Tag Archives: microscopy

Characterizing anatase titanium dixoide at the nanoscale

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An international collaboration of researchers combined atomic force microscopy (AFM) and scanning tunneling microscopy (STM) to characterize anatase titanium dixoxide. From a Sept. 14, 2015 news item on Azonano,

A [Japan National Institute for Materials Science] NIMS research team successfully identified the atoms and common defects existing at the most stable surface of the anatase form of titanium dioxide by characterizing this material at the atomic scale with scanning probe microscopy. This work was published under open access policy in the online version of Nature Communications on June 29, 2015.

A June 29, 2015 NIMS press release, which originated the news item, includes the paper’s abstract in numbered point form,

  1. The research team consisting of Oscar Custance and Tomoko Shimizu, group leader and senior scientist, respectively, at the Atomic Force Probe Group, NIMS, Daisuke Fujita and Keisuke Sagisaka, group leader and senior researcher, respectively, at the Surface Characterization Group, NIMS, and scientists at Charles University in the Czech Republic, Autonomous University of Madrid in Spain, and other organizations combined simultaneous atomic force microscopy (AFM) and scanning tunneling microscopy (STM) measurements with first-principles calculations for the unambiguous identification of the atomic species at the most stable surface of the anatase form of titanium dioxide (hereinafter referred to as anatase) and its most common defects.
  2. In recent years, anatase has attracted considerable attention, because it has become a pivotal material in devices for photo-catalysis and for the conversion of solar energy to electricity. It is extremely challenging to grow large single crystals of anatase, and most of the applications of this material are in the form of nano crystals. To enhance the catalytic reactivity of anatase and the efficiency of devices for solar energy conversion based on anatase, it is critical to gain in-depth understanding and control of the reactions taking place at the surface of this material down to the atomic level. Only a few research groups worldwide possess the technology to create proper test samples and to make in-situ atomic-level observations of anatase surfaces.
  3. In this study, the research team used samples obtained from anatase natural single crystals extracted from naturally occurring anatase rocks. The team characterized the (101) surface of anatase at atomic level by means of simultaneous AFM and STM. Using single water molecules as atomic markers, the team successfully identified the atomic species of this surface; result that was additionally confirmed by the comparison of simultaneous AFM and STM measurements with the outcomes of first-principles calculations.
  4. In regular STM, in which an atomically sharp probe is scanned over the surface by keeping constant an electrical current flowing between them, it is difficult to stably image anatase surfaces as this material presents poor electrical conductivity over some of the atomic positions of the surface. However, simultaneous operation of AFM and STM allowed imaging the surface with atomic resolution even within the materials band gap (a region where the flow of current between the probe and the surface is, in principle, prohibited). Here, the detection of inter-atomic forces between the last atom of the atomically sharp probe and the atoms of the surface by AFM was of crucial importance. By regulating the probe-surface distance using AFM, it was possible to image the surface at atomic-scale while collecting STM data over both conductive and not conductive areas of the surface. By comparing simultaneous AFM and STM measurements with theoretical simulations, the team was not only able to discern which atomic species were contributing to the AFM and the STM images but also to identify the most common defects found at the surface.
  5. In the future, based on the information gained from this study, the NIMS research team will conduct research on molecules of technologically relevance that adsorb on anatase and characterize these hybrid systems by using simultaneous AFM and STM. Their ultimate goal is to formulate novel approaches for the development of photo-catalysts and solar cell materials and devices.

Here’s a link to and a citation for the paper,

Atomic species identification at the (101) anatase surface by simultaneous scanning tunnelling and atomic force microscopy by Oleksandr Stetsovych, Milica Todorović, Tomoko K. Shimizu, César Moreno, James William Ryan, Carmen Pérez León, Keisuke Sagisaka, Emilio Palomares, Vladimír Matolín, Daisuke Fujita, Ruben Perez, & Oscar Custance. Nature Communications 6, Article number: 7265 doi:10.1038/ncomms8265 Published 29 June 2015

This is an open access paper.

Corrections: Hybrid Photonic-Nanomechanical Force Microscopy uses vibration for better chemical analysis

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*ETA  Nov. 4, 2015: I’m apologizing to anyone wishing to read this posting as it’s a bit of a mess. I deeply regret mishandling the situation. In future, I shall not be taking any corrections from individual researchers to materials such as news releases that have been issued by an institution. Whether or not the individual researchers are happy with how their contributions or how a colleague’s contributions or how their home institutions have been characterized is a matter for them and their home institutions.

