Discussion of developments surrounding the transformation of the scanning transmission electron microscope from an imaging platform into a manipulation platform.
The broad lined_type_ic_sn_2012_ap_and_the_nature_of_relatvistic_supernovae_l...Sérgio Sacani
Artigo mostra como os astrônomos deduziram que a supernova SN 2012ap, é o elo perdido que faltava para a construção completa da árvore genealógica das supernovas.
The broad lined_type_ic_sn_2012_ap_and_the_nature_of_relatvistic_supernovae_l...Sérgio Sacani
Artigo mostra como os astrônomos deduziram que a supernova SN 2012ap, é o elo perdido que faltava para a construção completa da árvore genealógica das supernovas.
I gave 1 hour seminar at ANSTO (Australian Nuclear Science and Technology Organization) to introduce my approach to magnetism. I see myself as an experimental physicist who is studying magnetism by using neutron scattering techniques. Throughout my career, I had learned local structure analysis (PDF), magnetic structural analysis, and inelastic neutron scattering technique to investigate superconductor, multiferroics, antiferromagnets, helimagnets, and frustrated magnets. I was trying to explain my approach to magnetism as an experiment physicist to both professional scientists and novices.
This talk was presented by Prof. Daniele Faccio, leader of the Extreme light research group at the Glasgow University. This presents overview of the research conducted in his group.
Dr. Toma Susi (University of Vienna, Austria) invited talk at the MRS Spring Meeting 2018 in Phoenix, AZ titled "Towards atomically precise manipulation of 2D nanostructures in the
electron microscope".
Plenary lecture of the XIV SBPMat Meeting, given by Prof. Ichiro Takeuchi (University of Maryland, USA) on September 30, 2015, in Rio de Janeiro (Brazil).
(PhD Dissertation Defense) Theoretical and Numerical Investigations on Crysta...James D.B. Wang, PhD
(I'm no longer in this academic field, and thus sharing my PhD dissertation slide here to anyone who would be interested in it)
=================================================
In order to prevent the spurious wave reflections and to improve the computational efficiency in nanomechanical simulation, this dissertation performs a series of theoretical/numerical studies on the crystalline nano material, including nanomechanics of monatomic lattice, isothermally non-reflecting boundary condition, fast updating of neighbor list, and the application/simulation in laser-assisted nano-imprinting.
The presentation file on workshop on Neutron and X-ray Characterisation on Caloric Materials, introduction to neutron scattering experiment with triple axis spectrometer for material scientist
Los días 22 y 23 de junio de 2016 organizamos en la Fundación Ramón Areces un simposio internacional sobre 'Materiales bidimensionales: explorando los límites de la física y la ingeniería'. En colaboración con el Massachusetts Institute of Technology (MIT), científicos de este prestigioso centro de investigación mostraron las propiedades únicas de materiales como el grafeno, de solo un átomo de espesor, y al mismo tiempo más resistente que el acero y mucho más ligero.
It includes topics regarding the Electron and ion spectroscopy. It consist of results of minute research done on the topics like electron spectroscopy for chemical analysis, auger spectroscopy, secondary ion mass spectroscopy, surface spectroscopic techniques and is very helpful for the analysis and presentation point of view.
I gave 1 hour seminar at ANSTO (Australian Nuclear Science and Technology Organization) to introduce my approach to magnetism. I see myself as an experimental physicist who is studying magnetism by using neutron scattering techniques. Throughout my career, I had learned local structure analysis (PDF), magnetic structural analysis, and inelastic neutron scattering technique to investigate superconductor, multiferroics, antiferromagnets, helimagnets, and frustrated magnets. I was trying to explain my approach to magnetism as an experiment physicist to both professional scientists and novices.
This talk was presented by Prof. Daniele Faccio, leader of the Extreme light research group at the Glasgow University. This presents overview of the research conducted in his group.
Dr. Toma Susi (University of Vienna, Austria) invited talk at the MRS Spring Meeting 2018 in Phoenix, AZ titled "Towards atomically precise manipulation of 2D nanostructures in the
electron microscope".
Plenary lecture of the XIV SBPMat Meeting, given by Prof. Ichiro Takeuchi (University of Maryland, USA) on September 30, 2015, in Rio de Janeiro (Brazil).
