היפוקסורקימל תילארשיה הדוגאה
Israel Society for Microscopy
th
May 13 th -14 th , 2014 |
| 2014 ,יאמב 13-14
The Maurice and Gabriela Goldschleger
Conference Foundation at the
Weizmann Institute of Science
The Irving and Cherna Moskowitz
Center for Nano and Bio-Nano Imaging at the Weizmann Institute of Science
The Russell Berrie Nanotechnology Institute (RBNI),
Technion

ISM 2014 - The 48th Annual Scientific Meeting of ISM
Weizmann Institute of Science, Rehovot
The conference lunch is provided by the generous sponsoring of Eisenberg
Bros. Ltd.
The conference evening Beer & Sushi snacks are provided by the generous sponsoring of El-Mul Technologies and
AVBA Hi Tech services Ltd.
The Maurice and Gabriela Goldschleger
Conference Foundation at the Weizmann Institute of Science.
The Irving and Cherna Moskowitz Center for Nano and Bio-Nano Imaging at the Weizmann Institute of
Science.
The Russell Berrie Nanotechnology Institute
(RBNI), Technion.
The Ilse Katz Institute for Nanoscale Science &
Technology, Ben-Gurion University of the Negev.

ISM 2014 - The 48th Annual Scientific Meeting of ISM
Weizmann Institute of Science, Rehovot
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2-5
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6-9
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10-11
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12-25
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26-39
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40-75
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76-105
- 1 -

ISM 2014 - The 48th Annual Scientific Meeting of ISM
Weizmann Institute of Science, Rehovot
th
MORNING SESSION
Materials + Life Sciences
Session Chair: Ofra Golani, Weizmann Institute
09:30 - 09:45
Ofra Golani (Weizmann Institute) –
Greetings
09:45 - 11:15
Aryeh Weiss (Bar-Ilan University) –
Introduction to Image Analysis and Processing
11:15 - 11:35
Session Chairs
11:35 - 12:20
12:20 - 13:05
13:05 - 14:00
Coffee Break
Life Sciences
Maayan Duvshani-Eshet,
Technion
Lior Liba (Faculty of Medicine -
Technion) -
Introduction to FIJI
Noga Kozer (Weizmann Institute) -
Introduction to CellProfiler
Lunch
AFTERNOON SESSION
Materials + Life Sciences
Materials Sciences
Yael Levi-Kalisman, Ben-Gurion
University
Uri Merhav (Volume Elements Ltd.) –
AVIZO: Making sense of 3D data - analysis and visualization techniques
Zahava Barkay (Tel-Aviv University) -
Introduction to EBSD
Session Chair: Ronit Popovitz-Biro, Weizmann Institute
14:00 - 14:45
14:45 - 15:30
Alex Berner (Technion) –
Spatial resolution in the SEM
Bruno Combettes (Andor) –
CCD camera in light microscopy
15:30 - 15:50
15:50 - 16:35
16:35 - 17:20
17:20
Coffee Break
Mhairi Crawford (Gatan) –
Introduction to TEM Cameras: CCD, CMOS and Direct Detection
Mauro Porcu (FEI) –
EDS spectroscopy: efficiency and applications of the FEI ChemiSTEM technology
Departure
- 2 -

ISM 2014 - The 48th Annual Scientific Meeting of ISM
Weizmann Institute of Science, Rehovot
08:30 - 09:30 Registration
PLENARY SESSION
Session Chair: Eyal Shimoni, ISM Chairperson
09:30 - 09:50
Michael Elbaum , Director of the Irving and Cherna Moskowitz Center for
Nano and Bio-nano Imaging, Weizmann Institute – Opening Remarks
Eyal Shimoni - Greetings & Presentation of the Lev Margulis Prize
09:50 - 10:35
10:35 - 10:55
10:55 - 11:40
Plenary Lecture: Angus I. Kirkland , University of Oxford, UK.
Understanding and Controlling Defects and Defect Dynamics in Carbon
Nanomaterials using Electron Microscopy
Coffee Break
Plenary Lecture: Clare M. Waterman
,
NIH, Bethesda Maryland, USA.
Using Quantitative Light Microscopy to Characterize the Cell Migration
Machinery
SOUND BITE SESSION
Session Chair: Maya Bar-Sadan, Ben-Gurion University
11:50 - 12:20 Posters Sound Bites
12:20 - 13:15
LIFE SCIENCES POSTERS
MATERIALS SCIENCE
POSTERS
VENDORS EXHIBITION
MICROGRAPH COMPETITION
ISM GENERAL ASSEMBLY
13:15 - 14:30
14:30 - 16:05
16:05 - 16:30
16:30 - 18:00
18:00 - 18:45
18:45
Lunch
PARALLEL SESSIONS
LIFE SCIENCES SESSION
MATERIALS SCIENCE SESSION
Coffee break
PARALLEL SESSIONS
LIFE SCIENCES SESSION
MATERIALS SCIENCE SESSION
Beer & Sushi + best poster & best micrograph nominations
Departure
- 3 -

ISM 2014 - The 48th Annual Scientific Meeting of ISM
Weizmann Institute of Science, Rehovot
Session Chair: Tzipi Cohen-Hyams, Technion
14:30 - 14:55
Dominique Chatain - Centre national de la recherche scientifique
(CNRS), France
Orientation Relationships of Cu Crystals on
α-Al2O3 Surfaces and Interface Morphology
14:55 - 15:15
Peri Landau - NRCN, Israel.
Deformation of As-fabricated and Helium Implanted 100nm-
Diameter Iron Nano-pillars
Invited
15:15 – 15:40
15:40 - 16:05
16:05 - 16:30
Lior Embon - Weizmann Institute of Science, Israel
Novel scanning SQUID-on-tip microscope for the imaging of magnetic phenomena at the nanoscale
Margulis
Daniel H. Rich - Ben Gurion University of the Negev, Israel
Probing Plasmonic Effects in GaAs/AlAs Core-shell Nanowires and InGaN/GaN Quantum Wells With Time-resolved
Cathodoluminescence
Invited
Coffee Break
Session Chair: Reshef Tenne, Weizmann Institute
16:30 - 16:55
16:55 - 17:15
** Session dedicated to the memory of Prof. Enrique Grünbaum **
Ilan Goldfarb - Tel Aviv University, Israel
My Last Work With Enrique –
Ge-Mediated Growth of Si On GaAs(001)
Adi Pantzer - Ben Gurion University of the Negev, Israel
Quantitative dopant mapping in silicon nanostructures by offaxis electron holography
17:15 - 17:35
17:35 - 18:00
Roy Shiloh - Tel Aviv University, Israel
Shaping electron beams
Wayne D. Kaplan - Technion, Israel
Equilibrium States at Interfaces: Combining Interface
Reconstruction and Adsorption
18:00 - 18:45
18:45
Beer & Sushi + Best Poster & Best Micrograph Nominations
Departure
Invited
Margulis
Invited
- 4 -

ISM 2014 - The 48th Annual Scientific Meeting of ISM
Weizmann Institute of Science, Rehovot
Session Chair: Yuval Garini, Bar-Ilan University
14:30 - 14:55
Alexander D. Bershadsky - Weizmann Institute of Science, Israel
& and National University of Singapore, Singapore.
Aspects of Self-Organization of Actin Cytoskeleton
14:55 - 15:15
Ron Saar Dover - Weizmann Institute of Science, Israel
Peptidoglycan Ultra-Structure and Nano-Mechanics in Live
Streptococcus is Revealed by PeakForce AFM
Invited
15:15 - 15:40 Invited
15:40 - 16:05
16:05 - 16:30
Sergio Marco - Institute Curie, France
Towards The Computation Of 3D-Chemical-Maps And The 3D
Visualization of Thick (>750nm thick) Biological Specimens
Mira Barda-Saad - Bar Ilan University, Israel
Dynamic conformational change within signaling molecular complex essential for actin polymerization comes to life using novel triple color FRET technology
Coffee Break
Invited
Session Chair: Kinneret Keren, Technion
16:30 - 16:55
16:55 - 17:15
Eran Meshorer - Hebrew University of Jerusalem, Israel
A Library of Endogenously Tagged Fluorescent Proteins in
Embryonic Stem Cells: Uses and Insights
Noga Kozer - Weizmann Institute of Science, Israel
High Content (Phenotypic) Screening in the Israel National
Center for Personalized Medicine
17:15 - 17:35
17:35 - 18:00
Daniel Blumenthal - Ben Gurion University of the Negev, Israel
Universal Approach to FRAP Analysis of Arbitrary Bleaching
Patterns
Danny Porath - Hebrew University of Jerusalem, Israel
Charge Transport in single DNA-Based Molecules
18:00 - 18:45
18:45
Beer & Sushi + Best Poster & Best Micrograph Nominations
Departure
Invited
Invited
- 5 -

ISM 2014 - The 48th Annual Scientific Meeting of ISM
Weizmann Institute of Science, Rehovot
1.
Alexander Pekin, Vladimir Ezersky, Amit Kohn and Yuval Golan
Optical and Electrical Characterization Of Semiconducting Nanoparticles Using
Transmission Electron Microscopy
2.
Amir Gabay and Wayne D. Kaplan
Electromagnetic Field Assisted Sintering of SiC
3.
Ayala Elkayam, Dalit Stolovas and Amit Kohn
Mechanical Damage to Silicon Wafers Caused by Nanoindentation
4.
Eran Amsellem and Amit Kohn
Characterization of Magnetic Tunnel Junctions with Zn-doped MgO barriers
5.
Eran Aronovitch, Shai Mangel ,Lothar Houben and Maya Bar-Sadan
Atomic characterization of bi-metallic photocatalyst nanoparticles
6.
Eran Gros, Dana Benes Dahan and Wayne D. Kaplan
SiO
2
Reduction During Sintering of SiC
7.
Galit Atiya, V. Mikhelashvili, Gadi Eisenstein and Wayne D. Kaplan
From Microscopic to Macroscopic Degrees of Freedom at Interfaces
8.
Gili Shalev and Louisa Meshi
Structure Solution of Th-V-Al Intermetallide Using Electron Diffraction Tomography
Method
9.
Hadas Strenlicht and Wayne D. Kaplan
The Mechanisms of Grain Boundary Motion
10.
Elizaveta Kossoy, Haim Weissman and Boris Rybtchinski
Nano-spirals and Nano-fibers: Self-Assembly Controlled by Coordination of Transition
Metals
11.
Alex Laikhtman, Igor Lapsker, Alexey Moshkovich, Vladislav Perfilyev and Lev Rapoport
Study the Influence of Temperature and Vanadium Content on Stick-Slip Phenomena under Friction on CrV(x)N Coatings
12.
H. Jiang, H.S. Ubhi, J. Goulden and Keith Dicks
EBSD Analysis of Large Sample Areas
13.
Liron Reshef Steinberger, Tamilla Gulakhmedov, Zahava Barkay, Ana Dotan and Shachar
Richter
Mechanical Properties of Biodegradable Composite Plastic Made of Jellyfish
- 6 -

ISM 2014 - The 48th Annual Scientific Meeting of ISM
Weizmann Institute of Science, Rehovot
14.
Mahdi Halabi and Shmuel Hayun
Inversion parameter and cations distribution of non-stoichiometric magnesium aluminate spinel
15.
Meital Shviro, Shlomi Polani and David Zitoun
Bimetallic and Hollow Nanocrystals Through Galvanic Replacement Reaction
16.
Olga Brontvein, Daniel G. Stroppa, , Daniel Feuerman, Vishakantaiah Jayaram, Lothar
Houben, K. P. J. Reddy, Jeffrey M. Gordon and Reshef Tenne
New High-Temperature Pb-Catalyzed Synthesis of Inorganic Nanotubes
17.
Olga Kleinerman, Yachin Cohen and Yeshayahu Talmon
Direct Imaging of Carbon Nanotubes in Super-Acid Solutions and Liquid Crystalline
Phases
18.
Pradipta Sankar Maiti, Lothar Houben and Maya Bar-Sadan
Solution Phase Synthesis and Aberration Corrected High-resolution Electron Microscopy
Studies of Ultrathin CdS x
Se
1-x
2D Nanosheets
19.
Ruth Moshe and Wayne D. Kaplan
The Solubility Limit of SiO
2
in
α
-Alumina at 1600°C
20.
Sagi Appel, Ayala Cohen and Maya Bar-Sadan
High Yield Exfoliation and Restacking of Single Layers of MoS
2
and WS
2
21.
Shai Mangel, Eran Aronovitch, Lothar Houben and Maya Bar-Sadan
Quantitatively Following growth processes of CdSe@CdS core-shell particles on the atomic scale
22.
Katya Gotlib-Vainshtein, Olga Girshevitz, Chaim N. Sukenik, David Barlam and Sidney R.
Cohen
Force microscopy study of novel, layered hard film with intermediate cushion for enhancing scratch and wear resistance
23.
Udayabhaskararao Thumu, Tino Zdobinsky and Rafal Klajn
Post-Synthetic Modifications of Binary Self-assembled Superlattices
24.
Roy Shiloh, Yuval Tsur, Yossi Lereah, Boris A. Malomed, Vladlen Shvedov, Cyril
Hnatovsky, Wieslaw Krolikowski, and Ady Arie
Unveiling the Orbital Angular Momentum and Acceleration of Electron Beams
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ISM 2014 - The 48th Annual Scientific Meeting of ISM
Weizmann Institute of Science, Rehovot
25.
Anat Akiva, Karina Yaniv, Lia Addadi and Steve Weiner
Tracking Calcium Transport and Bone Mineralization During Larval Zebrafish Tail
Formation
26.
Anat Shperberg-Avni, Reinat Nevo, Ofra Golani, Sharon Wolf, Eyal Shimoni, Dror Noy and
Ziv Reich
Electron Microscopy Study of State Transitions in Cyanobacteria
27.
Dvir Gur, Ben Leshem, Dan Oron, Steve Weiner and Lia Addadi
When Bright Becomes Brighter; Amplification of the Structural Colors in the Koi Fish
28.
Gal Mor Khalifa, David Kirchenbuchler, Michael Elbaum, Jonathan Erez, Lia Addadi and
Steve Weiner
Calcium mineralization pathways in foraminifera
29.
Giuliano Bellapadrona and Michael Elbaum
Fluorescent and crystalline cellular bodies generated ex-novo in human cells
30.
Ilana Shtein and Rivka Elbaum
Root contraction mechanism in monocotyledons
31.
Leo Goldstien, Daniel Blumenthal and Levi A. Gheber
Tracking Of Nano-Carrier Particles For Directed Drug Delivery
32.
Luba Kolik and Dganit Danino
Mechanistic aspects in the one-dimensional self-assembly of diacetylenic phospholipid -
DC
8,9
PC into tubular structures
33.
Maor Ronen and Yeshayahu Talmon
Complexes of Charged Lipids and Oppositely Charged Polyelectrolytes Characterized by
Cryo-TEM
34.
Maayan Nir-Shapira, Naama Koifman and Yeshayahu Talmon
Immunogold Labeling of Phosphatidylserine Liposomes by Annexin V in Cryo-TEM
Specimens
35.
Maya Schnabel-Lubovsky, Dror Seliktar and Yeshayahu Talmon
Nano-Scale Cell-Matrix Interactions through Amorphous Hydrogel Polymeric Networks
36.
Nadav Elad, Lucía Chávez-Gutiérrez, Sam Lismont, Wim Hagen, Katrien Horré, Muriel
Arimon, Sarah Veugelen, Oksana Berezovska, Carsten Sachse and Bart De Strooper
The dynamic conformational landscape of γ-secretase is altered by an Alzheimer’s disease causing mutation
- 8 -

ISM 2014 - The 48th Annual Scientific Meeting of ISM
Weizmann Institute of Science, Rehovot
37.
Netta Vidavsky, Sefi Addadi, Eyal Shimoni, Katya Rechav, Andreas Schertel, Steve Weiner and Lia Addadi
The initial stages of calcium accumulation and deposition during the formation of sea urchin embryonic spicules
38.
Noa Katz, Sarah Goldberg, Aya Friedman and Roee Amit
Tracking Transcriptional Kinetics in E.coli Using Live Imaging of RNA
39.
Rotem Gura, Daniel Kaganovich and Jeremy England
Characterizing the Motion of Proteins in the Cytosol Using Live Imaging of Photo-
Convertible Fluorophores
40.
Sari Natan, Assaf Zaritsky, Inbal Hecht, Judith Horev, Miriam Shaharabany and Ilan Tsarfaty
Studying Met Induced Bio-Physical Mechanisms of In Vitro and In Vivo Tumor Cell
Motility
41.
Sharon Grayer Wolf, Lothar Houben and Michael Elbaum
Cryo-Tomography of Vitrified Bacterial and Human Cells by Scanning Transmission
Electron Microscopy
42.
Pamela C. Cabahug, Keren Nisani-Bizer and Shlomo Trachtenberg
The Molecular and Spatial Organization of Fib – The Core of the Bacterial Linear Motor of Spiroplasma melliferum BC3
43.
Shachar Sherman, Dikla Nachmias and Natalie Elia
Live Super-Resolution Cell Imaging: Developing a Correlative Spinning-Disk – Structured-
Illumination Assay
44.
Ludmila Abezgauz, Inbal Abutbul-Ionita, Ellina Kaselman and Dganit Danino
Nanoparticle-phospholipid interactions: control of stability and structure
- 9 -

ISM 2014 - The 48th Annual Scientific Meeting of ISM
Weizmann Institute of Science, Rehovot
Prof. Angus I. Kirkland
Department of Materials, Oxford University, Parks Road, Oxford, OX13PH, UK.
Graphene, Carbon nanotubes and related 1D and 2D carbon nanomaterials are currently attracting considerable interest, due to their novel electronic, mechanical and structural properties. This talk will report recent structural studies of various types of defects in these materials using high resolution aberration corrected electron microscopy.
I will firstly describe experimental evidence for atomic displacements associated with shear strain in single-walled carbon nanotubes (SWNTs). This data indicates the existence of a dominant non-uniform shear strain that varies along the SWNT axis. The direction of shear is opposite to that expected from a simple force applied perpendicular to the axis to produce the bending, highlighting the complex atomistic strain behavior of beam bending mechanics in highly anisotropic structures.
The movement of dislocations in crystals is the key mechanism for plastic deformation in all materials. I will show studies of dislocation dynamics in graphene recorded with single atom sensitivity and examine dislocation movement together with analysis of the associated strain fields. Step-wise dislocation movement along the zig-zag lattice direction is mediated by a single bond rotation and along the arm-chair direction through the loss of two carbon atoms.
The strain fields deform the graphene lattice by elongation and compression of C-C bonds, shear and lattice rotations.
Finally I will describe the control over both the location and complexity of defect formation in graphene by controlled exposure to a focused electron beam. Examples of stable defect configurations will be described together with mechanistic pathways by which these can relax to simpler structures through bond rotations and surface adatom incorporation.
- 10 -

ISM 2014 - The 48th Annual Scientific Meeting of ISM
Weizmann Institute of Science, Rehovot
Clare M. Waterman
NIH, Bethesda Maryland, USA.
We aim to understand how specific proteins self-organize into dynamic higher-ordered cellscale macromolecular ensembles that mediate the morphological and physical processes driving directed cell migration.
The ability of vertebrate cells to directionally move is mediated by dynamic physical processes: shape and stiffness changes, generation of pushing and pulling forces, and frictional and adhesive interactions between the cell and the ECM.
The primary organelles responsible for cell shape, stiffness, force generation and ECM adhesion are the cytoskeletal polymer systems, actin filaments (F-actin) and microtubules
(MTs), and integrin-based focal adhesions (FAs). Control of cell migration processes originates at the biochemical level of nanoscale protein-protein interactions within these organelles, which in turn are translated into physical phenomena at the cell scale.
Critically, the orchestration of the biochemical and physical events must be precisely coordinated in space and time; i.e., if the new FAs in the cell front dissolve before the old
FAs in the cell rear, the cell will not move directionally. Thus, understanding the molecular mechanisms mediating cell migration require an approach that allows spatial and temporal resolution of the biochemical activities of the F-actin and MT cytoskeletons and FAs and the physical processes that their dynamics produce.
We utilize high-resolution quantitative light microscopy combined with biophysical techniques that allow spatially and temporally resolved measurements of protein association/dissociation rates and mechanical outputs in living cells. Using this in combination with systems biology and candidate molecule approaches and in vitro biochemistry, we achieve important insight into the molecular mechanisms governing the morphodynamics of cell migration. We also develop novel and innovative technologies that allow us to approach key unanswered questions in cell migration, which can in turn be adopted by others and benefit the field as a whole.
- 11 -

ISM 2014 - The 48th Annual Scientific Meeting of ISM
Weizmann Institute of Science, Rehovot
2
3
Dominique Chatain
Aix-Marseille University, CNRS, CINaM, UMR 7325, 13288 Marseille, France chatain@cinam.univ-mrs.fr
Metallic crystals of sizes ranging from micrometers to nanometers, prepared on oxide substrates, are used in many technologically important applications, such as catalysts and optical devices. Numerous studies have been dedicated to the impact of the size of the crystals on their properties. In this presentation, we focus on the orientation relationship (OR) of metallic particles on oxide surfaces and on the morphology of the interface between the oxide substrate and the metallic particle.
Interface structure characterizations at the macroscopic and the atomistic scales were performed by electron and near-field microscopies on submicron copper crystals equilibrated on different sapphire substrate orientations: (c(0001), a(11-20), r(1-102) and m(1-100)). The energetics of the interface and its anisotropy, the ORs, and the interface and triple line shapes were investigated to explain the particular and recurrent crystallographic alignments of copper and sapphire crystals.
We find that only two types of ORs are observed, and that unstable sapphire surfaces develop the same ORs as those that occur on stable sapphire substrates.
- 12 -

ISM 2014 - The 48th Annual Scientific Meeting of ISM
Weizmann Institute of Science, Rehovot
Peri Landau a,b , Qiang Guo b,c , Peter Hosemann d , Yongqiang Wang e , Julia R. Greer b,f a Department of Physics, NRCN, P.0.Box 9001, Beer Sheva, Israel 84190 b Department of Materials Science and Applied Physics, California Institute of Technology, 1200
East California Boulevard, Pasadena, CA, USA, 91125. c State Key Laboratory of Metal Matrix Composites, Shanghai Jiao Tong University, 800 Dongchuan
Road, Shanghai, P.R. China, 200240 d Department of Nuclear Engineering, University of California at Berkeley, Berkeley, CA, USA,
94720. e Ion Beam Materials Laboratory, Los Alamos National Laboratories, Los Alamos, NM, USA, 87545 f The Kavli Nanoscience Institute, California Institute of Technology
Ferritic and ferritic-martensitic steels are being considered for structural materials in the next generation nuclear reactors. For these applications, helium (He) accumulation due to the high appmHe/dpa ratio, represent a matter of concern rooted in the detrimental effects of irradiation on the mechanical performance. The investigations of the effects of ion beam irradiation on mechanical properties of iron represent a useful way to simplify the complexity of irradiation process. This study is focused on the mechanical response of nanometer-sized bcc iron pillars and the effects of mostly He bubbles on the mechanical behavior and deformation mechanisms.
<101>-oriented cylindrical single crystalline Fe samples with diameters of 100nm and heights of 1
µ m were uniformly implanted with 0.36±0.06 at. % helium throughout their gauge sections to produce 1.5nm-diameter He bubbles (Figure 1). Uniaxial compression tests were performed in a Hysitron Triboscope nanoindenter equipped with an 8μm-diameter diamond flat punch tip, operated under load controlled conditions at a nominally constant prescribed loading rate. In-situ uniaxial nano-tension experiments were performed in InSEM, a custom-built nano-mechanical instrument, comprised of a scanning electron microscope
(FEI Quanta200TM FEG) and a nanomechanical module similar to the nanoindenter
(Nanomechanics, Inc.) at a constant nominal strain rate of
∼
1 × 10-3s
-1
through a customwritten feedback loop. Selected implanted nano-pillars were lifted away from the substrate and glued onto the TEM grids by W deposition for microstructural analysis. Site-specific microstructural characterization was performed in a FEI TecnaiTM TF20 transmission electron microscope on the individual pillars. He bubble size and distribution was examined by through-focus imaging.
Uniaxial deformation experiments revealed a 40% higher yield and ultimate strengths in tension and a 25% higher yield strength and flow stress at 10% plastic strain in compression for implanted samples compared with as-fabricated ones. Observed tension-compression asymmetry in implanted pillars was attributed to the non-planarity of screw dislocation cores, to twinning-antitwinning deformation typical of bcc metals and the interaction between dislocations and He bubbles.
- 13 -