The August 10, 2015 ORNL news release with all the correct details has been added to the end of this post.*

A researcher at the University of Central Florida (UCF) has developed a microscope that uses vibrations for better analysis of chemical composition. From an Aug. 10, 2015 news item on Nanowerk,

It’s a discovery that could have promising implications for fields as varied as biofuel production, solar energy, opto-electronic devices, pharmaceuticals and medical research.

“What we’re interested in is the tools that allow us to understand the world at a very small scale,” said UCF professor Laurene Tetard, formerly of the Oak Ridge National Laboratory. “Not just the shape of the object, but its mechanical properties, its composition and how it evolves in time.”

An Aug. 10, 2015 UCF news release (also on EurekAlert), which originated the news item, describes the limitations of atomic force microscopy and gives a few details about the hybrid microscope (Note: A link has been removed),

For more than two decades, scientists have used atomic force microscopy – a probe that acts like an ultra-sensitive needle on a record player – to determine the surface characteristics of samples at the microscopic scale. A “needle” that comes to an atoms-thin point traces a path over a sample, mapping the surface features at a sub-cellular level [nanoscale].

But that technology has its limits. It can determine the topographical characteristics of [a] sample, but it can’t identify its composition. And with the standard tools currently used for chemical mapping, anything smaller than roughly half a micron is going to look like a blurry blob, so researchers are out of luck if they want to study what’s happening at the molecular level.

A team led by Tetard has come up with a hybrid form of that technology that produces a much clearer chemical image. As described Aug. 10 in the journal Nature Nanotechnology, Hybrid Photonic-Nanomechanical Force Microscopy (HPFM) can discern a sample’s topographic characteristics together with the chemical properties at a much finer scale.

The HPFM method is able to identify materials based on differences in the vibration produced when they’re subjected to different wavelengths of light – essentially a material’s unique “fingerprint.”

“What we are developing is a completely new way of making that detection possible,” said Tetard, who has joint appointments to UCF’s Physics Department, Material Science and Engineering Department and the NanoScience Technology Center.

The researchers proved the effectiveness of HPFM while examining samples from an eastern cottonwood tree, a potential source of biofuel. By examining the plant samples at the nanoscale, the researchers for the first time were able to determine the molecular traits of both untreated and chemically processed cottonwood inside the plant cell walls.

The research team included Tetard; Ali Passian, R.H. Farahi and Brian Davison, all of Oak Ridge National Laboratory; and Thomas Thundat of the University of Alberta.

Long term, the results will help reveal better methods for producing the most biofuel from the cottonwood, a potential boon for industry. Likewise, the new method could be used to examine samples of myriad plants to determine whether they’re good candidates for biofuel production.

Potential uses of the technology go beyond the world of biofuel. Continued research may allow HPFM to be used as a probe so, for instance, it would be possible to study the effect of new treatments being developed to save plants such as citrus trees from bacterial diseases rapidly decimating the citrus industry, or study fundamental photonically-induced processes in complex systems such as in solar cell materials or opto-electronic devices.

Here’s a link to and a citation for the paper,

Opto-nanomechanical spectroscopic material characterization by L. Tetard, A. Passian, R. H. Farahi, T. Thundat, & B. H. Davison. Nature Nanotechnology (2015) doi:10.1038/nnano.2015.168 Published online 10 August 2015

This paper is behind a paywall.

*ETA August 27, 2015:

August 10, 2015 ORNL news release (Note: Funding information and a link to the paper [previously given] have been removed):

A microscope being developed at the Department of Energy’s Oak Ridge National Laboratory will allow scientists studying biological and synthetic materials to simultaneously observe chemical and physical properties on and beneath the surface.

The Hybrid Photonic Mode-Synthesizing Atomic Force Microscope is unique, according to principal investigator Ali Passian of ORNL’s Quantum Information System group. As a hybrid, the instrument, described in a paper published in Nature Nanotechnology, combines the disciplines of nanospectroscopy and nanomechanical microscopy.

“Our microscope offers a noninvasive rapid method to explore materials simultaneously for their chemical and physical properties,” Passian said. “It allows researchers to study the surface and subsurface of synthetic and biological samples, which is a capability that until now didn’t exist.”

