques, cryo-ET and StA.  This reveals unprecedented details regarding different targeting pathways, shedding light on the interaction between importing proteins and their corresponding membrane-bound translocons. The consequences of these different modes of targeting and import site redistribution will be discussed in the context of mitochondrial protein biogenesis.


Legend to Figure 1

1. Top panel: mitochondria embedded in a layer of amorphous ice are imaged in the electron microscope.  Incremental tilts of the sample yield a series of projections from different viewing angles. The relative orientations of the mitochondrion (brown) and the macromolecular complex of interest (red) vary depending on the projection angle. Bottom panel: a 0° tilt projection image of a S. cerevisiae mitochondrion.

2. Top panel: a three-dimensional tomogram is reconstructed from the two-dimensional image series by computational back-projection. The molecular complex of interest is indicated (red, boxed). Bottom panel: a slice through a reconstructed tomogram of the mitochondrion shown in step 1. Labelled importing proteins (black spheres on the outer membrane are indicated (red arrowhead).

3. Top left and bottom panels: surface volume rendering is used to place complexes of interest back into three-dimensional space in order to visualize their distribution in a native-like context. Labelled preproteins (black spheres) are shown on the mitochondrial outer membrane (green). The inner membrane (blue) and crista membranes (yellow) are also shown. Top right panel: a slice through the reconstructed tomogram of a labelled preprotein (black sphere, red arrowhead) engaged in mitochondrial import.

Vicki GOLD (Frankfurt am Main, GERMANY), Piotr CHROŚCICKI, Piotr BRĄGOSZEWSKI, Agnieszka CHACINSKA
11:15 - 11:45 #8728 - LS08-S27 Three-dimensional maps of full-length huntingtin and linkage to development of Huntington’s disease.
Three-dimensional maps of full-length huntingtin and linkage to development of Huntington’s disease.

Among neurodegenerative diseases causing serious medical and social problems, in particular in association with an aging population, Huntington´s disease (HD) is classified as a representative one of nine polyglutamine (polyQ) tract disease families. The polyQ diseases cause dominantly inherited neurodegenerative disorders that typically manifests itself during midlife with motor, psychiatric and cognitive symptoms leading to death in 15-20 years after onset (Fig. 1). They evolve from an expansion of the CAG repeat tract in single responsible genes.

HD results from polyQ expansion at the N-terminal in the huntingtin protein (3,144 amino acid protein). The longer the repeat is, the earlier the onset of disease. A metastudy showed that the prevalence of HD in Europe, North America and Australia was 5.7 per 100 0001.

Genetic studies showed that huntingtin knock-out cause embryonic lethality implicating the important role of huntingtin during development2. Despite that huntingtin was identified to be responsible for HD two decades ago, little is known about its biological function nor the molecular mechanism of the pathogenesis. Even if the polyQ expansion in huntingtin occurs close to the N-terminus it is imperative to investigate the function of huntingtin in full-length context as the expansion is likely to modulate activities of the full-length protein. Huntingtin has several HEAT motifs without any known functional domain. Therefore, huntingtin was predicted to adopt an extended shape as shown in other HEAT repeat proteins.

For the present structural studies, allelic series of huntingtin with various polyQ lengths were successfully expressed and purified. We have obtained the overall structure of full-length huntingtin having 23 (Q23) and 78 (Q78) glutamines at medium-resolution by negatively-stained single-particle electron microscopy (EM) showing the protein adopts a spherical shape3 (Fig. 2). CD spectra were consistent with a predominant α-helical secondary structure. The position of the polyQ region could be mapped onto the structure following antibody-bound amino-terminal FLAG-tags of the Q23- and Q78-huntingtins. Furthermore, cross-linking mass spectrometry analysis revealed a modulated network of intramolecular contacts that together with the EM data suggests that huntingtin is composed of five structural domains. Thus, in a large size protein like huntingtin, HEAT repeat domains can be folded back to form a closed helical solenoid with functional sites in the internal cavity. The difference in structures of the EM maps of Q23 and Q78 huntingtin and between cross-linking patterns of the two species suggest modulation of the overall structure with increasing polyQ lengths.

  1. Pringsheim, T. et al. (2012) Mov Disord. 27, 1083-91.
  2. Nasir, J. et al. (1995) Cell 81, 811–823.
  3. Vijayvargia, R. et al. (2016) eLife, Mar 22;5. pii: e11184. doi: 10.7554/eLife.11184.

Taeyang JUNG, Ihnsik SEONG, Ji-Joon SONG, Hans HEBERT (Huddinge, SWEDEN)
11:45 - 12:00 #5482 - LS08-OP030 Structure and viability of atypical morphological forms of Lyme disease spirochetes.
Structure and viability of atypical morphological forms of Lyme disease spirochetes.

Spirochetes Borrelia burgdorferi sensu lato are the causative agents of Lyme disease transmitted by the hard ticks of the genus Ixodes. Spirochetes are motile bacteria with typical flat-wave morphology. These features are crucial for efficient dissemination and evasion of immune responses. However, several reports described presence of non-motile atypical morphologies, e.g. rod-shaped forms, looped/ring shaped forms and spherical/cystic forms called round bodies (RBs).  These forms were observed in the cerebral cortex of patient with chronic Lyme neuroborreliosis [1]. Recently, we proved long term survival of Borrelia in patients after extended antibiotic treatment by successful isolation of live spirochetes [2].

Now, we would like to answer questions, (i) whether RBs represent resistant forms of persisting Lyme disease spirochetes and (ii) whether the transformation of flat-waved spirochetes into RBs forms influences the capability to withstand unfavourable environmental conditions.

For this purpose, we studied morphology and three dimensional arrangements of spirochetes isolated from patients by transmission electron microscopy and electron tomography on serial resin sections and negatively stained spirochetes. Next, using a modification of our novel approach combining cryo-fluorescence and cryo-scanning electron microscopy, we interconnect viability assay with visualization of morphology at high resolution [3]. Viability of GFP expressing spirochetes in a response to host sera was assessed using propidium iodide exclusion method. Obtained results confirmed different susceptibility to different host sera, previously described by our colleagues [4]. We confirmed the formation/viability of RB forms under specific conditions. 

Acknowledgment: This work was supported by the TA CR (TE01020118), European FP7 project 278976 ANTIGONE, Czech-BioImaging (LM 2015062)


[1] Miklossy J, Kasas S, Zurn AD, et al. (2008) Persisting atypical and cystic forms of Borrelia burgdorferi and local inflammation in Lyme neuroborreliosis. J Neuroinflammation. 5: 40.

[2] Rudenko N, Golovchenko M, Vancova M, Clark K, Grubhoffer L, JH Oliver Jr. (2016) Isolation of live Borrelia burgdorferi sensu lato spirochetes from patients with undefined disorders and symptoms not typical for Lyme diseases. Clin Microbiol Infect 22: 267.

[3] Strnad M, Elsterová J, Schrenková J, Vancová M, Rego R, Grubhoffer L, Nebesářová J (2015): Correlative cryo-fluorescence and cryo-scanning electron microscopy as a straightforward tool to study host-pathogen interactions. Scientific Reports. Sci Rep. 5:18029.

[4] Tichá L, Golovchenko M, Oliver JH, Grubhoffer L, Rudenko N (2016): Sensitivity of Lyme Borreliosis Spirochetes to Serum Complement of Regular Zoo Animals: Potential Reservoir Competence of Some Exotic Vertebrates. Vector-Borne and Zoonotic Dis 16: 13–19. 

Marie VANCOVÁ (Ceske BUdejovice, CZECH REPUBLIC), Nataliia RUDENKO, Golovchenko MARYNA, Martin STRNAD, Tomáš BÍLÝ, Libor GRUBHOFFER, Jana NEBESÁŘOVÁ
12:00 - 12:15 #5881 - LS08-OP031 Novel in vivo imaging techniques to visualise renal morphology and function in acute kidney injury.
Novel in vivo imaging techniques to visualise renal morphology and function in acute kidney injury.

Introduction: The medical uses of optical imaging are revolutionizing medicine; optical imaging is undergoing explosive growth fuelled by advances in high-sensitivity detectors. These light based systems utilise multiphoton microscopy (MPM) to provide high resolution and quantitative imaging of cellular metabolism in in situ and in vivo biological tissues and organs – in space (three dimensions), in time, in spectra, and in fluorescence anisotropy (i.e. a total of 6 dimensions). MPM allows in vivo visualisation of intact kidney tissue at the single cell resolution, which is solved a long-standing critical technical barrier in renal research to study several complex and inaccessible cell types and anatomical structures. In this study, MPM was employed to visualise morphology changes and study the functions of acute kidney injury (AKI).

Methods: Glycerol-induced AKI model (elevated serum creatinine) can be used to mimic rhabdomyolysis, which was developed in male C57BL/6 mice (8-12 weeks) by intramuscular injection of 50% (v/v) glycerol /PBS (10 ml/kg) into the left hind leg. The control mice were injected by PBS using the same method. After 24 hours, kidneys were exposed to image using MPM for morphology examination in both groups. Since Rhodamine 123 (RH123) is a marker to measure P-glycoprotein (P-gp) transporter function, it was intravenously injected into control and AKI mice and imaged by MPM to evaluate the P-gp transporter function. Using a bolus injection of FITC labelled inulin, rapid quantification of glomerular filtration rate (GFR) was determined in both groups by directly imaging of inulin clearance from glomerulus. A LaVision Biotec Nikon MPM was used to image RH123 excretion from tubules. GFR was measured using a DermanInspect system equipped with the ultrashort (85 fs pulse width, 80 MHz repetition rate) pulsed mode-locked tunable Ti:sapphire laser (Mai Tai, Spectra Physics, 25 Mountain View, USA).

Results: The MPM images directly showed morphology changes in AKI mice compared to control group, where acute injury of tubular cells as indicated by reduced autofluorescence and cellular vacuolation (Fig.1). Intravital imaging showed that RH123 was rapidly excreted from tubules in control group but slowly eliminated from AKI model (Fig. 2), indicating P-gp transporter dysfunction in glycerol-induced AKI. As shown in Fig, 3, reduced glomerular permeability was also observed in AKI model, where FITC-labelled inulin (red color) was quickly cleared from glomerular at 30 mins after injection in control group, while fluorescence from FITC-labelled inulin was retained in glomerular in AKI model.

Conclusion: This advanced imaging technique can be used to rapid diagnosis and quantification of AKI induced morphology and functional changes.

Key words: Intravital imaging, Multiphoton microscopy, Morphology, Renal function, AKI

Xiaowen LIANG (Brisbane, AUSTRALIA), Haolu WANG, Germain GRAVOT, Xin LIU, Michael ROBERTS
12:15 - 12:30 #6844 - LS08-OP032 Organelle changes in a Huntington’s disease model using cryogenic soft x-ray tomography.
Organelle changes in a Huntington’s disease model using cryogenic soft x-ray tomography.

Huntington’s Disease, a neurodegenerative disorder characterized by movement and executive function disruption, is linked to an expanded and unstable CAG trinucleotide repeat which translates as a polyglutamine (Q) repeat in the protein product. Healthy controls demonstrate a fairly broad range of trinucleotide repeats and 40+ repeats have been described as pathological. Due to this expansion, exon 1 of the Huntingtin protein is aberrantly processed by cellular machinery leading to an unintended cleavage product (mHTT). Aggregates of mHTT exon 1 have been found in mouse models and in patient brain [1].

PC-12 cells were used as an HD model to study structures of mHTT aggregates in a cellular context and to study cell morphology changes due to the presence of mHTT. These cells inducibly express a truncated version of mHTT exon 1 (97Qs) tagged with eGFP in the presence of Ponasterone A [2]. PC-12 cells expressing mHTT-GFP exon 1 were grown on gold finder grids, cryo-immobilised by plunge freezing, and imaged. GFP fluorescence was used to identify cells of interest prior to imaging in cryogenic soft x-ray tomography (SXT). SXT makes use of x-rays in the “water window” (2.4 nm wavelength, 500 eV) where common biological elements such as carbon and nitrogen absorb x-rays and are therefore more visible, whereas water (vitreous ice) is relatively transparent. This allows whole, fully-hydrated cells to be imaged at approximately 40 nm resolution without requiring sectioning or staining techniques.

Seven overlapping tilt series were collected with a 0.5° step size and a tilt range of ±60°, followed by reconstruction in IMOD [3]. Figure 1 shows one of the seven reconstructions, featuring a large nucleus with nucleolar features and a crowded cytoplasmic space. Segmentation of these features was completed using HISS (Hierarchical Interactive Super-region Segmentation) followed by annotation of cellular features based on their inherent properties (Figure 2). Cytoplasmic organelles were classified using specific characteristics of the data, such as the average intensity of the organelle, the size of the organelle, the variance of the voxels that make up the organelle and the location of the organelle in the 3D volume (Figure 3).

Using these characteristics, clumps of collagen, empty vesicles, lipid droplets and mitochondria were classified and visually inspected for accuracy. (Note: collagen was used to aid in cell adherence, but due to aggregation issues produced large clumps localized to the surface of the carbon substrate.) The group termed “other organelles” is likely composed of various compartments such as lysosomes, endosomes, filled vesicles, etc, which are not differentiable by eye in soft x-ray images.

Next, population statistics for each organelle class, such as the average and standard deviation of the class’s size, shape, intensity and variance will be used to describe the morphology of a non-perturbed cell, and the changes due to perturbations, in this case, the presence of mHTT aggregates. In the future, correlated cryo-fluorescence light microscopy and SXT will be used to verify mitochondria, and identify subgroups of the “other organelles” class, such as lysosomes and early and late endosomes.

Identification of organelle specific characteristics in SXT will allow the unambiguous classification of various organelles. As a whole, this methodology can broadly describe the effects of various cellular perturbations such as disease, infection or treatment in a whole cell context.

  1. Hatters, D.M., 2012. Putting huntingtin “Aggregation” in View with Windows into the Cellular Milieu. Curr Top Med Chem.
  2. Apostol BL, et al., 2003. A cell-based assay for aggregation inhibitors as therapeutics of polyglutamine-repeat disease and validation in Drosophila. Proc Natl Acad Sci USA. 100(10):5950–5955.
  3. Mastronarde, D.N., 1997. Dual-axis tomography: an approach with alignment methods that preserve resolution. J. Struct. Biol. 120:343-352.
Michele DARROW (Didcot, UK), Wei DAI, Patrick MITCHELL, Imanol LUENGO, Wah CHIU, Elizabeth DUKE

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The Skin Imaging Society meeting

The Skin Imaging Society meeting

10:15 - 11:05 Invited lecture 2: Syndecans in epidermal biology. Patricia ROUSSELLE (LYON, FRANCE)
11:05 - 12:05 Session 4. Oral communications.

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EMAG Meeting

EMAG Meeting

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MS0: Nanoparticles: from synthesis to applications

MS0: Nanoparticles: from synthesis to applications

Chairmen: José CALVINO (Cadiz, SPAIN), Goran DRAZIC (Head of microscopy group) (Ljubljana, SLOVENIA), Christian RICOLLEAU (Professor) (Paris, FRANCE)
14:00 - 14:30 #8382 - MS00-S62 Understanding of atomic structures of nanoparticles on surfaces.
Understanding of atomic structures of nanoparticles on surfaces.

Metallic nanoparticles occupy special places in fundamental research and practical applications, not only because they bridge the gap between atoms and bulk matter but more importantly because some fascinating phenomena appear only at nanoscale level. Research has shown that the properties of nanoparticles are strongly affected by their size, shape, chemical composition as well as their supports.  Hence it is essential to gain full knowledge of their three-dimensional atomic structures, which is still a challenging task for nanoclusters and nanoalloys. 

After a brief overview of the current status of structure research on clusters and nanoalloys, I will discuss what an aberration-corrected scanning transmission electron microscopy (STEM) can offer in this area through an atom counting approach. I will then present two case studies from our recent work: (1) on control and manipulation of the size and atomic structure of Au clusters, formed via gas phase condensation and deposited on amorphous carbon films and MgO(100) surfaces; and (2) on structures of TiO2(110) supported Au-Rh nanoalloys, prepared through solution based chemical synthesis method, under effects of various thermal treatments.  In both cases, direct evidence of atomistic details of the clusters, nanoalloys as well as nanoparticle-support interfaces will be presented and their possible mechanisms will be discussed, together with computer modeling studies. Our emphasis will be on understanding the relationship between nanoparticle structures and their thermodynamics or kinetics.

Ziyou LI (Birmingham, UK)
14:30 - 15:00 #8386 - MS00-S63 Nanoparticle Structure and Dynamics Studied Using Controlled Atmosphere Transmission Electron Microscopy.
Nanoparticle Structure and Dynamics Studied Using Controlled Atmosphere Transmission Electron Microscopy.

Nanoparticle and catalysis research makes extensive use of transmission electron microscopy (TEM). In particular, environmental transmission electron microscopy (ETEM) has attracted considerable attention in recent years. This technique allows us to expose samples to gaseous environments at elevated temperatures in order to investigate local structural changes at the atomic level as the environment changes. Recently, the technique has also been used in nanowire, graphene and electron optical lithography research among others.

Recent developments in TEM instrumentation include monochromation of the electron source and aberration correction of both condenser and objective lenses. These developments have now been introduced onto the ETEM column. The improved spatial resolution and interpretability provided by these additions are beneficial for imaging the surface structure and dynamics of catalyst nanoparticles and provides exciting new possibilities for investigating chemical reactions. In order to take full advantage of this, an understanding of both the interaction of fast electrons with gas molecules and the effect of the presence of gas on high-resolution imaging is necessary.