ISM 2014 - The 48th Annual Scientific Meeting of ISM
Weizmann Institute of Science, Rehovot
Compressive stress-strain data in both sets of samples had three distinct regimes: (1) elastic loading followed by (2) discrete strain bursts during plastic flow with significant hardening up to strains of 5%, and (3) “steady state” discrete plasticity characterized by nearly-constant average flow stress. Each regime is discussed and explained in terms of competition in the rates of dislocation multiplication and dislocation annihilation.
Figure 1. (a) A SEM image of a typical over-plated 100nm-diameter Fe nano-pillar at an orientation that shows the shape and contour of the pillar's triangular-prismatic top. The facets in the top prism are inclined at ~45º to the pillar axis. (b) Bright field TEM image of a
Fe nano-pillar with the corresponding diffraction pattern. The pillar axis is close to the [101] direction. (c) Under-focus image of He bubbles that appear as bright dots with a dark fringe.
(d) Over-focus image of He bubbles that appear as dark dots with a bright fringe. The He bubbles form a herring-bone-like arrangement parallel to {110} planes throughout the pillar height. (e) Over-focus image of He bubbles at an orientation ~90º away from the orientation in (d) where the rectangular facet of the prism-shaped head is perpendicular to the electron beam, showing a uniform distribution of bubbles throughout the pillar height. A few bubbles are pointed to by the arrows in the image.
- 14 -

ISM 2014 - The 48th Annual Scientific Meeting of ISM
Weizmann Institute of Science, Rehovot
Lior Embon, Yonathan Anahory, Denis Vasyukov, Dorri Halbertal, Jo Cuppens, Yuri
Myasoedov, Michael L. Rappaport, Martin E. Huber, and Eli Zeldov
Department of Condensed Matter Physics, Weizmann Institute of Science, Rehovot, Israel
Achieving the level of sensitivity required for detecting the magnetic signal of a single electron is a “holy grail” of magnetic imaging. Superconducting QUantum Interference
Devices (SQUIDs), which were traditionally the most sensitive magnetometers, could not hitherto reach this goal due to their relatively large effective size (of the order of 1µm).
We have developed a scanning magnetic probe microscope based on a nanoSQUID which is fabricated on the apex of a sharp quartz tip. We pull a quartz tube into a pipette with a controlled diameter down to 50 nm and deposit a thin superconducting film onto the sides and the apex of the pipette. Using this process we form SQUIDs which are not only the smallest to date, but also have the unique advantage of being geometrically ideal for scanning probe microscopy.
Figure 1 - From the left: The SQUID geometry - a superconducting ring interrupted by two weak links. Schematic illustration of the pulled quartz tube with two gold electrodes connected to the superconducting leads. Inset – The superconducting ring on the apex with the two bridges between the leads forming two weak links. Two scanning electron microscope images of lead SOTs with effective diameters of
∅
56 nm and
∅
160 nm.
The SQUID-on-tip (SOT) based system possesses a record combination of high sensitivity, spatial resolution and operable magnetic fields together with a geometry which applies no constraints on the sample-probe distance. Our SQUIDs can operate at liquid
4
He temperatures in applied magnetic fields of up to 1 T, be made as small as 50 nm, and display an extremely low flux noise of 50 n
Φ
0
/Hz
1/2
. This corresponds to a record breaking spin sensitivity of
0.4 µ
B
/Hz
1/2
, about two orders of magnitude better than any previous SQUID and sufficient for the detection of the magnetic moment of a single electron [1].
The SOTs are mounted on a specially built scanning microscope which utilizes tuning fork based AFM feedback to bring the SOT to a scanning distance of only a few nanometers away from the sample. We can move our SOT coarsely within a range of a few millimeters and scan areas of up to 30
×
30 µm
2
.
- 15 -

ISM 2014 - The 48th Annual Scientific Meeting of ISM
Weizmann Institute of Science, Rehovot
Using these newly acquired capabilities we can directly image a wide range of nano-scaled magnetic phenomena which were completely out of reach up until now. My research focus is the investigation of vortices in type-II superconductors. I will show some results of this study, unravelling the static and dynamic behavior of these quantum entities under various conditions.
Figure 2 - Vortices in a superconducting hour-glass shaped lead film (50 nm thick) at 4.2 K as imaged by the scanning SQUID-on-tip microscope. All four images show the same area of
12
×
12 µm
2
. The bottom images show superconducting vortices penetrating the film in an external magnetic field of 27 G (left) and 54 G (right). The top images show the behavior of the vortex matter at the same fields in the presence of an applied current through the film
(from right to left). The current exerts a Lorentz force on the vortices (from bottom to top) resulting in instabilities, bifurcations, and channels along which the vortices flow at ultrasonic velocities.
1.
D. Vasyukov, Y. Anahory, L. Embon, D. Halbertal, J. Cuppens, L. Neeman, A. Finkler, Y.
Segev, Y. Myasoedov, M. L. Rappaport, M. E. Huber, and E. Zeldov, A scanning SQUID with single electron spin sensitivity. Nature Nanotech. 8, 639 (2013).
- 16 -

ISM 2014 - The 48th Annual Scientific Meeting of ISM
Weizmann Institute of Science, Rehovot
Daniel H. Rich
Department of Physics and The Ilse Katz Institute for Nanoscale Science and Technology, Ben-
Gurion University of the Negev, P.O.B 653, Beer-Sheva 84105, Israel, Email: danrich@bgu.ac.il.
An important focus in III-V nanowire research is the design of plasmonic metal/semiconductor composite structures to obtain novel optical device properties for applications in biological labeling/sensing, light-emitting diodes, lasers, and solar cells. With an appropriate choice of metal, possessing a surface plasmon frequency that is sufficiently close to the excitonic transition energy of the semiconductor, exciton coupling to surface plasmon polaritons (SPPs) can be enhanced. The coupling of excitons to SPPs in metalcoated GaAs/AlAs/GaAs core-shell nanowires and InGaN/GaN quantum wells (QWs) was probed using time-resolved cathodoluminescence (CL) on a SEM [1]. The GaAs/AlAs/GaAs nanowires and InGaN/GaN QWs were grown by molecular beam epitaxy (MBE) in separate systems. The nanowires were grown using the self-assisted VLS method on Si(111) [2].
Uniform diameter GaAs nanowires were grown with a high aspect ratio with no significant tapering and a pure zinc-blende structure, as revealed by TEM. Au, Al, and Ag films were deposited at near normal incidence onto the QW and nanowire samples at room temperature.
The surface roughness was studied with high resolution SEM and AFM. Excitons were generated in the metal-coated QWs and nanowires by injecting a pulsed high-energy electron beam through the thin metal films. Due to the opacity of the metal with respect to light/laser excitation from the top surface, CL is shown to be a particularly useful probe for the metal/QW and metal/nanowire samples (as well as for other metal-coated nanostructure systems) in that the high-energy electron beam can easily penetrate the metal films and create excess e h pairs in the semiconductor. The variable distance from the surface, at which excitons recombine, results in a range in the expected Purcell enhancement factor ( F p
) which describes the enhanced radiative recombination rate due to coupling of the excitons to the
SPP modes of the metal film. The SPPs can be converted to free-space photons if the propagating SPPs in the thin metal film are scattered by the surface/interface roughness or grain boundaries of the polycrystalline metal film, owing to the momentum change associated with the scattering that enables a matching with the
ω
vs k light dispersion relation. The
Purcell enhancement factor ( F p
) was obtained by direct measurement of changes in the temperature-dependent decay and radiative lifetimes caused by the exciton-SPP coupling. In order to analyze the coupling, we have developed a model for the average F p
in the Au and
Al covered nanowires by taking into account the dependence of F
P
on the distance from the metal film and the thickness of the film covering the nanowires possessing various crosssectional shapes [1]. The present study suggests a more general approach for treating metalcovered nanostructures and QWs in which exciton diffusion in the mesoscopic regime can influence the observed plasmonic effects.
References:
1.
Y. Estrin, D. H. Rich, A. V. Kretinin, and H. Shtrikman, Nano Lett. 13, 1602 (2013).
2.
P. Krogstrup, R. Popovitz-Biro, E. Johnson, M. Hannibal Madsen, J. Nygård and H.
Shtrikman, Nano Lett. 10, 4475 (2010).
- 17 -

ISM 2014 - The 48th Annual Scientific Meeting of ISM
Weizmann Institute of Science, Rehovot
Ilan Goldfarb 1 , Jose Louis Azar 2 , Amir Grisaru 2 , Enrique Grunbaum 2 RIP and Menachem
Nathan 2
1 Department of Materials Science and Engineering
2 Department of Physical Electronics, School of Electrical Engineering f aculty of Engineering, Tel Aviv University, Ramat Aviv, Tel Aviv 6997801, Israel
Epitaxial quality of Ge and Si-cap layers on GaAs(001) were investigated in situ by reflection high energy electron diffraction during growth and, subsequently, by scanning electron and scanning probe microscopy. Ge was grown on a (1
×
1)-GaAs(001) surface prepared by oxide desorption at 580°C in an As-free ultra-high vacuum. Its morphology, varying from reasonably flat layers with only atomic scale roughness to relatively large three-dimensional asperities, was found to crucially depend on the GaAs surface quality and growth temperature. The data presented in this work also accounts for the apparent discrepancies between various groups regarding the Ge/GaAs reconstruction; our detailed analysis proves that, at least under the experimental conditions described below, it is a mixture of (1
×
2) and
(2
×
1), rather than a (2
×
2) or c(2
×
2). Smooth Si growth was mainly impeded by a large lattice mismatch with the underlying Ge, initially replicating the Ge layer’s morphology and eventually forming discrete three-dimensional islands and continuous undulations. The study shows that flat epitaxial Si capping of GaAs should be possible by employing graded silicongermanium buffers.
Figure 1. Pre-growth evolution of GaAs(001) surface with annealing temperature.
References:
1.
I. Goldfarb, J.L. Azar, A. Grisaru, E. Grunbaum, M. Nathan, J. Appl. Phys. 93(5),
3057-3062 (2003).
- 18 -

ISM 2014 - The 48th Annual Scientific Meeting of ISM
Weizmann Institute of Science, Rehovot
Adi Pantzer a,b , Atsmon Vakahy b , Dror Horvitz b , Zohar Eliyahou Z”L a , Roie Yerushalmi c and Amit Kohn a a Department of Materials Engineering and Ilse Katz Institute for Nanoscale Science and
Technology, Ben-Gurion University of the Negev, Beer-Sheva 8410501, Israel b Micron Semiconductors Israel Ltd., Qiryat-Gat 82109, Israel c Institute of Chemistry and the Center for Nanoscience and Nanotechnology, The Hebrew
University of Jerusalem, Edmond J. Safra Campus, Givat Ram, Jerusalem, 91904, Israel.
Modern semiconductor devices function due to accurate dopant distribution at the nanoscale.
Off-axis electron holography (OAEH) in the transmission electron microscope (TEM) can map quantitatively the electrostatic potential in semiconductors with high spatial resolution 1,2 .
For the microelectronics industry, ongoing reduction of device dimensions, 3D device geometry, and failure analysis of specific devices require preparation of thin TEM samples, under 70 nm thick, by focused ion beam (FIB). Such thicknesses, which are considerably thinner than the values reported to date in the literature, are challenging due to FIB induced damage, surface depletion effects
3
, and low measurement signal.
Here, we report on quantitative dopant mapping of silicon PN nanostructures in the form of implanted junctions and nanowires. TEM samples were prepared in the FIB completed by low-energy (5 keV) ion milling, which reduced Si amorphization to 10 nm thick. Additional perpendicular FIB sectioning of the implanted junctions enabled a direct measurement of the
TEM sample thickness in order to determine accurately the crystalline thickness of the sample. Consequently, we find that the low-energy milling also resulted in a negligible thickness of electrically inactive regions, approximately 4 nm thick. The influence of TEM sample thickness, FIB induced damage and doping concentrations on the accuracy of the
OAEH measurements were examined by comparison to secondary ion mass spectrometry measurements as well as to 1D and 3D simulations of the electrostatic potentials 4,5 , see Fig. 1.
In the case of silicon nanowires, the unique vertical doping required cross-sectional preparation by the FIB in order to map the PN junction
5
, see Fig.2.
We conclude that OAEH measurements resulted in accurate determination of the potential variations in nanostructured Si-based PN junctions, for the doping levels examined here, in
TEM samples down to 50nm thick
6
.
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ISM 2014 - The 48th Annual Scientific Meeting of ISM
Weizmann Institute of Science, Rehovot
Figure 1. Comparison of potential profiles across the implanted PN junction derived from OAEH for TEM samples varying in thickness between 20 and 100nm to energy band potential measured by SIMS (1D-simulation).
Figure 2. Demonstrated experimental methodology on Si Nanowire: (a) Bright-field TEM image of the Si NW sample. (b) Thickness map calculated from energy-filtered TEM images.(c)
Thickness of the sample along the direction denoted in (b) in units of inelastic mean free path.(d)
Electron hologram.(e) Reconstructed phase image.(f) Potential profile extracted and calculated perpendicular to the junction along the direction denoted in (e).
References:
1. M. R. McCartney, David J. Smith et al ., Physical Review Letters 89 , 025502 (2002).
2. Bill Taylor, Martha R. McCartney et al ., Microscopy Microanalysis 12 , 295 (2006).
3. David Cooper et al ., Ultramicroscopy 108, 488 (2008).
4. IH. Tan, G.L. Snider et al ., Journal of Applied Phy sics 68 , 4071(1990); TCAD Sentaurus,
Synopsys, Inc., Mountain View, CA, (2012).
5. O. Hazut, R. Yerushalmi, A. Pantzer, A. Kohn et al ., submitted
6. A. Pantzer, D. Horvitz, A. Kohn et al , Dopant mapping in thin FIB prepared silicon samples by off-axis electron holography, Ultramicroscopy 138, 36 (2014).
- 20 -

ISM 2014 - The 48th Annual Scientific Meeting of ISM
Weizmann Institute of Science, Rehovot
Roy Shiloh, Yossi Lereah, Yigal Lilach, and Ady Arie
Department of Physical Electronics, Fleischman Faculty of Engineering, Tel Aviv University, Tel
Aviv 6997801, Israel
Electron beams, such as those used in the electron microscope, behave similarly to light beams. This similarity demands the application of knowledge and experience gained in optics to electron microscopy; simply put, in our research1 we wield electrons as one would light beams – using thin membranes as sophisticated optical elements
2
.
Electron beams are extensively used in microscopy, material studies and lithography. Today, beams are mainly shaped using magnetic or electric forces, allowing only simple shaping tasks such as focusing or scanning. Popular shaping methods used in phase microscopy include the well-known Hilbert and Zernike phase-plates
3,4
where recently complex shapes
5–8 were achieved using binary amplitude gratings. The ability to manipulate the shape of the electron-microscope’s beam is very important since it may enable us to apply well-based light-optics techniques to the microscope. We may envision some examples, including: structured illumination, a paradigm which is the basis for quantitative phase microscopy; super-resolution, a principle used to perform measurements beyond the diffraction limit; diffractive optical elements, that may be fashioned as lenses, high-order Zernike phase masks and computer-generated holograms - in general, giving us nearly-arbitrary control of the beam’s wavefront.
As part of our research, we strive to show that electron-beam shaping should not be an exotic field as it is currently considered. We demonstrate our shaping ideas by precise patterning of thin Silicon-Nitride (SiN) membranes: rather than applying electromagnetic forces, the beam is controlled by spatially modulating its wavefront. Much like light waves passing through glass and acquiring a phase-shift dependent on the material's refractive index, an electron passing through a SiN membrane will similarly accumulate a phase factor directly related to the thickness of the interacting material according to
9 ϕ =
2
π
λ
( n
−
1
) t
=
2
π
λ eU i
E
0
+
E
E 2 E
0
+
E t where
λ
is the electron's wavelength, E
0
and E are the electron's rest and kinetic energy, respectively, and e is the electron's charge. Upon choosing the material (hence the inner potential U i
), the variable quantity is the thickness t . A relatively thin film is sufficient, e.g. for a 200 keV electron, the required thickness to generate a
π
-phase shift is 42nm. The scattering through this film is fairly low (several percentages, depending on mode of operation) and may be considered a nearly pure phase plate for our purposes. We present several experimental examples from two of our papers: in the first
1
, we encode two computer-generated holograms: the letters “TAU” and a model of the atom with electrons circling a nucleus. These examples, depicted in Fig.1, include micrographs of the spatial thickness modulation in the insets. The holograms in this case were placed on the sample holder and designed to appear in the diffraction plane. In the second
2
, we investigate special beams from light optics – vortex and Airy beams – in the electron microscope. Vortex beams have already been intensively investigated in light optics, and recently some applications in
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ISM 2014 - The 48th Annual Scientific Meeting of ISM
Weizmann Institute of Science, Rehovot electron microscopy, such as magnetic chiral dichroism measurements
10
and manipulation of nano-particles
11
, have been suggested.
Our concepts may be utilized by scientists in various disciplines for advanced electron microscopy, through the design and fabrication of complex amplitude- or phase-plates for conditioning of the beam prior to specimen interaction, or the filtering of the beam (scattered or unscattered) post-specimen. One of the great advantages of our method is the ability to predict and generate a desired wavefront in the back-focal plane of a magnetic lens by manipulating it in the image plane, thus avoiding damage and charging effects to our phase plate, in contrast to Zernike phase plates, for example, which are placed in the back-focal plane and are prone to such problems
3
.
Figure 1. On-axis holograms: (A) “TAU” hologram produced by the mask in (B); inset: magnification showing ~60nm holes composing the pixels. (C) Electrons orbiting a nucleus hologram produced by the mask in (D); inset: magnification showing the centre of the mask.
Note: contrast and brightness levels in (C) were altered for visibility. *Patent pending.
References:
1.
Shiloh, R., Lereah, Y., Lilach, Y. & Arie, A. Sculpturing the Electron Wave Function.
13 (2014). at <http://arxiv.org/abs/1401.7174
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ISM 2014 - The 48th Annual Scientific Meeting of ISM
Weizmann Institute of Science, Rehovot
2.
Shiloh, R. et al.
Unveiling the orbital angular momentum and acceleration of electron beams. (2014). at <http://arxiv.org/abs/1402.3133>
3.
Danev, R. & Nagayama, K. Transmission electron microscopy with Zernike phase plate. Ultramicroscopy 88, 243–52 (2001).
4.
Nagayama, K. Another 60 years in electron microscopy: development of phase-plate electron microscopy and biological applications. J. Electron Microsc. (Tokyo).
60
Suppl 1, S43–62 (2011).
5.
Verbeeck, J., Tian, H. & Schattschneider, P. Production and application of electron vortex beams. Nature 467, 301–304 (2010).
6.
McMorran, B. J. et al.
Electron vortex beams with high quanta of orbital angular momentum. Science 331, 192–195 (2011).
7.
Voloch-Bloch, N., Lereah, Y., Lilach, Y., Gover, A. & Arie, A. Generation of electron Airy beams. Nature 494, 331–335 (2013).
8.
Saitoh, K., Hasegawa, Y., Hirakawa, K., Tanaka, N. & Uchida, M. Measuring the
Orbital Angular Momentum of Electron Vortex Beams Using a Forked Grating. Phys.
Rev. Lett.
111, 74801 (2013).
9.
Reimer, L. & Kohl, H. Transmission electron microscopy - physics of image formation . 587 (5th edition, {Springer}, 2008).
10.
Schattschneider, P., Löffler, S., Stöger-Pollach, M. & Verbeeck, J. Is magnetic chiral dichroism feasible with electron vortices? Ultramicroscopy 136, 81–5 (2014).
11.
Verbeeck, J., Tian, H. & Van Tendeloo, G. How to manipulate nanoparticles with an electron beam? Adv. Mater.
25, 1114–7 (2013).
- 23 -

ISM 2014 - The 48th Annual Scientific Meeting of ISM
Weizmann Institute of Science, Rehovot
Wayne D. Kaplan
Technion, Israel
Since the 1980s it has been recognized that grain boundaries can adopt a diffuse structural nature, characterized by a ~1nm thick disordered film [1]. More recently, the structure of grain boundaries has been described using diffuse interface theory, stating that the structure and chemistry of grain boundaries, interfaces and surfaces can go through two dimensional transitions between thermodynamic states (termed complexions) in order to minimize the interface energy [2]. As such, complexions for interfaces are analogous to phases in the bulk, although they are not bulk phases since they can’t exist without an adjacent bulk phase(s). In the past these conclusions were reached based on structural and chemical characterization of grain boundaries and interfaces correlated with properties [3], and more recently it has been shown that specific complexions can have a significant influence on grain boundary mobility, and thus the morphology of an evolving microstructure [4].
To date, almost all of these studies have been conducted at grain boundaries in single phase polycrystalline systems, which by definition are not at equilibrium, and in some cases it is not even clear if the identified complexions are at steady-state. Similar questions have been raised for studies on interfaces from thin film studies, where the deposition process used to form the samples may be very far from equilibrium.
This presentation will focus on an experimental approach to address the structure, chemistry, and energy of complexions at metal-ceramic interfaces which are fully equilibrated, from which it can be demonstrated that a change in complexion reduces interface energy (figure 1)
[5,6]. This will be compared with complexions at solid-liquid interfaces, where a region of ordered liquid exists adjacent to the interface at equilibrium (figure 2) [7-10], and the details of a reconstructed solid-solid interface where the
2.5 3 2.5 3 R30
reconstructed interface structure accommodates lattice mismatch for a nominally incoherent interface [11]. These three systems will be compared to known reconstructed solid surfaces, which can also be described as complexions, within a more generalized Gibbs adsorption isotherm.
Figure 1. Aberration corrected TEM micrograph (Cs~-5
µ m) of an equilibrated interface between a gold particle and a (0001) sapphire substrate. A 1.2nm thick intergranular film
(complexion) has equilibrated at the interface.
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ISM 2014 - The 48th Annual Scientific Meeting of ISM
Weizmann Institute of Science, Rehovot
Figure 2. Cs corrected (Cs=-
2.4μm) TEM micrograph of a liquid Al droplet located at the surface of solid Al
2
O
3
. The micrograph was acquired at T=750°C. The inset is the intensity line-scan perpendicular to the Al-Al
2
O
3
interface from the region marked on the micrograph by a black rectangle.
References:
1. D.R. Clarke, On the Equilibrium Thickness of Intergranular Glass Phases in Ceramic Materials,
Journal of the American Ceramic Society 70[1]:15-22 (1987).
2. M. Tang, W.C. Carter, R.M. Cannon, Grain Boundary Order-Disorder Transitions, Journal of
Materials Science, 41[23]:7691-7695 (2006).
3. R.H. French, H. Mullejans, D.J. Jones, G. Duscher, R.M. Cannon, M. Ruhle, Dispersion forces and
Hamaker constants for intergranular films in silicon nitride from spatially resolved-valence electron energy loss spectrum imaging, Acta Materialia, 46[7]:2271-2287 (1998).
4. S.J. Dillon, M.P. Harmer, Relating grain-boundary complexion to grain-boundary kinetics I:
Calcia-doped alumina, Journal of the American Ceramic Society, 91[7]:2304-2313 (2008)
5. M. Baram, D. Chatain, W.D. Kaplan, Nanometer-Thick Equilibrium Films: The Interface Between
Thermodynamics and Atomistics, Science, 332[6026]:206-209 (2011).
6. H. Sadan, W.D. Kaplan, Au-Sapphire (0001) Solid-Solid Interfacial Energy, Journal of Materials
Science, 41[16]:5099-5107 (2006).
7. S.H. Oh, Y. Kauffmann, C. Scheu, W.D. Kaplan, M. Ruhle, Ordered Liquid Aluminum at the
Interface with Sapphire, Science, 310[5748]:661-663 (2005).
8. S.H. Oh, M.F. Chisholm, Y. Kauffmann, W.D. Kaplan, W. Luo, M. R?hle, C. Scheu, Oscillatory
Mass Transport in Vapor-Liquid-Solid Growth of Sapphire Nanowires, Science, 330: 489-493 (2010).
9. Y. Kauffmann, S.H. Oh, C. T. Koch, A. Hashibon, C. Scheu, M. Ruhle, W.D. Kaplan, Quantitative analysis of layering and in-plane structural ordering at an alumina-aluminum solid-liquid interface,
Acta Materialia, 59[11]:4378-4386 (2011).
10. M. Gandman, Y. Kauffmann, C. T. Koch, W.D. Kaplan, Direct Quantification of Ordering at a
Solid-Liquid Interface Using Aberration Corrected Transmission Electron Microscopy, Physical
Review Letters, 110[8]:086106 (2013).
11. H. Meltzman, D. Mordehai, W.D. Kaplan, Solid–Solid Interface Reconstruction at Equilibrated
Ni–Al2O3 Interfaces, Acta Materialia, 60[11]:4359-4369 (2012).
- 25 -