ORNL’s instrument retains all of the advantages of an atomic force microscope while simultaneously offering the potential for discoveries through its high resolution and subsurface spectroscopic capabilities.

“The originality of the instrument and technique lies in its ability to provide information about a material’s chemical composition in the broad infrared spectrum of the chemical composition while showing the morphology of a material’s interior and exterior with nanoscale – a billionth of a meter – resolution,” Passian said.

Researchers will be able to study samples ranging from engineered nanoparticles and nanostructures to naturally occurring biological polymers, tissues and plant cells.

The first application as part of DOE’s BioEnergy Science Center was in the examination of plant cell walls under several treatments to provide submicron characterization. The plant cell wall is a layered nanostructure of biopolymers such as cellulose. Scientists want to convert such biopolymers to free the useful sugars and release energy.

An earlier instrument, also invented at ORNL, provided imaging of poplar cell wall structures that yielded unprecedented topological information, advancing fundamental research in sustainable biofuels.

Because of this new instrument’s impressive capabilities, the researcher team envisions broad applications.
“An urgent need exists for new platforms that can tackle the challenges of subsurface and chemical characterization at the nanometer scale,” said co-author Rubye Farahi. “Hybrid approaches such as ours bring together multiple capabilities, in this case, spectroscopy and high-resolution microscopy.”

Looking inside, the hybrid microscope consists of a photonic module that is incorporated into a mode-synthesizing atomic force microscope. The modular aspect of the system makes it possible to accommodate various radiation sources such as tunable lasers and non-coherent monochromatic or polychromatic sources.

…

ETA2 August 27, 2015: I’ve received an email from one of the paper’s authors (RH Farahi of the US Oak Ridge National Laboratory [ORNL]) who claims some inaccuracies in this piece.  The news release supplied by the University of Central Florida states that Dr. Tetard led the team and that is not so. According to Dr. Farahi, she had a postdoctoral position on the team which she left two years ago. You might also get the impression that some of the work was performed at the University of Central Florida. That is not so according to Dr. Farahi.  As a courtesy Dr. Tetard was retained as first author of the paper.

*Nov. 4, 2015: I suspect some of the misunderstanding was due to overeagerness and/or time pressures. Whoever wrote the news release may have made some assumptions. It’s very easy to make a mistake when talking to an ebullient scientist who can unintentionally lead you to believe something that’s not so. I worked in a high tech company and believed that there was some new software being developed which turned out to be a case of high hopes. Luckily, I said something that triggered a rapid rebuttal to the fantasies. Getting back to this situation, other contributing factors could include the writer not having time to get the news release reviewed the scientist or the scientist skimming the release and missing a few bits due to time pressure.*

Replacing metal with nanocellulose paper

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The quest to find uses for nanocellulose materials has taken a step forward with some work coming from the University of Maryland (US). From a July 24, 2015 news item on Nanowerk,

Researchers at the University of Maryland recently discovered that paper made of cellulose fibers is tougher and stronger the smaller the fibers get … . For a long time, engineers have sought a material that is both strong (resistant to non-recoverable deformation) and tough (tolerant of damage).

“Strength and toughness are often exclusive to each other,” said Teng Li, associate professor of mechanical engineering at UMD. “For example, a stronger material tends to be brittle, like cast iron or diamond.”

A July 23, 2015 University of Maryland news release, which originated the news item, provides details about the thinking which buttresses this research along with some details about the research itself,

The UMD team pursued the development of a strong and tough material by exploring the mechanical properties of cellulose, the most abundant renewable bio-resource on Earth. Researchers made papers with several sizes of cellulose fibers – all too small for the eye to see – ranging in size from about 30 micrometers to 10 nanometers. The paper made of 10-nanometer-thick fibers was 40 times tougher and 130 times stronger than regular notebook paper, which is made of cellulose fibers a thousand times larger.

“These findings could lead to a new class of high performance engineering materials that are both strong and tough, a Holy Grail in materials design,” said Li.

High performance yet lightweight cellulose-based materials might one day replace conventional structural materials (i.e. metals) in applications where weight is important. This could lead, for example, to more energy efficient and “green” vehicles. In addition, team members say, transparent cellulose nanopaper may become feasible as a functional substrate in flexible electronics, resulting in paper electronics, printable solar cells and flexible displays that could radically change many aspects of daily life.