(PhD Dissertation Defense) Theoretical and Numerical Investigations on Crysta...James D.B. Wang, PhD
(I'm no longer in this academic field, and thus sharing my PhD dissertation slide here to anyone who would be interested in it)
=================================================
In order to prevent the spurious wave reflections and to improve the computational efficiency in nanomechanical simulation, this dissertation performs a series of theoretical/numerical studies on the crystalline nano material, including nanomechanics of monatomic lattice, isothermally non-reflecting boundary condition, fast updating of neighbor list, and the application/simulation in laser-assisted nano-imprinting.
The presentation file on workshop on Neutron and X-ray Characterisation on Caloric Materials, introduction to neutron scattering experiment with triple axis spectrometer for material scientist
Los días 22 y 23 de junio de 2016 organizamos en la Fundación Ramón Areces un simposio internacional sobre 'Materiales bidimensionales: explorando los límites de la física y la ingeniería'. En colaboración con el Massachusetts Institute of Technology (MIT), científicos de este prestigioso centro de investigación mostraron las propiedades únicas de materiales como el grafeno, de solo un átomo de espesor, y al mismo tiempo más resistente que el acero y mucho más ligero.
It includes topics regarding the Electron and ion spectroscopy. It consist of results of minute research done on the topics like electron spectroscopy for chemical analysis, auger spectroscopy, secondary ion mass spectroscopy, surface spectroscopic techniques and is very helpful for the analysis and presentation point of view.
Similar to Atomic level manipulation of matter using Scanning Transmission Electron Microscopy (20)
Earliest Galaxies in the JADES Origins Field: Luminosity Function and Cosmic ...Sérgio Sacani
We characterize the earliest galaxy population in the JADES Origins Field (JOF), the deepest
imaging field observed with JWST. We make use of the ancillary Hubble optical images (5 filters
spanning 0.4−0.9µm) and novel JWST images with 14 filters spanning 0.8−5µm, including 7 mediumband filters, and reaching total exposure times of up to 46 hours per filter. We combine all our data
at > 2.3µm to construct an ultradeep image, reaching as deep as ≈ 31.4 AB mag in the stack and
30.3-31.0 AB mag (5σ, r = 0.1” circular aperture) in individual filters. We measure photometric
redshifts and use robust selection criteria to identify a sample of eight galaxy candidates at redshifts
z = 11.5 − 15. These objects show compact half-light radii of R1/2 ∼ 50 − 200pc, stellar masses of
M⋆ ∼ 107−108M⊙, and star-formation rates of SFR ∼ 0.1−1 M⊙ yr−1
. Our search finds no candidates
at 15 < z < 20, placing upper limits at these redshifts. We develop a forward modeling approach to
infer the properties of the evolving luminosity function without binning in redshift or luminosity that
marginalizes over the photometric redshift uncertainty of our candidate galaxies and incorporates the
impact of non-detections. We find a z = 12 luminosity function in good agreement with prior results,
and that the luminosity function normalization and UV luminosity density decline by a factor of ∼ 2.5
from z = 12 to z = 14. We discuss the possible implications of our results in the context of theoretical
models for evolution of the dark matter halo mass function.
THE IMPORTANCE OF MARTIAN ATMOSPHERE SAMPLE RETURN.Sérgio Sacani
The return of a sample of near-surface atmosphere from Mars would facilitate answers to several first-order science questions surrounding the formation and evolution of the planet. One of the important aspects of terrestrial planet formation in general is the role that primary atmospheres played in influencing the chemistry and structure of the planets and their antecedents. Studies of the martian atmosphere can be used to investigate the role of a primary atmosphere in its history. Atmosphere samples would also inform our understanding of the near-surface chemistry of the planet, and ultimately the prospects for life. High-precision isotopic analyses of constituent gases are needed to address these questions, requiring that the analyses are made on returned samples rather than in situ.
A brief information about the SCOP protein database used in bioinformatics.
The Structural Classification of Proteins (SCOP) database is a comprehensive and authoritative resource for the structural and evolutionary relationships of proteins. It provides a detailed and curated classification of protein structures, grouping them into families, superfamilies, and folds based on their structural and sequence similarities.