ISM 2014 - The 48th Annual Scientific Meeting of ISM
Weizmann Institute of Science, Rehovot
Alexander D. Bershadsky
Weizmann Institute of Science, Rehovot, Israel, and Mechanobiology Institute, National University of Singapore, Singapore.
Here, we address the processes of actin cytoskeleton self-organization driven by myosin II contractility at the local and global levels. Locally, the cytoplasm comprises a multi-nodal actomyosin network formed by small asters of actin filaments nucleated by DAAM1 formin and stabilized by the actin crosslinking protein filamin A. The asters are connected with each other by myosin II, so that the entire system forms extensive contractile network responsible for the maintenance of the cell shape. Globally, upon spreading on planar substrates, cells develop chiral arrays of actin filament bundles. In human fibroblasts plated on fibronectincoated circular islands, the process started with formation of a radially symmetrical actin pattern. Radial fibers (RFs) grew centripetally from peripheral focal adhesions in a formindependent fashion, while transverse fibers (TFs) moved centripetally along the RFs. The transverse fibers, which contain myosin IIA and consist of actin filaments with opposite polarity, are the structural elements solely responsible for the generation of contractile forces in the entire system. The radial pattern evolved spontaneously into a novel chiral pattern as a result of synchronous tilting of all RFs in the same direction and acquiring by TFs movement of a tangential component. We propose a novel mechanism of myosin IIA-driven retrograde flow where contractile stresses within transverse fibers drive their movement along radial fibers and promote the actin polymerization-dependent growth of radial fibers.
Computational modeling demonstrated that this mechanism explains the evolution of the radial pattern into the chiral pattern. Remarkably, the chiral pattern is characterized by a leftright asymmetry (handedness). We show that the sign of chirality can be regulated by actinassociated protein, alpha-actinin-1. Thus, self-organization of the actin cytoskeleton provides built-in machinery that potentially allows cells to distinguish between left and right.
- 26 -

ISM 2014 - The 48th Annual Scientific Meeting of ISM
Weizmann Institute of Science, Rehovot
Ron Saar Dover, Arkadi Bitler, Eyal Shimoni and Yechiel Shai
Department of Biological Chemistry, Department of Chemical Research Support
The Weizmann Institute of Science, Rehovot, Israel
Gram-positive bacteria are surrounded by a thick peptidoglycan layer that is strong and elastic, and determines the cell’s shape and mechanics. Peptidoglycan (PG) is comprised of linear glycan strands, made of GlcNAc-MurNAc disaccharides repeats that are connected by
short elastic peptides
1
. These building blocks construct a complex polymer, which cannot be crystallized and is not accessible to direct ultra-structural characterization
2
. Current structural models relay on indirect methods (chemical analysis
1
and NMR
3-5
). Recent advancement in high-resolution microscopy (AFM
6-8
and cryo-EM
9
) enabled direct visualization of the largescale PG architecture, and revealed that PG in elongated bacteria (rods and ovococci) is arranged around the cell’s long axis, probably to enable higher resistance to hoop stress
10
.
Yet, in the absence of high-resolution data, contradicting models were developed, postulating that PG either forms large helical ring-like cables
6,8
or arranged in a more uniform layered manner
7,9
.
Live-cell AFM enables to image the intact structure of surface PG8. We used a novel PFT-
AFM technique which offers high force sensitivity, minimal sample damage and improved spatial resolution10. In addition, simultaneous recording of individual tip-sample interaction using a quantitative nanomechanical mapping (QNM) mode generates detailed maps of surface mechanics11,12, and enabled to study how the PG structure affects its function in live group B streptococcus (GBS) (Fig. 1A). We report a new net-like arrangement formed by parallel cross-linking of strands into wider bands (Fig. 1B). We demonstrate how the peptidoglycan net expends and stiffen to restrict the cell swelling under high turgor pressure.
Peptidoglycan degradation destroyed the net-structure and remarkably enabled a first direct high-resolution characterization of single unstretched helical strands (Fig. 1C).
Understanding the basic structure of PG may allow future development of antibacterial therapeutics and bio-inspired nano-polymers.
- 27 -

ISM 2014 - The 48th Annual Scientific Meeting of ISM
Weizmann Institute of Science, Rehovot
Figure 1 . Peptidoglycan structure in live bacteria. A . Imaging single-live streptococcus using PFT-AFM. B . Peptidoglycan forms a turgor-responsive net-like ultra -structure. C .
Peptidoglycan degradation exposes single strands with right-handed helical structure.
References:
1. Vollmer, W., Blanot, D. & de Pedro, M.A. Peptidoglycan structure and architecture. FEMS
Microbiol Rev 32, 149-67 (2008).
2. Turner, R.D., Vollmer, W. & Foster, S.J. Different walls for rods and balls: the diversity of peptidoglycan. Mol Microbiol 91, 862-74 (2014).
3. Sharif, S., Singh, M., Kim, S.J. & Schaefer, J. Staphylococcus aureus peptidoglycan tertiary structure from carbon-13 spin diffusion. J Am Chem Soc 131, 7023-30 (2009).
4. Kern, T. et al. Toward the characterization of peptidoglycan structure and protein-peptidoglycan interactions by solid-state NMR spectroscopy. J Am Chem Soc 130, 5618-9 (2008).
5. Kim, S.J., Singh, M., Preobrazhenskaya, M. & Schaefer, J. Staphylococcus aureus peptidoglycan stem packing by rotational-echo double resonance NMR spectroscopy. Biochemistry 52, 3651-9
(2013).
6. Hayhurst, E.J., Kailas, L., Hobbs, J.K. & Foster, S.J. Cell wall peptidoglycan architecture in
Bacillus subtilis. Proc Natl Acad Sci U S A 105, 14603-8 (2008).
7. Wheeler, R., Mesnage, S., Boneca, I.G., Hobbs, J.K. & Foster, S.J. Super-resolution microscopy reveals cell wall dynamics and peptidoglycan architecture in ovococcal bacteria. Mol Microbiol 82,
1096-109 (2011).
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ISM 2014 - The 48th Annual Scientific Meeting of ISM
Weizmann Institute of Science, Rehovot
8. Andre, G. et al. Imaging the nanoscale organization of peptidoglycan in living Lactococcus lactis cells. Nat Commun 1, 27 (2010).
9. Beeby, M., Gumbart, J.C., Roux, B. & Jensen, G.J. Architecture and assembly of the Gram-positive cell wall. Mol Microbiol 88, 664-72 (2013).
10. Dufrene, Y.F., Martinez-Martin, D., Medalsy, I., Alsteens, D. & Muller, D.J. Multiparametric imaging of biological systems by force-distance curve-based AFM. Nat Methods 10, 847-54 (2013).
11. Pittenger, B., Erina, N. & Su, C. Quantitative Mechanical Property Mapping at the Nanoscale with
PeakForce QNM. Application Note, Veeco Instruments Inc (2010).
12. Alsteens, D., Trabelsi, H., Soumillion, P. & Dufrene, Y.F. Multiparametric atomic force microscopy imaging of single bacteriophages extruding from living bacteria. Nat Commun 4, 2926
(2013).
- 29 -

ISM 2014 - The 48th Annual Scientific Meeting of ISM
Weizmann Institute of Science, Rehovot
Sylvain Trepout 1 , Cédric Messaoudi 1 , Philippe BASTIN 2 , Sergio Marco 1
1, Institut Curie Recherche & INSERM, U759, 91405 Orsay Cedex, France.
2, Institut Pasteur, CNRS URA 2581, Parasitology & Mycology Department, Institut Pasteur, 25, rue du Docteur Roux, 75015 PARIS, FRANCE
Structural description of cellular structures has been crucial for the understanding of normal and pathological life processes. However, for a long period of time, the depiction of cell components was limited to static two-dimension draws or pictures. Emergence of fluorescence microscopy and electron tomographies overcame this limit by adding a temporal and/or spatial dimension with improved accuracy and resolution along time. Nowadays, afore mentioned developments, allow a new challenge, thus far impossible, being accessible: the
3D study of the chemical elements distribution in the cell. 3D chemical mapping unlocks new prospects in the understanding of pathologies, such as neurodegenerative diseases by providing access to the detailed visualization of metal accumulation in the cellular volume; in nano-medicine by characterizing the location and composition of internalized nano-particles; or in basic research, by making possible the tracking of labeled drugs.
Uses and limitations of acquisition procedures and freeware for 3D chemical mapping [1] will be presented and illustrated by examples of afore mentioned biological applications. A particular attention will be paid to describe new methods allowing the observation of thick biological specimens (thick > 700nm) by using focal-STEM. In this approach, dynamic focus correction during acquisition [2] is combined with an acquisition scheme and with a specific image processing method. In this method virtual full-focused images are computed, using wavelet estimation of the depth of focus [3], from STEM images recorded at different defocus. The virtual focused images are used to precisely compute geometrical transforms between images at different tilt angles. These geometrical transforms are used to combine the tilt series at different focus in a final 3D reconstruction obtained by ART [4]. The method was applied to compute the 3D reconstruction of a T. brucei 750 nm thick section. Figure 1 shows the improvement in the accuracy of the observed details.
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ISM 2014 - The 48th Annual Scientific Meeting of ISM
Weizmann Institute of Science, Rehovot
Figure 1. Sections of tomograms from T. brucei showing the improvement in the accuracy of the observed details after using focal-STEM 3D reconstruction. A) Standard reconstruction of a 750nm thick section. B) Reconstruction after using focal-STEM approach of the same data shown in (A). C) Graph representing the voxel intensity of the region boxed in red. Blue line plot corresponding to the standard reconstruction, red line plot from the focal-STEM section.
Image under the plot: zoom of the selected region.
References:
1.
C. Messaoudi, N. Aschman, M. Cunha, T. Oikawa, C.O.S. Sorzano, S. Marco.
EFTEM-TomoJ: 3D chemical mapping by EFTEM including SNR improvement by
PCA and volume improvement by noise suppression during the ART reconstruction process. Microsc. Microanal. 28:1-9. (2013).
2.
J. Feng, A.P. Somlyo, A.V. Somlyo, Z. Shao. Automated electron tomography with scanning transmission electron microscopy. J. Microsc.,228:406-12.
( 2007).
3.
B. Forster, D. Van De Ville, J. Berent, D. Sage, M. Unser. Complex Wavelets for
Extended Depth-of-Field: A New Method for the Fusion of Multichannel Microscopy
Images. Mic. Res. Tech., 65:33-42 (2004).
4.
C. Messaoudi, T. Boudier, C.O.S. Sorzano, S. Marco. TomoJ: tomography software for 3D reconstruction in transmission electron microscopy. BMC Bioinformatics .
8 :288-297. (2007).
Acknowledgment:
Authors want to thanks ANR for funding by grant 11-BSV8-0016.
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ISM 2014 - The 48th Annual Scientific Meeting of ISM
Weizmann Institute of Science, Rehovot
Fried S, Pauker HM, Reicher B, Elad N and Barda-Saad M
The Mina and Everard Goodman Faculty of Life Sciences,
Bar-Ilan University, Ramat-Gan 5290002, Israel
The Wiskott-Aldrich syndrome protein (WASp) is an actin nucleation promoting factor that is exclusively expressed in hematopoietic cells, where it plays a key regulatory role in cytoskeletal dynamics, promoting multiple cellular processes, e.g., motility, adhesion, and endocytosis. Mutations of the gene encoding WASp result in WASp instability, leading to partial or complete WASp deficiency. WASp dysregulation causes the primary immunodeficiencies, Wiskott-Aldrich syndrome (WAS), or its milder form, X-linked thrombocytopenia (XLT). WAS and XLT are genetic diseases in which interference with cytoskeleton (i.e., actin) reorganization results in bleeding and impaired immune response, leading to recurrent infections, autoimmune diseases, and hematopoietic malignancies.
Ninety-five percent of WASp is in a complex with the WASp interacting protein (WIP) that serves as WASp chaperone and, indeed, mutations within the WASp homology 1 domain
(WH1) that impair the WIP:WASp interaction dramatically decrease WASp stability. Here, we demonstrated the dynamic molecular nature of the WIP:WASp complex by using highresolution live-cell molecular-imaging technologies, including triple-color Förster resonance energy transfer (3-FRET). 3-FRET is based on using three separate fluorophores, where the first fluorophore serves as a FRET donor to the two others, a second one that can both act as an acceptor to the first one and as a donor to the third one, and a third that serves as a FRET donor for interactions with both other fluorophores. Thus, the 3-FRET technique allows energy transfer to occur via three distinct possible FRET pathways, allowing for the simultaneous tracking of three-way interactions that are not possible to investigate using traditional, two-color FRET. By using the unique advantages offered by 3-FRET, we discovered WIP autoinhibition and its effects on WIP:WASp complex formation. Utilizing 3-
FRET analysis, we have found that in resting T cells, WIP binds WASp at two sites: the
WH1 and the VCA domains. A conformational change in WIP structure releases its autoinhibition and alters, rather than abolishes, WIP;WASp interaction. This partial dissociation enables the exposure of WASp WH1 domain to ubiquitylation, thereby promoting its degradation. Since immune cells must strike a delicate balance between activation and degradation of WASp, WASp represents a critical junction of cellular outcomes, with implications not only for immunepathologies, but also for actin homeostasis.
Thus, our research provides novel insights into the regulation of the actin cytoskeleton in immune cells in health and disease.
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ISM 2014 - The 48th Annual Scientific Meeting of ISM
Weizmann Institute of Science, Rehovot
Eran Meshorer
Department of Genetics, The Institute of Life Sciences, The Hebrew University of Jerusalem,
Jerusalem 91904, Israel
Embryonic stem cells (ESCs), with their dual capacity to self-renew and differentiate, are commonly used to study differentiation, epigenetic regulation, lineage choices and more. We developed a library of over 200 clones of mouse ESCs using a gene-tagging approach, with each clone expressing a fluorescent tagged protein (YFP or Cherry) under the control of its own endogenous promoter. We show the power of this library to track proteins in living cells; identify heterogeneously expressing proteins; measure the dynamics of endogenously labeled proteins; screen for proteins that are recruited to sites of DNA damage; pull-down tagged fluorescent fusion proteins using anti-Cherry antibodies and test for interaction partners; and screen, using live imaging of differentiating clones, for novel pluripotency-related factors.
Using the latter approach, we identified SET nuclear oncogene (SET), a multifunctional linker histone chaperone, which remarkably, shifts from the SETα to the SETβ isoform by alternative promoter usage during early ESC differentiation. We further show that SET is essential for active pro liferation and differentiation of ESCs, and that SETα helps maintain a hyperdynamic chromatin state in ESCs while SETβ is essential during early neuronal differentiation. This work provides the first endogenously labeled fluorescent tag library in
ESCs, and identifies a novel chromatin regulator of proliferation and differentiation in ESCs.
- 33 -

ISM 2014 - The 48th Annual Scientific Meeting of ISM
Weizmann Institute of Science, Rehovot
Noga Kozer, Alexander Plotnikov, Haim Barr, Amir Gelman, Adi Abada Manelis
Vladislav Krupalnik
The Nancy & Stephen Grand Israel National Center for Personalized Medicine, Weizmann Institute of Science, Rehovot, Israel
High content screening (HCS) is a method that is used in biological research and drug discovery to identify substances such as small molecules, peptides or RNAi that alter the phenotype of a cell in a desired manner. High content screening includes any method used to analyze whole cells or components of cells with simultaneous readout of several parameters.
The Wohl Institute for Drug Discovery has established a small molecule screening facility in the INCPM with the goal of providing cutting edge technologies to the Israeli research community and promoting collaborations of outstanding biologists, clinicians, and chemists to facilitate probe discovery. Currently, the HCS unit maintains a compound library of 60,000 molecules, including known drugs, natural products, and peptides. Using automated workstations we miniaturize cell-based assays to small volume format in 384-well plates and screen up to 16,000 compounds daily using automated microscopy and cytometry. Acquired images are analyzed for phenotypic changes such as increases or decreases in the production of cellular entities and/or changes in the morphology of the cell. We use commercial and open source image analysis tools to generate multiple parameters from the images and combine them to develop a screening assay that will yield the most relevant compounds
(“hits”) that change the biology of interest in the desired manner.
Here, we present collaborations with two basic research labs in the Weizmann Institute of
Science which form the basis of ongoing chemical biology discovery projects.
Elazar lab –siRNA screen to identify genes that interfere with ubiquitination signals for entry into the autophagy cycle.
Hanna lab – turning the clock back: small molecule screen to identify inducing agents for transformation of fibroblasts to stem cells.
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ISM 2014 - The 48th Annual Scientific Meeting of ISM
Weizmann Institute of Science, Rehovot
Figure 1. Image processing output of one of the assays developed. Shown are four sites from two representing wells from 384 wells plate. A-D and E-H are sites from control, and stimulated cells, respectively. Note the segmentation of nuclei and phagosomes that facilitates sample classification.
Figure 2. Genedata Screener High Content Extension supports massive, multi-featured data, typical for High Content Screening. One of the HCS tools used by our unit at Weizmann
Institute of Science.
- 35 -

ISM 2014 - The 48th Annual Scientific Meeting of ISM
Weizmann Institute of Science, Rehovot
Universal Approach to FRAP Analysis of Arbitrary Bleaching Patterns
Daniel Blumenthal†, Leo Goldstien†, Michael Edidin‡ and Levi A. Gheber†.
†The Avram and Stella Goldstein-Goren Department of Biotechnology Engineering, Ben Gurion
University of the Negev, Beer-Sheva, ISRAEL. ‡Department of Biology, Johns Hopkins University,
Baltimore, MD, USA
Fluorescence recovery after photobleaching (FRAP) is a classical biophysical method, that has been used extensively in the study of numerous systems, particularly cell membranes. It consists of irreversibly photobleaching a fluorescently labeled diffusing species, and then following the fluorescence recovery over time. The fluorescence recovers due to diffusion of bleached molecules outside the bleached area and unbleached molecules diffusing into the bleached area, thus, by analyzing the fluorescence recovery dynamics it is possible to extract the diffusion coefficient of the fluorescent species. While the experimental setup is relatively simple, th`e interpretation of the results is complex, severely limiting the quantitative use of the technique.
With the introduction of digital imaging and the Laser Scanning Confocal Microscope
(LSCM), a multitude of variations of the technique became possible, all of which result in a stack of digital images, from which a recovery curve can be directly extracted. While these modern options offer high flexibility and extend the availability of the method to a wide community of users, the initial and boundary conditions are too complex to allow a precise closed, analytical solution of the diffusion problem, and thus quantitative extraction of the diffusion coefficient. Comparative studies are still possible, based on observation of higher or lower mobility of compared species.
Figure 1 - FRAP and its corresponding simulated recovery
(A) the first FRAP series image (post bleach) is used as the basis of the simulated recovery. (B - D) FRAP series showing recovery of the bleached spot. (E - G) Simulated recovery series
We have developed a fast algorithm that allows the extraction of diffusion coefficients given a stack of images representing a FRAP experiment, and acquired with any method, for a completely arbitrary geometry of the initially bleached area. The algorithm treats the first post-bleach frame as the initial and boundary conditions, and simulates the diffusion of the fluorescent molecules starting with this time point (Figure 1). Thus, no characterization of the bleaching profile is required, since this information is encoded in the image. The lack of closed analytical solutions for complex geometries is not a limiting factor, since the diffusion equation is effectively solved numerically by iterative simulation.
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ISM 2014 - The 48th Annual Scientific Meeting of ISM
Weizmann Institute of Science, Rehovot
We validated our approach using a well characterized diffusing molecule (DiIC
18
) and
against the well-established analytical procedures or Gaussian (Axelrod, Koppel et al. 1976) and box bleaching geometries (Ellenberg, Siggia et al. 1997). Furthermore, we show that the
algorithm is able to deduce the diffusion coefficient for an arbitrary bleaching geometry and even for bleaching a third of a cell (Figure 2). Our experiments yield statistically similar results, both for geometries compatible with the analytical methods, and for arbitrary bleaching geometries (Figure 3).
Figure 2 - Example of a Random Shape Bleaching Pattern
(A,B) Bleaching a random shape pattern. (C,D) Bleaching a third of the cell
1.30E-08
1.10E-08
9.00E-09
7.00E-09
5.00E-09
3.00E-09
Mean Calculated D
Mean Simulated D
1.00E-09
Gauss Box Shape
Bleaching Geometry
Third Cell
Figure 3 - Comparing Calculated and Simulation Diffusion Coefficients
(Two leftmost columns) Comparison of mean diffusion coefficient extracted with the two different models. (Two rightmost columns) the mean simulation-extracted diffusion coefficient of a random shape and third of a cell. Error bars represent SEM.
The authors gratefully acknowledge a grant from the US-Israel Binational Science
Foundation, #2009345.
References:
1.
Axelrod, D., D. E. Koppel, et al. (1976). "Mobility Measurements by Analysis of
Fluorescence Photobleaching Recovery Kinetics." Biophysical Journal 16(2): A217-A217.
2.
Ellenberg, J., E. D. Siggia, et al. (1997). "Nuclear membrane dynamics and reassembly in living cells: Targeting of an inner nuclear membrane protein in interphase and mitosis."
Journal of Cell Biology 138(6): 1193-1206.
- 37 -