Cellulose fibers can easily form many hydrogen bonds. Once broken, the hydrogen bonds can reform on their own—giving the material a ‘self-healing’ quality. The UMD discovered that the smaller the cellulose fibers, the more hydrogen bonds per square area. This means paper made of very small fibers can both hold together better and re-form more quickly, which is the key for cellulose nanopaper to be both strong and tough.

“It is helpful to know why cellulose nanopaper is both strong and tough, especially when the underlying reason is also applicable to many other materials,” said Liangbing Hu, assistant professor of materials science at UMD.

To confirm, the researchers tried a similar experiment using carbon nanotubes that were similar in size to the cellulose fibers. The carbon nanotubes had much weaker bonds holding them together, so under tension they did not hold together as well. Paper made of carbon nanotubes is weak, though individually nanotubes are arguably the strongest material ever made.

One possible future direction for the research is the improvement of the mechanical performance of carbon nanotube paper.

“Paper made of a network of carbon nanotubes is much weaker than expected,” said Li. “Indeed, it has been a grand challenge to translate the superb properties of carbon nanotubes at nanoscale to macroscale. Our research findings shed light on a viable approach to addressing this challenge and achieving carbon nanotube paper that is both strong and tough.”

Here’s a link to and a citation for the paper,

Anomalous scaling law of strength and toughness of cellulose nanopaper by Hongli Zhu, Shuze Zhu, Zheng Jia, Sepideh Parvinian, Yuanyuan Li, Oeyvind Vaaland, Liangbing Hu, and Teng Li. PNAS (Proceedings of the National Academy of Sciences) July 21, 2015 vol. 112 no. 29 doi: 10.1073/pnas.1502870112

This paper is behind a paywall.

There is a lot of research on applications for nanocellulose, everywhere it seems, except Canada, which at one time was a leader in the business of producing cellulose nanocrystals (CNC).

Here’s a sampling of some of my most recent posts on nanocellulose,

Nanocellulose as a biosensor (July 28, 2015)

Microscopy, Paper and Fibre Research Institute (Norway), and nanocellulose (July 8, 2015)

Nanocellulose markets report released (June 5, 2015; US market research)

New US platform for nanocellulose and occupational health and safety research (June 1, 2015; Note: As you find new applications, you need to concern yourself with occupational health and safety.)

‘Green’, flexible electronics with nanocellulose materials (May 26, 2015; research from China)

Treating municipal wastewater and dirty industry byproducts with nanocellulose-based filters (Dec. 23, 2014; research from Sweden)

Nanocellulose and an intensity of structural colour (June 16, 2014; research about replacing toxic pigments with structural colour from the UK)

I ask again, where are the Canadians? If anybody has an answer, please let me know.

SINGLE (3D Structure Identification of Nanoparticles by Graphene Liquid Cell Electron Microscopy) and the 3D structures of two individual platinum nanoparticles in solution

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It seems to me there’s been an explosion of new imaging techniques lately. This one from the Lawrence Berkelely National Laboratory is all about imaging colloidal nanoparticles (nanoparticles in solution), from a July 20, 2015 news item on Azonano,

Just as proteins are one of the basic building blocks of biology, nanoparticles can serve as the basic building blocks for next generation materials. In keeping with this parallel between biology and nanotechnology, a proven technique for determining the three dimensional structures of individual proteins has been adapted to determine the 3D structures of individual nanoparticles in solution.

A multi-institutional team of researchers led by the U.S. Department of Energy (DOE)’s Lawrence Berkeley National Laboratory (Berkeley Lab), has developed a new technique called “SINGLE” that provides the first atomic-scale images of colloidal nanoparticles. SINGLE, which stands for 3D Structure Identification of Nanoparticles by Graphene Liquid Cell Electron Microscopy, has been used to separately reconstruct the 3D structures of two individual platinum nanoparticles in solution.

A July 16, 2015 Berkeley Lab news release, which originated the news item, reveals more details about the reason for the research and the research itself,

“Understanding structural details of colloidal nanoparticles is required to bridge our knowledge about their synthesis, growth mechanisms, and physical properties to facilitate their application to renewable energy, catalysis and a great many other fields,” says Berkeley Lab director and renowned nanoscience authority Paul Alivisatos, who led this research. “Whereas most structural studies of colloidal nanoparticles are performed in a vacuum after crystal growth is complete, our SINGLE method allows us to determine their 3D structure in a solution, an important step to improving the design of nanoparticles for catalysis and energy research applications.”