Using an FEI Titan ETEM equipped with a monochromator and an aberration corrector on the objective lens, we have investigated sintering of supported metal nanoparticles often used in catalysis. A model system consisting of supported gold nanoparticles were prepared by sputter-depositing the metal onto graphene and boron nitride substrates. These samples were imaged under hydrogen at increasing temperatures. Gas was introduced into the environmental cell using digitally controlled mass flow controllers providing accurate and stable control of the pressure in the cell. As the temperature was increased, migrating particles were observed on the support. As they came into contact, a neck was formed between the particles and subsequently, the particles coalesced entirely (Fig. 1). Growth patterns have also been investigated for platinum and palladium nanoparticles supported on silicon oxide substrates. Here, anomalously large particles were observed as the particles were sintered in oxygen atmospheres at temperatures at elevated temparatures. Such large particles have also been observed for industrial catalysts. In this study, we will try to elucidate the mechanisms of metal nanoparticle sintering.

The analytical capabilities of the microscope can be further augmented by adding stimuli such as optical or electrical though the sample holder. Using a holder capable of exposing the sample to light, the redox properties of cuprous oxide have been investigated. Cuprous oxide has been identified as an active catalyst for the water splitting and hydrogen evolution from an ethanol solution. However, Cu2O suffers from photocorrosion. This phenomenon was investigated using controlled atmosphere transmission electron microscopy. Fig. 2 shows how the photoinduced degradation of cuprous oxide to metallic copper under an aqueous atmosphere using bright-field imaging, electron diffraction and electron energy-loss spectroscopy. All three techniques show the transformation from oxide to metal.

Effects of imaging in various elemental as well as di-molecular gases and their effect on imaging and spectroscopy in the environmental transmission electron microscope will also be discussed.

Thomas Willum HANSEN (Kgs. Lyngby, DENMARK)
15:00 - 15:15 #4573 - MS00-OP178 On the mechanism of metal-induced crystallization: an in situ TEM study of nanosized Au/Ge films.
On the mechanism of metal-induced crystallization: an in situ TEM study of nanosized Au/Ge films.

Thin crystalline germanium (c-Ge) and silicon (c-Si) films are widely used in current microelectronic and nanoelectronic devices, such as thin film transistors and highly efficient solar cells. However, Si or Ge films grown from the vapor phase are usually amorphous. Crystallization of such films requires annealing temperatures above 500°C, which are often incompatible with the fabrication processes used in industry. Yet, when a semiconductor film of amorphous germanium (a-Ge) or amorphous silicon (a-Si) is in contact with a metal that forms an eutectic phase diagram (e.g, Au, Ag, Al, Bi, Pd), the crystallization temperature of the amorphous film is reduced significantly. This effect is commonly known as “metal-mediated” or “metal-induced crystallization” (MIC). Despite numerous studies of the MIC effect, the reaction mechanism is still unclear, although the interaction at the interface between metal and semiconductor seems to play a key role in activating the process. In this context, the main motivation of the current work is to understand the mechanism of metal-induced crystallization of semiconductor films in eutectic binaries by studying the interfacial interactions in these systems. Layered films formed by the sequential condensation of components in vacuum are a convenient model system, since the thickness of the film or the size of particles is comparable with the width of the interface boundary in a binary system. By heating such a system in a transmission electron microscope,  the interaction between the metal and the semiconductor film can be observed directly in real time.


We have selected gold-germanium (Au-Ge) films as a model system. Layered Au/Ge films are prepared by the condensation of an amorphous continuous film of Ge of 5 nm, followed by the deposition of a 0.2-0.3 nm Au film on top of the Ge film. KCl crystals covered by an arc-deposited 5 nm carbon layer prior to the deposition of Ge and Au are used as a substrate. The structure and morphology of the films were studied in situ in a FEI TECNAI G2 F20 X-TWIN transmission electron microscope within the 20-400°C range with a Gatan 652 Double Tilt Heating Holder. It has been shown that the process of solid state de-wetting of a 0.2-0.3 nm Au films occurs in the 150-200°C temperature range and results in an a-Ge film uniformly covered with Au nanoparticles with an equivalent diameter of 4.4 nm. The eutectic melting of these Au nanoparticles occurs at temperatures 200-250°C and is accompanied by both an abrupt change of the film morphology and crystallization of the a-Ge film. Long-term annealing of the film at a temperature below the eutectic point does not lead to a change in the mean particle size or to the appearance of c-Ge. Instead, the capillary motion of liquid eutectic particles on Ge surface has been observed (Fig. 1). At higher temperatures, this process intensifies and the motion of the particles becomes visible directly by TEM. This effect leads to the crystallization of a whole surface of amorphous germanium film and causes a drastic change in the Au film morphology. In addition, the formation of metastable fcc Ge phase is found and is shown to drive the capillary motion of eutectic particles. Fig. 2 shows TEM images of the same area of the film taken at 370°C with an interval of 10 seconds between each image. From Fig 2a to Fig 2b, it is evident that the eutectic nanoparticles move, leaving c-Ge behind. However, a more detailed examination of the HRTEM images of the crystalline Ge film shown in Figure 2 exhibit an unexpected feature. In particular, the Fast Fourier Transform (FFT) of region I in Figure 2a, which corresponds to a beam direction of B=[110], shows forbidden reflections for the diamond structure, namely {200} type planes (d=0.283 nm). The appearance of such reflections seems to indicate the crystallization of germanium into a metastable fcc phase, which is then converted into the diamond structure.

Aleksandr KRYSHTAL (Krakow, POLAND), Alexey MINENKOV, Paulo FERREIRA
15:15 - 15:30 #6475 - MS00-OP190 The Determining Role of Solution Chemistry in Radiation-Induced Nanoparticles Synthesis in the STEM.
The Determining Role of Solution Chemistry in Radiation-Induced Nanoparticles Synthesis in the STEM.

In the last decades, radiolytic synthesis routes have exploited the chemical effects of the absorption of high-energy radiation on precursor solutions, to form nanostructures by reproducing a selective reducing/oxidizing environment. Radiation chemical synthesis provides a powerful means to form nuclei which are homogeneously distributed in the whole volume and where the growth rate can be easily controlled.[1] The latter has recently been achieved using liquid cell electron microscopy, with examples of formation kinetics of particles in polar (water)[2] and non-polar (toluene)[3] solvents following a linear relation with applied dose rate. Fine control of particles size with conventional radiation sources typically requires increasing the production of radicals (thus applying “high doses”). On the contrary, the challenge in the scanning transmission electron microscope (STEM), where incident doses are inherently higher by orders of magnitude, is to reduce drastically such production. To illustrate this, we recently proposed the use of non-polar systems (toluene), which are not typically used for radiolytic synthesis outside the STEM, as a solvent that produces much lower amount of radiolytic ionic species upon electron irradiation, as compared to water or other polar solvents such as alcohols (Figure 1 shows an example of


Thus far, most experiments in the liquid cell involved the use of water as a solvent, which explains the large amount of work dedicated to understanding the effects of the electron beam in aqueous conditions. Radiation chemical yields in water are large due to the relatively low bond energies in water molecules, meaning highly reactive oxidizing and reducing radicals and species are created in about an equal amount.[4] Reproducing net reducing conditions for nanoparticle growth can be achieved with the addition of substances that convert primary radicals into free reducing radicals (using OH· scavengers, for instance). The use of organic solvents in the liquid cell allows for tuning the polarity of the medium, giving access to a broader range of synthesis conditions but producing more complex radiolytic products. Here I will discuss, revisiting a number of examples from the literature and presenting our most recent work, general methods for finding more suitable synthesis environments for controlled nanoparticles formation in the liquid cell. Much of the presentation will focus on the solvent radiolysis which is what predominantly dictates the species and yields involved in the chemical processes leading to nanostructure synthesis.[4]



[1] J. Belloni, Catal. Today, 2006, 113, 141-156; S.-H. Choi et al., Colloids Surf., A, 2005, 256, 165-170; J. Belloni et al., New J. Chem., 1998, 22, 1239-1255; M. A. J. Rodgers and Farhataziz, Radiation Chemistry: Principles and Applications, VCH Publishers, New York, N.Y. , 1987.

[2] D. Alloyeau et al., Nano Lett., 2015, 15, 2574-2581; J. H. Park et al., Nano Lett., 2015, 15, 5314-5320.

[3] P. Abellan et al., Langmuir, 2016, 32, 1468-1477.

[4] SuperSTEM is the UK EPSRC National Facility for Aberration-Corrected STEM, supported by the Engineering and Physical Science Research Council (PA). Part of this work was supported by the Chemical Imaging Initiative, under the Laboratory-Directed Research and Development Program at Pacific Northwest National Laboratory (PNNL) and by the US Department of Energy, Office of Science, Office of Basic Energy Sciences, and was performed in part using the facilities located in the William R. Wiley Environmental Molecular Sciences Laboratory, a DOE national scientific user facility sponsored by the DOE’s Office of Biological and Environmental Research and located and the PNNL. PNNL is operated by Battelle for DOE.

Patricia ABELLAN (Daresbury, UK), Ilke ARSLAN, Naila AL HASAN, Nigel D. BROWNING, James E. EVANS, Jay W. GRATE, Ayman M. KARIM, Ivan T. LUCAS, Trevor H. MOSER, Lucas R. PARENT, Chiwoo PARK, Taylor J. WOEHL
15:30 - 15:45 #6303 - MS00-OP187 Advanced Electron Tomography of Assemblies of Nanoparticles.
Advanced Electron Tomography of Assemblies of Nanoparticles.

Nano assemblies are two- or three-dimensional (3D) collections of nanoparticles. The properties of the assemblies are determined by the number of particles, their position, shape and chemical nature as well as the bonding between them. If we are able to determine these parameters in 3D, we will be able to provide the necessary input for predicting the properties and we can guide the synthesis and development of new assemblies or superstructures. A detailed structural characterization is therefore of utmost importance.

Electron tomography is a versatile and powerful tool that has been increasingly used in the field of materials science. Also for the investigation of nanoassemblies, electron tomography has been of high value as illustrated in Figure 1 [1-3]. However, to extract quantitative information, optimization of the electron tomography experiment is required, especially for large assemblies or assemblies consisting of more than one type of nanoparticle. Here, we will show how advanced electron microscopy,  in combination with novel reconstruction algorithms, enables us to determine the number of particles, their stacking, interparticle distances and outer morphology. This will be illustrated for very large assemblies consisting of spherical nanoparticles [4], assemblies that contain anisotropic particles (Figure 2) and binary assemblies (Figure 3) consisting of particles with different sizes or different compositions [5,6].

Going a step further is the investigation of self assembly and oriented attachment at the atomic scale. Using annular bright field scanning transmission electron microscopy, the possible effect of polarity can be investigated, whereas high angle annular dark field scanning transmission electron microscopy in combination with advanced computational techniques enables the investigation of the interfacial planes in two-dimensional superlattices from nanocrystals [7]. Finally, we will discuss the use of exit wave reconstructions to investigate the effect of surface ligands on self assembly.

[1] S. Bals, B. Goris, L.M. Liz-Marzán, G. Van Tendeloo, Angewandte Chemie 53 (2014) 10600

[2] T. Altantzis, B. Goris, A. Sánchez-Iglesias, M. Grzelczak, L.M. Liz-Marzán, S. Bals, Particle and Particle Systems Characterization 30 (2013) 84

[3] M.P. Boneschanscher, W. Evers, J.J.Geuchies, T. Altantzis, B. Goris, F.T. Rabouw, S.A.P. van Rossum, H.S.J. van der Zant, L.D.A. Siebbeles, G. Van Tendeloo,I. Swart, J. Hilhorst, A. Pethukov, S. Bals, D. Vanmaekelbergh, Science 344 (2014) 1377

[4] D. Zanaga, F. Bleichrodt, T. Altantzis, N. Winckelmans, W.J. Palenstijn, J. Sijbers, B. de Nijs, M.A. van Huis, A. Sánchez-Iglesias, L.M. Liz-Marzán, A. van Blaaderen, K.J. Batenburg, S. Bals, G. Van Tendeloo, Nanoscale 8 (2016) 292

[5] M. Grzelczak, A. Sanchez-Iglesias, L. M. Liz-Marzán, Soft Matter 9 (2013) 9094-9098

[6] T. Altantzis, Z. Yang, S. Bals, G. Van Tendeloo, M.-P. Pileni, Chemistry of Materials 28 (2016) 716

[7] E. Javon, M. Gaceur, W. Dachraoui, O. Margeat, J. Ackermann, M. Ilenia Saba, P. Delugas, A. Mattoni, S.Bals, G. Van Tendeloo, ACS Nano 9 (2015) 3685


S.B., D.Z. and N.C. acknowledge financial support from European Research Council (ERC Starting Grant # 335078-COLOURATOMS). The research leading to these results has received funding from the European Union Seventh Framework Programme under Grant Agreements 312483 (ESTEEM2). 

Sara BALS (Antwerpen, BELGIUM), Thomas ALTANTZIS, Daniele ZANAGA, Bart GORIS, Nathalie CLAES, Gustaaf VAN TENDELOO
15:45 - 16:00 #6757 - MS00-OP196 Electron Microscopy of Copper Nanoparticle Growth.
Electron Microscopy of Copper Nanoparticle Growth.

Understanding processes leading to the formation of nanoparticles is of utmost importance for tailoring their size, shape and spatial arrangements, which are crucial for the nanoparticles’ use in heterogeneous catalysis. As the nanoparticle growth involve processes at or across atomic surfaces, observation made in situ at high-spatial resolution would be beneficial for elucidating the nanoparticle growth mechanism. In recent years, transmission electron microscopy (TEM) has become a powerful technique for studying nanoparticles. With TEM, individual nanoparticles can be observed at atomic-resolution and in reactive gas environments [1]. This capability opens up new possibilities for uncovering dynamics of nanoparticles immersed in gas environments. Here, we employ such in situ TEM capabilities to study the growth of Cu nanoparticles supported on SiO2 by the reduction of a homogeneous precursor consisting of Cu phyllosilicate platelets (Fig. 1) [2, 3]. The homogeneous precursor represents an important class of industrial catalyst precursor material for which local TEM observations can directly be related to the catalyst at a macro-scale.

By monitoring the individual nanoparticles over time, quantitative information about the nucleation time and size evolution of the Cu nanoparticles were obtained from TEM image series (Fig. 2). To employ such quantitative data in a kinetic description of the reduction process, it is imperative to reduce the influence of the electron beam on the process to a negligible level. To achieve that, we developed a low dose-rate TEM imaging procedure in which several regions of the sample was monitored in parallel in a dose-fragmentated way [1,4,5,6].  This strategy allows for a direct evaluating of the role of the electron dose-rate, accumulated dose and dose history, which were all found to play a role on the growth process (Fig. 1C). Based on this evaluation, the role of the electron beam was quantitatively assessed and used to pinpoint illumination conditions that allowed the observation of the inherent thermal reduction process.

In view of this detailed analysis, quantitative data were extracted from the time-resolved TEM image series to describe the thermally induced growth of the Cu nanoparticles supported on SiO2 (Fig 1B). By comparing the quantitative TEM data of the process with kinetic models, it was found that the growth process was best characterized as an autocatalytic reaction with either diffusion- or reaction-limited growth of the nanoparticles. This finding is significant because the autocatalytic reaction limits probability for secondary nucleation and because the platelike precursor structure restricts the diffusion. This describes a way to synthesize nanoparticles with well-defined sizes, which in turn offers a more stable catalyst[7]. In this way, in situ observations made by electron microscopy provide mechanistic and kinetic insights that can guide the formation of metallic nanoparticles for catalytic applications in a rational way.


[1] S. Helveg, J. Catal. 328, 102 (2015)

[2] R. van den Berg et. al., J. Am. Chem. Soc. 138, 3433 (2016)

[3] R. van den Berg et. al., Catal. Today (2015)

[4] C. Holse et. al., J. Phys. Chem. 119, 2804 (2015)

[5] J. R. Jinschek and S. Helveg, Micron 43, 1156 (2012)

[6] S. Helveg et. al., Micron 68, 176 (2015)

[7] S. B. Simonsen et. al., J. Am. Chem. Soc. 132, 7968 (2010)

16:00 - 16:15 #6872 - MS00-OP197 In situ TEM measurements of mechanical properties of individual spherical BN nanoparticles of different morphologies.
In situ TEM measurements of mechanical properties of individual spherical BN nanoparticles of different morphologies.

Boron nitride (BN) nanostructures exhibit excellent mechanical properties. For example, the in situ tensile tests on individual BN nanotubes (BNNTs), which were conducted in situ in a transmission electron microscope (TEM) column, demonstrated the strength and Young’s modulus of ~33 GPa and ~1.3 TPa, respectively [1].Such superb mechanical properties of BN nanostructures make them very attractive materials as a reinforcement phase in lightweight composites. Besides nanotubes, nano-BN can be obtained in the form of spherical nanoparticles (BNNPs) with different morphologies – solid or hollow, with smooth or rough surfaces. High electrical and chemical resistance, thermal stability and biocompatibility of BNNPs were reported but their mechanical properties have not been detailed yet.

BNNPs in the present study were synthesized by CVD technique. By changing technological parameters of CVD process particles of various morphologies were obtained. For each type of individual BNNPs in situ compression tests were accomplished in a TEM column. As-synthesized BNNPs were dispersed in acetone and the suspension was placed onto a Si wafer. The truncated cone-like shape indenter with a diameter of top circle of 1 μm was used. Elastic moduli were determined for all tested particles. The obtained results (Fig. 1) show that the high strength enables the hollow spherical BNNPs to withstand a considerable compressive deformation before failure (up to 50% of the hollow particle diameter). The structures also demonstrated a high percentage of elastic recovery.

1. X.L. Wei, M.S. Wang, Y.Bando, D.Golberg, “Tensile tests on individual multiwalled boron nitride nanotubes,” Adv. Mater. 22 (2010), 4895-4899.


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IM2: Micro-Nano Lab and dynamic microscopy

IM2: Micro-Nano Lab and dynamic microscopy

Chairmen: Francisco José CADETE SANTOS AIRES (VILLEURBANNE CEDEX, FRANCE), Niels DE JONGE (Saarbrücken, GERMANY), Gerhard DEHM (Düsseldorf, GERMANY)
14:00 - 14:30 #8433 - IM02-S37 Enabling and doing structural biology in situ.
Enabling and doing structural biology in situ.