Deep Behavioral Phenotyping in Systems Neuroscience for Functional Atlasing a...Ana Luísa Pinho
Functional Magnetic Resonance Imaging (fMRI) provides means to characterize brain activations in response to behavior. However, cognitive neuroscience has been limited to group-level effects referring to the performance of specific tasks. To obtain the functional profile of elementary cognitive mechanisms, the combination of brain responses to many tasks is required. Yet, to date, both structural atlases and parcellation-based activations do not fully account for cognitive function and still present several limitations. Further, they do not adapt overall to individual characteristics. In this talk, I will give an account of deep-behavioral phenotyping strategies, namely data-driven methods in large task-fMRI datasets, to optimize functional brain-data collection and improve inference of effects-of-interest related to mental processes. Key to this approach is the employment of fast multi-functional paradigms rich on features that can be well parametrized and, consequently, facilitate the creation of psycho-physiological constructs to be modelled with imaging data. Particular emphasis will be given to music stimuli when studying high-order cognitive mechanisms, due to their ecological nature and quality to enable complex behavior compounded by discrete entities. I will also discuss how deep-behavioral phenotyping and individualized models applied to neuroimaging data can better account for the subject-specific organization of domain-general cognitive systems in the human brain. Finally, the accumulation of functional brain signatures brings the possibility to clarify relationships among tasks and create a univocal link between brain systems and mental functions through: (1) the development of ontologies proposing an organization of cognitive processes; and (2) brain-network taxonomies describing functional specialization. To this end, tools to improve commensurability in cognitive science are necessary, such as public repositories, ontology-based platforms and automated meta-analysis tools. I will thus discuss some brain-atlasing resources currently under development, and their applicability in cognitive as well as clinical neuroscience.
Nutraceutical market, scope and growth: Herbal drug technologyLokesh Patil
As consumer awareness of health and wellness rises, the nutraceutical market—which includes goods like functional meals, drinks, and dietary supplements that provide health advantages beyond basic nutrition—is growing significantly. As healthcare expenses rise, the population ages, and people want natural and preventative health solutions more and more, this industry is increasing quickly. Further driving market expansion are product formulation innovations and the use of cutting-edge technology for customized nutrition. With its worldwide reach, the nutraceutical industry is expected to keep growing and provide significant chances for research and investment in a number of categories, including vitamins, minerals, probiotics, and herbal supplements.
Richard's aventures in two entangled wonderlandsRichard Gill
Since the loophole-free Bell experiments of 2020 and the Nobel prizes in physics of 2022, critics of Bell's work have retreated to the fortress of super-determinism. Now, super-determinism is a derogatory word - it just means "determinism". Palmer, Hance and Hossenfelder argue that quantum mechanics and determinism are not incompatible, using a sophisticated mathematical construction based on a subtle thinning of allowed states and measurements in quantum mechanics, such that what is left appears to make Bell's argument fail, without altering the empirical predictions of quantum mechanics. I think however that it is a smoke screen, and the slogan "lost in math" comes to my mind. I will discuss some other recent disproofs of Bell's theorem using the language of causality based on causal graphs. Causal thinking is also central to law and justice. I will mention surprising connections to my work on serial killer nurse cases, in particular the Dutch case of Lucia de Berk and the current UK case of Lucy Letby.
(May 29th, 2024) Advancements in Intravital Microscopy- Insights for Preclini...Scintica Instrumentation
Intravital microscopy (IVM) is a powerful tool utilized to study cellular behavior over time and space in vivo. Much of our understanding of cell biology has been accomplished using various in vitro and ex vivo methods; however, these studies do not necessarily reflect the natural dynamics of biological processes. Unlike traditional cell culture or fixed tissue imaging, IVM allows for the ultra-fast high-resolution imaging of cellular processes over time and space and were studied in its natural environment. Real-time visualization of biological processes in the context of an intact organism helps maintain physiological relevance and provide insights into the progression of disease, response to treatments or developmental processes.