Alivisatos, who also holds the Samsung Distinguished Chair in Nanoscience and Nanotechnology at the University of California Berkeley, and directs the Kavli Energy NanoScience Institute at Berkeley (Kavli ENSI), is the corresponding author of a paper detailing this research in the journal Science. The paper is titled “3D Structure of Individual Nanocrystals in Solution by Electron Microscopy.” The lead co-authors are Jungwon Park of Harvard University, Hans Elmlund of Australia’s Monash University, and Peter Ercius of Berkeley Lab. Other co-authors are Jong Min Yuk, David Limmer, Qian Chen, Kwanpyo Kim, Sang Hoon Han, David Weitz and Alex Zettl.

Colloidal nanoparticles are clusters of hundreds to thousands of atoms suspended in a solution whose collective chemical and physical properties are determined by the size and shape of the individual nanoparticles. Imaging techniques that are routinely used to analyze the 3D structure of individual crystals in a material can’t be applied to suspended nanomaterials because individual particles in a solution are not static. The functionality of proteins are also determined by their size and shape, and scientists who wanted to image 3D protein structures faced a similar problem. The protein imaging problem was solved by a technique called “single-particle cryo-electron microscopy,” in which tens of thousands of 2D transmission electron microscope (TEM) images of identical copies of an individual protein or protein complex frozen in random orientations are recorded then computationally combined into high-resolution 3D reconstructions. Alivisatos and his colleagues utilized this concept to create their SINGLE technique.

“In materials science, we cannot assume the nanoparticles in a solution are all identical so we needed to develop a hybrid approach for reconstructing the 3D structures of individual nanoparticles,” says co-lead author of the Science paper Peter Ercius, a staff scientist with the National Center for Electron Microscopy (NCEM) at the Molecular Foundry, a DOE Office of Science User Facility.

“SINGLE represents a combination of three technological advancements from TEM imaging in biological and materials science,” Ercius says. “These three advancements are the development of a graphene liquid cell that allows TEM imaging of nanoparticles rotating freely in solution, direct electron detectors that can produce movies with millisecond frame-to-frame time resolution of the rotating nanocrystals, and a theory for ab initio single particle 3D reconstruction.”

The graphene liquid cell (GLC) that helped make this study possible was also developed at Berkeley Lab under the leadership of Alivisatos and co-author Zettl, a physicist who also holds joint appointments with Berkeley Lab, UC Berkeley and Kavli ENSI. TEM imaging uses a beam of electrons rather than light for illumination and magnification but can only be used in a high vacuum because molecules in the air disrupt the electron beam. Since liquids evaporate in high vacuum, samples in solutions must be hermetically sealed in special solid containers – called cells – with a very thin viewing window before being imaged with TEM. In the past, liquid cells featured silicon-based viewing windows whose thickness limited resolution and perturbed the natural state of the sample materials. The GLC developed at Berkeley lab features a viewing window made from a graphene sheet that is only a single atom thick.

“The GLC provides us with an ultra-thin covering of our nanoparticles while maintaining liquid conditions in the TEM vacuum,” Ercius says. “Since the graphene surface of the GLC is inert, it does not adsorb or otherwise perturb the natural state of our nanoparticles.”

Working at NCEM’s TEAM I, the world’s most powerful electron microscope, Ercius, Alivisatos and their colleagues were able to image in situ the translational and rotational motions of individual nanoparticles of platinum that were less than two nanometers in diameter. Platinum nanoparticles were chosen because of their high electron scattering strength and because their detailed atomic structure is important for catalysis.

“Our earlier GLC studies of platinum nanocrystals showed that they grow by aggregation, resulting in complex structures that are not possible to determine by any previously developed method,” Ercius says. “Since SINGLE derives its 3D structures from images of individual nanoparticles rotating freely in solution, it enables the analysis of heterogeneous populations of potentially unordered nanoparticles that are synthesized in solution, thereby providing a means to understand the structure and stability of defects at the nanoscale.”

The next step for SINGLE is to recover a full 3D atomic resolution density map of colloidal nanoparticles using a more advanced camera installed on TEAM I that can provide 400 frames-per-second and better image quality.