To visualize and analyse molecular structures in their native state and in their cellular context is the overarching aim of in situ structural biology. In the classical structural biology approach purified molecules are investigated isolated from their ‘neighbours’, far from the intricate macromolecular interaction network and thus disentangled from the cellular factory. We have seen stunning results of such isolated molecular structures at atomic or near-atomic resolution obtained by single-particle cryo-electron microscopy (cryo-EM), a direct result of the development and exploitation of direct electron detection devices. However, many supra- and macromolecular assemblies involved in key cellular processes cannot be studied in isolation; their function is so deeply rooted in their cellular context that it is impossible to isolate them without disrupting their structural integrity. Thus the challenge for us now is to apply cryo-EM to protein complexes and other biological objects within their native environment, namely within cells [1,2].

The biggest obstacle in obtaining high-resolution three-dimensional (3D) information on the cellular level is the sample thickness. Resolution scales with thickness in transmission electron microscopy (TEM) and thus minimal invasive preparation methods are needed for several micrometer-sized specimens (e.g. mammalian cells). Cryo-focused ion beam milling or more general FIB micromachining is an alternative to traditional preparation methods. It allows the fabrication of self-supported lamellae, suitable for high-resolution cryo-electron tomography (cryo-ET) studies [3]. These lamellae open up ‘windows’ to the cellular interior, covering tens of square micrometers. They are electron transparent and ‘thin enough’ to obtain molecular resolution information in the cellular context. However, the fidelity with which macromolecules can be visually identified in cryo-electron tomograms is not only related to sample thickness, but on the characteristic ‘material properties’ of the biological samples. Living cells are inherently crowded, but the degree of molecular crowding can vary greatly from one cell type to another (e.g. yeast is denser than algae) and between different regions within a single cell (e.g. the nucleoplasm is denser than the cytoplasm). Thus, a compromise has to be found between what details one would like to see and how big the final tomographic volume should be. Moreover the volume represented in a typical FIB lamella is only a very small fraction of the cell. Retaining low-abundance and dynamic subcellular structures or macromolecular assemblies within such limited volumes requires precise targeting of the FIB milling process. This fact necessitates the introduction of correlative light and electron microscopy (CLEM) in all three dimensions [4]. Together, a sample’s thickness, molecular crowding and the accuracy with which structures can be targeted will ultimately determine the level of detail that can be resolved by cryo-ET.

Here, we present our approaches towards in situ structural biology, - capturing three-dimensional structure within cells at high resolution, unaltered by sample preparation. We will give an overview on recent advances in sample preparation, data collection and data processing, including technology for FIB milling, correlative light and electron microscopy, phase plate imaging and direct electron detection. We demonstrate that these developments can be used in a synergistic manner to produce 3D images of mammalian cells in situ of unprecedented quality, allowing for direct visualization of macromolecular complexes and their spatial coordination in unperturbed eukaryotic cellular environments.

[1] Mahamid J. et al. Science 2016, 351 (6276), 969-972.

[2] Engel BD. et al. PNAS USA 2015, 112 (36): 11264–11269.

[3] Rigort A. and Plitzko JM. Archives of Biochemistry and Biophysics 2015, 581: 122-130.

[4] Arnold J. et al. Biophysical Journal 2016, 110 (4): 860–869.

Juergen PLITZKO (Martinsried, GERMANY), Julia MAHAMID, Benjamin ENGEL, Sahradha ALBERT, Miroslava SCHAFFER, Jan ARNOLD, Yoshiyuki FUKUDA, Maryam KHOSHOUEI, Radostin DANEV, Wolfgang BAUMEISTER
14:30 - 14:45 #7069 - IM02-OP079 Studying biological samples in their native liquid environment using electron microscopy.
Studying biological samples in their native liquid environment using electron microscopy.

It is now possible to study biological systems (e.g. eukaryotic cells) at nanometer spatial resolution in their native liquid environment using electron microscopy [1-3]. In contrast to conventional procedures, these new methods do not involve complex preparation steps like embedding, cutting, or freeze-sectioning. It is further possible to minimize negative drying artifacts by adjusting experimental conditions that represent the native state as close as possible, i.e. the presence of water. Several different approaches meeting these requirements have been developed to study whole cells of different sizes:

Method 1: Two silicon microchips with electron transparent windows can be used to realize a microfluidic chamber that is sealed from the vacuum in the electron microscope (Figure 1). The chamber between the two microchips is thick enough to contain whole cells, yet thin enough to ensure a sufficient transmission of electrons. It is further possible to create bubbles in the liquid cell compartment by inducing a high density of electron dose on the sample. This increases the obtained contrast due to the minimized amount of scattering solvent. The liquid cell compartment can be used in a standard Transmission electron microscope (TEM). Method 2: Environmental scanning electron microscopy (ESEM) can be used to study cells covered in a thin layer of liquid surrounded by a saturated water atmosphere. The thickness of the liquid layer is controlled by adjusting the temperature and the environmental pressure within the vacuum chamber. Method 3: The wet sample is attached to an electron transparent support (e.g. graphene, carbon, silicon nitride) and covered with a thin membrane (e.g. mono or multilayer graphene) to realize a thin layer of liquid around the sample [4]. This method allows for high resolution imaging as the amount of solvent is reduced to a minimum. It can be used in any conventional TEM and SEM with scanning transmission electron microscopy (STEM) detection. The presence of water can be confirmed by beam-induced bubbles.

Each of these three methods can be used to study the location and stoichiometry of transmembrane proteins within the intact plasma membrane [2, 3] with relevance to cancer research [5]. Nanoparticles, specifically attached to proteins, provide enough contrast for imaging (Figure 2).  Also correlative light- and electron microscopy is readily possible, so that large numbers of cells can be screened, while selected regions can be studied with high resolution [5].


[1]       de Jonge, N., Peckys, D.B., Kremers, G.J., Piston, D.W. Proc Natl Acad Sci 106, 2159-2164, 2009.

[2]       Peckys, D.B., Baudoin, J.P., Eder, M., Werner, U., de Jonge, N., Scientific reports 3, 2626, 2013.

[3]       Peckys, D.B., de Jonge, N., Microscopy and microanalysis 20, 346-365, 2014.

[4]       Walker, M. I.; Weatherup, R. S.; Bell, N. A. W.; Hofmann, S.; Keyser, U. F. Appl. Phys. Lett. 2015, 106, 023119.

[5]       Peckys, D.B., Korf, U., de Jonge, N., Sci Adv 1, e1500165, 2015.

Acknowledgements: We thank E. Arzt for his support through INM.  Research in part supported by the Leibniz Competition 2014. R.S.W. acknowledges a Research Fellowship from St. John’s College, Cambridge and a Marie Skłodowska-Curie Individual Fellowship (Global) under grant ARTIST (no. 656870) from the European Union’s Horizon 2020 research and innovation programme.

14:45 - 15:00 #6123 - IM02-OP062 Environmental tomography of liquid latex suspensions in STEM.
Environmental tomography of liquid latex suspensions in STEM.


   ESEM (Environmental Scanning Electron Microscopy) allows the observation of liquids under specific conditions of pressure and temperature. Moreover, when working in the transmission mode, i.e. in STEM (Scanning Transmission Electron Microscopy), nano-objects can be analyzed inside a liquid. Those acquired images are quite similar to those obtained in TEM (Transmission Electron Microscopy) using a closed cell [1]. By implementing a Peltier stage in the tomography device which was developed for the characterization of the 3D structure of non-conductive and low-contrast materials [2], the acquisition of image series of wet samples (wet-STEM tomography) [3]. Moreover, in situ evaporation of water can be performed to study the materials evolution from the wet to the dry state.

  In our experiment, SBA-PMMA, a copolymer derived from styrene and metacrylic acid esters in aqueous solution, is chosen as the sample. A 3% PMMA shell, which plays the role of steric surfactant, has already included in the SBA particles. Some other surfactants can be introduced to further stabilize the latex for some special applications [4].

  We first present measurements of the sample temperature using different experimental conditions, to show that the sample can be preserved in the dry state. Then, we show series of tilted images that are acquired during in situ hydration / dehydration experiments. Reconstructed volumes are obtained using the image processing softwares etomo and Fiji (see Figure 1), and the resolution is calculated using Fourier Shell Correlation (FSC). The influence of irradiation damage on the reconstructed volumes are discussed.

  Afterwards, the volumes are segmented (see Figure 2) and quantified to follow the evolution of the microstructural parameters during water evaporation.  This shows the potentialities of wet-STEM tomography for the characterization of suspensions from the wet to the dry state.


[1] de Jonge, N., Ross, F.M. Nature Nanotechnology, 6, 695-704 (2011)

[2] Jornsanoh, P. Ultramicroscopy, 111, 1247-1254(2011)

[3] Masenelli-Varlot, K., Malchère, A. Microscopy and Microanalysis, 20, 366-375(2014)

[4] Faucheu, J., et al. Langmuir, 25, 10251-10258(2009)


The authors acknowledge the Consortium Lyon-Saint Etienne de Microscopie (CLYM) for the access to the microscope, the China Scholarship Council (CSC) and Institut Universitaire de France for financial support.


Solid oxide cells (SOC) have the potential of playing a significant role in the future efficient energy system scenario. In order to become widely commercially available, an improved performance and durability of the cells has to be achieved [1]. Conventional scanning and transmission SEM and TEM have been often used for ex-situ post mortem characterization of SOFCs and SOECs [2,3]. However, in order to get fundamental insight of the microstructural development of SOFC/SOEC during operation conditions in-situ studies are necessary [4]. The development of advanced TEM chips and holders makes it possible to undertake analysis during exposure to the SOFC/SOEC sample of reactive gas flow, elevated temperatures and electrical biasing in combination. This allows the study of nanostructure development under temperature and electrode polarisation conditions similar to operation conditions.

In this work, we have for the first time performed in-situ analysis of a symmetric cell inside a TEM under different configurations. In order to be able to perform in-situ experiments while drawing a current through the sample, we used a homemade TEM chip [5,6] and an 80-300kV Titan ETEM (FEI Company) equipped with an image corrector and a differential pumping system.

A symmetric cell was prepared by depositing a cell consisting of three thin films on a strontium titanate (STO) single crystal substrate by pulsed laser deposition (PLD). Lanthanum strontium cobaltite La0.6Sr0.4CoO3-δ (LSC) was chosen as electrode and yttria stabilized zirconia ZrO2: 8% mol Y2O3 (YSZ) as electrolyte, see figure 1. High resolution TEM analysis on PLD samples after the deposition, did not reveal any second phase formation at the interface between YSZ and LSC. The in-situ experiment was firstly conducted in vacuum at temperature between 25 oC and 900 oC. Secondly, it was repeated in presence of oxygen with an oxygen partial pressure of about 2 mbar and a maximum temperature of 750 oC. Subsequently, the symmetric cell will be exposed to oxygen at 600 oC and 1 V overpotential within the ETEM. In order to do that, a symmetric cell has been placed on the chip with the use of a focus ion beam (FIB) microscope, see figure 2. To do so, a lamella was first extracted by the bulk sample and attached to a conventional TEM grid. Afterwards, the grid was tilted by 90 degrees and the lamella was detached once again and placed on the chip.

 STEM-EDS investigation was used for ex-situ post mortem analysis. Finally, a bulk symmetric cell, coming from the same batch as the in-situ treated TEM samples, was tested in a furnace with similar environmental conditions. This comparison is vital for distinguishing possible surface diffusion effects caused by having a thin lamella for in-situ TEM analysis. Electrochemical properties were also investigated by electrochemical impedance spectroscopy (EIS).

In the figure 3 the cell was heat treated at 400 oC in vacuum, whereas in figure 4, the cell was treated at the same temperature but in presence of oxygen, with PO2 of 2 mbar. Comparing the two figures, the cell exposed to oxygen showed structural changes in the LSC thin film in comparison with the sample heated in vacuum. These changes refer to the formation of grains as is confirmed by electron diffraction patterns.


[1] A. Atkinson et al., Nature Materials 2004, 3, 17-27.

[2] R. Knibbe et al., Journal of The Electrochemical Society 2010, 157, B1209-B1217.

[3] N. Imanishi et al., Solid State Ionics 2006, 177, 2165-2173.

[4] M. L. Traulsen et al., ECS Transactions 2015, 66, 3-20.

[5] C. Kallesøe et al., Nano Letters 2012, 12, 2965-2970.

[6] S. B. Alam et al., Nano Letters 2015, 15, 6535-6541.

Fabrizio GUALANDRIS (Roskilde, DENMARK), Søren Bredmose SIMONSEN, Mogens Bjerg MOGENSEN, Kristian MØLHAVE, Simone SANNA, Jakob Birkedal WAGNER, Luise Theil KUHN
15:15 - 15:30 #6348 - IM02-OP067 On the applicability of electron diffraction to precisely measure temperature in TEM.
On the applicability of electron diffraction to precisely measure temperature in TEM.

With the overwhelming success of in situ electron microscopy, fueled by the recent advances in instrumentation, an everlasting question in electron microscopy comes into focus again: the precise determination of the temperature of the sample, especially in in situ heating experiments [1]. So far temperature is determined by sensors (thermocouples, resistance thermometers) placed close to the sample. In this work we elaborate on the applicability of parallel beam electron diffraction in TEM to precisely measure temperature directly on the sample and on a local scale.


Well defined metallic particles are applied on the sample surface using a dewetting process after thin film deposition. SAED is used to determine the lattice spacing from ring patterns averaging over a large number of particles. The determined lattice spacing can be translated into temperature using reference data on thermal expansion. To test the performance of this approach, a MEMS-based sample heating system from DENSsolutions is used inside of a double corrected FEI Titan Themis³ 300. Various metals (Ag, Au, Pt) are used to cover different temperature ranges. Fig. 1 shows image and diffraction pattern of a typical setup.


To allow for the highest precision, a proper alignment of the microscope is crucial. Therefore a method to assure perfect beam parallelity has been developed in this project, based on the change in diffraction pattern upon changing the sample position relative to the eucentric height. The accuracy of the evaluation based on peak fitting to the azimuthally averaged radial profile critically depends on the determination of the center and correction of astigmatism in the ring pattern. An algorithm has been employed allowing for correction of the astigmatism to the fourth order in the ring pattern (exemplarily shown in Fig. 2). The error due to the evaluation method can be estimated from the results of the evaluation of 100 subsequent diffraction patterns at a constant temperature shown in Fig. 3. The position of the (220) ring of Pt is determined to be 7.27183 ± 0.00023 nm-1 (corresponding to a temperature accuracy of approximately ± 3.5 K).


The temperature accuracy can be tailored to the particular application by selecting a different metal. Low melting metals show a higher thermal expansion increasing the sensitivity of the temperature measurement, but, on the other hand, limiting the maximum usage temperature because of melting or sublimation. Fig. 4 demonstrates the applicability of the presented approach. Ag particles have been used to measure the temperature during a dynamic in situ experiment, showing a very good agreement with the temperature reading from the holder.



Financial support by the German Research Foundation (DFG) via research training group GRK 1896 “In-situ microscopy with electrons, X-rays and scanning probes” and cluster of excellence EXC 315 “Engineering of advanced materials” is gratefully acknowledged.


[1] F. Niekiel, P. Schweizer, S.M. Kraschewski, B. Butz, E. Spiecker, Acta Mater. 90 (2015), pp. 118-132

Florian NIEKIEL (Erlangen, GERMANY), Simon M. KRASCHEWSKI, Julian MÜLLER, Benjamin BUTZ, Erdmann SPIECKER
15:30 - 15:45 #6422 - IM02-OP068 Dynamical Holographic Moirés : Time average holographic interferometry.
Dynamical Holographic Moirés : Time average holographic interferometry.

Electron holography (EH) enable a sensitivity to electromagnetic fields at the nanoscale in a Transmission Electron Microscope (TEM) through the Aharonov-Bohm effect (which was by far experimentally demonstrated with EH [1]).  Beside EH we consider here the Moirés pattern than can arise with the fringe network of a hologram. Moirés originate from a superposition of two networks  and their use in electron microscopy enable to reveal hidden details within crystal stacks (from stacking faults in crystals to graphene misalignments).

The technique presented in this contribution propose to reach one step beyond the sensitivity that is actually achieved in EH by combining it with Moirés. The basic idea of what we call Dynamical Holographic Moirés (DHM) is to superpose various and controlled states of the sample under observation within the same out-of-axis hologram giving rise to the apparition of Moirés in a holographic interferogram. Holographic interferometry was initially designed in optics [2] and then implemented in its double exposure at the beginning of electron holography development. Our approach can be described as the implementation of time-average holographic interferometry by an application of in situ experiment with EH.

The system in use here is a Hard Disk Drive writing head that has been mounted to be characterized in operando by EH [3]. We can easily switch the writing pole state between two different states and thus reverting the magnetic flux sense. The DHM method [4] was thus used to fully characterize the magnetic flux escaping from such a magnetic pole in a quantitative way. By far, the obtained interferogram are directly quantized in term of magnetic flux quantum () linked to phase shift via the Aharonov-Bohm effect. A typical phase image of the system along with an interferogram are displayed in Fig 2. The main advantages of this new TEM technique, namely frequential analysis, electron optic distorsion and disturbed reference problem or direct quantification, will be discussed.

References :

[1]            Tonomura A.  Rev. Mod. Phys. 59, 639–669 (1987)
[2]            Heflinger, L. O.  et al.  Journal of Applied Physics 37, 642–649 (1966)
[3]            Einsle, J. F. et al.   Nano Res. 1–9 (2014)
[4]            Gatel, C. et al.   Under review

Christophe GATEL, Aurélien MASSEBOEUF (Toulouse), Florent HOUDELLIER, Etienne SNOECK
15:45 - 16:00 #5954 - IM02-OP061 Atoms in Motion: Electron beam induced dynamics in experiment and simulation.
Atoms in Motion: Electron beam induced dynamics in experiment and simulation.