In this webinar we give an overview of advanced applications of the IVM system in preclinical research. IVIM technology is a provider of all-in-one intravital microscopy systems and solutions optimized for in vivo imaging of live animal models at sub-micron resolution. The system’s unique features and user-friendly software enables researchers to probe fast dynamic biological processes such as immune cell tracking, cell-cell interaction as well as vascularization and tumor metastasis with exceptional detail. This webinar will also give an overview of IVM being utilized in drug development, offering a view into the intricate interaction between drugs/nanoparticles and tissues in vivo and allows for the evaluation of therapeutic intervention in a variety of tissues and organs. This interdisciplinary collaboration continues to drive the advancements of novel therapeutic strategies.
Seminar of U.V. Spectroscopy by SAMIR PANDASAMIR PANDA
Spectroscopy is a branch of science dealing the study of interaction of electromagnetic radiation with matter.
Ultraviolet-visible spectroscopy refers to absorption spectroscopy or reflect spectroscopy in the UV-VIS spectral region.
Ultraviolet-visible spectroscopy is an analytical method that can measure the amount of light received by the analyte.
What is greenhouse gasses and how many gasses are there to affect the Earth.moosaasad1975
What are greenhouse gasses how they affect the earth and its environment what is the future of the environment and earth how the weather and the climate effects.
Cancer cell metabolism: special Reference to Lactate PathwayAADYARAJPANDEY1
Normal Cell Metabolism:
Cellular respiration describes the series of steps that cells use to break down sugar and other chemicals to get the energy we need to function.
Energy is stored in the bonds of glucose and when glucose is broken down, much of that energy is released.
Cell utilize energy in the form of ATP.
The first step of respiration is called glycolysis. In a series of steps, glycolysis breaks glucose into two smaller molecules - a chemical called pyruvate. A small amount of ATP is formed during this process.
Most healthy cells continue the breakdown in a second process, called the Kreb's cycle. The Kreb's cycle allows cells to “burn” the pyruvates made in glycolysis to get more ATP.
The last step in the breakdown of glucose is called oxidative phosphorylation (Ox-Phos).
It takes place in specialized cell structures called mitochondria. This process produces a large amount of ATP. Importantly, cells need oxygen to complete oxidative phosphorylation.
If a cell completes only glycolysis, only 2 molecules of ATP are made per glucose. However, if the cell completes the entire respiration process (glycolysis - Kreb's - oxidative phosphorylation), about 36 molecules of ATP are created, giving it much more energy to use.
IN CANCER CELL:
Unlike healthy cells that "burn" the entire molecule of sugar to capture a large amount of energy as ATP, cancer cells are wasteful.
Cancer cells only partially break down sugar molecules. They overuse the first step of respiration, glycolysis. They frequently do not complete the second step, oxidative phosphorylation.
This results in only 2 molecules of ATP per each glucose molecule instead of the 36 or so ATPs healthy cells gain. As a result, cancer cells need to use a lot more sugar molecules to get enough energy to survive.
Unlike healthy cells that "burn" the entire molecule of sugar to capture a large amount of energy as ATP, cancer cells are wasteful.
Cancer cells only partially break down sugar molecules. They overuse the first step of respiration, glycolysis. They frequently do not complete the second step, oxidative phosphorylation.
This results in only 2 molecules of ATP per each glucose molecule instead of the 36 or so ATPs healthy cells gain. As a result, cancer cells need to use a lot more sugar molecules to get enough energy to survive.
introduction to WARBERG PHENOMENA:
WARBURG EFFECT Usually, cancer cells are highly glycolytic (glucose addiction) and take up more glucose than do normal cells from outside.
Otto Heinrich Warburg (; 8 October 1883 – 1 August 1970) In 1931 was awarded the Nobel Prize in Physiology for his "discovery of the nature and mode of action of the respiratory enzyme.
WARNBURG EFFECT : cancer cells under aerobic (well-oxygenated) conditions to metabolize glucose to lactate (aerobic glycolysis) is known as the Warburg effect. Warburg made the observation that tumor slices consume glucose and secrete lactate at a higher rate than normal tissues.
Slide 1: Title Slide
Extrachromosomal Inheritance
Slide 2: Introduction to Extrachromosomal Inheritance
Definition: Extrachromosomal inheritance refers to the transmission of genetic material that is not found within the nucleus.
Key Components: Involves genes located in mitochondria, chloroplasts, and plasmids.