“We plan to image defects in nanoparticles made from different materials, core shell particles, and also alloys made of two different atomic species,” Ercius says. [emphasis mine]

“Two different atomic species?”, they really are pushing that biology analogy.

Here’s a link to and a citation for the paper,

3D structure of individual nanocrystals in solution by electron microscopy by Jungwon Park, Hans Elmlund, Peter Ercius, Jong Min Yuk, David T. Limme, Qian Chen, Kwanpyo Kim, Sang Hoon Han, David A. Weitz, A. Zettl, A. Paul Alivisatos. Science 17 July 2015: Vol. 349 no. 6245 pp. 290-295 DOI: 10.1126/science.aab1343

This paper is behind a paywall.

Microscopy, Paper and Fibre Research Institute (Norway), and nanocellulose

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In keeping with a longstanding interest here in nanocellulose (aka, cellulose nanomaterials) the Norwegian Paper and Fibre Research Institute’s (PFI) ??,??, 2015 announcement about new ion milling equipment and a new scanning electron microscope suitable for research into cellulose at the nanoscale caught my eye,

In order to advance the microscopy capabilities of cellulose-based materials and thanks to a grant from the Norwegian Pulp and Paper Research Institute foundation, PFI has invested in a modern ion milling equipment and a new Scanning Electron Microscope (SEM).

Unusually, the entire news release is being stored at Nanowerk as a July 3, 2015 news item (Note: Links have been removed),

“There are several microscopy techniques that can be used for characterizing cellulose materials, but the scanning electron microscope is one of the most preferable ones as the microscope is easy to use, versatile and provides a multi-scale assessment”, explains Gary Chinga-Carrasco, lead scientist at the PFI Biocomposite area.

“However, good microscopy depends to a large extent on an adequate and optimized preparation of the samples”, adds Per Olav Johnsen, senior engineer and microscopy expert at PFI.

“We are always trying to be in front in the development of new characterization methods, facilitating research and giving support to our industrial partners”, says Chinga-Carrasco, who has been active in developing new methods for characterization of paper, biocomposites and nanocellulose and cannot hide his enthusiasm when he talks about PFI’s new equipment. “In the first period after the installation it is important to work with the equipment with several material samples and techniques to really become confident with its use and reveal its potential”.

…

The team at PFI is now offering new methods for assessing cellulose materials in great detail. They point out that they have various activities and projects where they already see a big potential with the new equipment.

Examples for these efforts are the assessment of porous nanocellulose structures for biomedical applications (for instance in the NanoHeal program) and the assessment of surface modified wood fibres for use in biocomposites (for instance in the FiberComp project).

Also unusual is the lack of detail about the microscope’s and ion milling machine’s technical specifications and capabilities.

The NanoHeal program was last mentioned here in an April 14, 2014 post and first mentioned here in an Aug. 23, 2012 posting.

Final comment, I wonder if Nanowerk is embarking on a new initiative where the company agrees to store news releases for various agencies such as PFI and others who would prefer not to  archive their own materials. Just a thought.

“This is the best microscope we could ever dream of”—Rice University (US) gets new microscope

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I believe it’s Emilie Ringe who’s hosting this video about the new microscope at Rice University (Texas, US) and, as you will be able to tell, she’s thrilled.

A June 29, 2015 news item on Nanotechnology Now explains some of Ringe’s excitement,

Rice University, renowned for nanoscale science, has installed microscopes that will allow researchers to peer deeper than ever into the fabric of the universe.

The Titan Themis scanning/transmission electron microscope, one of the most powerful in the United States, will enable scientists from Rice as well as academic and industrial partners to view and analyze materials smaller than a nanometer — a billionth of a meter — with startling clarity.

The microscope has the ability to take images of materials at angstrom-scale (one-tenth of a nanometer) resolution, about the size of a single hydrogen atom.

Images will be captured with a variety of detectors, including X-ray, optical and multiple electron detectors and a 4K-resolution camera, equivalent to the number of pixels in the most modern high-resolution televisions. The microscope gives researchers the ability to create three-dimensional structural reconstructions and carry out electric field mapping of subnanoscale materials.