With the availability of aberration-correctors, scanning transmission electron microscopy (STEM) has become one of the most versatile tools for the characterization of nanostructured materials. In combination with electron energy loss spectrometers (EELS) and energy dispersive X-ray (EDX) detectors in principle chemical information can be extracted at atomic resolution. Due to the high current densities occurring in a highly focused electron beam, however, STEM has to be classified as destructive method in many cases.[1] This is especially true for small metallic clusters with a high percentage of low-coordinated atoms, which are interesting in particular for heterogeneous catalysis.

In this work electron beam induced dynamics was studied via transient STEM HAADF image sequences for different nanostructured material systems like bimetallic alloys and clusters. All clusters were synthesized by means of the superfluid helium droplet method, which guarantees their high purity.[2] Furthermore, we present a methodology for the simulation of elastic electron damage processes using an algorithm based on molecular dynamics and Monte Carlo techniques.[3] Figure 1a shows simulation results for a bimetallic AuAg-cluster which exhibits selective Ag-sputtering and a rapid change of morphology during electron radiation. In Figure 1b HAADF image time series of an Au-CrOx core-shell nanowire can be seen. Due to electron beam enhanced diffusion of Au atoms in CrOx, significant morphology changes of the Au core can be observed after a few seconds of electron beam exposure, even at 60 keV electron energy.

Deeper understanding of electron beam induced dynamics can not only help to develop strategies to prevent sample damage, which is important especially for analytical and quantitative STEM analysis. Electron induced motion of single atoms on the surface or inside crystalline materials may also be useful to estimate surface energies, analyse defect generation and investigate diffusion processes.[4,5] Figure 1c shows the electron beam mediated diffusion of Au atoms on and inside an Al-matrix, for instance.

Moreover, electron beam induced chemical reactions can be used to tailor nanostructures with properties not obtainable otherwise. We show how Ni clusters transform into single crystalline, hollow and toroidal NiO clusters, consisting of less than 3000 Ni atoms, during electron exposure (see Figure 1d and e). The transformation is mediated by adsorbed water and driven by a nanoscale Kirkendall effect. We studied the oxidation process via HAADF time-lapse series and EELS analysis.




[1]    R. Egerton, Ultramicroscopy 2013, 127, 100.

[2]    P. Thaler, A. Volk, D. Knez et al., The Journal of chemical physics 2015, 143, 134201.

[3]    A. Santana, A. Zobelli, J. Kotakoski et al., Phys. Rev. B 2013, 87.

[4]    A. Surrey, D. Pohl, L. Schultz, B. Rellinghaus, Nano letters 2012, 12, 6071.

[5]    W. Xu, Y. Zhang, G. Cheng et al., Nature communications 2013, 4, 2288.




Our research is supported by the European Union within the 7th Framework Programme (FP7/2007-2013) under Grant Agreement no. 312483 (ESTEEM2) as well as by the Austrian Research Promotion Agency (FFG). 

Daniel KNEZ (Graz, AUSTRIA), Alexander VOLK, Philipp THALER, Wolfgang ERNST, Ferdinand HOFER
16:00 - 16:15 #6712 - IM02-OP073 Improved gas holder for in-situ TEM studies.
Improved gas holder for in-situ TEM studies.

In-situ TEM studies using an environmental cell (nanoreactor) play an important role in not just giving an understanding the corrosion mechanisms at a sub-micron scale, but also on the influence of heat-treatment on the microstructural change and corrosion behaviour of these alloys. One of the main requirements of for these in-situ TEM studies is the leak tightness of the nanoreactor. This is achieved by gluing the top and the bottom chips together with water glass or commercially available cyanoacrylate compounds. The drawback of this method is the chips are inseparable after the in-situ TEM study, making it impossible to carry out any further investigations on the same specimen. To overcome this drawback, we worked on upgrading the nanoreactor by redesigning the TEM holder to avoid gluing. This made it possible not only to assemble the nanoreactors in a more reliable way but also separate the two halves after the in-situ TEM study. This has opened up opportunities to carry out investigations like tomography, AFM measurements and other surface characterization studies on the same specimen, adding more to the mechanisms observed from the in-situ TEM studies.


Using this holder, we studied the corrosive attack of an Al alloy that has been heat-treated at 250 °C in an environment of oxygen bubbled through aqueous HCl of pH 3. After corrosion, STEM-tomography has been carried out to understand the propagation of the corrosive attack. Most of the Al alloys have the unique property of improving their strength by the mechanism known as precipitation hardening. This involves a special heat-treatment given to the alloys where alloying elements are added to aluminium, heated to an elevated temperature (usually above 500 °C) to form a single-phase solid solution, and then quenched rapidly to room temperature. On quenching, a super-saturated solid solution is obtained, from which a distribution of numerous fine nano-sized precipitates in the matrix can be obtained by heating at slightly elevated temperatures (typically ranging from 100 to 250 °C). Figure 1 shows the precipitation of numerous S-type nanoprecipitates in the matrix of a FIB specimen of AA2024, heat-treated at 250 °C for 3 minutes. While the formation of the S-type precipitates contributes to a significant increase in the strength of the alloy, the Mg-rich S-type precipitates and the formation of precipitate-free-zones next to the grain boundary have a severely detrimental effect on the corrosion behaviour of this alloy.


The corrosion behaviour of the heat-treated specimen can be investigated by assembling a nanoreactor. The heat-treated specimen was also exposed to a gas mixture of oxygen bubbled through aqueous HCl at room temperature, at a pressure of 1 bar.  The snapshots from a movie recorded during the in-situ corrosion experiment are shown in Figure 2.  In contrast to the specimen prior to heat-treatment, Figure 1, exposure to the reactive gas mixture of oxygen bubbled through aqueous HCl causes an immediate attack as shown in Figure 1(a). The bubble-like features observed all over the specimen indicate this, more prominently next to the grain boundary precipitates. As the exposure time increases, the corrosion attack progresses as observed by the growth of circular features all over the matrix after exposure of 15 min (Figure 2b) and approximately 30 min (Figure 2c). STEM-ADF tilt-series confirms that the circular feature observed all over the specimen are pits initiating from the surface of the sample. The high-density of the S-type precipitates, enriched in Mg and Cu act as numerous galvanic couples leading to such an attack.



The authors gratefully acknowledge the ERC project 267922 for the financial support.


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MS2: 1D and 2D materials

MS2: 1D and 2D materials

Chairmen: Raul ARENAL (Zaragoza, SPAIN), Ursel BANGERT (Limerick, IRELAND)
14:00 - 14:30 #8679 - MS02-S70 Properties of low-dimensional electron-beam-sensitive objects by spherical and chromatic aberration-corrected low-voltage high-resolution transmission electron microscopy and spectroscopy.
Properties of low-dimensional electron-beam-sensitive objects by spherical and chromatic aberration-corrected low-voltage high-resolution transmission electron microscopy and spectroscopy.

Spherical aberration correction has become inevitable in materials science for atomic-resolution imaging of conventional objects by transmission electron microscopy at medium accelerating voltages (80-300kV). However, low-Z and radiation-sensitive low-dimensional objects often require lower accelerating voltages because the threshold for knock-on damage is below 80kV for these materials. Unfortunately, the resolution of spherical aberration-corrected transmission electron microscopy at an accelerating voltage less than 80 kV with a standard Schottky type or field-emission electron source is strongly limited by the chromatic aberration of the objective lens. Here we report on our approach to achieve atomic resolution at voltages in the range between 20-80kV in transmission electron microscopy [1,2,3]. We apply the newly-developed aberration corrector that corrects for both, spherical and chromatic aberration of the objective lens.  First experimental results of low-dimensional objects will be presented.

            The performance of the SALVE (Sub-Angstrom Low-Voltage Electron microscopy) microscope enables atomic-resolution imaging and high-resolution energy-filtered (EF)-TEM with large energy windows even at 20kV accelerating voltage. Obviously, no damping of the contrast transfer function by chromatic aberration has to be considered in the image calculation routine, although image spread due to thermal magnetic field noise [4] needs to be taken into account as a new source of contrast transfer damping. The envelope now results from image-spread and residual defocus [5]. Image calculations are performed in dependence of the electron dose [6]. Figure 1 shows experimental HRTEM images of single-layer graphene at 30kV; as the usable aperture is about 65mrad, consequently an information limit of 107pm has been achieved. The comparison of the line profiles through the calculated and experimental images of a defect in graphene demonstrates that a good match has been obtained assuming Si substitutions. Moreover, on the example of TiO2 we demonstrate the new capabilities for EFTEM imaging. We now can use an energy window of about 20 eV where the defocus changes by only about 2 nm. This enables previously reported high-resolution EFTEM [7] imaging but at low accelerating voltages.

In addition, we discuss the importance of sophisticated sample preparation approaches [8,9] and show results in imaging and spectroscopy on low-dimensional objects [10-15].


[1] U. Kaiser, J. Biskupek, J.C. Meyer, J. Leschner, L. Lechner, H. Rose, M. Stöger-Pollach, A.N. Khlobystov, P. Hartel, H. Müller, M. Haider, S. Eyhusen and G. Benner Ultramicroscopy 111 (2011), p. 1239.
[2] www.salve-projcet.de
[3] M. Linck, P. Hartel, S. Uhlemann, F. Kahl, H. Müller, J. Zach, and M Haider, M. Niestadt and M. Bischoff, J. Biskupek, Z. Lee, T. Lehnert, F. Börrnert, H. Rose, and U. Kaiser (2016) submitted.
[4] S. Uhlemann Physical Review Letters 111(4) (2013), 046101.
[5] M. Haider, P. Hartel, H. Müller, Microsc. Microanal. 16(2010), 393.
[6] Z. Lee, H. Rose, O. Lehtinen, J. Biskupek, U. Kaiser, Ultramicroscopy 145 (2014), 3.
[7] K. W. Urban, J. Mayer, J. R. Jinschek, M. J. Neish, N. R. Lugg, and L. J. Allen, Phys. Rev. Lett. 110, (2013), 185507.
[8] G. Algara-Siller, O. Lehtinen, A, Turchanin, U. Kaiser, Appl. Phys. Lett. 104 (2014) 153115.
[9] G. Algara-Siller, S. Kurasch, M. Segeti, O. Lehtinen, U. Kaiser, Appl. Phys. Lett. 103 (2013) 20310.
[10] G. Algara-Siller, N. Severin, S. Chong, T. Björkman, R. Palgrave, A. Laybourn, M. Antonietti, Y.  Khimyak, A. Krasheninnikov, J. P. Rabe, U. Kaiser, A. Cooper, A. Thomas, M. Bojdys, Angewandte Chemie, 53 (2014) 7450.
[11] O. Lehtinen, L. Tsai, R. Jalil, R. R. Nair, J. Keinonen, U. Kaiser and I. V. Grigorieva, Nanoscale, 6 (2014) 6569.
[12] O. Lehtinen, N. Vats, G. Algara-Siller, P. Knyrim, U. Kaiser, Nano Lett. 15 (1) (2015) 235.
[13] T. Zoberbier, T. W. Chamberlain, J. Biskupek, M. Suyetin, A. G. Majouga, E. Besley, U. Kaiser, A. N. Khlobystov, Small (2016) accepted.
[14] A.  Markevich,  S. Kurasch, O. Lehtinen, O. Reimer, N. Hohlbein, X. Feng, K. Müllen, A. Turchanin,
A N. Khlobystov, U. Kaiser, and E. Besley, Nanoscale (2016) accepted.
[15] A. Botos, J. Biskupek, T. W. Chamberlain, G. A. Rance, C. Stoppiello, J. Sloan, Z. Liu, K. Suenaga, U. Kaiser, A. N. Khlobystov, JACS (2016) accepted.
[16] The authors greatly acknowledge funding from the German Research Foundation (DFG) and the Ministry of Science, Research and the Arts (MWK) of the federal state Baden-Württemberg, Germany in the frame of the SALVE project.

14:30 - 14:45 #5810 - MS02-OP219 Quantitative STEM analysis of multiscale CNT assemblies.
Quantitative STEM analysis of multiscale CNT assemblies.

Carbon nanotubes (CNTs) and their macroscopic assemblies have shown their potential as advanced conductors. The assembly of individual CNT’s into hierarchical structures is determined either by their interactions (bottom-up self-assembly) or during the fabrication process (top-down strategy). Hence, to tailor the macroscopic functional properties (e.g. electrical conductivity or porosity) of assemblies, a detailed understanding on how interactions create multiscale morphologies and finally function is required. STEM is widely employed for the nanoscale analysis of (in)organic materials. However, (S)TEM imaging of hierarchical CNT assemblies has several limitations. For instance, CNT/polymer composites are only composed of light elements which results in low contrast between the phases. Moreover, they are beam sensitive. We have optimized the contrast between the CNT’s and the polymer phase combining experiments and simulations at limited electron dose [1]. In addition, a hierarchical morphology extends across several length scales, hence, depending on the area of imaging, interpretations could vary, questioning the representativeness of the analysis. Our approach to imaging of representative volumes of hierarchical materials included the development of a toolbox to acquire large-areas at high-resolution, which in essence brings STEM closer to a bulk characterization technique [2].

With these technical developments and relevant image analysis tools, the processing-structure-property relationship of porous CNT assemblies and CNT/polymer composites (PNCs) have been studied on a scale that was previously impossible. We will illustrate the potential of the methodology on examples of: 1) CNT compacts where the final structure and electrical conductivity can be controlled by the polydispersity and aspect ratio of the CNT population (Figure 1) [3]; 2) CNT/polymer composites where residual CNT-CNT interactions during compounding lead to inhomogeneous but highly conducting CNT networks [4]; and 3) CNT alignment can be induced by spin-coating of polymer latex-CNT mixture which exhibit directionally varying electrical conductivity (Figure 2) [5]. In above investigations it has becomes clear that CNT-CNT contacts play a crucial role in the formation of least resistance pathway. At present we are investigation such contacts in details employing electron tomography combined with template matching to deduce the contact number and contact area per unit volume. In summary, we are developing (S)TEM towards bulk characterization tool for the analysis of beam sensitive hierarchical materials over multiple length scale which are materials of scientific and technological importance.


[1] K. Gnanasekaran, G. de With, H. Friedrich, Quantification and optimization of STEM image contrast for beam sensitive materials, (2016) submitted.

[2] K. Gnanasekaran, R. Snel, G. de With, H. Friedrich, Ultramicroscopy, 160 (2016) 130-139.

[3] K. Gnanasekaran, G. de With, H. Friedrich, J. Phys. Chem. C, 118 (2014) 29796-29803.

[4] K. Gnanasekaran, H. Friedrich, G. de With, Process dependent electrical percolation in mesoscale networks of multi-walled carbon nanotubes in polymer nanocomposites, (2016) submitted.

[5] M.A. Moradi, K.L. Angoitia, S. van Berkel, K. Gnanasekaran, H. Friedrich, J.P. Heuts, P. van der Schoot, A.M. van Herk, Langmuir, 31 (2015) 11982-11988.


The research leading to these results has received funding from the European Union Seventh Framework Programme (FP7-MC-ITN) under grant agreement No. 264710. The authors would like to thank the Directorate-General for Science, Research and Development of the European Commission for financial support of the research.

Karthikeyan GNANASEKARAN (Eindhoven, THE NETHERLANDS), Gijsbertus DE WITH, Heiner FRIEDRICH
14:45 - 15:00 #5935 - MS02-OP220 Investigating the loss spectrum of individual carbon nanotubes at high energy resolution in real and momentum space.
Investigating the loss spectrum of individual carbon nanotubes at high energy resolution in real and momentum space.

Over the last quarter of a century Electron Energy Loss Spectroscopy (EELS) has proved itself as an excellent tool for investigating the plasmonic [1-5] and electronic [1, 3, 4] response of carbon nanotubes: either by attaching a spectrometer to a Scanning Transmission Electron Microscope STEM [4, 5] or using a purpose built stand-alone spectrometer [1-3].  While STEM-EELS provides superior spatial resolution to that of a stand-alone spectrometer, it was not until recent improvements in electron source monochromation that the energy resolution of the two techniques became comparable. This was demonstrated by Sato and Terauchi [4] who used TEM –EELS to identify peaks in the loss spectrum of individual CNTs attributable to inter-band transitions between van Hove singularities (vHs) in the CNTs' electronic density of states.  


As an extension of the work of Sato and Terauchi [4], the present study is focused on the spatial and momentum dependence of the loss spectrum of individual CNTs. Fig. 1A shows loss spectra acquired from the single walled CNT in Fig. 1B using both a penetrating (1) and an aloof beam geometry (2), (3). The spectra in Fig. 1A are primarily characterised by peaks attributed to vHs (black arrows) [1, 3, 4], and, the π and π+σ plasmon resonances [1-5].  The apparent red-shift of the two plasmon peaks with increasing distance to the tube centre is consistent with literature [5]. Note the lack of a comparable red-shift for the “vHs peaks” as well as a significant change in fine structure of the high energy shoulder of the π plasmon peak.


Resolving the CNT loss spectrum in momentum space allows for access to information not readily available in real space. Specifically, the momentum resolved spectra in Fig. 1C reveal that the vHs peaks are non-dispersive (no peak shift with increasing momentum transfer), consistent with a reported measurement of a “bulk” sample of purified single wall CNTs [1]. Furthermore, it is shown that the “π peak” comprises two distinct plasmon modes: “π1“ and “π2”.  The π1 peak is non-dispersive, thus indicating confinement perpendicular to the CNT axis, while the π2 peak is dispersive, which in turn indicates significant plasmon propagation along the CNT axis [2, 3]. 



[1] T Pichler et al., PRL 80 (1998) p. 4729.

[2] C Kramberger et al., PRL 100 (2008) 196803.

[3] C Kramberger et al., Nanotechnology 24 (2013) 405202.

[4] Y Sato and M Terauchi, Microsc. Microanal. 20 (2014) p. 807.

[5] M Kociak et al., PRB 61 (2000) 13936, BW Reed and M Sarikaya, PRB 64 (2001) 195404,

O Stéphan et al., PRB 66 (2002) 155422.