Slide 3: Mitochondrial Inheritance
Mitochondria: Organelles responsible for energy production.
Mitochondrial DNA (mtDNA): Circular DNA molecule found in mitochondria.
Inheritance Pattern: Maternally inherited, meaning it is passed from mothers to all their offspring.
Diseases: Examples include Leber’s hereditary optic neuropathy (LHON) and mitochondrial myopathy.
Slide 4: Chloroplast Inheritance
Chloroplasts: Organelles responsible for photosynthesis in plants.
Chloroplast DNA (cpDNA): Circular DNA molecule found in chloroplasts.
Inheritance Pattern: Often maternally inherited in most plants, but can vary in some species.
Examples: Variegation in plants, where leaf color patterns are determined by chloroplast DNA.
Slide 5: Plasmid Inheritance
Plasmids: Small, circular DNA molecules found in bacteria and some eukaryotes.
Features: Can carry antibiotic resistance genes and can be transferred between cells through processes like conjugation.
Significance: Important in biotechnology for gene cloning and genetic engineering.
Slide 6: Mechanisms of Extrachromosomal Inheritance
Non-Mendelian Patterns: Do not follow Mendel’s laws of inheritance.
Cytoplasmic Segregation: During cell division, organelles like mitochondria and chloroplasts are randomly distributed to daughter cells.
Heteroplasmy: Presence of more than one type of organellar genome within a cell, leading to variation in expression.
Slide 7: Examples of Extrachromosomal Inheritance
Four O’clock Plant (Mirabilis jalapa): Shows variegated leaves due to different cpDNA in leaf cells.
Petite Mutants in Yeast: Result from mutations in mitochondrial DNA affecting respiration.
Slide 8: Importance of Extrachromosomal Inheritance
Evolution: Provides insight into the evolution of eukaryotic cells.
Medicine: Understanding mitochondrial inheritance helps in diagnosing and treating mitochondrial diseases.
Agriculture: Chloroplast inheritance can be used in plant breeding and genetic modification.
Slide 9: Recent Research and Advances
Gene Editing: Techniques like CRISPR-Cas9 are being used to edit mitochondrial and chloroplast DNA.
Therapies: Development of mitochondrial replacement therapy (MRT) for preventing mitochondrial diseases.
Slide 10: Conclusion
Summary: Extrachromosomal inheritance involves the transmission of genetic material outside the nucleus and plays a crucial role in genetics, medicine, and biotechnology.
Future Directions: Continued research and technological advancements hold promise for new treatments and applications.
Slide 11: Questions and Discussion
Invite Audience: Open the floor for any questions or further discussion on the topic.
Atomic level manipulation of matter using Scanning Transmission Electron Microscopy
1. Atomic level manipulation of matter using
Scanning Transmission Electron Microscopy
Ondrej Dyck
Center for Nanophase Materials Science
Oak Ridge National Laboratory
Oak Ridge, TN
2. E v o l u t i o n o f i m a g i n g : d e s c r i p t i o n , u n d e r s t a n d i n g , c o n t r o l
Need to find out :
• Why do atoms do it ?
• How we direct them
to do what we want ?
X-ray and
neutron
scattering:
where the atoms
are on average
Electron and
probe
microscopy:
where exactly
are the atoms
Dynamic
microscopies:
what atoms do Nanotechnology
Beyond Moore
Molecular Machines
Present
Time
3. S c a n n e d p r o b e t e c h n i q u e s
D. Eigler, 1990
M. Simmons, 2012
Single Atom Transistor
4. E m e r g i n g f i e l d o f e l e c t r o n - b e a m m a n i p u l a t i o n
5. W h y n o w ?
Interest in machine
learning through time
2007
2018
• Aberration correction
• 2D materials
• End of Moore’s law
• Quantum race
• Artificial intelligence
6. A t o m i c F a b r i c a t i o n i n S T E M : P i e c e s o f t h e p u z z l e
7. E - b e a m I n d u c e d P h e n o m e n a
Electron-irradiation “damage”
Elastic
(electron-nucleus)
scattering
Inelastic
(electron-electron)
scattering
Deposition, e.g
hydrocarbon
contamination
Mass loss
Structural damage
Specimen heating
E-beam sputtering
Atomic displacement Electrostatic charging
Direct nuclear recoil
Dependent on electron energy,
beam fluence, and atomic
number
Direct nuclear recoil and
ejection
Electron-electron energy
transfer
Dependent on beam current
and material; usually negligible
Absorbed electrons
Sample conductivity
Backscattered electrons
Secondary emission (Auger)
Radiolysis
Electronic excitations
Non-reversible decay
Altered chemical bonds
Depends on current density,
sample chemistry, and temp.