ISM 2014 - The 48th Annual Scientific Meeting of ISM
Weizmann Institute of Science, Rehovot
Danny Porath
Institute of Chemistry and Center for Nanoscience and Nanotechnology, The Hebrew University of
Jerusalem, 91904 Israel
A
DNA and DNA-based polymers have been at the focus of molecular electronics owing to their programmable structural versatility. The variability in the measured molecules and experimental setups, caused largely by the contact problem, has produced a wide range of partial or seemingly contradictory results, highlighting the challenge to transport significant current through individual DNA-based molecules. A well-controlled experiment that would provide clear insight into the charge transport mechanism through a single long molecule deposited on a hard substrate has never been accomplished. In this seminar I will report on detailed and reproducible charge transport in G4-DNA, adsorbed on a mica substrate. Using a novel benchmark process for testing molecular conductance in single polymer wires, we observed currents of tens to over 100 pA in many G4-DNA molecules over distances ranging from tens to over 100 nm, compatible with a long-range hopping between multi-tetrad segments. With this report, we answer a long-standing question about the ability of individual polymers to transport significant current over long distances when adsorbed a hard substrate, and its mechanism. These results may re-ignite the interest in DNA-based wires and devices towards a practical implementation of these wires in programmable circuits.
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ISM 2014 - The 48th Annual Scientific Meeting of ISM
Weizmann Institute of Science, Rehovot
References :
[1] "Direct measurement of electrical transport through DNA molecules", Danny Porath, Alexey
Bezryadin,Simon de Vries and Cees Dekker, Nature 403, 635 (2000).
[2] "Charge Transport in DNA-based Devices", Danny Porath, Rosa Di Felice and Gianaurelio
Cuniberti, Topics in Current Chemistry Vol. 237, pp. 183-228 Ed. Gary Shuster. Springer Verlag,
2004.
[3] “Direct Measurement of Electrical Transport Through Single DNA Molecules of Complex
Sequence”, Hezy Cohen, Claude Nogues, Ron Naaman and Danny Porath, PNAS 102, 11589 (2005).
[4] “Long Monomolecular G4-DNA Nanowires”, Alexander Kotlyar, Nataly Borovok, Tatiana
Molotsky, Hezy Cohen, Errez Shapir and Danny Porath, Advanced Materials 17, 1901 (2005).
[5] “Electrical characterization of self-assembled single- and double-stranded DNA monolayers using conductive AFM”, Hezy Cohen et al., Faraday Discussions 131, 367 (2006).
[6] “High-Resolution STM Imaging of Novel Poly(G)-Poly(C)DNA Molecules”, Errez Shapir, Hezy
Cohen, Natalia Borovok, Alexander B. Kotlyar and Danny Porath, J. Phys. Chem. B 110, 4430
(2006).
[7] "Polarizability of G4-DNA Observed by Electrostatic Force Microscopy Measurements", Hezy
Cohen et al., Nano Letters 7(4), 981 (2007).
[8] “Electronic structure of single DNA molecules resolved by transverse scanning tunneling spectroscopy”, Errez Shapir et al., Nature Materials 7, 68 (2008).
[9] “A DNA sequence scanned”, Danny Porath, Nature Nanotechnology 4, 476 (2009).
[10] “The Electronic Structure of G4-DNA by Scanning Tunneling Spectroscopy”, Errez Shapir, et.al., J. Phys. Chem. C 114, 22079 (2010).
[11] “Energy gap reduction in DNA by complexation with metal ions”, Errez Shapir, G. Brancolini,
Tatiana Molotsky, Alexander B. Kotlyar, Rosa Di Felice, and Danny Porath, Advanced Maerials 23,
4290 (2011).
[12] "Quasi 3D imaging of DNA-gold nanoparticle tetrahedral structures", Avigail Stern, Dvir Rotem,
Inna Popov and Danny Porath, J. Phys. Cond. Mat. 24, 164203 (2012).
[13] "Comparative electrostatic force microscopy of tetra- and intra-molecular G4-DNA", Gideon I.
Livshits, Jamal Ghabboun, Natalia Borovok, Alexander B. Kotlyar, Danny Porath, submitted (2014).
[14] "Long-range charge transport in single G4-DNA molecules", Gideon I. Livshits et. al., submitted
(2014).
- 39 -

ISM 2014 - The 48th Annual Scientific Meeting of ISM
Weizmann Institute of Science, Rehovot
Alexander Pekin, Vladimir Ezersky, Amit Kohn and Yuval Golan
Department of Materials Engineering, and the Ilse Katz Institute for Nanoscale Science and
Technology, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel
Semiconducting materials attract scientific and technological attention, as their optical and electrical properties change significantly when their size is reduced to the nanometer scale.
Optical properties, i.e. light absorption, light reflection, fluorescence, and refractive index are usually measured using a large ensemble of particles , meaning that the result represents an average property. In many cases, the size and shape of the particles in the characterized sample, which are the very reason for their unique properties, are not identical. Moreover, even if the particles are identical, surface effects cannot be separated from the bulk. Though sophisticated light-optics methodologies exist in order to measure single particles, the morphology of the measured particle remains unknown[1].
Electrical measurements of semiconducting nanoparticles, i.e. band gap width, charge carrier concentration, conductivity, band bending at interfaces, and the dielectric constant are even more challenging. Because of the nanoscale size of these particles, it is challenging to apply electric contacts and perform a measurement. In some cases, it is not even possible to measure the average properties of many particles because of isolating ligands which are attached on the surface of the particles. Some studies[2] use scanning probe microscopy, however they are usually limited both in spatial resolution and in the information which can be retrieved from these experiments.
This work applies transmission electron microscopy (TEM) for sub nanometer analytical characterization of these properties in PbS, CdS and SnS nanoparticles and heterojunctions based on two methodologies: First, electron energy loss spectroscopy (EELS) measurements were performed. The low loss region of the spectra was examined for information regarding the valance electrons, the dielectric function, effective electron density and the band gap [3].
Energy filtered TEM (EFTEM) was used in order to map surface plasmons in the nanoparticles.
The complex dielectric function was measured with high (~1 nm) spatial resolution which allowed separating the bulk and surface contributions.
Second, for heterojunctions, the band alignment, can provide important insights into the optical and electrical behavior of hybrid nanostructures. One of our main goals was to measure the band bending resulting from a nanoscale heterojunction in a PbS/CdS nanostructure. This was done by off axis electron holography [4]. In this work, an intermediate spatial resolution (~ 1 nm) off-axis holography mode was developed and applied. First, we mapped the compounds in the nanostructure by measuring their mean inner potential and then attempted to measure band bending. The different compounds were successfully identified. Initial results for the band bending characterization will be presented.
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ISM 2014 - The 48th Annual Scientific Meeting of ISM
Weizmann Institute of Science, Rehovot
References:
[1] P. Michler, A. Imamoglu, M. D. Mason, P. J. Carson, G. F. Strouse and S. K. Buratto, “Quantum correlation among photons from a single qunatum dot at room temperature,” Letters to Nature , vol.
406, no. 6799, pp. 968-970, Jul. 2000.
[2] X. D. Cui, Primak, X. Zarate, J. Tomfohr, O. F. Sankey, L. Moore, T. Moore, D. Gust, G. Harris, and S. M. Lindsay, “Reproducible measurement of single-molecule conductivity.,” Science , vol. 294, no. 5542, pp. 571–574, Oct. 2001.
[3] R. F. Egerton, “Electron energy-loss spectroscopy in the TEM,” Reports Prog. Phys.
, vol. 72, no.
1, p. 016502, Jan. 2009.
[4] M. R. McCartney and D. J. Smith, “Electron Holography: Phase Imaging with Nanometer
Resolution,” Annu. Rev. Mater. Res.
, vol. 37, no. 1, pp. 729–767, Aug. 2007.
- 41 -

ISM 2014 - The 48th Annual Scientific Meeting of ISM
Weizmann Institute of Science, Rehovot
Amir Gabay and Wayne D. Kaplan
Department of Materials Science & Engineering, Technion, Haifa, Israel
Recently, there is a renewed interest in electromagnetic field assisted sintering (FAST)
[1,2,3]. In this method a green body is exposed to an electric field and elevated temperatures.
The exposure to an electric field causes faster sintering rates compared to conventional sintering methods, resulting in a finer microstructure at the point of full density [3].
FAST can result in improved properties of the material, such as strength, transparency, and conductivity. However, there is a debate in the literature regarding the mechanism(s) of
FAST, and understanding the mechanism is critical to implementation of the method.
In this study, FAST is investigated, focusing on SiC as a model system. Experiments were conducted to shed light on the fundamental mechanism(s) behind FAST, and include a quantitative comparison between the effective grain boundary mobility after FAST versus conventional sintering.
References:
1.
Cologna, Marco, Boriana Rashkova, and Rishi Raj. “Flash Sintering of Nanograin Zirconia in
<5 s at 850°C.” Journal of the American Ceramic Society 93(11):3556–59, 2010.
2.
Cologna, Marco, Andre L. G. Prette, and Rishi Raj. “Flash-Sintering of Cubic Yttria-
Stabilized Zirconia at 750°C for Possible Use in SOFC Manufacturing.” Journal of the
American Ceramic Society 94(2):316–19, . 2011.
3.
Hayun, S. et al, “Microstructure and mechanical properties of silicon carbide processed by
Spark Plasma Sintering (SPS).” Ceramics International 38(8):6335–40, 2012.
- 42 -

ISM 2014 - The 48th Annual Scientific Meeting of ISM
Weizmann Institute of Science, Rehovot
Ayala Elkayam, Dalit Stolovas and Amit Kohn
Department of Materials Engineering, Ilse Katz Institute for Nanoscale Science and Technology,
Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel
Handling and positioning of silicon wafers during manufacture and metrology can cause local damage, cracks which render the wafer unusable, and even wafer breakage within the processing tools. In processing and metrology tools, the stage supports the wafer with contact points, for example conductive needles that are required for electrical bias. These contact points between needles and wafer is a source for damage and contamination that we are studying by controlled nanoindentation tests.
Previous nanoindentation studies showed formation of slip-planes, dislocations, stacking faults, twins, cracks
[1,2]
and phase transformations
[3,4]
in the vicinity of the indent. However, those studies applied significant pressure, up to15 GPa, while typical pressure loads in the processing tools are lower and importantly for our study, can be optimized in order to minimize the contact area.
Our aim is to determine the conditions for onset of, and subsequent processes of mechanically induced damage to Si(001) wafers due to indenter contact, e.g. load magnitude, load rate, and indenter geometry. Additionally, an experimental objective is to examine capabilities of microscopy and spectroscopy methodologies to detect this initial damage.
Nanoindentation experiments were performed in three loads (2.5, 5, and 20mN) using a 2µmdiameter spherical diamond indenter. Elastic strain/stress distributions following these indentations were calculated using finite-element simulations in order to predict the onset of crystalline phase transformations (expected above 12GPa) and amorphization (expected above 3GPa). These calculations show uneven distribution of stress reaching its highest value underneath the indenter tip. Even for the lowest applied force of 2.5mN (Fig. 1a), stress in some regions exceeds 12GPa, so structural defects and phase transformations are expected.
Figure 1. Stress distribution (in GPa) calculated using Patran-Marc software elastic simulations
[5]
. Two dimensional indenter-surface model, with 2µm-diameter spherical
- 43 -

ISM 2014 - The 48th Annual Scientific Meeting of ISM
Weizmann Institute of Science, Rehovot diamond indenter applying force of (a) 2.5mN, (b) 5mN, (c) 20mN on a Si(001) substrate.
The inlaid blue regions mark the displaced material, and the black arrows indicate the color code associated with crystalline phase transformation.
We searched for phase transformations in the vicinity of the indents by Raman spectroscopy and electron backscattered diffraction. We searched for mechanical damage by atomic force microscopy (AFM) and scanning electron microscopy. For example, in the case of AFM, topography mapping of the indents (Figure 2), do not show residual damage to the Si surface following the 2.5mN indentation. In the case of the higher load indentations, qualitative agreement was observed between the AFM measurements and the finite-element simulations.
(a) (b) (c)
Figure 2. AFM topography mapping of (a) 2.5 mN indentation showing no evidence of residual indentation. (b) 5mN indentation, 600nm diameter, 14nm depth and no pile-up.
(c) 20mN indentation, 1.1µm diameter, 42nm depth and 7nm pile-up.
References:
1. H. Saka, et al., Transmission electron microscopy of amorphization and phase transformation beneath indents in Si. Phil. Mag. A, Vol.82(10), 1971-1981 (2002).
2. Y.Q. Wu, et al., Nanoscratch-induced deformation of single crystal silicon. J. Vac. Sci. Technol. B,
Vol.27(3), 1374-1377 (2009).
3. S.R. Jian, et al., Nanoindentation-induced phase transformation in (110)-oriented Si single-crystals.
Curr. Opin. Solid State Mater. Sci., Vol.14, 69-74 (2010).
4. J.E. Bradby, et al., In situ electrical characterization of phase transformations in Si during indentation. Phys. Rev. B, Vol.67(8), 085205 (2003)
5. Patran-Marc Mentat, MSC software Corp., Santa Ana, CA, USA
Acknowledgments:
Dr. David Barlam and Prof. Roni Shneck (Ben-Gurion University of the Negev) for support with finite-element simulations.
- 44 -

ISM 2014 - The 48th Annual Scientific Meeting of ISM
Weizmann Institute of Science, Rehovot
Eran Amsellem and Amit Kohn
Department of Materials Engineering, Ilse Katz Institute for Nanoscale Science and Technology,
Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel
Magnetic tunnel junctions (MTJ) are devices based on spin-dependent tunneling between two ferromagnetic electrodes separated by a thin (1-3nm) insulating barrier[1]. MTJ devices are mostly used as read head sensors in hard disk drives and show promise for magnetoresistive random access memory (MRAM). The tunneling resistance of the junction depends on the relative magnetic alignment of the two ferromagnetic layers with parallel alignment resulting in lower resistivity than antiparallel. This phenomenon, caused by spin-dependent electron tunneling, is quantified by the fractional change in resistance termed as the tunneling magnetoresistance (TMR) ratio.
At present, switching the magnetization direction in the ferromagnetic electrodes of MRAM devices are achieved by magnetic fields produced by current carrying wires. A more efficient approach for this magnetic switching is using a spin-polarized current [2]. Therefore, spintransfer torque MRAM are better information storage devices in terms of scalability but require generating a large enough spin polarized current to operate. In standard MgO based
MTJs, these currents are high resulting in power dissipation specifically due to the tunneling barrier, thus degrading the reliability of the device. Liu et al [3] presented a theoretical study examining the effect of impurity doping and alloying effects of the tunneling MgO barrier on the spin polarized tunneling current in Fe/MgO/Fe MTJs. They predict that doping the epitaxial MgO barrier with Zn results in a significant nonlinear quenching of the junction resistance while the TMR ratio is less affected, only linearly reduced. Additionally, study of doped MgO barriers can gain a better understanding of spin-dependent and spin independent tunneling processes.
Consequently, the objective of this research was a systematic study of epitaxial MgO based
MTJs in which the barrier was doped at increasing levels of Zn, nominally up to Mg
0.7
Zn
0.3
O.
MTJ structures were grown by molecular beam epitaxial growth on an MgO(001) substrate.
Devices were fabricated by a UV optical lithography process. Transport measurements support calculations and show that device properties can be optimized by Zn doping, namely more significant reduction of the junction resistance compared to the TMR ratio.
Characterization of the MTJ devices was undertaken by transmission electron microscopy
(TEM) by preparing cross-sectional samples using a focused ion beam. TEM analysis is necessary to confirm the structure of these devices, and to determine Zn composition and distribution within the barrier. For the Mg
0.8
Zn
0.2
O barrier, we show that the MTJ structure is crystalline and epitaxial: Fe[010](001)//Mg
0.8
Zn
0.2
O [110](001)//Fe[010](001). The barrier remains NaCl-type MgO ( Fm m accuracy of this measurement. High-angle annular dark-field STEM, Energy dispersive Xray and electron energy-loss spectroscopies did not detect Zn segregation.
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ISM 2014 - The 48th Annual Scientific Meeting of ISM
Weizmann Institute of Science, Rehovot
Figure 1. High-resolution cross-sectional TEM image of the entire MTJ device showing the epitaxial growth and relations of: Fe[010](001)/Mg
0.8
Zn
0.2
O [110](001)/Fe[010](001); insets are power spectra of the regions denoted schematically by the red rectangles.
This project is undertaken in collaboration with Dr. S.-G. Wang, State Key Laboratory of
Magnetism, Institute of Physics, China, and with Dr. R. Ward, Clarendon Laboratory, Oxford
University, U.K. The project is funded by the Israel Ministry of Science and Technology,
China-Israel project 3-9742.
References:
1. Yuasa, S., and D. D. Djayaprawira. "Giant tunnel magnetoresistance in magnetic tunnel junctions with a crystalline MgO(001) barrier." Journal of Physics D: Applied Physics 40 (2007): R337.
2. Ralph, R.A. Buhrman, J.A. Katine, “Spin-transfer effects in nanoscale magnetic tunnel junctions.”
Appl. Phys. Lett. 85 (2004) 1205
3. Liu, Dongping, Xiufeng Han, and Hong Guo. "Junction resistance, tunnel magnetoresistance ratio, and spin-transfer torque in Zn-doped magnetic tunnel junctions." Physical Review B 85 (2012):
245436.
4. Zhuang, L., and K. H. Wong. "Microstructure and optical properties of MgxZn1-xO thin films grown by means of pulsed laser deposition." Thin Solid Films 516 (2008): 5607-5611.
- 46 -

ISM 2014 - The 48th Annual Scientific Meeting of ISM
Weizmann Institute of Science, Rehovot
Eran Aronovitch
1
, Shai Mangel
1
,Lothar Houben
2
, Maya Bar-Sadan
1*
1 Chemistry Department, Ben Gurion University of the Negev, Beer Sheba, Israel
2 Peter Grünberg Institut 5 and Ernst Ruska Centre for Microscopy and Spectroscopy with
Electrons, Forschungszentrum Jülich GmbH, 52425 Jülich, Germany
The search for alternative clean and renewable energy source is a pressing major issue that has been occupying scientists in the last few decades. Most of the efforts are directed towards attaining energy from the sun and water by using semiconductor nanoparticles as photocatalysts that absorb the solar radiation. This radiation energy leads to the creation of an excited electron and a hole. The use of heterogenic core-shell nano-composites can help increase the charge separation and reduce the particle dissolution by confining the holes to the core and allowing the electrons to be delocalized in both core and shell. CdSe@CdS coreshell nanorods with a bi-metallic tip composed of gold and palladium may act as a sink for the excited electrons. The presence of the metal tip on the nano-rod can enhance the transfer of electrons from the semiconductor nanorod to the aqueous solution, which in turn reduces water to produce hydrogen.
Here we use the CdSe@CdS/metal hybrid nanostructures as a case study to explore the relationship between atomic structure at the interface of the metals with the semiconductor and the bimetallic structure with the overall catalytic properties of the nanostructures. For that purpose, we first investigate the atomic structure of such nanoparticles through various
HR(S)TEM methods both for imaging and analytical purposes. Phase reconstruction (focal series reconstruction) method was used in order to uncover the atomic columns positions and hence the polarity of the nanostructure.
References:
1. Navarro Yerga, R.M., et al., Water Splitting on Semiconductor Catalysts under Visible-Light
Irradiation. ChemSusChem, 2 (6): p. 471-485, (2009).
2. Manna, L., E. Scher, and A.P. Alivisatos, Shape Control of Colloidal Semiconductor Nanocrystals.
Journal of Cluster Science, 13 (4): p. 521-532, (2002).
3. Mokari, T., et al., Selective Growth of Metal Tips onto Semiconductor Quantum Rods and
Tetrapods. Science, 304 (5678): p. 1787-1790, (2004).
4. Li, X., et al., Light-Induced Selective Deposition of Metals on Gold-Tipped CdSe-Seeded CdS
Nanorods . Journal of the American Chemical Society, 133 (4): p. 672-675, (2010).
- 47 -

ISM 2014 - The 48th Annual Scientific Meeting of ISM
Weizmann Institute of Science, Rehovot
2
Eran Gross, Dana Benes Dahan, and Wayne D. Kaplan
Department of Materials Science and Engineering, Technion, Haifa, Israel
Pressureless solid phase sintering of silicon carbide powder compacts to a monolithic high density material is generally achieved by adding boron and carbon as sintering additives and sintering at about 2100°C. While the role of boron in the sintering process is thought to increase grain boundary diffusion [1] the role of carbon is thought to be the reduction of a native SiO
2
layer found on the SiC powder particles:
SiO
2
+ 3C = SiC + 2CO
This mechanism was suggested based on chemical analysis of the gas flow during sintering and thermo gravimetric methods [2].
The goals of this work were first to develop and characterize a pressureless sintering process for SiC, and secondly to directly characterize the SiO
2
reduction mechanism using TEM of
SiC samples subjected to alternating oxidation and reduction processes.
SiC samples were prepared by mixing 6H SiC powder (0.7 µm), amorphous boron (0.5 – 1 wt.%), phenolic resin as a source of free carbon and a binding agent, acetone as a mixing medium and an organic dispersing agent, and deflocculant. After ball-milling the suspension was dried, ground, and sieved. Cylindrical discs (20mm in diameter) were formed by uniaxial pressing at 27 MPa, followed by cold isostatic pressing (CIP) at 350 MPa. The green bodies were sintered at 2100°C. Single crystals (0001) of 6H SiC served as reference samples for reduction-oxidation experiments, where TEM samples were made by mechanical milling followed by Ar ion milling. The TEM samples were oxidized at 1400°C in air, carbon coated and thermally reduced at 1400°C in flowing He.
Characterization of the single crystal TEM sample using HRTEM at each stage showed the formation of a thick oxide layer, which was then reduced in the presence of carbon during the second thermal treatment, thus providing direct experimental evidence for the reduction mechanism which enables solid state sintering of SiC.
References:
1.
A. Malinge, A. Coupé, Y. Le Petitcorps, R. Pailler, Pressureless sintering of beta silicon carbide nanoparticles, Journal of the European Ceramic Society, 32[16]:4393-
4400, 2012.
2.
W. J. Clegg, Role of Carbon in the Sintering of Boron-Doped Silicon Carbide, Journal of the American Ceramic Society, 83[5]:1039-1043, 2000.
- 48 -

ISM 2014 - The 48th Annual Scientific Meeting of ISM
Weizmann Institute of Science, Rehovot
Galit Atiya 1 , V. Mikhelashvili 2 , Gadi Eisenstein 2 , and Wayne D. Kaplan 1
1 Department of Materials Science & Engineering, Technion – IIT, Haifa, Israel
2 Department of Electrical Engineering, Technion – IIT, Haifa, Israel
Metal-ceramic interfaces determine the mechanical and functional properties of many technologically important material systems, and thin metal films on ceramic substrates have an important role in technological applications and in fundamental science. Since thin films are not stable and tend to break-up into particles, solid-state dewetting has become a common method used to produce catalysts for carbon nanotubes, nanowires, nano-crystal arrays for memory, and photo-electronic devices [1,2,3,4,5]. Despite the wide range of applications, the kinetic mechanism(s) by which Pt dewetting occurs, and the mechanism(s) dependence on the surface and interface structure and chemistry which define the thermodynamic driving force for dewetting, were not studied in detail. Furthermore, interfaces in general, and metalceramic interfaces in particular, can be extremely complex with regards to atomistic structure and adsorption, and the microscopic degrees of freedom (DOF) such as surface reconstruction can have a critical role in defining the macroscopic DOF (i.e. the orientation relationship (OR) at equilibrium). The main goal of this study is to experimentally determine the influence of microscopic DOF on the macroscopic DOF, and the kinetic mechanisms of solid-state Pt dewetting [6,7,8,9].
In this study, SrTiO
3
(100) substrates were chemically etched using a buffered HF solution
(NH
4
F 35.6%, HF 6.4%, pH ~ 4.5) to achieve TiO
2 termination [10]. Pt films were deposited using electron beam evaporation at room temperature. The samples (including TEM samples of bare SrTiO
3
) were annealed for 10 hours at 1150˚C, in a sapphire tube furnace under two different atmospheres: flowing Ar+7%H
2
(99.9999%) at an oxygen partial pressure of P(O
2
)
~10 -20 atm, and flowing Ar+2%O
2
(99.999%) at a P(O
2
) ~10 -2 atm The P(O
2
) was measured at the exit port of the furnace using a zirconia oxygen detector (Cambridge Sensotec, Rapidox
2000).
During annealing the Pt films dewetted via the formation of holes that grew with increasing annealing time and via grain boundary grooving. However, surface reconstruction, driven by the minimization of surface energy, depends on the P(O2) used for dewetting (equilibration), and this in turn can affect both the kinetics of dewetting and the final equilibrium state. The surface reconstruction was determined from reconstructed exit-wave functions using experimentally acquired aberration-corrected focal series and the TrueImage software, complimented by high angle annular dark field (HAADF) high resolution scanning transmission electron microscopy (HRSTEM), which showed that the SrTiO3 termination changed from TiO2 to SrO, and thus different morphologies at equilibrium. In-situ transmission electron microscopy of the bare SrTiO3 showed that macroscopic reconstruction
(faceting) during annealing is motivated by the minimization of surface energy. Equilibrated samples were used to determine the equilibrium crystal shape of Pt and the Pt-SrTiO3 interface energy [ Error! Bookmark not defined.
].
References:
- 49 -