SuperSTEM is the UK National Facility for aberration-corrected STEM and is funded by the UK Engineering and Physical Sciences Research Council (EPSRC). N Dellby and TC Lovejoy (Nion Company, WA, USA) are thanked for useful discussions and advice. U Bangert (University of Limerick, Ireland) is thanked for providing CNT samples. 

Fredrik S. HAGE (Daresbury, UK), Quentin M. RAMASSE
15:00 - 15:15 #5967 - MS02-OP221 Calcium Cobal Oxide: the first oxide-based misfit nanotube - from nanostructure to properties.
Calcium Cobal Oxide: the first oxide-based misfit nanotube - from nanostructure to properties.

        Though misfit layered compounds (MLC) have been known for some time,1 the interest in these materials has increased in recent years. Their unique structure allows them to behave like electron crystal, showing a phonon glass behavior and then, exhibiting superior thermoelectric properties.2 MLC can be considered as inter-grown materials with a general formula [(MX)1+x]m[TX2]n, where M is a rare earth (Pb, Sb, etc); T is Ti, V, Cr, Nb, etc. and X is S, Se.1 In 2011, nanotubes (NTs) based on MLC were synthetized for the first time in large amounts.3 Later, the syntheses were generalized to many other chalcogenide systems which were extensively studied at the local scale by TEM and associated techniques.4 However, until now, analogous synthesis of oxide-based MLC NTs has not been demonstrated yet.

        Here, we report a chemical strategy for the synthesis of calcium cobalt oxide-based misfit NTs. A combination of high-resolution STEM (HRSTEM)-HAADF imaging (including image simulations), spatially-resolved EELS (SR-EELS), electron diffraction, and density functional theory (DFT) calculations are used to discover the formation of new phase within these nanotubes. This new phase significantly differs from bulk starting material, inducing different electronic properties.


        The bulk starting material, Ca3Co4O9, has a misfit layered structure (Fig. 1), consisting of alternate stacking of CoO2 layers and Ca2CoO3 layers with a periodicity of 1.05 nm along the c axis. After the hydrothermal synthesis of Ca3Co4O9, several NTs (inset of Fig. 2a) are observed with typical lengths of several hundred nanometers. Sandwiched between bright layers (spaced by 0.86 nm), two other atomic layers, with weaker intensities, can be distinguished (purple arrows in Fig. 2a). These facts suggest that one layer from the initial bulk structure is now missing.

        To achieve further insight into the chemical nature of this missing layer, SR-EELS elemental quantification was performed by using the Ca-L2,3 and Co-L2,3 edges (Fig. 2b). The bright layers perfectly match the areas with the lowest Ca/Co ratio (red arrows in Fig. 2b) and correspond to one of the two cobalt sub-systems (CoO2 or CoO). Following the same reasoning, the two layers are related to the Ca sub-system (CaO) and the Co sub-system (CoO2 or CoO), respectively. Thus, it can be concluded that one CaO layer is missing in the NT.

        A novel structure CaCoO2-CoO2 was created by removing one CaO layer from the bulk structure which was then optimized by DFT structural relaxation. To confirm this new structure, we have performed a comparison between the experimental and simulated HRSTEM-HAADF images, using the DFT-relaxed structure as input for the simulation. As it can been seen from Fig. 3, there is an excellent agreement between the simulated and experimental micrographs. The excellent consistency between HRSTEM, SR-EELS, and DFT calculations support and confirm our proposed structure for the new calcium cobaltite phase.


        In light of this new structural and chemical information, a growth mechanism for these NTs is proposed. In addition, we will detail the electronic properties of the new MLC phase which we predict as semiconducting in nature in contrast with the bulk phase which is metallic.5,6


1. J. Rouxel, A. Meerschaut, and G. Wiegers, J. Alloys Compd. 229, 144 (1995)

2. Putri, Y. E.; Wan, C.; Wang, Y.; Norimatsu, W.; Kusunoki, M.; Koumoto, K. Scr. Mater. 66 (11), 895–898 (2012)

3. G. Radovsky, R. Popovitz-Biro, M. Staiger, K. Gartsman, C. Thomsen, T. Lorenz, G. Seifert, and R. Tenne, Angew. Chem. Int. Ed. 50, 12316 (2011).

4. L.S. Panchakarla, L. Lajaunie, R. Tenne, R. Arenal. J. Phys. Chem. C  (2015), In Press.

5. L.S. Panchakarla, L. Lajaunie, A. Ramasubramaniam, R. Tenne, R. Arenal, Submitted

6. This research has received funding from the EU under Grant Agreement 312483-ESTEEM2, Grant Agreement 604391 Graphene Flagship and the Spanish Ministerio de Economia y Competitividad (FIS2013-46159-C3-3-P).

15:15 - 15:30 #6418 - MS02-OP225 Exciton and Plasmon Mapping at the Nanoscale.
Exciton and Plasmon Mapping at the Nanoscale.

Excitons and plasmonic interactions, which are effectively responsible for the transfer of energy within devices such as solar cells, LEDs and semiconductor circuits, have been understood in theory for decades. However, the photophysical behaviour within materials has always been rather difficult to understand and be directly observed.  

Surface structure, localised thickness variations and presence of edges are bound to influence the macroscopic properties of the materials. Understanding the local surface structure and chemistry of these materials at the nanoscale is crucial in order to reach the full potential of the materials for real-life applications. Hence, there is a need to fully characterise the physical and chemical properties from the bottom up i.e. at the level of individual atoms and to map the optoelectronic properties where they happen.


Due to recent technical improvements we can now access parts of the low loss electron energy-loss (LL EEL) spectra which had previously been inaccessible. This opens up new possibilities to study nanomaterials not only at unprecedented energy but also – contrary to bulk optical techniques – with a spatial resolution at the nanoscale, as described by Zhou, Dellby [1]. Although some significant progress has been made recently in unravelling the physical origins of the LL EEL features as shown by Tizei, Lin [2], significant gaps in our understanding of the signals and their origins remain. In the study presented here, we used for the first time a combination of experimental monochromated LL STEM EEL spectroscopy and theoretical calculations using time-dependent density functional theory (TDDFT) as well as the Bethe-Salpeter equation (BSE) to study the optical properties of MoS2 at the nanoscale with the aim to understand the origins of the peaks and regional variations of the complete LL EEL spectrum. We report that we identified and resolved as well as mapped mid-bandgap excitonic signals at ~1.88eV and at ~2.08eV on MoS2 flakes using monochromated LL EELS (figure 1) and confirmed their origin by BSE calculations; we also identified and mapped several plasmonic peaks (figure 1) using LL EELS combined with TD DFT. Furthermore, we observed great spatial variations in the LL EELS signal when comparing the edge to inner regions of a flake, i.e. with increasing number of layers, and we show how these can be largely attributed to beam geometry effects. The effects of the experimental set-up on the low loss EELS signal will be discussed.


1.         Zhou, W., et al., Monochromatic STEM-EELS for Correlating the Atomic Structure and Optical Properties of Two-Dimensional Materials. Microscopy and Microanalysis, 2014. 20(S3): p. 96-97.

2.         Tizei, L.H.G., et al., Exciton Mapping at Subwavelength Scales in Two-Dimensional Materials. Physical Review Letters, 2015. 114(10).

Hannah NERL (Dublin, IRELAND), Kirsten WINTHER, Fredrik HAGE, Kristian THYGESEN, Lothar HOUBEN, Quentin RAMASSE, Valeria NICOLOSI
15:30 - 15:45 #6375 - MS02-OP224 High resolution EELS on individual carbon nanotubes by monochromated TEM.
High resolution EELS on individual carbon nanotubes by monochromated TEM.

            Single-walled carbon nanotube (SWNT) has been known to exhibit a wide range of electronic properties upon its atomic arrangement [1,2]. However it is still difficult to directly correlate the distinct electronic properties with its atomic structure from an individual carbon nanotube. Here, we successfully demonstrate highly localized electronic properties of individual carbon nanotubes with precise atomic structures by means of transmission electron microscopy (TEM) consisting of a monochromator.

            We have used a JEOL TEM (TripleC#2) equipped with a Schottky field emission gun, a double Wien filter monochromator and delta correctors. The energy resolution is adjustable from 30 to 200 meV by choosing the energy selecting slits in the dispersion plane of the monochromator. We have performed the electron energy loss spectroscopy (EELS) on individual freestanding SWNTs with the scanning TEM (STEM) mode at 60 kV. The target SWNTs are also imaged by both STEM/TEM modes to fully assign their atomic structures.

           Figure 1(a) presents a TEM image of two closely aligned SWNTs (inset) and their C K-edge (C1s) spectra. The chirality of thicker SWNT (top) and thinner one (bottom) are assigned as (9, 7) and (6, 5), respectively. Each spectrum has several sub-peaks on the π* response and exhibits completely different features. The line shape analysis [3] suggests that the π* response of (6, 5) tube consists of four sub-peaks related to the van Hove singularity (vHs) (1s →E1*, E2*, E3* and  E4*) and a broad π* resonance (Fig. 1(b)). The position of the sub-peaks fairly consists with the vHs in the shifted ab-initio DOS [3] (inset in Fig. 1(b)). The relative intensities are possibly influenced by core-hole effects. The valence-loss spectra taken from the same SWNTs also exhibit the peaks related to the vHs (Ei → Ei* (i=1,2,…)). However it is difficult to distinguish the two closely aligned SWNTs from the valence-loss spectra because the large delocalization mixes the peaks for both SWNTs. This means that the core-loss spectra has a much higher special resolution and reflects more localized electronic structures.

            Then, we have experimentally investigated how the core-loss spectra changes corresponding to nonperiodic structures. Figure 2 shows STEM images of a typical hybrid SWNT and its C K-edge (C1s) spectra. We have confirmed from TEM image (not shown here) that the hybrid SWNT involves a serial junction between the thinner (11, 1) semiconducting part and the thicker (10, 10) metallic part. The C K-edges (i to x) presented in Figs. 2(b) and 2(c) are obtained when the electron probe is scanned across the broken lines (i to x) in Fig. 2(a). The π* peaks in the junction part (iv to vii) are different form the spectra for either (10, 10) and (11, 1) and show new peaks (black arrows in Fig. 2(c)) reflecting the distinct electronic structures. Such a highly localized measurement of electronic properties for individual carbon nanotubes has never been realized by any other methods.



[1] N. Hamada, S. Sawada, and A. Oshiyama, Phys. Rev. Lett. 68 (1992), p.1579.

[2] R. Saito, M. Fujita, G. Dresselhaus, and M. S. Dresselhaus, Phys. Rev. B 46 (1992), p.1804.

[3] K. De Blauwe et al., D. J. Mowbray, Y. Miyata, P. Ayala, H. Shiozawa,  A. Rubio, P. Hoffmann, H. Kataura, and T. Pichler, Phys. Rev. B 82 (2010), p.125444.

Ryosuke SENGA (Tsukuba, JAPAN), Thomas PICHLER, Kazu SUENAGA
15:45 - 16:00 #6886 - MS02-OP233 Layer specific optical band gap measurement at nanoscale in MoS2 and ReS2 van der Waals compounds by high resolution electron energy loss spectroscopy.
Layer specific optical band gap measurement at nanoscale in MoS2 and ReS2 van der Waals compounds by high resolution electron energy loss spectroscopy.

Atomically thin monolayer transition metal dichalcogenides (TMDs) are a new class of two dimensional nano-material with promising optoelectronic, energy and novel device applications. One of the important features of many TMDs is that they undergo a crossover from indirect band gap in the bulk to direct band gap in the monolayer form [1]. While the monolayer properties of TMDs are unique (e. g. direct band gap), it may be illusive while fabricating practical devices because the cross over to indirect band gap occurs due to unavoidable electronic packaging and the property could change in close proximity of foreign substance. Therefore, there is an urge to stabilize such novel properties arising from the monolayer in the interface or in the bulk form. With this goal there is a candidate material already reported in the family, i.e. crystalline 1T-ReS2 [2]. In this work we have exploited high resolution electron energy loss spectroscopy (HREELS) to perform layer specific direct measurement of optical band gaps of two important van der Waals compounds, MoS2 and ReS2 at nanoscale. Areas with mono, bi, tri and multilayers of MoS2 and ReS2 have been identified using a electron microscope. The atomic resolution image of mono and multilayer MoS2 and ReS2 have been given in figure 2. For monolayer MoS2, the twin excitons (1.8 and 1.95 eV) originating at the K point of the Brillouin zone are observed. The band gap values have been deduced after plotting Tauc-like plots for both direct and indirect band gaps from the EELS absorption spectra. An indirect band gap of 1.27 eV is obtained from the multilayers regions (see figure 1). Indirect to direct band gap crossover is observed which is consistent with the previously reported strong photoluminescence from the monolayer MoS2. For ReS2 the band gap is direct and a value of 1.52 and 1.42 eV are obtained for the monolayer and multilayers, respectively (see figure 1). A direct to indirect band gap transition has been observed in MoS2 going from monolayer to bilyer but no such transition is observen in ReS2 The results demonstrate the power of HREELS technique as a nanoscale optical absorption spectroscopy tool.
[1] K. Mak, C. Lee, J. Hone, J. Shan, and T. F. Heinz, Phys. Rev. Lett. 105, 136805 (2010).
[2]S. Tongay, H. Sahin, C. Ko, A. Luce, W. Fan, K. Liu, J. Zhou, Y-S Huang, H. Ching-Hwa , J. Yan, D. F. Ogletree, S. Aloni, J. Ji, S. Li, J. Li, F.M. Peeters, and J. Wu, Nat. Comm. 5, 3252 (2014).

[3] K. Dileep, R. Sahu, Sumanta Sarkar, Sebastian C. Peter, and R. Datta, J. Appl. Phys. 119, 114309 (2016).

Dileep KRISHNAN (Dublin, IRELAND), Rajib SAHU, Sebastian PETER, Ranjan DATTA
16:00 - 16:15 #6863 - MS02-OP232 STEM and EELS investigation of graphene nanoribbons epitaxially grown over SiC.
STEM and EELS investigation of graphene nanoribbons epitaxially grown over SiC.

Graphene nanoribbons grown on the (1-10n) and (-110n) facets of SiC have demonstrated exceptional electronic properties as ballistic transport along their long direction and a band gap in the small direction [1]. In order to understand these electronic properties, we have performed (S)TEM (HAADF, LAADF, ABF, EELS) investigation in combination with STM and ARPES measurements. The (S)TEM have been performed on X-section sample as it can be schematically seen in the figure 1. Using Cs corrected STEM at 60 keV voltage, the structural aspect of the graphene can be maintained for high resolution investigation and EELS spectromicroscopy. In particular we will describe the origin of the metal-semiconductor junction as observed in these graphene [2] and this will be discussed in term of curvature effect, quantum confinement on a complex reconstructed step as presented in figure 2 [3].


[1] Exceptional ballistic transport in epitaxial graphene nanoribbons, J. Baringhaus, M. Ruan, F. Edler, A. Tejeda, M. Sicot, A. Taleb-Ibrahimi, A.-P. Li, Z. Jiang, E.H. Conrad, C. Berger, C. Tegenkamp, and W.A. de Heer, Nature 506, 349 (2014).

[2] A wide band gap metal-semiconductor-metal nanostructure made entirely from graphene, J. Hicks, A. Tejeda, A. A. Taleb-Ibrahimi, M.S. M.S. Nevius, F. F. Wang, K. K. Shepperd, J. J. Palmer, F. Bertran, P. Le Fèvre, J. Kunc, W.A. de Heer, C. Berger, E.H. Conrad, Nature Physics 9, 49 (2013).

[3] Atomic structure of epitaxial graphene sidewall nanoribbons:  flat graphene, miniribbons and confinement gap, Irene Palacio, Arlensiú Celis, Maya N. Nair, Alexandre Gloter, Alberto Zobelli, Muriel Sicot, Daniel Malterre, Meredith S.  Nevius, Walt A. de Heer, Claire Berger, Edward H. Conrad, Amina Taleb-Ibrahimi and Antonio Tejeda, Nano letters 15, 182-189 (2015).


Alexandre GLOTER (orsay), Irene PALACIO , Arlensiu CELIS, Maya NARAYANAN NAIR, Alberto ZOBELLI, Muriel SICOT, Daniel MALTERRE, Claire BERGER, Walt DE HEER, Ed CONRAD, Amina TALEB, Antonio TEJEDA

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MS3: Semiconductors and devices

MS3: Semiconductors and devices

Chairmen: Catherine BOUGEROL (Grenoble, FRANCE), Vincenzo GRILLO (Modena, ITALY)
14:00 - 14:30 #8350 - MS03-S73 Atomic-Scale Compositional Fluctuations in Ternary III-Nitride Nanowires.
Atomic-Scale Compositional Fluctuations in Ternary III-Nitride Nanowires.

Ternary InGaN and AlGaN alloys have been sought after for the application of various optoelectronic devices spanning a large spectral range between the deep ultraviolet (DUV) and infrared (IR), including light-emitting diodes, and laser diodes. Conventional planar devices suffer from a high density of dislocations due to the large lattice mismatch, which together with the non-ideal alloy mixing, are established as the cause for various phase separation, surface segregation, and chemical ordering processes commonly observed in nitride alloys. Growth in a nanowire (NW) geometry can overcome these processes by providing enhanced strain relaxation at the free surfaces. In both InGaN and AlGaN, their superior operational characteristics can be attributed to enhanced charge carrier localization at alloy inhomogeneities down to the atomic-scale. Atomic-level chemical ordering in wurtzite InGaN and AlGaN epilayers, describing preferential site occupancy of the cation sublattice by the group III atoms, has been reported mostly with a 1:1 periodicity along the [0001] growth direction [1]. Reports of atomic ordering in cubic ternary III-V alloys (including III-As and III-P) have remained limited to planar thin films; its prevalence within NWs had not been explored.