Polymerization of hydrocarbons
Adapted from Egerton and Malac, Micron (2004)
8. E - b e a m - i n d u c e d P h e n o m e n a
Crystallization of amorphous material
Elastic-plastic transition
Ferroelectric domain switching
Phase transitions
Vacancy formation and dynamics
Creation of molecular bonds
Atomic motion
Sculpting (erosion)
Liquid electrochemistry
S. Jesse et. al. (2015) Small
J. Kotakoski et. al. (2014) Nat. Com.H. Komsa et. al. (2012) Phys. Rev. Lett.
O. Dyck et. al. submitted T. Susi et. al. (2017) arXiv
9. E - b e a m I n d u c e d P h e n o m e n a
Electron beam induced
fragmentation
Catalytic growth of C nano-onions
Oku et. al., J. Mat. Chem. (1998)Gonzales-Martinez et. al., Nanoscale (2016)
Fullerene formation
Chuvilin et. al., Nat. Chem. (2010)
Nanotube welding
Terrones et. al., Phys. Rev. Lett. (2002)
10. E - b e a m I n d u c e d P h e n o m e n a
Nanotube growth
Gonzalez-Martinez et. al., Nano Letters (2014)
Formation of 2D Fe and ZnO
Zhao et. al., Science (2014)
Quang et. al., ACS Nano (2015)
Catalytic etching via Fe
nanoparticle
Wang et. al., Sci. Rep. (2012)
11. E - b e a m I n d u c e d P h e n o m e n a
Single atom catalytic activity
Ta et. al., Nano Res. (2017)
Ni M2,3 EELS
Ramasse et. al., ACS Nano (2012)
Catalyst-free formation
of graphene from a-C
Börrnert et. al., Adv. Mat. (2012)
Nanowire formation via
e-beam sculpting
Lin et. al., Nat. Nano. (2014)
12. E - b e a m I n d u c e d P h e n o m e n a
Nanoparticle nucleation and growth
(liquid cell)
Liao et. al., Science (2014)
Creation of point defects (WS2)
Zhou et. al., Nano Lett. (2013)
Crystallization in Strontium titanate
Jesse et. al., Small (2015)
13. E - b e a m I n d u c e d P h e n o m e n a
Dyck et. al., J. Vac. Sci. Tech. B (2017)
Patterning of C Dopant movement through 3D crystal
Jesse et. al., arXiv (2017)
Movement and assembly of
single atoms in 2D materials
Dyck et. al., arXiv (2017)
14. E - b e a m I n d u c e d P h e n o m e n a
• There are a wealth of e-beam induced phenomena to explore
• Specialized holders offer additional parameters to explore
(heating, cooling, electrical biasing, gas/liquid cell,
nanomanipulators etc.)
• Aberration correction and 2D materials have allowed the
addressing of single atoms in STEM
How do we develop fabrication techniques at the atomic scale?
15. D e t e c t i o n
Imaging
Spectroscopy
Ptychography
Compressed sensing
3D imaging
Super-resolution
Read-out speed
Signal to noise ratio
Data generation from
beam-sample
interactions.
16. I n t e r p r e t a t i o n
Machine Intelligence
DFT Modelling
Molecular Dynamics
Image Simulation
Offline analysis
Library building
Physical insight
Real-time analysis
Decision making
What are we looking at?
17. R e a c t i o n D e c i s i o n
Prior Experience
Physical Laws
Libraries
Machine Intelligence
DFT Modelling
Molecular Dynamics
Image Simulation
What do we want to
make happen? How can
we alter parameters to
achieve this?