ISM 2014 - The 48th Annual Scientific Meeting of ISM
Weizmann Institute of Science, Rehovot
1.
Yu R, Song H, Zhang X-F, Yang P, Thermal Wetting of Platinum Nanocrystals on Silica Surface,
Journal of Physical Chemistry B 109: 6940 (2005)
2. J.-M. Lee, B.-I. Kim, Thermal dewetting of Pt thin film: Etch-masks for the fabrication of semiconductor nanostructures, Materials Science and Engineering: A, 449-451[769-773, 2007.
3. S. Sebastian, et al., Sub-10 nm structures on silicon by thermal dewetting of platinum,
Nanotechnology, 21[50]:505301, 2010.
4. E. Shaffir, I. Riess, W. D. Kaplan, The mechanism of initial de-wetting and detachment of thin Au films on YSZ, Acta Materialia, 57[1]:248-256, 2009.
5. C. V. Thompson, Solid-State Dewetting of Thin Films, Annual Review of Materials Research,
42[1]:399-434, 2012.
6. E. Jiran, C. V. Thompson, Capillary instabilities in thin, continuous films, Thin Solid Films,
208[1]:23-28, 1992.
7. E. Rabkin, Metastable porosity in thin polycrystalline films, Scripta Materialia, 69[10]:764-767,
2013.
8. G. Atiya, V. Mikhelashvili, G. Eisenstein, W. Kaplan, Solid-state dewetting of Pt on (100) SrTiO3,
Journal of Materials Science, 1-12, 2014. DOI: 10.1007/s10853-013-7966-5
9. A. Altberg, G. Atiya, V. Mikhelashvili, G. Eisenstein, W. Kaplan, The equilibrium orientation relationship between Pt and SrTiO3 and its implication on Pt films deposited by physical vapor phase deposition, Journal of Materials Science, 1-11, 2013. DOI:10.1007/s10853-013-7941-1.
10. M. Kawasaki, A. Ohtomo, T. Arakane, K. Takahashi, M. Yoshimoto, H. Koinuma, Atomic control of SrTiO3 surface for perfect epitaxy of perovskite oxides, Applied Surface Science,
107[0]:102-106, 1996.
- 50 -

ISM 2014 - The 48th Annual Scientific Meeting of ISM
Weizmann Institute of Science, Rehovot
Gili Shalev and Louisa Meshi
Department of Materials Engineering, Ben Gurion University of the Negev, Beer-Sheva 84105,
Israel
In intermetallic compounds, based on f-elements, having particular electronic configuration, the interaction between the unstable f-electrons and the conduction electrons may yield formation of heavy fermion ground state [1]. A large number of A (actinide)-based aluminides have been characterized as heavy-fermion systems. Among them two Al-rich A-
T-Al (where T is transition metal) series with many representatives were found: cubic
AT
2
Al
20
(belonging to the Cr
2
Mg
3
Al
18
structure type) [2, for example] and hexagonal
A
4
T
6
Al
43
(belonging to the Ho
6
Mo
4
Al
43
structure type) [3, for example]. During our study of related Th-V-Al system - ThV
2
Al
20
phase was identified. Its structure was assumed to be isotypical to AT
2
Al
20
. Rietveld analysis was performed on powder X-ray data, taken from this material, and exact location of atomic coordinates determined.
Current research was undertaken with a purpose to perform full structure solution of this material using electron diffraction (ED), which became more reliable at the last decades due to the use of beam precession (PED) that substantially reduces the influence of dynamical effects. There exist two main ED data collection methodologies: 1) collection of different
PED patterns at zone axis patterns (zonal data) [4]; and 2) collection of "off-axis" ED patterns with small angular steps between them (with and w/o precession) (Electron
Diffraction Tomography (EDT) or Rotation Electron Diffraction (RED) approaches) [5,6].
Structure of several intermetallic compounds was already solved using zonal PED data by our group [7]. However this approach provides limited completeness of data, thus, structure solution of complex alluminides is extremely difficult to perform using zonal PED data.
EDT, on the other hand, was developed in order to increase completeness of data. Successful structure solution of ThV
2
Al
20
phase using EDT method as well as comparison of the structural model derived from electron data to the model received from X-ray data will be presented.
References:
1. H.R. Ott. Materials Research, Vol 17, pp.13-33, (1987)
2. S. Niemann, W. Jeitschko. Journal of Solid State Chemistry, Vol 114, pp.337-341, (1995).
3. S. Niemann, W. Jeitschko. Z. Metallkd, Vol 85, pp.345-349, (1994).
4. R. Vincent, P.A. Midgley. Ultramicroscopy, Vol 53, pp.271-282 (1994).
5. U. Kolb, T. Gorelik, C. Kübel, M.T. Otten, D. Hubert. Ultramicroscopy, Vol 107, pp.507-513 ,
(2007).
6. D. Zhang, P. Oleynikov, S. Hovmöller, X.Zou. Zeit. für Kristall., Vol 225, pp.94-102, (2010).
7.
S. Samuha, Y. Krimer, L. Meshi. Submitted to J. Appl. Cryst.
- 51 -

ISM 2014 - The 48th Annual Scientific Meeting of ISM
Weizmann Institute of Science, Rehovot
Hadas Strenlicht and Wayne D. Kaplan
Department of Materials Science & Engineering, Technion – IIT, Haifa, Israel
The kinetics of grain boundary motion can be experimentally determined, however the mechanism by which a grain boundary migrates has not yet been determined. One of the models proposed to describe grain boundary motion is the terrace-ledge-kink (TLK) model.
This model suggest that the process of grain boundary migration is via diffusion of atoms to the grain surface (terrace), then atoms diffuse along the surface, attach to step sites, and finally diffuse along the step into a kink site [ 1,2 ].
In order to determine the mechanism of grain boundary migration, two model systems have been defined based on grain boundaries between a single crystal and polycrystalline SrTiO
3 and general boundaries in polycrystalline SrTiO
3
. These boundaries are characterized using aberration corrected transmission electron microscopy (TEM), with the goal to identify steps which following the TLK model are hypothesized to be the active mechanism for grain boundary motion. This work will present analysis of the nature of the steps and dislocations found at the above boundaries.
References:
1. H. Gleiter, Mechanism of Grain Boundary Migration , Acta Metallurgica, 17[5]:565-&,
1969.
2. H. Gleiter, Theory of Grain Boundary Migration Rate , Acta Metallurgica, 17[7]:853-&,
1969.
- 52 -

ISM 2014 - The 48th Annual Scientific Meeting of ISM
Weizmann Institute of Science, Rehovot
Elizaveta Kossoy, Haim Weissman and Boris Rybtchinski* Department of Organic
Chemistry, Weizmann Institute of Science, Rehovot 76100, Israel
Coordination chemistry is a powerful synthetic tool in supramolecular chemistry. In the current work, we demonstrate how coordination bonds can direct the assembly morphology based on strong hydrophobic interactions. We compare between self-assembled structures of three complexes of the first row transition metals (zinc, cobalt and nickel), having the identical set of ligands and differing only by the central metal ion. In aqueous medium, aggregation of the complexes is induced by hydrophobic interactions between the ligands.
However, final shapes of the resulting assemblies depend on the preferred geometry of the coordination spheres typical for the particular metal center. The self-assembly process was characterized by UV/Vis spectroscopy, zeta potential measurements and cryogenic transmission electron microscopy (cryo-TEM). Coordination of zinc(II) and cobalt(II) leads to formation of unique nanospiral assemblies, while complexation of nickel(II) leads for formation of straight nanofibers. Notably, coordination bonds are utilized not as connectors between elementary building blocks, but as directing intermolecular interactions, enabling unique control of supramolecular geometry.
Scheme 1 : Synthesis of the compounds 2 4 .
- 53 -

ISM 2014 - The 48th Annual Scientific Meeting of ISM
Weizmann Institute of Science, Rehovot
Figure 1. An example of nano-spirals formation in a solution of 2 (1·10
-4
M) in 5% THF in water as demonstrated by cryo-TEM; Inset: HR-cryo-TEM image of the fine details of the assemblies (scale bar: 100 nm; 25 nm in the inset).
- 54 -

ISM 2014 - The 48th Annual Scientific Meeting of ISM
Weizmann Institute of Science, Rehovot
Alex Laikhtman, Igor Lapsker, Alexey Moshkovich, Vladislav Perfilyev, and Lev Rapoport
Sciences Department, Holon Institute of Technology (HIT), Holon 5810201, Israel
The aim of this work is to investigate the stick–slip phenomenon under friction of CrV(x)N
(x=0%, 12%, 27%, and 35%) coatings at room and high temperatures. To study stick–slip phenomena, a new ball on flat device with a heated chamber for experiments at up to 500 °C was developed at the Holon Institute of Technology.
The effects of vanadium (V) content and the temperature on the friction and stick–slip parameters for the contact pair: coating-ceramic ball were analyzed. The amplitude – a difference between the maximal and minimal values of the friction force, the static force (at the beginning of friction) and the kinetic friction force (average value in the steady state) were chosen for the description of the stick–slip phenomenon.
The surface morphology, the structure and the mechanical properties of coatings were analyzed by SEM, AFM and XRD techniques. The hardness and roughness parameters before and after friction were measured.
It was shown that the addition of V up to 27–35% in CrV(x)N coatings increased the hardness and roughness and decreased the grain size. These parameters are responsible for the improved tribological properties of coatings with high a content of V. Friction of the
CrV(0)N coating rubbed at room temperature is accompanied by strong sticking. At room temperature CrVxN coatings feature strong sticking effects in the friction experiments. High values of the stick–slip parameters are explained by mechanical “catching” and adhesion on the contact spots due to high roughness and transfer of Si films on the surface of the coating.
Low values of the wear and stick–slip parameters under friction of Cr
0
.
65
V
0
.
35
N at high temperatures (T = 500–700°C) is associated with the formation of V
2
O
5
oxide phase providing easy shearing of tribofilms in the interface of rubbed surfaces (Figure 1).
Figure 1. SEM images of CrV(35)N coating near the rubbed surface
(a) and in the wear track after friction at temperature of 500oC (b).
- 55 -

ISM 2014 - The 48th Annual Scientific Meeting of ISM
Weizmann Institute of Science, Rehovot
H. Jiang, H.S. Ubhi, J. Goulden, K. Dicks
Oxford Instruments NanoAnalysis, Halifax Road, High Wycombe, HP12 3SE, UK
In material characterization, it is very important to collect statistically representative datasets.
The interpretation of data collected from small sample areas may not fully describe the sample. The requirement to collect EBSD and EDS data simultaneously over larger sample areas is not new, but as EBSD and EDS technology improves, it is possible to acquire ever larger datasets from larger areas and at higher speeds, while maintaining the highest quality results.
Recent development for large area mapping within AZtec offers several benefits. Firstly the power to analyse large sample areas. Secondly the capability to see both nano scale detail and micro scale features in the same data set. Finally it aids in collecting representative and statistically significant data sets, typically over coarse grain material, non-uniform microstructures or materials containing scattered phases.
The example below shows a large area map collected over 2.7cm by 8.2cm of a silicon wafer where some of the individual grains are over a cm in size.
2 cm
Large area mapping is required to obtaining representative statistics on coarse grain materials. Data was collected using Oxford Instruments AZtec. Sample courtesy of Sam
Huang, Gigastorage Corporation, Taiwan
For these applications to be successful there are some key requirements. Maintaining the sample focus over the area is critical. In addition, data collected from multiple fields must be accurately aligned so that it can be montaged, investigated and reanalysed as a single data entity.
This study will present examples where large area maps of both EBSD and EDS data is collected at high resolution over large areas.
- 56 -

ISM 2014 - The 48th Annual Scientific Meeting of ISM
Weizmann Institute of Science, Rehovot
Liron Reshef Steinberger 1 , Tamilla Gulakhmedov 1 , Zahava Barkay 2 , Ana Dotan 3 , Shachar
Richter 1
1 Center for Nanoscience and Nanotechnology, Tel-Aviv University, Israel
2 Wolfson Applied Materials Research Center, Tel-Aviv University, Israel
3 Israel Plastics and Rubber Center, Shenkar College of Engineering and Design,
Ramat-Gan, Israel
Plastics are widely used around the world, since they are light, strong and durable and their production process is simple and inexpensive. Plastics, however, have some serious ecological issues related to the fact that the raw material comes from petroleum contributing to the exhaustion of natural resources and global warming. More important, is the fact that most synthetic plastics are not biodegradable. Proteins may provide an answer for the fabrication process of biodegradable materials due to their physical and chemical attributes.
Proteins can be easily processed into polymers via classical chemical processes, such as crosslinking and do not require major changes to existing processes. Mucin and Collagen proteins can be used for this purpose. These proteins are widely available in Jellyfish.
Jellyfish are of special interest due to their large protein content. Furthermore, Jellyfish have became an ecological disturbance worldwide being multiplied at a concerning rate. In many countries, including Israel, Jellyfish cause severe problems for various industries.
In this current study, we are focusing on the process of fabricating biodegradable composite plastics from Jellyfish proteins derived from Rhopilema nomadic Jellyfish, a species which is massively found in Israeli coast. The gelatinous part of the Jellyfish was processed into biodegradable composite plastics and other innovative materials for different applications by addition of various crosslinkers in order to produce a biopolymer. After the gelatinous part of the Jellyfish was processed with crosslinkers, it was dried in order to produce the raw bioplastic. Here we characterize the bioplastic mechanical properties by stress-strain measurements and correlate it with morphological properties using environmental scanning electron microscopy (ESEM) at low vacuum mode.
Tensile tests were performed on different composite bioplastics in order to obtain stressstrain curves (Figure 1). The curves show that the addition of crosslinkers makes the Jellyfish biopolymer stronger and more rigid. The ultimate tensile stress (UTS), strain at UTS and
Young’s modulus obtained values (mean ± standard deviation) were 24±12MPa, 1.8±0.6 % and 1550±730 MPa, respectively, after averaging the measurements of samples from Figure
1. ESEM images of the fractured specimens after failure (Figure 2a) show that Jellyfish aggregations are dispersed through all crosslinker surfaces. ESEM images of the composite bioplastic specimen cross sections can significantly emphasize this evidence (Figure 2c).
Furthermore, ESEM imaging revealed that crosslinkers have a multi layered structure, which could explain the improvement of mechanical properties after adding crosslinkers to the
Jellyfish biopolymer. Additionally, we have found that, failure path of the composite bioplastic is jagged than the one of 100% crosslinker plastic (Figures 2a, 2b). In order to
- 57 -

ISM 2014 - The 48th Annual Scientific Meeting of ISM
Weizmann Institute of Science, Rehovot validate that these composite bioplastics are biodegradable, the biodegradability degree was investigated. The biodegradation test was performed according to ISO 14855-2. It was found that the degree of biodegradation of the sample was about 90% after 4 weeks and was higher than the reference sample, meeting the standard requirements.
In conclusion, we demonstrate noble composite bioplastic materials based on renewable resources and show the significance of using ESEM at low vacuum mode for surface characterizing. The tensile stress-strain results of the composites were correlated with the
ESEM characterization. These green and biodegradable plastics may prove useful for many applications, such as medical (drug delivery), electronic and food packaging applications.
Figure 1 –Tensile stress-strain curves. The cross section width was measured by micrometer. a b c
Figure 2 – ESEM imaging after tensile test: a) crosslinked Jellyfish biopolymer, b) 100% crosslinker plastic and c) a composite bioplastic specimen cross sections
- 58 -

ISM 2014 - The 48th Annual Scientific Meeting of ISM
Weizmann Institute of Science, Rehovot
Mahdi Halabi and Shmuel Hayun
Department of Materials Engineering, Ben-Gurion University of the Negev, P. 0. Box 653, Beer-
Sheva 84105, Israel
The effect of composition and sintering condition of magnesium aluminate spinel on cations distribution and inversion parameter was studied by Electron Energy Loss Spectroscopy
(EELS). MgO·nAl2O3 powders with 0.95<n<1.07 were synthesized by a solution combustion method. The structural analysis (FTIR and XRD) indicated that the nano
MgO·nAl2O3 powders are disordered and the Al+3 cations placed in booth tetrahedral and octahedral sites. In order to study the effect of sintering conditions on the structural arrangement and grain boundaries composition two sintering methods were used; Spark
Plasma Sintering (SPS) and pressure-less sintering. The spinel phase after the pressure-less sintering shifts to a more ordered state, i.e. less tetrahedral and more octahedral sites were occupied by the Al+3 cations. The SPS samples, however, show an almost fully ordered state, even though the powders were exposed to a lower temperature and shorter time.
Complementary information on the cations segregation at the grain boundaries was obtained by the relative composition quantification of aluminum and magnesium K-edges. The inversion parameter was determined using the energy loss near-edge spectra (ELNES) method. The effect of sintering condition on grain boundary composition will be discussed.
References :
[1] J.Bruley, "Spectrum-Line Profile Analysis of a Magnesium Aluminate Spinel Sapphire Interface,"
Microsc. Microanal. Microstruct, pp. 1-18, 1995.
[2] K. v. Benthem, "Methods for ELNES-quantification: characterization of the degree of inversion of
Mg–Al-spinels," Micron 31, p. 347–354, 2000.
[3] A.Mussi, "inversion defects in Mg-Al Spinel elaporated by pressuless sintering, pressuless sintering plus hot isostatic pressing, and spark plasma sintering," Scripta Materialia, pp. 516-519,
2009.
- 59 -

ISM 2014 - The 48th Annual Scientific Meeting of ISM
Weizmann Institute of Science, Rehovot
Meital Shviro, Shlomi Polani and David Zitoun
Bar Ilan University, Department of Chemistry and Bar Ilan Institute of Nanotechnology and
Advanced Materials (BINA), Ramat Gan 52900, ISRAEL
The ability to control the shape of metal nanocrystals is very important to application such as catalysis, magnetism and plasmonics. Here we report on the synthesis of monodisperse and shape control Ni and NiPt nanocrystals and electroless deposition of Au and Pd on selective areas of the nanocrystals. Metallic core are synthesized from metal-organic precursors while galvanic displacement and/or chemical reduction allows for the second metal decoration.
Depending on the phase diagram and diffusion processes, the particles rearrange at low temperature (below 150°C) by alloying or demixing processes. This soft chemical route yields core/shell, dendrites or hollow morphologies.
Each bimetallic system shows very different growth pathways which we interpret as three different growth mechanisms: galvanic displacement at low temperature, metal assisted growth and overgrowth at high temperature. Combined high resolution transmission electron microscopy (HRTEM), XRD and magnetic measurements demonstrate the diffusion processes taking place in the nanocrystal. This result is a nice example of chemical rearrangement which we apply to hydrogen oxidation electrocatalysis.
Figure 1. Schema of galvanic displacement mechanism (left) and TEM images of hollow octahedral nanocrystals (right)
References:
Nickel nanocrystals: cubes, pyramids and tetrapods from fast reaction M. Shviro and D. Zitoun RSC
Adv., 2013 , 3 (5), 1380 – 1387
- 60 -

ISM 2014 - The 48th Annual Scientific Meeting of ISM
Weizmann Institute of Science, Rehovot
Olga Brontvein 1 , Daniel G. Stroppa 2 , Daniel Feuerman 3 , Vishakantaiah Jayaram 4 ,
Lothar Houben 2 , K. P. J. Reddy 4 , Jeffrey M. Gordon 3 and Reshef Tenne 1,*
Department of Materials and Interfaces, Weizmann Institute of Science, Israel.
Institute of Solid State Research and Ernst Ruska Centre for Microscopy and Spectroscopy with
Electrons, Forschungszentrum Jülich GmbH, Germany.
Department of Solar Energy and Environmental Physics, Jacob Blaustein Institutes for Desert
Research, Ben-Gurion University of the Negev, Israel.
Department of Aerospace Engineering, Indian Institute of Science, India. reshef.tenne@weizmann.ac.il
Inorganic fullerene-like structures and inorganic nanotubes became a world popular research subject in recent years. So far a number of synthetic routes have been developed for production of inorganic nanotubes made of layered materials were developed with particular control of morphology and their quantity.
A new procedure for the synthesis of MoS
2
nanotubes is represented here, and additionally demonstrated for MoSe
2
, WS
2
, and WSe
2
. Highly concentrated sunlight creates continuous high temperatures, strong temperature gradients, and extended hot annealing regions, which, together with a metallic (Pb) catalyst, are conducive to the formation of different inorganic nanotubes. Structural characterization (including atomic resolution images) reveals a threestep reaction mechanism. In the first step, MoS
2
platelets react with water - air residues, decompose by intense solar irradiation, and are converted to molybdenum oxide.
Subsequently, the hot annealing environment leads to the growth of Pb-stabilized MoO
3
−x nanowhiskers. Shortly afterward, the surface of the MoO
3
−x starts to react with the sulfur vapor supplied by the decomposition of nearby MoS
2
platelets and becomes enveloped by
MoS
2
layers. Finally, the molybdenum oxide core is gradually transformed into MoS
2
nanotubes
1
.
Similar Pb-stabilized MoO
3-x
nanowhiskers were created using high pressure shock wave system which produces extremely high temperature. In the second step these nanowhiskers were converted into MoS
2
INT using H
2
S gas in a reducing atmosphere.
These findings enable future scaling up of synthesized products and open up many opportunities for similar syntheses of as yet unattained nanotubes from other metal chalcogenides.
- 61 -

ISM 2014 - The 48th Annual Scientific Meeting of ISM
Weizmann Institute of Science, Rehovot
References :
1.Brontvein, O.; Stroppa, D. G.; Popovitz-Biro, R.; Albu-Yaron, A.; Levy, M.; Feuerman, D.;
Houben, L.; Tenne, R.; Gordon, J. M., New High-Temperature Pb-Catalyzed Synthesis of
Inorganic Nanotubes. Journal of the American Chemical Society 2012, 134 (39), 16379-
16386.
- 62 -