InGaN/GaN dot-in-a-wire nanostructures grown on Si(111) by molecular beam epitaxy (MBE) were recently developed to achieve more controlled light emission across the entire visible spectrum [2], and characterized using aberration-corrected scanning transmission electron microscopy (STEM) [3]. High-angle annular dark-field (HAADF) Z-contrast imaging shows the InGaN quantum dots (QDs) with atypical oscillating HAADF image intensity at the atomic-level along the c-axis growth direction, exhibiting alternating bright/dark atomic-planes within the QDs [3]. Electron diffraction patterns obtained from the QDs show the presence of otherwise forbidden superlattice reflections, unambiguously confirming the presence of 1:1 bilayer atomic ordering [1]. In addition, atomic-resolution elemental mapping using electron energy-loss spectroscopy (EELS) shows significant In-enrichment in alternating c-planes matching the maxima in the ADF signal collected concurrently, with a deviation from the local mean composition by >25%. Corresponding annular bright field imaging (ABF) enables the visualization of light elements like N, and was used to directly deduce the NWs as N-face polarity. It also indicates that the In-atoms have a preferential occupation at the lower-coordination site along a pyramidal surface facet, which is the first experimental evidence [3] validating the existing theoretical structure model for ordered InGaN layers [4].


Compositional inhomogeneities were also investigated in MBE-grown self-catalyzed AlGaN NWs, which exhibit high luminescence efficiency in the DUV range [5]. With increasing Al concentration, atomic-scale compositional modulations can be induced due to differences in Ga- and Al-adatom migration and incorporation at the growth front. The modulating HAADF intensities were confirmed as Ga-rich/Al-rich regions using EELS elemental mapping at atomic-resolution. Furthermore, their QD/quantum dash-like nature was determined based on multi-orientation views of the same atomic-scale Ga-rich regions. Such atomic-scale compositional modulations in AlGaN can provide energy band fluctuations leading to strong three-dimensional confinement of charge carriers [6].


[1] P. Ruterana, G. Nouet, W. Van der Stricht et al., Appl. Phys. Lett., 72, 1742-1744 (1998)

[2] H.P.T. Nguyen, K. Cui, S. Zhang et al., Nano Lett., 12, 1317-1323 (2012)

[3] S.Y. Woo, M. Bugnet, H.P.T. Nguyen et al., Nano Lett., 15(10), 6413–6418 (2015)

[4] J.E. Northrup, L. Romano and J. Neugebauer, Appl. Phys. Lett., 74, 2319–2321 (1999)

[5] S. Zhao, S.Y. Woo, M. Bugnet et al., Nano Lett., 15(12), 7801–7807 (2015)

[6] The authors are grateful to NSERC for supporting this research. The microscopy was carried out at the Canadian Centre for Electron Microscopy, a National facility supported by NSERC, CFI and McMaster University.

Steffi Y WOO, Matthieu BUGNET (Ontario, CANADA), Hieu P T NGUYEN, Songrui ZHAO, Zetian MI, Gianluigi A BOTTON
14:30 - 14:45 #5193 - MS03-OP238 Insight on the fine structure of semiconductor nanowires down to single atom detection: correlation to their physical properties.
Insight on the fine structure of semiconductor nanowires down to single atom detection: correlation to their physical properties.

Nanotechnology allows modifying the structure of nanoobjects down to the atomic scale. Low dimensional quantum structures can be embedded in a nanowire system in order to modify its properties at will. Electronic and optoelectronic devices benefit from the new advances in growth methodologies, with a fine control of the elemental species locally deposited.

In the present work, we will present how an accurate knowledge on the atomic positions, down to single atom detection, may help to deeply understand the improved properties of our complex nanowire heterostructures. We will show how from scanning transmission electron microscopy (STEM), it is possible to obtain precise 3D atomic models that can be used as input for the simulation of its physical properties. Finally, these theoretical properties will be cross-correlated to the experimental measurements obtained locally on our nanowire systems.

Some of the presented works will include: the effect of the isotope distribution on the phononic behavior of nanowires, the measurement of the internal electric fields in quantum structures and the influence of doping on the compensation of the polarization field, or the influence of polarity and the atomic arrangement on the photonic and electronic properties of single heterostructured nanowires.

1.    J. Arbiol et al., Nanoscale 4, 7517 (2012).

2.    M. Heiss, J. Arbiol et al., Nature Materials 12, 439 (2013).

3.    J. Arbiol, et al., Materials Today 16, 213 (2013).

4.    M. de la Mata, J. Arbiol, et al., Journal of Materials Chemistry C 1, 4300 (2013).

5.    J. Müßener, J. Arbiol, et al., Nano Letters, 14, 5118 (2014).

6.    F. Schuster, J. Arbiol, et al., ACS Nano, 8, 4376 (2014)

7.    Gozde Tutuncuoglu, Jordi Arbiol, et al., Nanoscale, 7, 19453 (2015)

8.    M. de la Mata, J. Arbiol, et al., Nano Letters, 16, 825 (2016)

Jordi ARBIOL (Bellaterra, SPAIN), Aziz GENÇ, Reza R. ZAMANI, María DE LA MATA
14:45 - 15:00 #6604 - MS03-OP247 Quantification of the HAADF contrast from the nanometer scale down to the single atomic column: application to quantum cascade lasers.
Quantification of the HAADF contrast from the nanometer scale down to the single atomic column: application to quantum cascade lasers.

The emission wavelength of quantum cascade lasers can potentially be continuously tuned from the short (2µm) to the long (15µm) infrared, making them an ideal candidate for infrared emitters in a region where materials with the appropriate gap are scarce. The challenge with QCLs lies in the complexity of the epitaxial structure. Indeed, in a typical InGaAs/InAlAs/InP structure the active region is often comprised of thirty stages, each stage containing an alternation of twenty or more InGaAs wells and InAlAs barriers, the thicknesses of which range between 7 and 40 Angstrom. Properly optimizing the epitaxial process therefore requires feedback on the thickness and, most importantly, the composition of each individual well and barrier in the layer, as even small deviations can make or break the end device. Currently, even in the most advanced transmission electron microscopes, equipped with state of the art EDX systems it is not possible to obtain quantitative information on the composition of layers that are thinner than 15 Angstrom. Quantifying the chemical information in the Z-Contrast of HAADF images [1] therefore provides the only solution to obtain the kind of quantitative feedback required for QCLs. The present paper discusses how to obtain such chemical mappings in InGaAs/InAlAs QCLs by combining HAADF-STEM, EDX and also X-ray Diffraction and how the information collected from these mappings is used to optimize the QCL structure [2]. The paper also discusses how this information is fed to numerical models to model the performance of the end device and optimize the QCL design. Finally, the paper forays into the quantification of the contrast of single atomic columns, ultimate step in the analysis.


[1] K. Pantzas, G. Patriarche, D. Troadec, S. Gautier, T. Moudakir, S. Suresh, L. Largeau, O. Mauguin, P. L. Voss, and A. Ougazzaden, Nanotechnology, 23, 455707 (2012)

[2] K. Pantzas, G. Beaudoin, G. Patriarche, L. Largeau, O. Mauguin, G. Pegolotti, A. Vasanelli, A. Calvar, M. Amanti, C. Sirtori, and I. Sagnes, Semiconductor Science and Technology, accepted for publication (2016)

Konstantinos PANTZAS (Marcoussis), Gilles PATRIARCHE, Ludovic LARGEAU, Maria AMANTI, Angela VASANELLI, Carlo SIRTORI, Grégoire BEAUDOIN, Isabelle SAGNES
15:00 - 15:15 #6317 - MS03-OP244 The influence of atomic size effect on the quantitative compositional analyses by means of local lattice parameter measurements.
The influence of atomic size effect on the quantitative compositional analyses by means of local lattice parameter measurements.

A quantitative analysis of the chemical alloy composition down to the near atomic scale is a key issue for understanding  physical properties of semiconductor nanostructures. One method that is commonly applied to this problem is ‘strain mapping’ in a high-resolution transmission electron microscopy (HRTEM) image. The idea is to measure the out-of-plane lattice parameter locally in the HRTEM image and to calculate a local chemical composition within a specific probe volume using elastic continuum theory (see e.g. Refs. [i,ii]. Prerequisites for this approach are that (i) the HRTEM image contrast yields local information about the mean atomic position along the projection direction and (ii) the probe volume possesses a tetragonal distortion, i.e. the local in-plane lattice parameter is fixed to that of the substrate. We show that the latter assumption only holds for comparatively large probe volumes, while it is a poor approximation as the probe volume approaches the near atomic scale. Such small probe volumes, however, are mandatory for studying small composition variations to distinguish e.g. statistical alloy fluctuations from clustering effects. For demonstration, we have performed HRTEM multislice image simulations using relaxed supercells that correspond to realistic sample thicknesses of around 10 nm. The supercells were relaxed using an interatomic potential that has been fitted to DFT calculations[iii]. The supercells contain typical (In,Ga)N quantum structures, such as wells or dots, coherent to GaN. Fig. 1 shows a random Indium distribution within a quantum well, as determined by counting the ratio of Ga and In atoms within a probe volume of (0.519 x 0.317 x 10) nm³ (corresponding to the GaN unit cell times the sample thickness). Fig. 2 displays the c-lattice parameter map, measured in the corresponding HRTEM image simulation. As can be seen by naked eye, the out-of-plane lattice parameter map does only poorly reflect the true In distribution within the supercell. Even a non-existing ordering phenomena might be mistakenly interpreted from the c-lattice parameter map. As we will show, this effect stems from local strain fields caused by In fluctuations in the alloy, which do not only extent in out-of-plane but also in in-plane directions, making the Indium quantification error prone. We have developed a novel approach, which measures next to the out-of-plane, also the local in-plane lattice parameter to extract the local chemical composition. This method allows a much more reliable calculation of the chemical composition from these complex strain fields. Fig. 3 shows the resulting ‘strain revised’ c*-lattice parameter of the (In,Ga)N quantum well, which reveals a much better agreement with the actual In distribution. In addition to the theoretical works, we will also demonstrate first experimental images, where the feasibility of our approach is demonstrated. We propose that our method is versatile, working also for other compounds and is not limited to 2D objects but also applies for quantum wires or dots.

[i] A. Rosenauer, 1, D. Gerthsen and V. Potin, Phys. Stat. Sol. (a) 203, 176 (2006)

[ii] T.P. Bartel and C. Kisielowski, Ultramicroscopy 108, 1420 (2008)

[iii] E. C. Do, Y.-H. Shin and B.-J. Lee J. Phys.: Condens. Matter, 21, 325801 (2009)

15:15 - 15:45 #8302 - MS03-S73B Quantitative STEM - From composition to atomic electric fields.
Quantitative STEM - From composition to atomic electric fields.

The image intensity in high-angle annular dark field STEM images shows a strong chemical sensitivity. As it is also influenced by specimen thickness, crystal orientation as well as characteristics of illumination and detector, a standard-free quantification of composition requires a comparison with accurate image simulation, for which we use the frozen lattice approach of the STEMsim program taking the non-uniform detector sensitivity into account. The experimental STEM intensity is normalized with respect to the incident electron beam. For the quantification of a STEM image it is subdivided into Voronoi cells in which the intensity is averaged. Analysis of the composition in a ternary semiconductor layer such as InxGa1-xN requires measuring the specimen thickness in regions with known composition by comparison with the simulated STEM intensity. Interpolation of the obtained thickness into the layer with unknown composition yields a map of the specimen thickness. Finally, specimen thickness and STEM intensity are compared with simulations computed as a function of composition resulting in a map of the In-concentration x. In alloys containing atoms with different covalent radii (e.g. In and Ga in InxGa1-xN) static atomic displacements occur, which are computed with empirical potentials and included in the simulation. As an application example Fig. 1a shows an array of core-shell nanowires. One single nanowire is depicted in Fig. 1b. The core-shell area marked by a yellow frame is shown in Fig. 1c. Figs. 1d and 1f show high-resolution STEM images of the core-shell regions corresponding to the top and the bottom of a nanowire, respectively. The maps of the measured In-concentration given in Figs. 1e and 1g reveal an increasing thickness of the layer along the growth direction. In the upper part, the layer shows variations of the In-concentration clearly beyond the random-array fluctuations as was shown by a comparison with image simulation.

In the second part of the talk we present results on measurements of atomic electric fields. Differential phase contrast STEM detects the field-induced angular deflection of the electron beam with a segmented ring detector (J. Chapman et al., Ultramicroscopy 3 (1978), 203) assuming that the Ronchigram is homogeneously filled and shifted as a whole in the presence of electromagnetic fields (N. Shibata et al., Nat. Phys. 8 (2012), 611). These assumptions were tested by simulation for 1.3 nm thick GaN. Fig. 2b shows Ronchigrams simulated for 6x6 scan positions within the region marked in Fig. 2a. The dominant effect of the atomic electric field is a complex redistribution of intensity within a Ronchigram. By fundamental quantum mechanical arguments, we take the complex intensity distribution in the Ronchigram into account (K. Müller et al., Nat. Commun. 5 (2014), 5653). The intensity in a certain pixel of the recorded Ronchigram is proportional to the probability that the corresponding momentum is observed. Thus, a center-of-gravity type summation yields the expectation value for the momentum. To relate the electric field in the specimen to the observed momentum transfer, Ehrenfest’s theorem is applied. For thin specimens, the expectation value of the momentum is found to be proportional to the projection of the electric field along the optical axis, convolved with the intensity distribution of the incident STEM probe. We demonstrate the potential of this approach in both simulation and experiment. For the GaN simulation in Fig. 2c we find the electric field depicted in Fig. 2d. Atomic sites appear as sources of the field which has a magnitude of up to 1.5 V/pm. As only the convolution of the true field with the probe intensity can be measured, the field strength decreases in the direct vicinity of atomic sites. In a first experiment, 20x20 Ronchigrams of SrTiO3 with a thickness of 2.5 nm have been recorded on a conventional charge-coupled device (CCD), yielding the electric field in Fig. 2e. We also report on pilot experiments with the ultrafast pnCCD camera (K. Müller et al., Appl. Phys. Lett. 101 (2012), 212110) which was operated at read-out rates of up to 4 kHz. For example, Fig. 2f shows the momentum transfers recorded at a MoS2 mono/bilayer interface, demonstrating that fast detectors are the key for atomic-scale materials analyses at a reasonable field of view.

15:45 - 16:00 #5755 - MS03-OP239 Analysis of strain and composition in GeSi/Si heterostructures by electron microscopy.
Analysis of strain and composition in GeSi/Si heterostructures by electron microscopy.

Electronic properties of GeSi/Si-based metal oxide semiconductor field effect transistors (MOSFETs) are strongly influenced by the geometry, composition and strain state of the Ge containing source/drain stressor regions and the Gate channel in between. In the first part of our contribution, we hence present quantitative STEM Z-contrast evaluations of the Ge composition in MOSFETs with different stressor geometries and verify the results with energy-dispersive analyses of X-rays (EDX) using the chemiSTEM system mounted on an FEI Titan facility. To evaluate the strain distribution within the gate channel and the stressors, we used nano-beam electron diffraction employing a delay-line detector (DLD, [1]) which enhances the acquisition speed for the 4-dimensional data set (diffraction patterns as a function of the STEM raster position) to 10ms/image.

As illustrated in Fig.1 the top of the DLD consists of a microchannel plate (MCP) stack that causes a cascade of secondary electrons for each 300keV electron impinging on the detector. The heart of the DLD are 2 meandering wires shown in blue and red in which each cascade causes electrical pulses travelling towards the ends of the wires. Depending on the incident position of the electron a characteristic time delay between the arrivals of the 2 conjunct pulses at the ends of a wire is measured with high accuracy, giving the coordinate of incidence perpendicular to the meander. By crossing two such delay-lines the point (x,y) and time τ of incidence can be detected. Thus the DLD allows for both the recording of a continuous stream of single electron events processed by a time-to-digital converter (TDC) with a time precision in the picosecond range and the in-situ integration of the signal over a certain frame time to obtain conventional images. Note that no pixel raster is involved here. The two modes of operation are illustrated in the right part of Fig. 1.

An example for a MOSFET exhibiting 2 Ge regimes of 22% and 37% within the stressors is shown in Fig. 2 for the strain measurement along the [001] direction and in Fig. 3 for a measurement along the [110] direction. Here a STEM raster of 100x100 pixels was used with a dwell time of 40ms. Figure 2 was obtained by evaluating the position of the 004 CBED disc using the radial gradient maximisation method [2] whereas the 220 reflection was measured to obtain Fig.3. Two strain regimes are observed inside the GeSi stressors due to the different regimes of Ge contents. The gate channel exhibits compressive strain of up to 3% laterally and an expansion below 1% along [001]. Concerning the influence of the acquisition speed on strain precision, recording 10,000 diffraction patterns took 6.5min here, yielding a strain precision of 0.12% in terms of the standard deviation determined in unstrained Si regions. The same experiment at twice the scan speed (dwell time of 20ms) yields the same average strain distributions, however, at the precision of 0.18%.

In the second part, we report a systematic study on the epitaxy of GeSi on Si (111) as a function of growth temperature. In particular, temperatures of 400, 450 and 550°C have been used and the strains along [111] and [1-11] have been measured. Using elasticity theory, composition maps were derived from the strain results, yielding the three Ge profiles in Fig.4. Obviously growth at 400 and 450°C leads to islands of pure Ge whereas the Ge content drops to 60% if the temperature is raised to 550°C. We finally discuss our results with respect to Si/Ge interdiffusion which causes a gradual change of composition at the interface.

[1] K. Müller-Caspary, A. Oelsner, P. Potapov, Applied Physics Letters 107 (2015), 072110.

[2] K. Müller and A. Rosenauer et al., Microscopy and Microanalysis 18 (2012), 995.

[3] Funding: Deutsche Forschungsgemeinschaft (DFG) under contract MU3660/1-1.

16:00 - 16:15 #6572 - MS03-OP246 Analysis of the Sb and N distribution in GaAsSb/GaAsN superlattices for solar cell applications.
Analysis of the Sb and N distribution in GaAsSb/GaAsN superlattices for solar cell applications.