18. R e a c t i o n
Beam Control
Feedback
Stability
Perform some action, monitor
and correct errors and state of
the sample.
electron beam
Specimen Advanced
DAQ
Fast Direct
Electron
Detection
To scan coils, or
in situ holder
ADF/ABF
19. P u t t i n g t h e p u z z l e t o g e t h e r : c r y s t a l l i z a t i o n
electron beam
Specimen Advanced
DAQ
To scan coils, or
in situ holder
Start inside crystal,
Fast advance
Amorphous/crystalline
interface
Growth of new crystalline atomic layer
Beam advances to next atomic layer
Crystalline detection threshold
FFT reveals real-time frequency distributions
Stephen Jesse
20. P u t t i n g t h e p u z z l e t o g e t h e r : c r y s t a l l i z a t i o n
After
2 nm
Before
2 nm
Beam induced dopant motion
Paul Snijders
Andrew Lupini
Beth Hudak
21. P u t t i n g t h e p u z z l e t o g e t h e r : d e f e c t p o s i t i o n i n g
Stephen Jesse
22. P u t t i n g t h e p u z z l e t o g e t h e r : d e f e c t p o s i t i o n i n g I
Series of fast spiral scans (~50 ms/scan) at a chosen
location. The rapid change in brightness indicates the
formation of a hole.
X
Hole formation
Time
23. P u t t i n g t h e p u z z l e t o g e t h e r : b e a m - i n d u c e d h e a l i n g
• Start with pristine,
cleaned graphene lattice
• Material at ~1200 C
• Electron beam at 100 kV
• Drill hole using spiral scan
• The formed hole is
metastable
• If we continuously
scan at 100 keV, the
hole will grow as edge
atoms are easily
removed
• If we turn the beam
off, or scan elsewhere,
the hole will heal in
less than a minute
24. P u t t i n g t h e p u z z l e t o g e t h e r : b e a m - i n d u c e d h e a l i n g
60 kV with light room-temperature contamination
E-beam deposited
multi-layer graphene
25. P u t t i n g t h e p u z z l e t o g e t h e r : d e f e c t p o s i t i o n i n g I I
Graphene Lattice Viewed Edge-on
26. P u t t i n g t h e p u z z l e t o g e t h e r : d e f e c t p o s i t i o n i n g I I
Graphene Lattice Viewed Edge-on
27. P u t t i n g t h e p u z z l e t o g e t h e r : d e f e c t p o s i t i o n i n g I I
Agitate
source
material
Create
hole/defect
Position
beam
Dyck et. al., Appl. Phys. Lett. (2017)
Scan over large area
to mobilize Si atoms
Drill hole100 kV Si dopant positioning
28. P u t t i n g t h e p u z z l e t o g e t h e r : d e f e c t p o s i t i o n i n g I I I
Susi et. al., Ultramicroscopy (2017)
Positioning single dopant atoms
within a graphene lattice
12
Dyck et. al., Appl. Phys. Lett. (2017)
Toma Susi
Jannik Meyer
Jani Kotakoski
29. P u t t i n g t h e p u z z l e t o g e t h e r : d e f e c t p o s i t i o n i n g I V
Dyck et. al., arXiv (2017)
Assembly of primitive, few atom structures from single dopant atoms
Elisa Jimenez-Izal Anastasia N.
Alexandrova
30. P u t t i n g t h e p u z z l e t o g e t h e r : d e f e c t p o s i t i o n i n g V
• Stationary beam prevents real-time sample monitoring
• Drift causes frequent “misses”
• Need to detect when a structural change happens
• Need to automatically (and intelligently) position beam
• We need help from the machine
31. P u t t i n g t h e p u z z l e t o g e t h e r : d e f e c t p o s i t i o n i n g V
Custom software/hardware for beam control and feedback
Stephen Jesse
Overview
scan pattern
Dwell time
Raw overview
Filtered
overview
Sum of spiral scans
Real-time image of
manipulation mode
32. P u t t i n g t h e p u z z l e t o g e t h e r : d e f e c t p o s i t i o n i n g V
Automated drift compensation
Drift compensation off Drift compensation on
33. P u t t i n g t h e p u z z l e t o g e t h e r : d e f e c t p o s i t i o n i n g V
34. P u t t i n g t h e p u z z l e t o g e t h e r : d e f e c t p o s i t i o n i n g V
Next step: Automated beam positioning for atomic movement
Rule: chose the closest
neighboring lattice position
to the target
35. P u t t i n g t h e p u z z l e t o g e t h e r : d e f e c t p o s i t i o n i n g V
Spiral Scan + Compressive Sensing
Conventional scan pathStop and wait for
scan coil hysteresis Significant oversampling
Can we scan continuously?