ISM 2014 - The 48th Annual Scientific Meeting of ISM
Weizmann Institute of Science, Rehovot
Olga Kleinerman, Yachin Cohen and Yeshayahu Talmon
Department of Chemical Engineering, Technion - Israel Institute of Technology, Haifa 32000, Israel
During recent years it has been demonstrated that carbon nanotubes (CNTs) spontaneously dissolve in chlorosulfonic acid (Davis et al., 2009), and at high concentrations form a liquid crystalline phase (Davis et al., 2004). Actually, chlorosulfonic acid (CSA) is the only solvent for CNT, to form thermodynamically stable solutions and liquid crystalline phases, from which carbon fibers can be spun. Fiber spinning from a liquid crystal state is essential for the high degree of CNT orientation in the fibers, and hence preserving the intrinsic unique properties of individual CNT in the spun fiber (Behabtu et al., 2013).
The transition between the isotropic and the liquid crystalline phases depends strongly on the
CNT type, concentration, and solvent strength. Combination of direct cryogenic transmission- and cryogenic scanning-electron (cryo-TEM and cryo-SEM) imaging of
CNT/CSA solutions at different concentrations allowed us, for the first time to follow phase transformation at nanometric level; from diluted solution to the isotropic phase, through the biphasic region, to the pure liquid crystalline phase (LC), used as the "dope" for fiber spinning. To allow direct imaging of superacid solutions we developed unique cryo-EM specimen preparation and imaging methodologies, suitable for highly acidic systems. Those techniques preserve the native nanostructure in the system, without harming the expensive equipment and the operator (Kleinerman et al., 2013).
Presented cryo-EM images (Fig. 1a) are the first direct validation of Flory's model describing phase transitions in rigid-rod polymers (Flory P.J, 1956) in CNT/superacid systems (Fig. 1b).
The correlation between direct imaging of the "dope" in its liquid state and of fiber, spun from the "dope" (Fig. 2) allowed us to study the effect of CNT behavior in the solution on final fiber structure and alignment, which are directly related to fiber mechanical and electrical properties. By combination of x-ray analysis, with focused ion beam (FIB) fiber cross-sectioning, and high-resolution electron microscopy for morphological and chemical analysis, we have provided nanometric structural information of the fibers, in terms of CNT alignment, degree of purity and porosity.
- 63 -

ISM 2014 - The 48th Annual Scientific Meeting of ISM
Weizmann Institute of Science, Rehovot
Figure 1: (a) Cryo-EM micrographs of CNT/CSA solution, showing liquid crystalline phase development as a function of nanotube concentration (from left to right CNT concentration is
increased). Dilute, semi-dilute and isotropic phases are cryo-TEM micrographs. Biphasic and fully liquid crystalline phases are cryo-SEM images. (b) A model of aligned phase development in rigid-rod polymer solution, as predicted by Flory's model in 1956 (Flory P.J,
1956) and schematically presented by Doi and Edwards in 1986 (Doi, M.& Edwards S.F.,
1986).
Figure 2: (a) Room temperature HR-SEM image of CNT fiber surface, spun from the LC
"dope" of CNT (3%wt) in CSA . (b) cryo-SEM image of the "dope": CNT (3%wt) in CSA.
References :
1.
Behabtu N., Young C.C., Tsentalovich D.E., Kleinerman O., Wang X., Ma A.W.K., Bengio
E.A., Ter Waarbeek R.F., De Jong J.J., Hoogerwerf R.E., Fairchild S.B., Ferguson J.B.,
Maruyama B., Kono J., Talmon Y., Cohen Y., Otto M.J. & Pasquali M., Strong, light,
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ISM 2014 - The 48th Annual Scientific Meeting of ISM
Weizmann Institute of Science, Rehovot multifunctional fibers of carbon nanotubes with ultrahigh conductivity. Science 339, 182-186,
(2013).
2.
Davis V.A., Ericson L.M., Parra-Vasquez A.N.G., Fan H., Wang Y., Prieto V., Longoria J.A.,
Ramesh S., Saini R.K., Kittrell C., Billups W.E., Adams W.W., Hauge R.H., Smalley R.E. &
Pasquali M., Phase behavior and rheology of SWNTs in superacids. Macromolecules 37, 154-
160, (2004).
3.
Davis V.A., Parra-Vasquez A.N.G., Green M.J., Rai P.K., Behabtu N., Prieto V., Booker R.D.,
Schmidt J., Kesselman E., Zhou W., Fan H., Adams W.W., Hauge R.H., Fischer J.E., Cohen Y.,
Talmon Y., Smalley R.E. & Pasquali M., True solutions of single-walled carbon nanotubes for assembly into macroscopic materials. Nat. Nanotechnol. 4, 830-834, (2009).
4.
Doi, M.and Edwards, S. F., The Theory of Polymer Dynamics; Oxford University Press: Oxford,
325, (1986).
5.
Flory P. J., "Phase Equilibria in Solutions of Rigid Particles", Proc. Roy. Soc. (London), A234,
73-89 (1956).
6.
Kleinerman, O., Parra-Vasquez, A.N.G., Green M.G., Behabtu, N., Judith Schmidt J., Kesselman
E., Young, C.C, Cohen, Y., Pasquali, M., and Talmon, Y., Cryogenic-Temperature Electron
Microscopy for Direct Imaging of Carbon Nano-Allotropes Dissolved in Super-acids (paper in preparation), (2013).
7.
Kleinerman, O., Adnan, M., Ma, A., Behabtu, N., Bengio, A., Park, C., Pasquali, M., and
Talmon, Y. True Solutions of Boron Nitride Nanotubes (paper in preparation), (2013).
8.
Ramesh S., Ericson L.M., Davis V.A., Saini R.K., Kittrell C., Pasquali M., Billups W.E., Adams
W.W., Hauge R.H. & Smalley R.E., Dissolution of pristine single walled carbon nanotubes in superacids by direct protonation. J Phys Chem B 108, 8794-8798, 2004.
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ISM 2014 - The 48th Annual Scientific Meeting of ISM
Weizmann Institute of Science, Rehovot
x
1-x
Pradipta Sankar Maiti 1 , Lothar Houben 2 and Maya Bar-Sadan 1 *
1 Department of Chemistry, Ben-Gurion University of the Negev, Be'er Sheva, Israel
2
Ernst Ruska Center, Juelich, Germany
Two-dimensional (2D) semiconductor nanostructures, with the properties similar to quantum wells (QW), have attracted a lot of interest from many researchers in recent years. These structures can be easily prepared in solution phase with controlled and uniform thickness that is small compared to their lateral dimensions. The 2-D nanostructures have appealing combination of properties: physical properties close to the quantum wells and chemical properties similar to the colloidal quantum dots. Furthermore, alloying these semiconductors also provide us additional degree of freedom which can be used to tune their properties by varying their composition. These alloyed semiconductors can open new possibilities in band gap engineering and as well as developing tunable emitters.
Here, we report the solution phase synthesis of the ultrathin 2-D CdS x
Se
1-x nanosheets as well as their properties. We show how the relative amount of S and Se can drastically affect the shape, size and optical properties of these structures. We also present the C c
and C s
corrected high-resolution electron microscopy (HR-TEM) studies for these 2D systems. Structural, compositional and optical characterizations are presented using UV-visible absorption and fluorescence spectroscopy, atomic force microscopy (AFM) and powder X-diffraction
(PXRD).
References:
1. Ithurria, S.; Tessier, M. D.; Mahler, B.; Lobo, R. P. S. M.; Dubertret, B.; Efros, A. L. Colloidal nanoplatelets with two-dimensional electronic structure. Nature Materials, Volume 10, 936-941,
(2011).
2. Son, J. S.; et al. Large-Scale Soft Colloidal Template Synthesis of 1.4 nm Thick CdSe Nanosheets.
Angew. Chem., Int. Ed. Volume 48, 6861–6864, (2009).
3. Liu, Y. H.; Wang, F.; Wang, Y.; Gibbons, P. C.; Buhro, W. E. Lamellar Assembly of Cadmium
Selenide Nanoclusters into Quantum Belts. J. Am. Chem. Soc. Volume 133, 17005–17013, (2011).
- 66 -

ISM 2014 - The 48th Annual Scientific Meeting of ISM
Weizmann Institute of Science, Rehovot
2
Ruth Moshe and Wayne D. Kaplan
Department of Materials Science & Engineering, Technion – IIT, Haifa, Israel
Polycrystalline alumina (Al
2
O
3
) is widely used as a structural ceramic material mainly due to its high hardness and fracture strength, creep and corrosion resistance, low density, and mechanical strength at high temperatures. These macroscopic properties of mass-produced alumina strongly depend on the composition of the powder used for the sintering process, and the microstructure of the sintered body, where dopants and impurities are known to affect sintering rates and grain growth. It has been shown that MgO promotes sintering and normal grain growth, whereas Si results in secondary glass phases and abnormal grain growth [1].
There are conflicting reports in the literature whether Si is detrimental to sintering of alumina when it is in solution, since the solubility limit of Si in alumina at the sintering temperature has not been determined [2]. It has been demonstrated that ppm level solubility limits of cations in alumina can be determined by conducting fully standardized wavelength dispersive spectroscopy (WDS) on saturated (two-phase) samples quenched from high temperature [3-
5]. In this study, the solubility limit of Si in Al
2
O
3
is investigated using WDS from samples quenched from 1600°C in order to further understand the effect of impurities on the microstructural evolution of alumina.
References :
1. K. L. Gavrilov, S. J. Bennison, K. R. Mikeska, J. M. Chabala, R. Levi-Setti, Silica and
Magnesia Dopant Distributions in Alumina by High-Resolution Scanning Secondary Ion Mass
Spectrometry, Journal of the American Ceramic Society, 82[4]:1001-1008, 1999.
2. S. J. Dillon, M. P. Harmer, Relating grain boundary complexion to grain boundary kinetics II:
Silica-doped alumina, Journal of the American Ceramic Society, 91[7]:2314-2320, 2008.
3. L. Miller, A. Avishai, W. D. Kaplan, Solubility Limit of MgO in Al
2
O
3
at 1600°C, Journal of the American Ceramic Society, 89[1]:350-353, 2006.
4. L. Miller, W. D. Kaplan, Solubility Limits of La and Y in Aluminum Oxynitride at 1870°C,
Journal of the American Ceramic Society, 91[5]:1693-1696, 2008.
5.
R. Akiva, A. Berner, W. D. Kaplan, The Solubility Limit of CaO in α-Alumina at 1600°C,
Journal of the American Ceramic Society, 96[10]:3258-3264, 2013.
- 67 -

ISM 2014 - The 48th Annual Scientific Meeting of ISM
Weizmann Institute of Science, Rehovot
2
2
Ayala Cohen, Sagi Appel and Maya Bar-Sadan
Chemistry Department, Ben-Gurion University, Israel.
Recent advances in nanotechnology, following the discovery of graphene, has led researchers to look for new fabrication methods of defect free 2D structures. Transition metal dichalcogenide (TMD) compounds, such as MoS
2
and WS
2
, have been extensively researched in the past decade, due to their Graphite-like laminated structure. The semiconductive nature of TMD compounds makes them compatible for various electrical and thermoelectric applications. The efficiency of a thermoelectric material is characterized by its figure of merit (ZT). ZT=α 2 T/κρ, where α is the Seebeck coefficient, T is the absolute temperature, κ is the thermal conductivity and ρ is the electrical resistivity.
Each MoS
2
and WS
2
layer is comprised of strong covalent bonds within the layer, while the layers themselves interact via weak Van-Der Waals interactions, this unique configuration makes it relatively easy to produce 2D structures out of them. A combined compound of
Mo x
W
1-x
S
2 has been shown to reduce the lattice thermal conductivity κ
L
within the layer, thus improving the thermoelectric figure of merit (ZT).
This study examines an exfoliation method in which ultrasonic sound waves are applied on
MoS
2
and WS
2
dissolved in liquid solutions, this method has shown to produce large concentrations of defect-free single layers. Moreover, a restacking process of exfoliated
MoS
2
and WS
2
layers in exact ratios was conducted, in the prospect of achieving similar properties to chemically synthesized Mo x
W
1-x
S
2
. This method could be preferable to the replacement of single atoms within a given compound, as it doesn't require the breaking of covalent bonds and is easily scalable.
- 68 -

ISM 2014 - The 48th Annual Scientific Meeting of ISM
Weizmann Institute of Science, Rehovot
Shai Mangel 1 , Eran Aronovitch 1 , Lothar Houben 2 and Maya Bar-Sadan 1
1 Chemistry Department, Ben Gurion University of the Negev, Beer Sheba, Israel
2 Peter Grünberg Institut 5 and Ernst Ruska Centre for Microscopy and Spectroscopy with
Electrons, Forschungszentrum Jülich GmbH, 52425 Jülich, Germany
Colloidal CdSe@CdS nanoparticles are one of the most extensively researched systems in nanoscience, due to their optical and electronic size dependent properties. While reports on the optical properties of single particles are available, the quantitative characterization of atomic order on a single particle level, which has a crucial role in determining the physical properties, and the growth mechanism that resulted in that specific rearrangement, are still generally missing.
The use of advanced Cc and Cs corrected High-Resolution TEM in 80kV and phase reconstructions procedures enable us to follow their growth process and determine the polarity of the particles by identifying the terminating facets. The use of these high resolution characterizations techniques allow us to observe the stacking faults formation at different domains in the particle during its growth and to investigate the influence of the deposition of the shell on the atomic rearrangement of the core.
Here we report that after the deposition process we observe an increase in the stacking faults formation, which are mostly expressed as phase transition in the particle crystal structure and located mainly at the estimated shell area and its close surrounding.
The structural and optical characterizations are presented using UV-vis absorption,
Fluorescence and XRD.
References:
1. Yin, Y. and A.P. Alivisatos, Colloidal nanocrystal synthesis and the organic-inorganic interface.
Nature, 2005. 437(7059): p. 664-670.
2. Murray, C.B., D.J. Norris, and M.G. Bawendi, Synthesis and Characterization of Nearly
Monodispere CdE (E = S, Se, Te) Semiconductor Nanocrystallites Journal of the American
Chemical Society, 1993. 115(19): p. 8706-8715.
- 69 -

ISM 2014 - The 48th Annual Scientific Meeting of ISM
Weizmann Institute of Science, Rehovot
Katya Gotlib-Vainshtein 1 , Olga Girshevitz 1 , Chaim N. Sukenik 1* , David Barlam 2 and
Sidney R. Cohen 3*
1 Department of Chemistry and Institute of Nanotechnology & Advanced Materials Bar Ilan
University, Ramat-Gan ISRAEL,
2
Department of Mechanical Engineering Ben Gurion University, Beer Sheva, Israel;
3 Department of Chemical Research SupportWeizmann Institute of Science, Rehovot ISRAEL
In this work, scanning force microscopy (SFM) is used to measure tribological characteristics of a novel, compound film. Hard coatings are often applied to engineering surfaces for reduction of friction and wear. Here, we show that a soft, flexible, intermediate layer placed between substrate and hard outer coating provides considerable enhancement of the wear protection. Previously, we demonstrated that such compound films provide a means to controllably tune surface stiffness, thus opening interesting nanomechanical applications.
1
Titania films of several nm thickness are coated onto substrates of silicon, kapton, polycarbonate, and polydimethylsiloxane (PDMS) and the scratch resistance is measured by
SFM. When PDMS is applied as an intermediate layer between any harder substrate and the thin titania outer layer, marked improvement in the scratch resistance is achieved. This is shown by quantitative wear tests on silicon and kapton substrates, by coating them with
PDMS which is subsequently capped by a titania layer with thickness ranging from several nm to several tens of nm. In addition to the improvement in scratch/wear resistance, nanofriction studies performed in the SFM showed that the PDMS cushion layer reduced friction coefficient of titania coating by more than a factor of two.
To demonstrate a technological application of such coatings, they were applied to the common lens material polycarbonate – 40 nm titania (deposited by liquid phase deposition
2
) on a several micrometer-thick PDMS “cushion”. In scratch tests, load to failure was increased by 5x without any detrimental effect on the optical properties of the polycarbonate. This work thus demonstrates, a simple, robust, and practical means of improving tribological properties.
The physical basis of this effect is explored by means of Finite Element Analysis, and we suggest a model for friction reduction based on the "cushioning effect” of a soft intermediate layer.
- 70 -

ISM 2014 - The 48th Annual Scientific Meeting of ISM
Weizmann Institute of Science, Rehovot
Figure 1. Atomic force microscope images of polycarbonate (PC) surfaces with different surface treatment, after scratch tests at the indicated loads.
References:
1. K. Gotlib-Vainshtein, O. Girshevitz, C.N. Sukenik, D. Barlam, E. Kalfon-Cohen, S.R. Cohen,
Oxide Surfaces with Tunable Stiffness. J. Phys. Chem. C 117, 22232-22239 (2013).
2. O. Girshevitz, Y. Nitzan, C.N. Sukenik, Solution-deposited amorphous titanium dioxide on silicone rubber. Chem. Mater., 20, 1390-1396 (2008).
- 71 -

ISM 2014 - The 48th Annual Scientific Meeting of ISM
Weizmann Institute of Science, Rehovot
Udayabhaskararao Thumu, Tino Zdobinsky and Rafal Klajn*
Department of Organic Chemistry, Weizmann Institute of Science, Rehovot 76100, Israel.
Ordered arrays or superlattices consisting of nanocrystals (NCs) with different well-defined diameters represent an important class of materials, which have been used for the fabrication of diverse NC-based devices.
1,2
Recent advances in monodisperse NC synthesis and selfassembly enable the creation of multicomponent superlattices in which two or three types of
NCs are co-crystallized into ordered structures. In particular, binary NC superlattices
(BNSLs) consisting of two NC components distinct in size and/or composition have attracted due to their intriguing diverse superlattice structures as well as wide applications in electronic and magnetic devices. Despite these advances, little progress has been made to date in the structural control over the desired structure of superlattices. Here, we used novel UV mediated and post modification methods to create self-assembly of Au
25 into single and 3D cluster sheets and uncommon FCC packed Fe
3
O
4
NCs and Au nanoparticles with welldefined distances between them, respectively.
- 72 -

ISM 2014 - The 48th Annual Scientific Meeting of ISM
Weizmann Institute of Science, Rehovot
Figure 1. TEM image of as-synthesized, AB-type 13.2 nm Fe
3
O
4 and 5.4 nm Au NC BNSLs
(a) are incubated in solutions of aq. KCN (b) and aq. HCl at pH 5 for 48 hours (c). Novel SLs are seen upon dissolution of gold NCs and Fe
3
O
4
NCs in presence of aq. KCN and HCl solutions, respectively. Schematic representation of SLs obtained upon the dissolution of gold
NCs (represented in yellow color) and Fe
3
O
4
NCs (represented in blue color).
References:
1. Talapin, D. V. Lee, J. S. Kovalenko, M. V. Shevchenko, E. V. Chem. Rev. 110, 389–458, (2010).
2. Murray, C. B. Kagan, C. R. Bawendi, M. G. Science 270 , 1335–1338, (1995).
- 73 -

ISM 2014 - The 48th Annual Scientific Meeting of ISM
Weizmann Institute of Science, Rehovot
Roy Shiloh
1
, Yuval Tsur
1
, Yossi Lereah
1
, Boris A. Malomed
1
, Vladlen
Shvedov
2
, Cyril Hnatovsky
2
, Wieslaw Krolikowski
2
and Ady Arie
1
1
Department of Physical Electronics, Fleischman Faculty of Engineering, Tel Aviv University, Tel
2
Aviv 6997801, Israel
Laser Physics Centre, The Australian National University, Canberra ACT 0200, Australia
New forms of electron beams have been intensively investigated recently, including vortex beams carrying orbital angular momentum, and Airy beams propagating along a parabolic trajectory in free-space. Their traits may be harnessed for applications in materials science, electron microscopy and interferometry, and so it is important to measure their properties with ease. In this poster we present methods to quantify these beams’ parameters without need for additional fabrication or non-standard microscopic tools. Our experimental results are backed by numerical simulations and analytic derivations.
Recently it became possible to generate special shapes of electron beams. One of these special beams is the vortex beam [1] having a helical wavefront structure and a phase singularity on axis. Its azimuthal phase dependence is 𝑒 𝑖𝑙𝜙
, where l is the topological charge, and 𝜙
is the azimuthal angle. Each electron carries an orbital angular momentum of ℏ𝑙
[1]. Another interesting beam is the Airy beam, having the transverse form of the Airy function, i.e.
𝐴𝑖 ( ⁄
0
)
, where 𝑥
0
defines the transverse scale. It is shape-preserving along a parabolic trajectory in free-space with a “self-acceleration” coefficient
⁄ 𝑥 𝑘 2
, where 𝑘 is the wave number [2]. As possible applications, vortex beams were used in electron energy loss spectroscopy in order to characterize the magnetic state of a ferromagnetic material [1], while Airy beams were proposed for the realization of a new type of an electron interferometer [2]. In order to utilize these new types of electron beams, it is required to develop methods that allow one to easily determine their main attributes - the orbital angular momentum in the case of a vortex beam or the self-acceleration coefficient in the case of an
Airy beam.
In this poster, we first show that by deliberately applying astigmatism to a vortex beam, it is converted to a different type of beam (Hermite-Gauss), in which the topological charge is easily quantified, appearing as dark stripes in the micrograph (Fig 1 left).
We then use the same principle to investigate the self-acceleration of 2D Airy beams. We present the first encounter of Airy beams with special transformations, specifically the astigmatic transformation. We find an analytic relation (Fig. 1 right, e) between the selfacceleration coefficient and the asymptotic angle of the beam's envelope (marked as v in Fig.
1 right, d).
- 74 -

ISM 2014 - The 48th Annual Scientific Meeting of ISM
Weizmann Institute of Science, Rehovot
Figure 1. (Left figure) TEM diffraction image of (a) vortices generated by a charge 3 fork grating, (zero-order blocked); (b) corresponding vortices under astigmatism; (c) fork mask.
(Right figure) Astigmatic Airy beams. (a) Images of the transformed beams; (b) simulated
Airy beams (right) and their corresponding astigmatic transformation (left); (c) Micrographs of the lowest and highest self-acceleration Airy masks; (d) same as (b), for higher selfacceleration; (e) self-acceleration dependence of the hyperbola asymptotic angle v.
In conclusion, we present a method of measuring the orbital angular momentum of electron vortex beams by means of the astigmatic transformation. The transformation is applied literally by the turn of a knob in any TEM. Since the orbital angular momentum can be transferred between the electron beam and the internal electron states in an atom, this method can be readily applied for microscopic studies of materials [3]. We then apply astigmatism to
Airy beams, and measure the Airy beam's self-acceleration. Our results warrant further theoretical investigation into the astigmatic transform of other beams to which it may be relevant, such as Bessel beams [4] and beams with arbitrary caustic curves [5], unveiling their underlying propagation parameters.
References :
1. J. Verbeeck, H. Tian, P. Schattschneider, Production and application of electron vortex beams.
Nature , 467 , 301–4, (2010).
2. N. Voloch-Bloch, Y. Lereah, Y. Lilach, A. Gover, A. Arie, Generation of electron Airy beams.
Nature , 494 , 331–335, (2013).
3. S. Lloyd, M. Babiker, J. Yuan, Quantized orbital angular momentum transfer and magnetic dichroism in the interaction of electron vortices with matter. Physical Review Letters , 108, 074802,
(2012).
4. V. Grillo, E. Karimi, G. C. Gazzadi, S. Frabboni, M. R. Dennis, R. W. Boyd. Generation of nondiffracting electron Bessel beams. Physical Review X , 4, 011013, (2014).
5. L. Froehly, F. Courvoisier, A. Mathis, M. Jacquot, L. Furfaro, R. Giust, P. A. Lacourt, J. M.
Dudley. Arbitrary accelerating micron-scale caustic beams in two and three dimensions. Optics
Express , 19, 16455–65, (2011).
- 75 -