Dilute nitride III–V alloys have attracted a lot of attention in the last decade due to its wide tunability of both band gap and lattice constant that makes them a potential candidate in multi-junction solar cell technology. For certain, these alloys can be used to improve the conventional lattice matched three-junction solar cell by the replacement of Ge bottom cell and/or also by adding a fourth junction with a bandgap of 1 eV, which is predicted to provide efficiencies beyond 50%.1 In this sense, the GaAs1-x-ySbxNy quaternary alloys have a surplus due to the Sb-surfactant effect and the possibility of an independent tuning of the electron and hole confinements.2 However, the composition control in GaAsSbN materials present important challenges, and undesired phenomena such as segregation, clustering or phase separation are typically observed. A possible route to overcome these handicaps is the use of superlattices, based on the fine stacking of ternary and/or binary thin layers, which could, in addition, offer extra advantages (such as a greater collection efficiency). In any case, it is expected that the spatial separation of Sb and N atoms would improve the composition control and therefore facilitate a smaller lattice mismatch deviation with respect to the substrate. The present work analyses the Sb and N distribution in different GaAsSb/GaAsN superlattice structures grown lattice matched to GaAs substrates by molecular beam epitaxy. The nominal contents of Sb and N are 6.12% and 2.7%, respectively, and the periodicity is varied from a few MLs to ~20 nm. The samples were then characterised by different transmission electron microscopy techniques (TEM) and the results supported by X-ray diffraction (XRD) and cross-sectional scanning tunneling microscopy (X-STM) data.

Firstly, compositionally sensitive 002 dark field (DF) imaging was carried out in order to estimate the compositional distribution and periodicity, where the Sb and N rich areas depict a brighter or darker intensity than the GaAs ones, respectively (Figure 1a). Although the periodicity is close to planned, the intensity analysis revealed a compositional deviation with respect to the nominal design, especially in the Sb distribution. Certainly, although N atoms seem to be confined into the GaAsN layers exhibiting greater stability against interdiffusion, Sb atoms are spread along the whole structure. The precise control over the N position in the supperlattice is confirmed by atomic scale X-STM images in which individual N atoms are directly observed. The low contents of Sb and N unable the application of high angle annular dark field (HAADF) conditions in STEM images (Figure 1.b). Instead, ADF images are used, since N yields a brighter contrast due to the distortion that produces in the structure3,4 (Figure 1c) and compared with electron dispersive x-ray (EDX) maps acquired simultaneously, that allow us to determine the distribution and the overall content of Sb (Figure 1d). All these analysis pointed out to a lower incorporation both of Sb and N that depends on the period of the structure. More important, a strong interdiffusion of Sb is evidenced. The Sb content reaches its maximum value at the top of the GaAsSb layer and a minimum at the top of the GaAsN layer (Figure 2). As consequence, there is a phase difference between the ADF images and the EDX maps that must be taken in consideration. The system moves away from the original design, where the Sb content adopts a sawtooth distribution and the square superlattice structure is preserved mainly by the N distribution. The influence of the period of the superlattice on these effects is discussed.


We acknowledge the Spanish MICINN–MINECO for funding through Project MAT2013-47102-C2, and SCCYT-UCA for technical support.


1 A. Luque, J. Appl. Phys. 110, 031301 (2011)

2 J. M. Ulloa et al. Appl. Phys. Lett. 100, 013107 (2012)

3 M. Herrera et al. Phys. Rev. B, 80, 125211 (2009)

4 T. Grieb et al., Ultramicroscopy, 117, 15-23 (2012) 


Daniel F. REYES (Chiclana de la Frontera, SPAIN), Veronica BRAZA, Alicia GONZALO, Antonio D. UTRILLA, Davide F. GROSSI, Paul M. KOENRAAD,, Alvaro GUZMAN, Adrian HIERRO, Jose M. ULLOA, Teresa BEN, David GONZALEZ

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MS4: Complex materials and nanocomposites

MS4: Complex materials and nanocomposites

Chairmen: Rick BRYDSON (Leeds, UK), Marc SCHMUTZ (Strasbourg, FRANCE)
14:00 - 14:30 CryoTEM in Materials Science. Nico SOMMERDIJK (EINDHOVEN, THE NETHERLANDS)
14:30 - 14:45 #5836 - MS04-OP250 Direct visualization and quantification of three-dimensional ferritin crystallization on the nanoscale.
Direct visualization and quantification of three-dimensional ferritin crystallization on the nanoscale.

We present the proof of concept that a real space tomography approach can be used for the quantification of local ordering in tiny crystals of ferritin. This work is driven by the need for a  fundamental understanding of crystal growth of weakly interacting proteins on a molecular level. At present, only tentative ideas exist about interactions in particular in solution and during crystallization. Offering simplicity and controllability the condensation of ferritin molecules from solution was chosen as an ideal system to get insight into the nucleation and crystallisation mechanism that leads to ordered crystals. 

The approach involves cryo-fixation of aging stages of ferritin condensation from solution and subsequent three-dimensional scanning transmission electron miscoscopy (STEM) tomography (Fig. 1a). Cryo-STEM tomograms were recorded and analysed to yield the three-dimensional ferritin particle coordinates for the real-space refinement of the structure of ferritin agglomerates. 3D pair correlation functions for ordered nanocrystals of a few hundred ferritin particles reproduce well and up to higher coordination shells the crystal structure that was reported from synchrotron experiments on macrocrystals. The local order within ferritin agglomerates is further refined quantitatively by order parameter mapping with the resolution of a single lattice site based on a data-base correlation technique (Fig. 1b).

14:45 - 15:00 #5982 - MS04-OP253 Characterization of Janus gold nanoparticles obtained via spontaneous binary polymer shell segregation.
Characterization of Janus gold nanoparticles obtained via spontaneous binary polymer shell segregation.

Janus nanoparticles are nanoparticles (NPs) displaying two sides of different chemical nature which makes them of high interest. The formation of the Janus shell provides the NPs an amphiphilic character, which can therefore self-assemble in a tunable fashion by varying different experimental parameters such as size, polymer ratio and temperature. Here, Au NPs coated by polyethylene glycol (PEG) and both polystyrene (PS) and poly(N-isopropylacrylamide) (PNIPAM) were investigated. [1] The true Janus character of the NPs was determined by electron tomography. Characterization of polymer coated particles by electron microscopy is challenging due to the low contrast of the organic materials. The goal was to distinguish the two different polymers in two types of particles (PEG+PNIPAM and PEG+PS coated Au NPs). Different approaches were used to improve the contrast between the two polymers. The PEG+PNIPAM particles were characterized by specific staining of the hemispheres while the character of the PEG+PS particles was investigated by the growth of silica.


First, the PEG+PNIPAM coated NPs were stained with 3 mM CuSO4.5H2O solution to generate sufficient contrast in the Transmission Electron Microscope (TEM). PNIPAM-coated NPs showed damage of the polymer upon electron beam irradiation. For PEG-coated NPs a stable shell was observed. In an attempt to distinguish PNIPAM and PEG, PEG+PNIPAM coated particles were stained and investigated with TEM (Fig. 1). Since conventional TEM images are 2D projections from a 3D object, electron tomography was performed. It must be noted that the conventional technique for tomography in materials science, high angle annular dark field scanning TEM (HAADF-STEM), could not be applied due to the large difference in atomic number Z for Au and the elements in the polymer shell. Instead, Bright-Field TEM tomography was applied. Images were acquired over the largest possible range (-76° to +76°) every 2°, aligned and reconstructed by the SIRT (Simultaneous Iterative Reconstruction Technique) algorithm in the Astra Toolbox. [2] The obtained 3D reconstruction displayed rather low contrast between the shell and the background. Manual segmentation based on the orthoslices (xy-, yx- and zx-direction) could be carried out. This method provided a 3D reconstruction that clearly confirms the formation of stained half-shells (Fig. 3).


In the second case of PEG+PS coated Au NPs, an attempt of staining with calcium phosphate was carried out. In TEM images hemispheres could be observed, but selective staining could not be confirmed. Due to the high affinity of PEG by silica, PEG is able to act as a primer to promote silica condensation. Since PS is hydrophobic and does not allow silica nucleation, the silica shell was expected to occur only at the parts of the NPs that are coated by PEG (Fig. 2).

Either staining or silica shell growth over PEG-coated areas resulted in the observation of semi-shells (Janus character) in Au NPs by TEM and electron tomography.


[1] A. M. Percebom, et al., Chem. Comm., 52 (2016), 4278-4281.

[2] W.van Aarle, et al., Ultramicroscopy, 157, (2015), 35.

[3] The authors S.B. and N.C. gratefully acknowledge the European Research Council, ERC grant N°335078 – Colouratom.

Nathalie CLAES (Antwerpen, BELGIUM), Ana. M PERCEBOM, Juan J. GINER-CASARES, Sara BALS, Watson LOH, Luis M. LIZ-MARZÁN
15:00 - 15:30 #6345 - MS04-S75B Imaging Dynamic Processes in Liquids: Application for Batteries.
Imaging Dynamic Processes in Liquids: Application for Batteries.

The development of in-situ liquid stages for the (S)TEM presents many opportunities to study dynamic processes important for next generation energy storage, transport and conversion systems.  However, to use the microscope to study these systems we must be aware of the effect of the electron beam in controlling/altering the experiment. Fortunately, the effect of the beam current can be calibrated and understood in terms of its effect on the nucleation and growth of nanoparticles from solution.  Here, we demonstrate the beam effect by analyzing the degradation mechanisms in Li battery electrolytes. Figure 1 shows the degradation mechanisms for lithium hexafluoroarsenate (LiAsF6) in 1,3-dioxolane, DOL (Figure 1a) and dimethyl carbonate, DMC (Figure 1b). There are different mechanisms of breakdown in each case – the size, shape and morphology of the precipitates is different. These results demonstrate that the electron beam has the potential to mimic electrochemical reduction, and therefore must be taken into account during in-situ electrochemical measurements to ensure results are free from artifacts.

Having calibrated the electron dose for the particular electrolyte, we can now use an operando electrochemical cell to investigate the role and mechanism of electrolyte additives during Li deposition/stripping. We prepared two electrolytes, LiPF6 in propylene carbonate (PC) with different trace-amounts of water. Figure 2A shows a comparison of the cyclic voltammograms for the two electrolytes and Figure 2B shows the corresponding amount of Li deposited/stripped during these cycles (Figure 2C and D shows representative STEM images of the process). The higher concentration of water, leads to an increased concentration of highly conducting LiF in the SEI layer, leading to a larger grain size through increased diffusion of Li ions during battery cycling. SEM images show Li deposited on a Cu electrode surface in the presence of 10 ppm (Figure 2E) and 50 ppm (Figure 2F) of water at a current density of 1mA/cm2 for 15 h.  The Li deposits in the electrolyte containing 10 ppm shows a typical dendritic microstructure. However, the electrolyte with 50 ppm of water forms smooth, thin and dense dendritic layer. This result provides crucial insides into the performance of Li metal anodes and their successful incorporation into the next generation battery system.



This research is part of the Chemical Imaging LDRD Initiative at PNNL, a multi-program laboratory operated by Battelle for the U.S. DOE under Contract DE-AC05-76RL01830.  This work was partially supported by JCESR, an Energy Innovation Hub funded by DOE-BES. A portion of the research was performed using EMSL, a national scientific user facility sponsored by DOE-BER and located at PNNL. C.P. acknowledges support from the FSU COFRS Award 032968, the Ralph E. Powe Junior Faculty Enhancement Award, and NSF-CMMI-1334012.

15:30 - 15:45 #6275 - MS04-OP256 Atomic structure of the ultrathin amorphous aluminium oxide barrier in Al/AlOx/Al Josephson junctions.
Atomic structure of the ultrathin amorphous aluminium oxide barrier in Al/AlOx/Al Josephson junctions.

Amorphous materials are widely used in many technologically important devices and structures. In Josephson junctions, amorphous aluminium oxide film with a thickness of a few nanometers is used as tunnel barrier [1]. The atomic structure of this thin amorphous oxide film determines the tunnelling properties of the junction. However, the disordered nature, the miniaturized dimension and the close proximity to the adjacent crystalline contacts of the oxide barrier are challenging aspects of the direct investigation of the atomic structure of the tunnel barrier layer.


In this work, we have unveiled the microscopic structure of the ultrathin (<2 nm) aluminium oxide barrier in Al/AlOx/Al Josephson junctions via transmission electron microscopy. Scanning transmission electron microscopy (STEM) and electron energy loss spectroscopy (EELS) were used to reveal the detailed atomic structure and the chemical bonding in the junction. By combining nano-beam electron diffraction (NBED) and pair distribution function (PDF) analysis with reverse Monte Carlo (RMC) refinement [2] we unravelled the atomic structure of the nanosized AlOx barrier. The technique of combining NBED-PDF and RMC enabled us to treat the crystalline Al contacts and the amorphous AlOx barrier layer as integrated parts in the system and take the interfacial interaction between Al and AlOx into account while retrieving the atomic structure information.


The atomic structure of the AlOx tunnel barrier layer resembles the structure in bulk Al2O3 in terms of bond length distribution, bond angle distribution, and connectivity of the elemental structure units. However, the average coordination number of the Al atoms in the barrier is around 3.4, which is lower than that in other amorphous aluminium oxide systems [3]. The combined NBED and RMC simulation showed that the miniaturized dimension of the oxide barrier and the presence of the interfacial interaction between crystalline Al and amorphous AlOx give rise to an oxygen deficiency at the metal/oxide interfaces in the junction. This is of importance since atomic defects such as oxygen vacancies at the interfaces are possible origins of the two-level systems that contribute to the decoherence and noise in superconducting quantum circuits based on Josephson junctions.


[1] Oliver, W. D. & Welander, P. B. Materials in superconducting quantum bits. MRS Bull. 38, 816–825 (2013).

[2] Cockayne, D. J. H. The study of nanovolumes of amorphous materials using electron scattering. Annu. Rev. Mater. Res. 37, 159–187 (2007).

[3] Gutiérrez, G. & Johansson, B. Molecular dynamics study of structural properties of amorphous Al2O3. Phys. Rev. B 65, 104202 (2002).

Lunjie ZENG (Gothenburg, SWEDEN), Dung Trung TRAN, Cheuk-Wai TAI, Gunnar SVENSSON, Eva OLSSON
15:45 - 16:00 #6273 - MS04-OP255 Structure determination of a disordered, complex zeolite by combining rotation electron diffraction and HRTEM.
Structure determination of a disordered, complex zeolite by combining rotation electron diffraction and HRTEM.

Zeolites are porous materials with important industrial applications [1]. Their structures are complex, and sometimes disordered which makes their structure characterization difficult using conventional methods. Electron diffraction (ED) combined with high resolution transmission electron microscopy (HRTEM) is a very powerful method for determination of complex or disordered structures from nano-and submicron-sized crystals. In this work, we used Rotation Electron Diffraction (RED) [2] combined with HRTEM imaging and powder X-ray diffraction (PXRD) to solve and characterize the structure of the complex germanosilicate IM-18 [3]. The RED method combines discrete goniometer tilt steps (2.0-3.0°) with fine beam tilt steps (0.05-0.20°) to collect 3D ED data from a single particle. More than 1000 ED frames can be collected in less than one hour. Moreover, both sharp spots and diffuse streaks indicating the disorder could be seen from the 3D reciprocal lattice reconstructed from the RED data. IM-18 was first prepared more than 8 years ago, but its structure remained unsolved [3]. RED data of IM-18 consisting of 649 ED frames were collected covering a tilt range of 119.46° with a tilt step of 0.20°. RED data were collected at 200 kV using the software RED – data collection on a JEOL JEM2100 TEM. The RED data processing software was used for unit cell determination, indexing, and intensity extraction.

We have developed a method and a software, QFocus, for structure projection reconstruction from a through-focus series of HRTEM images acquired with a constant step of defocus changes [4]. The defocus value and two-fold astigmatism were then determined for each image in the series. A contrast transfer function (CTF) correction was performed on each image and a final image representing the projected potential of the specimen was reconstructed by averaging all CTF-corrected images. Several through-focus series of 12 HRTEM images with a defocus step of 85.3Å were taken from IM-18 along the b-axis, and the structure projections were reconstructed using QFocus.

The unit cell parameters of IM-18 were obtained from the 3D reciprocal lattice reconstructed from the RED data (Fig. 1), and refined against the PXRD data. The crystal of IM-18 is monoclinic (P2/m) with a = 10.336 Å, b = 14.984 Å, c = 17.734 Å, β = 106.9° (Fig. 2A). The structure was solved from the RED intensities by using direct methods and further confirmed by using HRTEM images (Fig. 2B) and PXRD data. IM-18 contains three-dimensional intersecting channels defined by 8, 10, 8 vertex-sharing (Ge, Si)O4 tetrahedra along a-, b- and c-axis, respectively. Disorder was determined from the reconstructed HRTEM images (Fig. 2C).

We have shown here that the RED method can help to solve the structures from diffraction intensities and give the information about the disorder in the materials. The structure projection reconstruction method is important for beam sensitive materials, because it allows fast data collection without the need of manually optimizing the defocus. The contrast of the reconstructed HRTEM image is greatly improved and the image can be directly interpreted in terms of structure projection.


This project is supported by the Swedish Governmental Agency for Innovation Systems (VINNOVA) and the Swedish Research Council (VR), and the Knut and Alice Wallenberg Foundation (KAW) through a project grant 3DEM-NATUR.



1) M. E. Davis, Nature, 2002, 417, 813-821.

2) W. Wan, J. Sun, J. Su, S. Hovmöller, X. Zou, J. Appl. Cryst. 2013, 46, 1863-1873.

3) Y. Lorgouilloux, J.-L. Paillaud, P. Caullet, J. Patarin, N. Bats, French patent 2,923,477. 2007 Nov 11.

4) W. Wan, S. Hovmöller, X. Zou, Ultramicroscopy, 2012, 115, 50-60.