Can we sample “just enough”?
36. P u t t i n g t h e p u z z l e t o g e t h e r : d e f e c t p o s i t i o n i n g V
Lissajous scan paths
Is there a scan path that
optimizes data collection?
Do we need an image?
37. P u t t i n g t h e p u z z l e t o g e t h e r : d e f e c t p o s i t i o n i n g V
Next step: Automated atom position recognition
Rapid-scanned image
(simulated) with 5 times
more noise than signal
FFT of the image revealing
periodicity
Ring filtered image can be
compared to an expected
lattice generated from the
FFT to find atom positions.
We help the computer by
giving it an assumption: it
is looking at a lattice of
some kind and this is what
is important.
38. P u t t i n g t h e p u z z l e t o g e t h e r : d e f e c t p o s i t i o n i n g V
Next step: Automated atom position recognition
Raw data from microscope Ring filtered image
Atom positions found
• Rapid scan fast “peak” at the sample
• Lower electron dose less chance of
unintentional sample modification
• Computer knows where atoms are atomic
movement can be automated
39. I n t e r p r e t a t i o n : b u i l d i n g l i b r a r i e s
One C atom displaced Two C atoms displaced
Anastasia N.
Alexandrova
Elisa Jimenez-Izal
• What atomic configurations can be stable?
• Are they useful/have interesting physics?
• How would they look in STEM?
40. I n t e r p r e t a t i o n : A u t o m a t e d D e f e c t C l a s s i f i c a t i o n
Convolutional Neural Network
Pixel-wise localization and classification
Maxim Ziatdinov Artem Maksov
M. Ziatdinov et al., ACS Nano 11, 12742 (2017)
M. Ziatdinov et al., arXiv:1801.05133 (2018)
A. Maksov et al., arXiv:1803.05381 (2018)
Experiment cNN output
Time
C lattice atoms Si dopants Vacancies
41. I n t e r p r e t a t i o n : A u t o m a t e d D e f e c t C l a s s i f i c a t i o n
Analysis of Atomic Defect Kinetics During E-beam
Induced Transformations in WS2
ConvNet + Gaussian mixture model
42. N a n o - M a c h i n e s
Sensors
(multimodal)
Signal processing
and control
Locomotion
Power unit
Nature provides us with examples
incredibly well adapted machines
- Autonomous
- Adaptable
- Self-growing
- Self-healing
- Self-replicating
- Capable of (limited)
network formation
25-200 nm30 nm
Viruses are
the smallest
organisms
43. N a n o - M a c h i n e s
• Not even nature gives us examples of “high level” functionality on the
nanometer scale
• They don’t do anything “on purpose”, no decisions being made
• General problem: We are trying to integrate to many dissimilar functionalities in
an extremely small package
– Thinking (signal processing, decision making, feedback etc)
– Motility
– Energy sources (internal, chemistry, control fields?)
44. N a n o - M a c h i n e s
What if we use a single atom or small atom assembly as an
functional element of a moving nanomachine, and defer
control and power functions to external entities?
Remove thinking and energy source from the machine itself
45. Scanning over this bright
nanoparticle caused it to start
eating the carbon raft it was
stuck to.
As the
nanoparticle eats
the carbon it is
pulled along the
edge of the bilayer
46.
47. N a n o - M a c h i n e s
Dyck et. al., J. Vac. Sci. Tech. B (2017)
Patterning of C
Single layer
Double layer
Triple layer
Maybe heat and custom beam control can
direct the deposition rate and produce
patterning of graphene on graphene
Nanoparticle
Pathway defined by in situ
grown graphene
48. N a n o - M a c h i n e s
600 oC
600 oC
Trigger on intensity
rather than frequency
Graphitic nanowires
grown at various
temperatures