ISM 2014 - The 48th Annual Scientific Meeting of ISM
Weizmann Institute of Science, Rehovot
Anat Akiva a , Karina Yaniv b , Lia Addadi a and Steve Weiner a a. Department of Structural Biology, Weizmann Institute of Science, Rehovot, Israel. b. Department of Biological Regulation, Weizmann Institute of Science, Rehovot, Israel.
In order to produce their mineralized skeletons, many vertebrates groups first form a transient amorphous mineral phase, which then transforms into the mature crystalline phase. An open question in biomineralization concerns the pathway through which ions are sequestered from the environment, transported, concentrated and aggregated within the soft tissues, to form the transient mineral phases. Here we study calcium transport and mineral formation in the forming zebrafish larva caudal fin in vivo. We exploit the availability of transgenic zebrafish carrying fluorescent reporters within blood vessels to explore the intimate relations between bone, bone-related cells, and the circulatory system during bone development.
In this study we use complementary advanced techniques that allow characterization of the native mineralizing tissue: ( i ) correlative confocal fluorescence microscopy of transgenic fish and calcium staining, which provides views of the developing tail in vivo; ( ii ) Cryo-Scanning
Electron Microscopy of rapidly frozen tail specimens, allowing high-resolution images of the intact tissue, not damaged by chemical fixation and drying; ( iii ) Synchrotron micro-beam Xray fluorescence mapping, which provides information on the mineral composition of the particles and their locations; ( iv ) Simultaneous fluorescence and Raman imaging on a living fish1, allowing real time spectroscopy of the mineral aggregates.
Our results show that mineral aggregates and intracellular mineral vesicles are located in close proximity to blood vessels. Some of the intracellular mineral vesicles were observed in cells which also carry an endothelial fluorescent marker. This might imply the existence of a common lineage for endothelial and osteoblast cells. Raman spectroscopy coupled with fluorescence imaging performed on a living fish, shows the presence of a disordered calcium phosphate phase with characteristic features of an OCP-like phase in mineral aggregates located between bones.
The achievement of in vivo correlative confocal imaging and spectroscopy of cells and mineral in a living animal advances our understanding of bone mineralization pathways in vertebrates, including humans.
References:
1. M. Bennet, A. Akiva, D. Faivre, G. Malkinson, K. Yaniv, S. Abdelilah-Seyfried, P. Fratzl, and A. Masic, 'Simultaneous Fluorescence-Raman Imaging of Bone Mineralization in Living
Zebrafish Larvae', Biophysical Journal, 106 (2014), L17-L19.
- 76 -

ISM 2014 - The 48th Annual Scientific Meeting of ISM
Weizmann Institute of Science, Rehovot
Anat Shperberg Avni, Reinat Nevo, Ofra Golani, Sharon Wolf, Eyal Shimoni,
Dror Noy and Ziv Reich.
Department of Biological Chemistry, Weizmann Institute of Science, Rehovot, Israel.
State transitions are rapid-response adaptation processes that allow oxygenic phototrophs to maintain high photosynthetic yields under fluctuations in light intensity and/or quality. They involve changes in the distribution of light energy to the two photosystems. While the mechanism of state transitions in higher plants and green algae is quite well characterized and understood, the manner by which they operate in cyanobacteria is not clear. We address this issue by employing two electron microscopy (EM) techniques; freeze-fracture EM and electron microscope tomography (EMT), and by using mutant strains deficient in different components of the phycobilisome (PBS) – the large, soluble molecular assembly that mediates peripheral light harvesting in these organisms.
Figure 1. Freeze-fracture. In order to determine the organization of PSI and PSII in the thylakoid membranes, high-pressure frozen cells, wildtype and PBS mutant (∆PC), were freeze-fractured and visualized using cryo-SEM. The density of the proteins on the two fractured membrane faces, the EF (exoplasmic face) and the PF (protoplasmic face) is significantly different. PSII has been shown to reside in the EF, while monomeric and trimeric PSIs are localized to the PF. While comparing the data set of state II (dark-adapted) to state I (far red illumination), it can immediately be seen that PSII complexes that arranged in rows are more abundant in state I.
- 77 -

ISM 2014 - The 48th Annual Scientific Meeting of ISM
Weizmann Institute of Science, Rehovot
Dvir Gur, Ben Leshem, Dan Oron, Steve Weiner and Lia Addadi a Department of Structural Biology, Weizmann Institute of Science, Rehovot, 76100 (Israel)
One very interesting function of biogenic organic crystals is in the production of structural colors. Structural colors are caused by the interaction of light with structures that have periodicities comparable to the wavelength of visible light. Animals from different phyla have independently evolved ways to produce structural colors using intra-cellular arrays of thin plate-shaped guanine crystals interspersed with cytoplasm. A well-studied example is the
Japanese Koi fish ( Cyprinus carpio ) whose scales’ metallic luster originates from periodically arranged thin guanine crystals [1]. The crystals are enveloped by membranes and form from an amorphous precursor [2]. One variety, the Gin Rin, has scales with strikingly higher reflectance than the classic Koi. We used a correlative approach in which the reflecting scales and skin from both Gin Rin and classic Koi fish were measured by a custom made microscope consisting in a micro-spectrophotometer, two CCD cameras and a high numerical aperture objective. The custom built microscope enabled us to acquire the reflectance spectrum and an image of the epidermal layer and its associated scale, as well as to obtain the Fourier transform of the reflectance for the same location in the scale. This information was then correlated to the crystal arrangement as visualized by cryo-SEM on the same set of samples.
A mathematical simulation of the expected reflectance was then performed for each sample based on the data acquired on the crystal arrangement, and was compared to the measured reflectance (Figure 1).
Figure 1: Correlative representation of all the parameters measured or simulated for one Gin
Rin scale and one classic scale. i) Light microscope images. ii) cryo-SEM images. iii)
Normalized measured reflectance. iv) Calculated reflectance. The measured reflectance was obtained by a micro-spectrophotometer and was normalized to the crystal stack coverage area in the scales (determined by the light microscope image). The geometric parameters used to calculate the reflectance were determined by cryo-SEM.
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ISM 2014 - The 48th Annual Scientific Meeting of ISM
Weizmann Institute of Science, Rehovot
We have found that the higher reflectance of the Gin Rin scales and skin is achieved using the same basic building blocks present in the classic Koi, i.e. alternating layers of the anhydrous guanine crystals and cytoplasm. However, we have found 4 different structural features that were different between the Gin Rin and the classic Koi: 1.The dermal layer underneath the scale of the Gin Rin appears much more densely covered with crystal stacks.
2. The orientation of the crystals relative to the scale surface is almost parallel in the Gin Rin and around 30° in the classic Koi 3. The number of layers of iridophores underneath the scale and the number of crystal stacks inside iridophores is much higher in the Gin Rin system.4.
Intercalation of different crystal stacks within the iridophores resulting in lower d-spacings between the crystals was found only in the Gin Rin and is absent in the classic Koi (Figure
2). The good agreement between the calculated reflectance spectrum and the measured reflectance spectrum confirms that the specific features observed in the Gin Rin structure all contribute to the extra-reflectance. In order to produce a structure with such features, control over not only the crystal size, morphology and orientation is required but also on the 3D assembly of the crystals, all indicating a very high degree of structural regulation.
Figure 2: cryo-SEM micrographs of high pressure frozen, freeze fractured scale and skin. a and b) iridiphore of a classic Koi fish, with one stack of parallel crystals. c and d) iridophore of a Gin Rin Koi fish showing two crystal stacks inside a single cell. Frequently the crystal stacks intercalate with each other resulting in a shorter distance between the crystals;
References:
1. A. Levy-Lior, E. Shimoni, O. Schwartz, E. Gavish-Regev, D.Oron, G. Oxford, S. Weiner,
L. Addadi, Advance Functional Materials. 2010, 20, 320 – 329.
2. Gur D, Politi Y, Weiner S, Addadi L (2013) Guanine-Based Photonic Crystals in Fish
Scales Form from an Amorphous Precursor. Angewandte Chemie International Edition
52(1):388-391.
- 79 -