Magdalena Ola CICHOCKA (Stockholm, SWEDEN), Yannick LORGOUILLOUX, Jie SU, Yifeng YUN, Wei WAN, Nicolas BATS, Jean-Louis PAILLAUD, Xiaodong ZOU
16:00 - 16:15 #6629 - MS04-OP257 Electron tomography combined with electron diffraction reveals the dissolution and phase transformation of KFI to CHA zeolites.
Electron tomography combined with electron diffraction reveals the dissolution and phase transformation of KFI to CHA zeolites.


Microporous alumminosilicates, zeolites, have been implemented in a large number of important industrial applications.[1] Their unique properties are to a large extent determined by their unique micropore structures with pores in the size range of small molecules. Though providing unique properties, the micropores also introduce obstacle when it comes to efficient mass transfer in the material. Introducing porosity on larger length scales will enhance the diffusion properties as well as increasing the accessibility to the chemically active micropores. In addition transformations between different zeolite phases with characteristic pore structures may be observed. Through electron tomography important knowledge about the internal pore structure can be obtained. By linking the results to information about the present crystalline phases, relationship between morphology, crystal structure and the relative orientation of intergrowing crystals from electron diffraction and high resolution TEM (HRTEM) imaging a comprehensive understanding of the material and its crystallization can be obtained.

Results and discussion

Micrometer sized single crystals of a cubic KFI zeolite were treated in in a controlled dissolution process with 1.2M Potassium hydroxide. This treatment partially dissolves the KFI crystals and creates a very peculiar sponge like morphology, see Fig 1a. The overall cubic morphology of the crystals was however preserved. Selected area electron diffraction (SAED) could confirm that the crystal despite its spongy texture remained a single crystal of KFI, Figure 1b.

In order to study the internal structure of the KFI crystals electron tomography was performed. A tilt series of 69 ADF-STEM projection images collected in the range of -76 - +60 degrees with a 2° tilt increment was used for the reconstruction. The reconstruction was performed using a SIRT reconstruction algorithm implemented in the ASTRA toolbox [2]. The electron tomography reconstruction clearly shows that the porosity penetrates through the entire spongy cubic crystal of KFI zeolite, see Fig 2 b-c. Both the tomography reconstruction as well as the ADF-STEM and HRTEM images, see Fig 1a and 2a, shows that some of the pores have a preference to run from the edges towards the center. From the HRTEM images in Fig xx it can be observed that the preferred termination surfaces are and surfaces.


Bright field TEM images shows that after the controlled dissolution process additional smaller well facetted crystals form on top of the micrometer sized spongy KFI cubes, see Fig XX. Through the use of SAED the smaller crystals could be identified to be a different trigonal zeolite, chabazite. The Potassium ions present during the dissolution direct the growth of chabazite based on the KFI structure. Interestingly the KFI and chabazite structures are intimately related as they are entirely built from the same building unit of 12 SiO4 tetrahedrons, called a double 6-ring. The only difference between the two structures is the packing of this building unit. The SAED patterns shows that the cubic KFI zeolite grows along its directions and that the chabazite crystals tend to grow epitaxially with its [101] direction aligned along the [100] direction of the KFI crystals structure.



T.W. acknowledges a Postdoctoral grant from the Swedish research council. S.B. acknowledges financial support in the form of an ERC starting grant.



1) Davis, M. E. Nature, 2002, 417, 813-821.

2) van Aarle, W., Bals, S., Sijbers, J. et. al. Ultramicroscopy, 2015, 157, 35-47

3) L. Van Tendeloo, E. Gobechiya, E. Breynaert, J. A. Martens and C. E. A. Kirschhock, Chemical communications, 2013, 49, 11737-11739.


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LS2: Cell organisation and dynamics

LS2: Cell organisation and dynamics

Chairmen: Isabelle ARNAL (Grenoble, FRANCE), Chris HAWES (Oxford, UK), Eija JOKITALO (University of Helsinki, FINLAND)
14:00 - 14:30 #8358 - LS02-S05 Probing cell behavior: Combining MEMS (microelectromechanical systems) technology with high resolution live cell imaging.
Probing cell behavior: Combining MEMS (microelectromechanical systems) technology with high resolution live cell imaging.

Cell biological experimentation has benefitted from the development of microdevices based on microfluidics and MEMS (microelectromechanical systems) technology. These devices exploit the possibility to create microscopic 3D structures that can be used to manipulate single cells. Furthermore, microdevices can be used to miniaturize laboratory functions (Lab-on-a-Chip). We developed an experimental platform with the specific aim to study tip growing cells, the TipChip [1]. The device allows positioning of single cells such as pollen grains or fungal spores at the entrances of serially arranged microchannels harboring microscopic experimental setups. The transport of the cells is mediated by fluid-flow. Once positioned in the device, the tip growing cells, pollen tubes, filamentous yeast or fungal hyphae, can be exposed to chemical gradients, microstructural features, integrated biosensors or directional triggers. The device is compatible with Nomarski optics and fluorescence microscopy and can thus be used for live cell imaging. Using the TipChip platform we investigated the growth mechanism in pollen tubes. The pollen tube is a cellular transport system that is generated to connect the male gametophyte with its female counterpart. Through this catheter-like protuberance the sperm cells are delivered from the pollen grain to the ovule nestled deep within the pistillar tissues. To be competitive, the pollen tube elongates extremely rapidly and it has to do so against the impedance of the apoplast of the transmitting tissue and through the maze of pistillar cells that separate the pollen grain from the ovule. Using calibrated micro-cantilevers we quantified the invasive force of the pollen tube and we found that sperm cell discharge can be triggered by mechanical constriction [2]. Further applications include exposure of cells to precisely calibrated electric fields and micron-sharp, tunable chemical gradients. The TipChip is therefore a highly versatile tool for the combined quantitative biophysical and optical investigation of polar growth in plant cells.





[1] Agudelo CG, Sanati Nezhad A, Ghanbari M, Naghavi M, Packirisamy M, Geitmann A. 2013. TipChip – a modular, MEMS (microelectromechanical systems)-based platform for experimentation and phenotyping of tip growing cells. Plant Journal 73:1057-1068

[2] Sanati Nezhad A, Naghavi M, Packirisamy M, Bhat R, Geitmann A. 2013. Quantification of cellular penetrative forces using Lab-on-a-Chip technology and finite element modeling. PNAS 110: 8093–8098

14:30 - 15:00 #7814 - LS02-S06 Structure and dynamics of the endoplasmic reticulum in cultured mammalian cells.
Structure and dynamics of the endoplasmic reticulum in cultured mammalian cells.

The endoplasmic reticulum (ER) is a large, single-copy, membrane-bound organelle that comprises an elaborate 3D network of structurally diverse subdomains: highly curved tubules, flat sheets, and parts that form contacts with nearly every other organelle of the cell. The ER is essential for the synthesis, modification, and transport of membrane and secretory proteins; it is also the site of cytosolic calcium level regulation and synthesis and transport of several lipids. To accommodate the vast range of functions, the ER network spreads throughout the cell, and its functions are distributed into structural subdomains according to their specific requirements. Many structural determinants of the network formation and maintenance have been described; however, it is not yet understood e.g. how different functions are distributed to the various subdomains, why the ER is constantly rearranging its architecture, and how the sheet/tubule –balance is maintained.
Proper ER operation requires an intricate balance within and in-between dynamics, morphology, and functions. While ER structure is in constant flux, it does not move en masse, and the network movement is achieved through dynamics of individual subdomains and through network remodelling, which are accomplished through interactions with the cytoskeleton. Combining live cell imaging, thin section TEM and two 3D-EM methods, we show that dynamic microtubules and actin filament arrays together contribute to the maintenance of ER sheet-tubule balance. Perturbations of microtubule or actin cytoskeleton readily shift the balance towards tubules or sheets, which in turn can result in formation of sheet remnants or long and less fenestrated abnormal sheets. We recently identified the unconventional motor protein myosin 1c localizing to and regulating the ER associated actin filament arrays. Manipulation of myo1c levels disturbed the dynamics of actin arrays and affected ER sheet morphology similarly to actin manipulations with drugs. Tubular ER phenotype of myo1c-depleted cells could be rescued with wild type myo1c, but not with a mutated form lacking the actin binding domain. We propose that ER -associated actin filaments have a role in maintaining the ER sheet-tubule balance and sheet structure by regulating sheet remodeling events, and thus support the maintenance of sheets as a stationary subdomain of the otherwise dynamic ER network.
Knowledge of the mechanisms behind the structural maintenance and dynamics will be the key towards deeper understanding of ER functions and their regulation, and eventually, in unravelling molecular mechanisms behind various ER-associated diseases.

Merja JOENSUU, Ilya BELEVICH, Helena VIHINEN, Darshan KUMAR, Olli RÄMÖ, Behnam LAK, Eija JOKITALO (University of Helsinki, FINLAND)
15:00 - 15:30 #8624 - LS02-S07 How do plants read their own shape ?
How do plants read their own shape ?

There is accumulating evidence that single cells in culture can sense mechanical cues to control their division, their growth and their fate. In a multicellular context, this implies that a given cell can use growth-derived stress and shape-derived stress to control its behavior. In this scenario, the presence of mechanical forces in tissues may thus be a way for the cell to know its position and control its differentiation accordingly, during development. Whereas this question is difficult to explore in animals, the relatively slow growth and simpler mechanics in plants make them ideal systems to investigate the contribution of “positional mechanical signals” in development. To illustrate this idea, I will present the microtubule response to mechanical stress in Arabidopsis at three different scales: at the single cell level, using the jigsaw puzzle shaped pavement cells; at the tissue scale, using the crease-shape boundary domain of the shoot apical meristem; at the whole organ scale, using the sepal, which exhibits a very reproducible shape despite high variability at the cell level. Beyond the cytoskeleton, mechanical cues are also controlling gene expression and our recent data suggest that the perception of mechanical stress acts in parallel to major hormones, like auxin, to regulate some of the master regulators of the shoot apical meristem. Altogether, this provides a picture in which mechanical forces add robustness to plant morphogenesis, by channeling the dynamics of cell effectors and molecular pathways.

15:30 - 15:45 #6579 - LS02-OP013 The 3-D organisation of the plant endomembrane system.
The 3-D organisation of the plant endomembrane system.

Recent advances in high resolution field emission scanning electron microscopy combined with the ability to section resin blocks within the microscope specimen chamber have revolutionised our ability to study cell structure in three dimensions.   Serial Block Face Scanning Electron Microscopy (SBFSEM) permits the collection of large three dimensional data sets from resin embedded material.  One of the major limitations of the technique is generating sufficient contrast in the specimen prior to resin embedding to permit sequential collection of relatively high magnification images. We use selective staining of membranes using the zinc iodide/osmium tetroxide impregnation technique to selectively highlight membranes of the secretory pathway. In this way the organisation of nuclear envelope, endoplasmic reticulum and Golgi membranes can be studied through reconstructions of data sets obtained from the Gatan 3-View system and reconstructed using Amira or Imaris.  Here we will describe the use of this technique to investigate the organisation of the endoplasmic reticulum in dividing root meristematic calls and the relationship between Golgi bodies and the tubular endoplasmic reticulum.

Chris HAWES (Oxford, UK), Maike KITTELMANN, Louise HUGHES
15:45 - 16:00 #5933 - LS02-OP012 A complex prokaryotic endomembrane system.
A complex prokaryotic endomembrane system.

Compartmentation is generally considered a feature of eukaryotic cells. One exception in the "prokaryotic world" is the marine hyperthermophilic Crenarchaeon Ignicococcus that exhibits a large inter-membrane compartment (IMC) between an inner (cytoplasmic) and an outer (cellular) membrane (CM and OCM) [1]. In addition, I. hospitalis supports the propagation of another archaeon - Nanoarchaeum equitans - on its surface [2]. Cryopreparation in combination with 3D methods (serial sectioning, FIB/SEM and electron tomography) enabled us to deliver a comprehensive insight into the anatomy of I. hopitalis and its contact to N. equitans. The 3D-models obtained, reveal a highly complex and dynamic endogenous membrane system with putative secretory function: The IMC makes up ~40% of the whole cell volume on average, but in few cells, it can reach an extent much larger than the volume of the cytoplasm. In the IMC, elongated protrusions of the cytoplasm are present. Apparently, these structures can constrict from or fuse with the CM or themselves. We also observed interactions of these protrusions with the OM via macromolecular, cylindrically shaped complexes. All interacting structures are connected via thin filaments (~3-6 nm in diameter), that span through the whole IMC and are presumably responsible for membrane dynamics. In addition, homologues in sequence and/or structure to eukaryotic proteins can be found in Ignicoccus, that are putatively involved in the system like their eukaryotic counterparts: small GTPases (Sar1/Arf like), Coatomer proteins, Sec61ß, proteins of the ESCRT-III system, a tethering complex component (Bet3) and the ATPase CDC48/p97 [3, 4]. Since Ignicoccus belongs to the recently proposed TACK superphylum, that is considered a sister group of eukaryotes [5], it is also tempting to speculate about a prokaryotic origin of the eukaryotic endogenous membrane system. Regarding the contact of N. equitans to I. hospitalis, a fusion of cytoplasms of both organisms was revealed, providing an important complement and explanation to recent proteomic [4], transcriptomic [6] and metabolomic [7] studies on this inter-archaeal system.

[1] Rachel et al., Archaea 1 (2002), 9

[2] Huber et al., Nature 417 (2002), 63

[3] Podar et al., Biology Direct 3 (2008), 2

[4] Giannone et al., PLOS One 6(8) (2011), e22942

[5] Guy & Ettema, Trends in Microbiology 19(12) (2011), 580

[6] Giannone et al., ISME Journal 9 (2015), 101

[7] Hamerly et al., Metabolomics, 11(4) (2015), 895

[8] supported by a grant of the Deutsche Forschungsgemeinschaft (DFG)

Thomas HEIMERL (Marburg, GERMANY), Jennifer FLECHSLER, Gerhard WANNER, Reinhard RACHEL
16:00 - 16:15 #6693 - LS02-OP015 Spatial relation of organelle membranes in the coccolith forming marine alga Emiliania huxleyi.
Spatial relation of organelle membranes in the coccolith forming marine alga Emiliania huxleyi.

The  marine unicellular alga Emiliania huxleyi forms a shell of calcite scales called coccoliths. It can form large blooms and thus is the most important sink for marine CO2 responsible for 33% of the marine CaCO3 production [1]. The coccoliths are first formed intracellular within an organelle called the coccolith vesicle and then leave the cell and interlock with one another to form the shell. Calcium ions required for calcite formation need to be transported from the external medium to the coccolith vesicle, raising the question of compartmentation of calcium ions during its way through the cell to the growing coccolith. Current hypotheses suggest influx of calcium through plasma membrane calcium channels, uptake from the cytoplasm in peripheral cisternae of the smooth endoplasmic reticulum, and vesicular transport to Golgi cisternae. Further accumulation of calcium is thought to occur within Golgy cisterns and Golgi vesicles via a V-type H+-ATPase driven Ca2+/H+-exchange mechanism before the vesicles fuse with the coccolith vesicle [2].

In order to contribute to the understanding in organelle interactions during coccolith formation, we used STEM tomography of high pressure frozen and freeze substituted E. huxley as well as chemically fixed material. The coccolith vesicle is confluent with membrane bound cisterns of an organelle called the reticular body. STEM tomography reveal seams of peculiar 7-10 nm thick particles at the inner side of membranes of the reticular body, Golgi cisterns and Golgy vesicles (Figure 1) suggesting that the latter fuse with the reticular body. In early stages the coccolith vesicle is devoid of these particles, however, they can be found in later stages, suggesting that the reticular body contributes to the growth of the coccolith vesicle. The coccolith vesicles is always close to the nuclear envelope [3]. Only in late stages just before the extrusion of the coccolith into the external medium it is apart from the nucleus. In these cases we often find a second coccolith growing within a young coccolith vesicle. Cryofixation followed by freeze substitution revealed that the coccolith vesicle forms a close junction with the outer membrane of the nuclear envelope (Figure 2). Over a distance of 500 nm and more this junction maintains a constant gap of about 4 nm between the two membranes. This finding opens the possibility of another pathway of calcium ions required for coccolith formation. The nuclear envelope is continuous with endoplamic reticulum and is thus part of the large intracellular calcium store having a calcium concentration between 100 and 300 mM [4] and contains calcium release channels required for calcium signalling [5]. Therefore, we propose a model in which calcium ions from the endoplasmic reticulum are released at the site of the junction of the nuclear envelope with the coccolith vesicle causing a large local increase of calcium within the gap between the adjacent membranes, which facilitates quick uptake of calcium into the coccolith vesicle by a Ca2+/2H+ exchange mechanism [6].

[1] M. D. Iglesias-Rodriguez et al. (2008). Science, 320 (5874): 336-340

[2] C. Brownlee and A. Taylor (2004). In: Thierstein H.R., Young, J.R. (Eds.), Coccolithophores.

     From molecular processes to global impact. Springer, Berlin, Heidelberg. pp. 31-49,

[3] P. Westbroek et al (1989). J. Protozool. 36, 368-373.

[4] O.H. Petersen et al (1998). Cell Calcium 23, 87-90.

[5] O.V. Gerasimenko et al (1996) Eur. J. Physiol. 432, 1-6.

[6] L. Mackinder et. al. (2011). Environ. Microbiol. 13, 3250-3265.

Andreas ZIEGLER (Ulm, GERMANY), Xiaofei YIN, Erika GRIESSHABER, Lothar MIERSCH, Thorsten B. REUSCH, Paul WALTHER, Wolfgang W. SCHMAHL

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EMS General Council

EMS General Council

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Annual SCUR meeting

Annual SCUR meeting

14:00 - 15:10 Session 5. Oral communications.
15:10 - 16:00 Invited lecture 3: Bedside assessment of multiphoton fluorescence lifetime imaging - from morphology to biochemical state. Volker HUCK (Mannheim, GERMANY)
16:30 - 17:30 Session 5. Oral communications.
17:30 - 17:45 Announcement of the prizes and closing of the SCUR meeting.