ISM 2014 - The 48th Annual Scientific Meeting of ISM
Weizmann Institute of Science, Rehovot
Gal Mor Khalifa 1 , David Kirchenbuchler 1 , Michael Elbaum 1 , Jonathan Erez 2 , Lia Addadi 1 and Steve Weiner 1
1.Weizmann Institute of science, Rehovot, Israel
2.Hebrew University,
Har ha-Tsofim, Jerusalem
Foraminifera are single celled marine protozoans that are widespread in oceans throughout the world. Many Foraminifera produce an outer protective shell made of calcite and together with coccolithophores are responsible for most of the calcium carbonate formed in the oceans. Foraminifera can be cultured making them an excellent model organism for studying intracellular bioimineralization processes. The calcitic radial foraminifera construct their shells by an extracellular biomineralization process. They are known to internalize sea water vacuoles into the cytoplasm by endocytosis, and these vacuoles play an important role in the mineralization process, but their exact function is not yet known. Calcium is known to be stored in the cytoplasm prior to its deposition in the shell wall but the location and phase of the stored calcium is also unknown.
The goal of this study is to track the course of calcium through the calcitic radial foraminifera cell and to uncover the mechanisms of its stabilization in storage organelles, and its deposition at the mineralization site.
We observe intact foraminifera, in vivo, and use the cell impermeable calcium indicator, calcein, to track the course of calcium in the foraminifera cell, following Bentov et al (2009).
We have developed a novel correlative cryo SEM- fluorescence technique. Using this technique we observe a freeze fractured foraminifera, under cryo conditions, both in scanning electron microscope and in the confocal fluorescence microscope, and correlate the images at every location in the sample. We obtain high resolution morphological and compositional characterization of cellular organelles in the foraminifera cell, and observe their spacial interaction with the forming mineral of the shell (SEM data). We further distinguish the calcium concentrating organelles by their fluorescent signal due to calcein labeling.
Our cryo SEM and cryo fluorescence observations support the presence of sea water vacuoles with a range of sizes between a micron to tens of microns, previously reported by Bentov et al. (2009). The prevalence of the sea water vacuoles increased towards the newer chambers.
We further observed many vesicles strongly labeled with calcein with a uniform size (about
2-3microns) and with a lifetime of several days in the cytoplasm. Occasionally we observed micron size calcein labeled mineral aggregates incorporated within sea water vacuoles (tens of micrometers). Calcein labeling of these mineral bodies indicates that these are calcium minerals.
The calcein labeled vesicles may be calcium concentrating organelles which serves as a storage phase in the cytoplasm. This is the first report of calcium mineral aggregates inside sea water vacuoles. To date the mineralization mechanism of calcitic radial foraminifera was considered to be entirely extracellular. These mineral aggregates may be a precursor phase for mineralization to be deposited at the mineralization site at the shell wall. The formation
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ISM 2014 - The 48th Annual Scientific Meeting of ISM
Weizmann Institute of Science, Rehovot process of these cytoplasmic mineral bodies, their incorporation into the sea water vacuoles and their involvement in the mineralization pathway is still an enigma. This finding reinforces the importance of sea water vacuoles in the biomineralization process, but sheds new light on their possible role in the mineralization process.
References:
1.
Bentov, S., C. Brownlee, and J. Erez, The role of seawater endocytosis in the bioimineralization process in calcareous foraminifera. Proceedings of the National
Academy of Sciences of the United States of America, 106, 21500-21504, (2009).
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ISM 2014 - The 48th Annual Scientific Meeting of ISM
Weizmann Institute of Science, Rehovot
Giuliano Bellapadrona and Michael Elbaum
Dept of Materials and Interfaces, Weizmann Institute of Science, Rehovot 76100, Israel.
A fully genetically encoded protein supramolecular assemblies (PSMA) system able to subcellular compartmentalization in human HeLa cells have been designed by combining in a single fusion construct (i) a nuclear localization signal, and the genes encoding for (ii) the ferritin heavy H chain subunit (HuFtH), well-known for its self-assembly properties, and for
(iii) Citrine fluorescent protein, the latter endowed with a weak dimerization interface.
In vivo confocal fluorescence and differential interference contrast (DIC) imaging showed extended PSMA structures forming upon the expression of the fusion construct exclusively in the nucleus of HeLa cells.
Citrine-HuFtH PSMA were found in plastic embedded sections of HeLa cells and showed a crystalline order by transmission electron microscopy.
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ISM 2014 - The 48th Annual Scientific Meeting of ISM
Weizmann Institute of Science, Rehovot
Site-specific mutagenesis of the Citrine dimerization interface clarified the mechanism of formation of Citrine-HuFtH PSMA formation. Finally, the functional properties of ferritin were shown to be retained by histological staining assay.
References :
Giuliano Bellapadrona and Michael Elbaum. Supramolecular protein assemblies in the nucleus of human cells. Angew Chem Int Ed Engl. 53(6):1534-7. (2014).
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ISM 2014 - The 48th Annual Scientific Meeting of ISM
Weizmann Institute of Science, Rehovot
1 Ilana Shtein and 1,* Rivka Elbaum
1 The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, The Hebrew University of Jerusalem, Robert H. Smith Faculty of Agriculture, Food and Environment.
* rivka.
elbaum@mail.huji.ac.il
Though being sessile organisms, plants have evolved numerous motion mechanisms for protection and dispersal. The most prominent form of monocotyledon movement is root contraction. This phenomenon is important for 1) securing an underground position in young seedlings or mature plants in order to escape potentially dangerous soil temperatures, uprooting or herbivory and 2) dispersal of daughter bulbs. Monocotyledon contracted roots often involve a contracted stele, collapsed outer cortex and contracted, accordion-like surface of the root. The accepted hypothesis is that the middle cortex cells swell, expand transversely and pull the root. However, the molecular and mechanistic details of the contraction process are largely unknown. We hypothesise that the arrangement of the cellulose microfibrils in the cell walls controls the pulling force. Therefore we examined root contraction in Pancratium maritimum seedlings in comparison to Allium cepa non-contractile roots. Three months old seedlings underground depth was 2.5 cm in P. maritimum and 0.2 cm in A. cepa. Cellulose microfibrils angles in different root regions were accessed via polarized light microscopy.
Our preliminary results indicate that the cellulose microfibril angles change in the cortex cells of P. maritimum. While the inner cortex cells show 20º angle, middle cortex expanded cells have 75º angle. In A. cepa the inner cortex cells show 18º angle, middle cortex expanded cells have 21º angle. Such difference in orientation might explain the differential ability to contract. In the future we intend to explore this phenomenon further and elucidate the root contraction process.
Figure 1. Contractile root of Pancratium maritimum exhibiting collapsed cells (A), noncontractile root of Allium cepa (B) and a PolScope image of P. maritimum root.
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ISM 2014 - The 48th Annual Scientific Meeting of ISM
Weizmann Institute of Science, Rehovot
Leo Goldstien † , Daniel Blumenthal † and Levi A. Gheber †§
† Avram and Stella Godstein-Goren Department of Biotechnology Engineering, Ben Gurion
University of the Negev, Beer Sheva, Israel; § Ilse Katz Institute for Nanoscale Science and
Technology, Ben Gurion University of the Negev, Beer Sheva, Israel
Delivery of therapeutic molecules to sub-cellular compartments allows for increased drug efficacy and reduction of undesired side effects. Though classic methods of drug design have achieved moderate success in these areas, this goal can be better served using nano-carriers.
Rational design of nano-carries allows for protection of the drugs from degradation, circumvention of immunogenic responses and release of drugs on target. While the design aspects of nano-carriers are well understood and established, few methods exist to monitor and report on essential events incurred by the carrier along its convoluted path to the target.
We show that by a combination of carefully chosen fluorescent labels and through application of Single Particle Tracking (SPT) methods, trajectories of such nano-carriers can be extracted in the context of living cells. Trajectory data can then be used for analysis of particle modes of motion (e.g. free diffusion, directed diffusion, tethered diffusion, etc.).
Such information can be indicative of random walk, active transport and trapping in endosomal compartments respectively, thus shedding light on nano-carrier dynamics and intra-cellular processes. These insights can then be further applied to the design process of nano-carriers, refining requirements and elucidating mechanisms. Combination of quantitative microscopy methods and computing techniques, allows the rational design of carriers conforming to the abovementioned requirements.
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ISM 2014 - The 48th Annual Scientific Meeting of ISM
Weizmann Institute of Science, Rehovot
8,9
Luba Kolik 1 and Dganit Danino 1,2
1,2 Department of Biotechnology and Food Engineering, Technion, Haifa, Israel
2 Russell Berrie Nanotechnology Institute, Technion – Israel Institute of Technology, Haifa 32000,
Israel
The self-assembly of biological and synthetic based lipids into micro- and nano- structures has been the subject of intense study in past years, both for basic research and for potential applications, ranging from controlled release to electroactive composites [1]. Lipids as phosphatidylcholine (PC), phosphatidylethanolamine (PE) and phosphatidylserines (PS) that are common in the plasma membranes, can exhibit a variety of lamellar phases in aqueous solution. Some of them (e.g., PS) as well as synthetic or mixed-lipid systems can form chiral aggregates in the form of cylindrical tubes, to minimize their free energy requirement.
The first class of tube-forming amphiphilic lipids was reported by Yager and Schoen in 1984
[2], from a diacetylenic phosphatidylcholine lipid, 1,2-bis (tricosa-l0,l2-diynoyl)-sn-glycero-
3-phosphocholine, designated DC
8,9
PC. Several theoretical approaches were suggested regarding the chiral self-assembly of synthetic phospholipids; however these theories of chiral packing do not consider the effect of solvent on tubule morphology. Addition of short chain alcohols was found to have a strong influence on bilayer uniformity, yet, little is known about the tendency towards single or multilayered tubular structures [3].
Cryo-transmission electron microscopy (cryo-TEM) is a powerful direct imaging technique which enables to capture intermediate structures (Fig 1) and follow dynamic processes. We used cryo-TEM to study the self-assembly pathway of DC
8,9
PC from liposomes to microtubes in different solvent environments, through the liquid crystalline to the gel phase transition.
Figure 1. DC
8,9
PC lipid intermediate membrane structures
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ISM 2014 - The 48th Annual Scientific Meeting of ISM
Weizmann Institute of Science, Rehovot
References:
1.
Schnur, J.M.; Shashindhar, R., Advanced Materials 1994 . 6(12), 971-974.
2.
Yager, P.; Schoen, P.E., Molecular Crystals and Liquid Crystals 1984 , 106(3-4): 371-
381.
3.
Ratna, B.R.; Baraltosh, S.; Kahn, B.; Schnur, J.M.; Rudolph, A.S.
, Faseb Journal
1992 . 6(1), A502-A502.
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ISM 2014 - The 48th Annual Scientific Meeting of ISM
Weizmann Institute of Science, Rehovot
Maor Ronen 1 and Yeshayahu Talmon 2
1 The Norman Seiden Multidisciplinary Graduate Program in Nanoscience and Nanotechnology and the
2 Department of Chemical Engineering, Technion-Israel Institute of Technology, Haifa 3200003,
Israel.
In recent years there has been increasing interest in the study of the mechanisms governing the complexation of polyelectrolytes and oppositely charged lipids. This is due to their interesting and still not completely understood phenomenology, and, more so, to the increased awareness of their potential for innovative applications in nano-medicine and nanobiotechnology, as in gene-delivery.
In this work we used direct-imaging cryo-TEM to study the structural evolution on the nanolevel, as the charge-ratio between a negative polyelectrolyte and a cationic lipid is changed.
Charge ratio (CR) is the ratio between the negatively charged groups of the polymer and the positively charged groups of the lipids. This system was composed of reduced bis(11ferrocenylundecyl)-dimethylammonium bromide (BFDMA), a positively charged synthetic double-tailed cationic lipid, and sodium poly(acrylic acid) (NaPAA), a negatively charged polyelectrolyte.
We observed different nanostructures with changing CR. First, the solution of pure BFDMA
(1mM) had only polydispersed population of large unilamellar vesicles, 200 nm to 1 µm, in diameter. Upon addition of appropriate amount of PAA to the BFDMA solution to give varying values of CR, we saw formation of the multilamellar complexes. The unilamellar vesicles started to add on more layers of cationic lipid, where the polyelectrolyte was sandwiched in the middle screening the electrostatic repulsion. As CR approached unity, the structures tended to aggregate and form larger complexes, since each complex was electrically neutral, which allows them to get into close proximity. Once they are close, they are attracted to each other by short-range interactions. Beyond CR of 1, aggregated clusters are not seen, and the structure average size decreases. However, at CR of 2 we observed structures that are facetted, while at other CR > 1 values, round multilamellar liposomes were dominant structure in solution.
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ISM 2014 - The 48th Annual Scientific Meeting of ISM
Weizmann Institute of Science, Rehovot
Figure 1 - Cryo-TEM Images: a) Pure BFDMA 1mM; b) BFDMA+PAA CR=0.5; c)
BFDMA+PAA CR=1; d) BFDMA+PAA CR= 2
Another two systems we investigated are composed of 1,2-dioleoyl-3-trimethylammoniumpropane (DOTAP) and NaPAA and DOTAP and poly(sodium 4-styrenesulfonate) (NaPSS).
Similar nanostructures were seen in those systems. While there is a difference between the structures, all of these structures are composed of multilamellar bilayers (Figure 2)
Figure 2 - Cryo-TEM Images: a) DOTAP+PAA CR=1; b) DOTAP+PSS CR=1.
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ISM 2014 - The 48th Annual Scientific Meeting of ISM
Weizmann Institute of Science, Rehovot
Maayan Nir-Shapira, Naama Koifman and Yeshayahu Talmon
The Norman Seiden Multidisciplinary Program for Nanoscience and Nanotechnology, Department of Chemical Engineering and the Russell Berrie Nanotechnology Institute (RBNI), Technion-Israel
Institute of Technology, Haifa 32000, Israel.
Immunochemistry is a powerful tool, based on the concept that specific antigens can be probed by complementary antibodies. In the last few decades the use of colloidal gold in transmission electron microscopy has grown at an enormous rate, and has become virtually the only method worth considering for ultrastructural studies of cellular antigens.
Immunogold labeling takes advantage of the high electron density of gold conjugated to antibodies, which in turn adsorb to a specific antigen. Although the probing molecules are often antibodies, other proteins bearing a specific affinity can be used.
Phosphatidylserine (PS) is a negatively charged phospholipid, found mostly in the inner leaflet of the cell membrane, facing the cytoplasm. Certain cell processes, such as apoptosis and microparticle shedding, involve PS migration to the outer leaflet. This phenomenon can be studied using the cellular protein, annexin V, which is highly affinitive to PS. Annexin V binding is Ca
2+dependent, which should be taken into account during the procedure.
Liposomes are spheroidal vesicles, composed of one or more lipid bilayers. They allow the easy and fairly realistic mimicking of bio-membranes; they can be built-up by only a few well-defined components, and hence allow better characterization of the physical principles underlying the self-organization processes observed in membranes. Immunogold labeling of
PS in mixed lipid bilayer will significantly contribute to the study of nano-scale domain formation mechanism. Up to date, these domains have been studied by direct imaging only on the micrometer scale, not on the nanoscopic scale. Understanding this phenomenon is important, because they are involved in a large variety of cellular functions and biological events.
Thus far, immunogold labeling has been performed in various ways, all of which eventually lead to room temperature imaging by TEM or SEM. Our work, presents, for the first time, immunogold labeling in cryo-TEM. Cryo-TEM preserves the liposomes as close as possible to their native state, thus providing a more reliable view of the nanostructure and its morphology. We attempted to label PS liposomes prepared by sonication. Labeling was performed in solution, using biotinilated annexin V and gold-conjugated streptavidin in a two-step process. We observed gold nanoparticles oriented in close proximity to the liposomes membranes. Many of the particles were bound to liposomes, as small as a few nanometers. The gold nanoparticles were not randomly spread in the solution, suggesting that the immunogold labeling in cryo-TEM was indeed successful.
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ISM 2014 - The 48th Annual Scientific Meeting of ISM
Weizmann Institute of Science, Rehovot
Maya Schnabel-Lubovsky 1,2 , Dror Seliktar 1,3 and YeshayahuTalmon 2,3
Departments of 1 Biomedical & 2 Chemical Engineering, and the 3 Russell Berrie Nanotechnology
Institute (RBNI), Technion-Israel Institute of Technology, Haifa, Israel.
Introduction
Cells are confined by the extracellular matrix (ECM), which encapsulates most tissue cells in the body. In this study we have use a hydrogel matrix made of fibrinogen and polyethyleneglycol (PEG) to study the nano-scale interactions associated with the interface between cells and the encapsulating milieu. The synthetic polymer provides control over the matrix properties, while the protein provides biofunctionality needed for cells to survive the encapsulation, including cell adhesion and degradation sites. Characterization of the cellbiomaterial interface at the nano-scale is done by scanning electron microscopy, but the drying techniques that are usually used to examine hydrogels lead to nano-structural artifacts.
To overcome these artifacts, cryogenic techniques are required. We have developed and tested a methodology to characterize cellular hydrogels using state-of-the-art cryogenic highresolution scanning electron microscopy (cryo-HR-SEM). The technique allows us to study the actual cell-hydrogel interface, while preserving the native state of the hydrated polymer network.
Materials and Methods
In this study we used a biosynthetic hydrogel made from PEGylated fibrinogen (PF) as an
ECM mimic. The hydrogel matrix was formed from the biocompatible fibrinogen-polymer adducts by light-activated free-radical polymerization in the presence of human foreskin fibroblasts (HFF). The HFF constructs were cultured for up to one week, and then visualized.
The characterization of the fully hydrated cellular hydrogels was performed on freezefractured samples using cryo-HR-SEM. Cryogenic transmission electron microscopy (cryo-
TEM) was also used forthe material characterization.
Results
A novel methodology to characterize cellular hydrogels using cryo HR-SEM and cryo-TEM was successfully applied to visualize hydrated cellular PF hydrogels to reveal unique features of the cell-ECM interface. For example, the results showed an amorphous polymer network of the PF hydrogel. Consequently, after vitrification, the samples were kept under controlled conditions, including vacuum and cryogenic temperatures to avoid structure artifacts. Figure
1 shows a cryo-HR-SEM image of PF containing HFFs embedded in the amorphous polymer network. Small vesicles, organelles, and the cell membrane are observed within the encapsulating PF milieu. Figure 2 shows a cryo-HR-SEM image of a fibrin matrix containing
HFF cells, whereby fibrous nanostructures are observed at the cell-ECM interface, consistent with fibrin’s fibrillar structure.
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ISM 2014 - The 48th Annual Scientific Meeting of ISM
Weizmann Institute of Science, Rehovot
Fig1. Cryo-HR-SEM image of an amorphous PFhydrogel containing HFF cells.
Fig2. Cryo-HR-SEM image of a fibrin scaffold containing HFF cells.
Discussion and Conclusions
Cryo-HR-SEM is an ideal method for investigating cellular hydrogels containing very high water content. This methodology was successfully demonstrated in showing the amorphous nature of the PF matrix encapsulating fibroblast, as well as with a cell-seeded fibrillar fibrin hydrogel. Accordingly, the Cryo-HR-SEM micrographs revealed important spatial and structural information about the cell-ECM interface.
References
1. Seliktar, D.,"Designing Cell-Compatible Hydrogels for Biomedical Applications".
Science, 336 (6085),1124-28, 2012.
2. Issman, L. and Talmon, Y., "Cryo-SEM Specimen Preparation Under Controlled
Temperature and Concentration Condition".Journal of Microscopy, 246 (1), 60-69, 2012.
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ISM 2014 - The 48th Annual Scientific Meeting of ISM
Weizmann Institute of Science, Rehovot
Nadav Elad 1,2 , Lucía Chávez-Gutiérrez 1,2 , Sam Lismont 1,2 , Wim Hagen 3 , Katrien Horré 1,2 ,
Muriel Arimon 4 , Sarah Veugelen 1,2 , Oksana Berezovska 4 , Carsten Sachse 3 and Bart De
Strooper 1,2
(1) VIB Center for the Biology of Disease, Leuven, Belgium
(2) Center for Human Genetics, KU Leuven, Belgium
(3) European Molecular Biology Laboratory, Heidelberg, Germany
(4) Massachusetts General Hospital, Harvard Medical School, Boston, USA
The structure and function of the γ-secretase proteases are of vast interest because of their critical role in a wide range of cellular processes and diseases. These proteases cleave integral membrane proteins within the lipid bilayer with a broad specificity. Their activity is involved in the pathogenesis of Alzheimer’s disease since they process the amyloid precursor protein to amyloid β (Aβ) peptides. Published single-particle electron microscopy structures provide a static view and the models proposed are rather divergent. We provide a novel, dynamic view of the complex presenting the conformational landscape of γ-secretase. We determined the molecular architecture of the enzyme using antibody labeled and substrate-bound complexes. A Familial Alzheimer’s Disease-linked mutation results in enrichment of extended-conformation complexes with increased flexibility, whereas a transition-state analogue inhibitor stabilizes a sub-population of particles with a compact conformation. We conclude that the function of γ-secretase involves large-scale conformational dynamics and that increased release of longer Aβ peptides correlates with alterations in the γ-secretase conformational landscape.
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ISM 2014 - The 48th Annual Scientific Meeting of ISM
Weizmann Institute of Science, Rehovot
Netta Vidavsky 1 , Sefi Addadi 2 , Eyal Shimoni 3 , Katya Rechav 3 , Andreas Schertel 4 , Steve
Weiner 1 and Lia Addadi 1
1 Department of Structural Biology, 3 Department of Chemical Research Support, Weizmann
Institute of Science, 2 B-nano LTD, Rehovot, Israel, 4 Carl Zeiss Microscopy GmbH, Oberkochen,
Germany
Sea water is the source of calcium ions for many marine organisms which deposit calcareous skeletons, including the sea urchin embryos which deposit calcite spicules. The embryos form the spicules before they are able to feed and obtain the calcium only from the surrounding sea water. The calcium ion pathway is mediated through tissue layers and is at least in part intracellular, and involves the formation of an amorphous calcium carbonate transient phase [1].
We track the passage of calcium ions by using in vivo confocal fluorescence microscopy and labeling the sea water with the fluorescent molecule calcein. We show that calcein initially appears dispersed inside the embryonic body cavity and subsequently observed as intracellular concentrated micrometer-size granules [2]. By using dynamic time-lapse monitoring of calcein we aim to better understand the order of the events leading to the dispersed and concentrated calcium states.
We show that the calcein-label faithfully maps the distribution of calcium and not of other ions by using the airSEM microscope that combines back scattered electron imaging, fluorescence microscopy and EDS at ambient conditions. By using cryo-SEM we show that some of the mineral-bearing granules are vesicles containing nanospheres of sizes 20-30nm, that are similar to the nanospheres present in the mature spicule. In order to assess the major role players of the calcium transport we obtained a 3D view of the spicule environment by applying cryo FIB-SEM (serial FIB milling and block face SEM imaging) method on high pressure frozen, unprocessed and unstained samples [3]. Cryo-FIB-SEM data cubes visualizing the ultrastructure is shown for the first time using this new approach.
The intracellular calcein-labeled vesicles observed are widely distributed inside the whole embryo, and not only inside the mesenchymal cells which envelope and form the spicules.
The vesicles are composed of a solid calcium phase, raising the intriguing possibility that cells and organelles other than the mesenchyme cells also take part in the mineralization process or contribute ions to other cellular metabolic processes.
References:
1. E. Beniash, J. Aizenberg, L. Addad, S. Weiner, Amorphous calcium carbonate transforms into calcite during sea urchin larval spicule growth, Proc. R. Soc. Lond. B, 264, 1997
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ISM 2014 - The 48th Annual Scientific Meeting of ISM
Weizmann Institute of Science, Rehovot
2. N.Vidavsky, S. Addadi, J. Mahamid, E. Shimoni, D. Ben-Ezra, M. Shpigel, S. Weiner, L.
Addadi, Initial stages of calcium uptake and mineral deposition in sea urchin embryos, Proc.
Natl. Acad. Sci. U.S.A., 111, 2014
3. A. Schertel, N. Snaidero, H. M. Hanc, T. Ruhwedel, M. Lauee, M. Grabenbauer, W.
Möbius, Cryo FIB-SEM: Volume imaging of cellular ultrastructure in native frozen specimens, J. Struct. Biol. 184, 2013
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ISM 2014 - The 48th Annual Scientific Meeting of ISM
Weizmann Institute of Science, Rehovot
Noa Katz, Sarah Goldberg, Aya Friedman and Roee Amit
The Faculty of Biotechnology and Food Engineering, Technion – Israel Institute of Technology
One of the intriguing questions in multicellular organism development is how precise differentiation of cells at the early developmental stages can occur when the expression of the proteins that govern differentiation is known to be noisy. Generally, many factors contribute to the protein expression level and to its variance. In this work we focus on transcription and on its contribution to the noise in protein expression.
We use synthetic single-copy plasmid constructs to study the kinetic properties of transcription for various promoters in E.coli
. In each construct, the promoter of interest initiates transcription of a region coding for multiple phage coat-protein binding sites. Upon transcription, RNA binding site s are formed, and fluorescent phage coat proteins (MS2, PP7) bind to them. Using single-cell fluorescent microscopy, we can monitor the fluorescence intensity of the bound proteins as a function of time and directly measure the kinetic properties of transcription. Our goal is to explore whether transcriptional apparatus that are characterized by different underlying components yield distinct noise responses
Figure 1. In vivo imaging of E.coli with a fluorescence "spot" indicating phage coat protein binding to the mRNA transcript
References:
1. Amit et. al., Cell 146, 2011.
2. Ninfa et. al., Cell 50, 1987.
3. So et. al., Nature Genetics 43, 2011.
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ISM 2014 - The 48th Annual Scientific Meeting of ISM
Weizmann Institute of Science, Rehovot
Rotem Gura 1,2 , Daniel Kaganovich 3 , Jeremy England 2
1 Computational and Systems Biology Graduate Program, Massachusetts Institute of Technology,
77 Massachusetts Ave, Cambridge MA 02139
2 Department of Physics, Massachusetts Institute of Technology, 77 Massachusetts Ave, Cambridge
MA 02139
3 Department of Cell and Developmental Biology, The Hebrew University in Jerusalem, Edmond J.
Safra Campus, Jerusalem 91904
To properly perform their function, many proteins must be free to move through the cytosol
(1,2). It is commonly assumed that proteins diffuse in the cytosol and that Brownian thermal fluctuations drive their motion. However, macromolecular crowding, extensive proteinprotein interactions, and dissipative energy flux, all of which take place in the cell, suggest that the cytosolic motion of proteins may be more complexly regulated (3,4).
To characterize protein motion in the cytosol, we developed a powerful method based on live imaging of photo-convertible proteins. We express photo-convertible Dendra2 (DDR) proteins or DDR fusions in Chinese hamster ovary (CHO) cells. We then use a laser pulse to photo-convert a sub-population of fluorophores within a small volume in the cytosol, and use a resonant-scanning confocal microscope to image the propagation of the photo-converted fluorophores throughout the cell.
Analyzing microscopy images generated in these experiments, we calculated effective diffusion coefficients for DDR fusion proteins with different functions, e.g. the model misfolded Ubc9Y68L enzyme and the molecular chaperone Hsp70. Our initial results show that while most of the examined proteins have similar effective diffusion coefficients, Hsp70-
DDR has a diffusion coefficient smaller than the rest by an order of magnitude. In addition, we tracked the mobility of DDR during various cellular perturbations, such as actin and tubulin depolymerization, and ATP depletion. Surprisingly, we did not observe a major change in the mobility of DDR in either of these cases.
Our method enables us to distinguish between the cytosolic motions of different proteins and to examine how cytosolic motion is affected by cellular perturbations.
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ISM 2014 - The 48th Annual Scientific Meeting of ISM
Weizmann Institute of Science, Rehovot
Figure 1. Top: photo-converted proteins propagate throughout the cytosol. Scale bar 1
μm.
Bottom: apparent diffusion coefficients are extracted from the microscopy images.
References:
1. Luby-Phelps, K., Cytoarchitecture and physical properties of cytoplasm: volume, viscosity, diffusion, intracellular surface area. Int Rev Cytol, 192, 189-221 (2000).
2. Dehmelt, L. & Bastiaens, P. I., Spatial organization of intracellular communication: insights from imaging. Nat Rev Mol Cell Biol, 11, 440-452 (2010).
3. Banks, D. S., & Fradin, C., Anomalous diffusion of proteins due to molecular crowding.
Biophysical Journal, 89(5), 2960–2971 (2005).
4. Balbo, J. et al., The shape of protein crowders is a major determinant of protein diffusion.
Biophysical Journal, 104(7), 1576-1584 (2013).
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ISM 2014 - The 48th Annual Scientific Meeting of ISM
Weizmann Institute of Science, Rehovot
Sari Natan 1 , Assaf Zaritsky 2 , Inbal Hecht 3 , Judith Horev 1 , Miriam Shaharabany 1 , Ilan
Tsarfaty 1
1 Sackler School of Medicine, Tel Aviv University, Ramat Aviv, Israel.
2 Blavatnik School of Computer Science, Tel Aviv University, Ramat Aviv, Israel.
3 School of Physics and Astronomy, The Raymond and Beverly Sackler Faculty of Exact Sciences,
Tel-Aviv University, Ramat Aviv, Israel.
Increased cell motility in tumors is an integral part of tumor development leading first to tumor growth and then to the emergence of metastases. The bio-physical mechanisms by which tumor cells navigate through the tumor into neighboring tissues are not fully understood. HGF/SF-Met signaling regulates cell motility. We further investigated the contribution of this signaling pathway on the bio-physical mechanisms that govern cell motility.
Tumor cell motility in vitro was studied using wound healing assays. We observed that in vitro wounds close in a wave like pattern. We have studied the molecular mechanism of the wave and the effects of Met activation and inhibition on its formation, discovering that the wave formation is largely influenced by HGF/SF-Met signaling; Met activation induces the wave and its direct or downstream inhibition hinders wave formation. We have also studied the organization of actin in cells treated with HGF/SF as compared to untreated cells. The simplicity of the 2D wound healing assay model led to fundamental insight into cell motility mechanisms, yet the model is missing key elements that effect cell motility in vivo. Thus, we continued our study of cell motility using a xenograft mammary adenocarcinoma tumors in which cells are tagged by the fluorescent protein mCherry (DA3-mCherry). This model was used to follow cell motility ex vivo in extravagated tumors and in vivo. Tumor cells were then imaged over time and Imaris analysis software was used to detect the volume of the tumor cells and to follow their progression throw the tissue over time. Our results demonstrate that Met activation increases cell velocity, acceleration and induces collective cell motility.
Met induced increased cell motility is a key factor in tumor growth and metastasis formation.
Better understanding of the bio-physical mechanisms that govern cell motility may indicate new targets for anti-Met and anti-Metastases targeted therapy.
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ISM 2014 - The 48th Annual Scientific Meeting of ISM
Weizmann Institute of Science, Rehovot
Sharon Grayer Wolf a , Lothar Houben b and Michael Elbaum c a Dept. of Chemical Research Support, Weizmann Institute of Science, Rehovot Israel b Ernst Ruska-Centre for Microscopy and Spectroscopy with Electrons, Julich Germany cDept.of
Materials and Interfaces, Weizmann Institute of Science, Rehovot Israel
Cryo-transmission electron tomography (CET) has emerged as a vital tool for structural biology studies of cells and viruses. Direct imaging of fully hydrated, vitrified material represents the state of the art for preservation of biological samples. Lacking heavy metal stains, CET relies on phase contrast typically obtained by defocusing the sample. The dependence on phase coherence, as well as cumulative radiation damage on frozen hydrated specimens, impose an inherent upper limit on sample thickness and usable tilt range. Even with energy filtration to remove the contribution of inelastic scattering, CET suffers from
"missing wedge" effects and low signal-to-noise ratio. Scanning transmission electron microscopy (STEM) circumvents the need for phase contrast with incoherent detection, and has recently been extended to biological tomography. However the weak electron scattering by light elements was thought to preclude its application to unstained cryogenic specimens.
We show this not to be the case
1
. To the contrary, we find that raster scanning permits a higher total dose than conventional wide-field imaging, and the independent STEM detection in bright and dark field detectors provides sufficient contrast to show detailed cellular architecture similar to that provided by wide-field tomography. An important difference is that the specimen remains dynamically in focus even at high very tilts up to 70°. This significantly improves the depth resolution in reconstructions. Sample thickness limitations are also relaxed. We demonstrate the cryo-STEM tomography (CSTET) method using unstained, vitrified bacteria and human epithelial cells.
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ISM 2014 - The 48th Annual Scientific Meeting of ISM
Weizmann Institute of Science, Rehovot
Figure 1. Volumetrically rendered STEM cryo-tomographic reconstruction with projection onto the XY plane of a cluster of bacteria.
References:
1.
S.G.Wolf, L. Houben, M. Elbaum, Cryo-scanning transmission electron tomography of vitrified cells. Nature Methods, 11(4), 423-8 (2014).
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ISM 2014 - The 48th Annual Scientific Meeting of ISM
Weizmann Institute of Science, Rehovot
Pamela C. Cabahug, Keren Nisani-Bizer and Shlomo Trachtenberg
Department of Microbiology and Molecular Genetics, IMRIC, The Hebrew University-Hadassah
Medical School, Jerusalem, Israel
Spiroplasmas (alongside with Mycoplasmas and Acholeplasmas) are members of the mollicutes representing the minimal, free-living and self-replicating forms of life [1].
Spiroplasmas are helical, wall-less bacteria and the only ones known to swim by means of a linear motor (rather than the near-universal rotary bacterial motor). The linear motor follows the shortest path along the cell’s helical membranal tube. The motor is comprised of a flat mono-layered ribbon of seven parallel fibrils and is believed to function in controlling cell helicity and motility through dynamic, coordinated, differential length changes of the fibrils.
The latter cause local perturbations of helical symmetry (changes in pitch, diameter, handedness and axial bending) essential for net directional displacement in low Reynolds number environments. The local perturbations travel along the helical cell body. The underlying fibrils’ core building block is a semi-circular tetramer of the 59kDa protein—Fib.
The fibrils’ differential length changes are believed to be driven by molecular switching of
Fib, leading, consequently, to axial-ratio and length changes of the tetrameric rings. To accommodate for mass and diffraction data, the tetramer is assumed to be comprised of two pairs of monomers with opposite polarities [2]. Using cryo-EM, diffractometry, singleparticle-analysis of isolated ribbons and sequence analyses of Fib, we determined the overall molecular organization of the Fib monomer, tetramer, fibril and linear motor of S. melliferum
BC3 that underlies cell geometry and motility [3]. Fib appears to be a bi-domained molecule of which the N-terminal half is apparently a globular phosphorylase. By a combination of reversible rotation and diagonal shift of Fib monomers, the tetramer adopts either a crosslike, non-handed, or a ring-like, handed, conformation. The sense of Fib rotation may determine the handedness of the linear motor and, eventually, that of the cell. Further change of the axial ratio of the ring-like tetramers controls fibril lengths and consequent helical geometry. Single-particle analysis of tetramer quadrants from adjacent fibrils, clearly demonstrates local differential fibril lengths.
References:
1. Trachtenberg, S .
, Schuck, P., Phillips, T.M., Andrews, S.B. and Leapman, R.L. (2014). A
Structural Framework for a Near-Minimal Form of Life: Mass and Compositional Analysis of the Helical Mollicute Spiroplasma melliferum BC3. PLoS ONE 9: e87921.
2. Trachtenberg, S., Andrews, S. B. and Leapman, R.D. (2003). Mass distribution and spatial organization of the linear bacterial motor of Spiroplasma citri R8A2. J. Bacteriol. 185:1987-
1994.
3. Cohen-Krausz, S., Cabahug, P. C
. and Trachtenberg, S.
(2011). The Monomeric,
Tetrameric and Fibrillar Organization of Fib –The Dynamic Building Block of the Bacterial
Linear Motor of Spiroplasma melliferum BC3. J. Mol. Biol. 410 : 194-213.
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ISM 2014 - The 48th Annual Scientific Meeting of ISM
Weizmann Institute of Science, Rehovot
Shachar Sherman, Dikla Nachmias and Natalie Elia
Department of Life-Sciences, Ben-Gurion University, Beer-Sheva, Israel
Research over the years has shown a tight relationship between proteins’ structure and function. Similarly, structural organization of protein complexes matches by design a functional demand. As the overall organization of molecules can be influenced by the environment, documenting a protein in its native, cellular environment is needed to infer its function.
Structured Illumination Microscopy (SIM) provides 3D super-resolution images allowing solving of protein complexes structural organization in cells at 100 nm resolution. But, SIM is slow, as a minimum of 15 images need to be captured from each focal plane to obtain final high-resolution information. Therefore, SIM is generally restricted to fixed cells. However, as biological processes occur in a timed fashion, the function of a protein complex cannot be fully understood without accounting for a temporal dimension.
Confocal spinning-disk technology allows capturing rapid fluorescent images of live cells, providing the high temporal resolution required for documenting biological processes. We have therefore developed a correlative protocol combining both technologies in which live cell imaging adjoins super-resolution.
In this approach cells are imaged live using a spinning disk confocal. At a specific time, cells are fixed and moved to a SIM microscope. A reference mark is set, and relative coordinates of specific cells are saved and transferred between systems. This mark-and-find approach makes the entire correlative assay possible. Piloted experiments in dividing MDCK cells expressing tubulin-GFP demonstrated the feasibility of this approach. A single experiment now has the substructural organization of a protein complex in a cell with an attached timestamp. By repeating this protocol and fixing cells at different time points a full superresolution description of a protein complex throughout an entire biological process can be obtained. Notably, this approach is compatible with any fluorescently tagged protein.
Methodology and additional correlative data will be presented and discussed.
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ISM 2014 - The 48th Annual Scientific Meeting of ISM
Weizmann Institute of Science, Rehovot
Ludmila Abezgauz, Inbal Abutbul-Ionita, Ellina Kaselman and Dganit Danino
Department of Biotechnology and Food Engineering,Technion – Israel Institute of Technology,
Haifa 32000, Israel
In the last years nanoparticles were extensively studied in medical application such as selective vehicles transport of active agents to the cell. Therefore, the study of nanoparticlephospholipid interactions is of great relevance for nanomedicine, especially nanotoxicity.
In this work we studied systems composed of phospholipid vesicles and silica nanoparticles
(SiNPs). We focused on the phase behavior of mixtures and mechanism of internalization of
SiNPs into vesicles. We observed that the addition of negatively charged silica particles to zwitterionic phospholipid vesicles leads to the formation of different colloidal structures, depending on multiple components including volume ratio (
β
: SiNPs/liposome), concentration of nanoparticles and storage time.
We used advanced techniques of cryo-transmission electron microscopy, static and dynamic light scattering, small angle neutron scattering, fluorescence correlation s pectroscopy, ζpotential measurements.
Figures: A. Schematic illustrations and cryo-TEM images of the nanoparticle-phospholipid complexes at
β
<1 and B.
β
>1. Cryo-TEM images revealed the different colloidal structures that form: decorated vesicles, vesicles with incorporated SiNPs covered with a supported lipid bilayer (SLB) and free particles covered by SLB.
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ISM 2014 - The 48th Annual Scientific Meeting of ISM
Weizmann Institute of Science, Rehovot
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