“Seeing single atoms is exciting, of course, and it’s beautiful,” said Emilie Ringe, a Rice assistant professor of materials science and nanoengineering and of chemistry. “But scientists saw single atoms in the ’90s, and even before. Now, the real breakthrough is that we can identify the composition of those atoms, and do it easily and reliably.” Ringe’s research group will operate the Titan Themis and a companion microscope that will image larger samples.

A June 29, 2015 Rice University news release, which originated the news item, provides more information about electron microscopes, incident electron beams, and the specifics of the second new piece of equipment being installed,

Electron microscopes use beams of electrons rather than rays of light to illuminate objects of interest. Because the wavelength of electrons is so much smaller than that of photons, the microscopes are able to capture images of much smaller things with greater detail than even the highest-resolution optical microscope.

“The beauty of these newer instruments is their analytical capabilities,” Ringe said. “Before, in order to see single atoms, we had to work a machine for an entire day and get it just right and then take a picture and hold our breath. These days, seeing atoms is routine.

“And now we can probe a particular atom’s chemical composition. Through various techniques, either via scattering intensity, X-rays emission or electron-beam absorption, we can figure out, say, that we’re looking at a palladium atom or a carbon atom. We couldn’t do that before.”

Ringe said when an electron beam ejects a bound electron from a target atom, it creates an empty site. “That can be filled by another electron within the atom, and the energy difference between this electron and the missing electron is emitted as an X-ray,” she said. “That X-ray is like a fingerprint, which we can read. Different types of atoms have different energies.”

She said the incident electron beam loses a bit of energy when it knocks an atom’s electron loose, and that energy loss can also be measured with a spectroscope to identify the atom. The X-ray and electron techniques are independent but complementary. “Typically, you use either/or, and it depends on what element you’re looking at,” Ringe said.

The second instrument, a Helios NanoLab 600 DualBeam microscope, will be used for three-dimensional imaging, analysis of larger samples and preparation of thin slices of samples for the more powerful Titan next door.

Both tools reside in the university’s Brockman Hall for Physics, which opened in 2011 and features sophisticated vibration-dampening capabilities. The microscopes require the best possible isolation from vibration, electric fields and acoustic noise to produce the best images, Ringe said.

“We have wanted a high-end microscopy facility at Rice because so many of us are working on nanomaterials,” said Pulickel Ajayan, a professor and founding chair of Rice’s Department of Materials Science and NanoEngineering. “This has been an issue because in order to be competitive you have to have the best atomic-scale characterization techniques. This will put us in business in terms of imaging and understanding new materials.”

He said the facility will position Rice as one of the most competitive institutions to recruit students and faculty, attract grants and publish groundbreaking results.

“A visual image of something on an atomic level can give you so much more information than a few numbers can,” said Peter Rossky, a theoretical chemist and dean of Rice’s Wiess School of Natural Sciences. Comparing images of the same material taken by an older electron microscope and the Titan Themis was like “the difference between a black-and-white TV and high-definition color,” he said.

Ringe said Rice’s Titan is a fourth-generation model manufactured in the Netherlands. It’s the latest and most powerful model and the first to be installed in the United States.

“Taking a complex image — not just a picture but a spectrum image that has lots of energy information — in the older model would take about 35 minutes,” she said. “By that time, the electron beam has destroyed whatever you were trying to look at.

“With this generation, you have the data you need in about two minutes. You can generate a lot more data more quickly. It’s not just better; it’s enabling.”

Edwin Thomas, the William and Stephanie Sick Dean of Rice’s George R. Brown School of Engineering, expects the new instruments to ignite the already strong research culture at the university. “This is going to influence the kind of people who will be attracted to apply to and then come to Rice,” said Thomas, a materials scientist. “I’m sure there will be people on campus who, once they find out the capabilities, are going to shift their compasses and take advantage of these machines. The whole point is to have an impact on science and society.”

Rice plans to host a two-day workshop in September to introduce the microscopes and their capabilities to the research community at the university and beyond. [emphasis mine] Beginning this summer, Ringe said, the electron microscopy center will be open to Rice students and faculty as well as researchers from other universities and industry.

Ringe looks forward to bringing researchers into the new microscopy lab — and to the research that will emerge.

“I hope everyone’s going to come out with a blockbuster paper with images from these instruments,” she said. “I would like every paper from Rice to have fantastic, crystal-clear, atomic-resolution images and the best possible characterization.”

To sum this up, there are two new pieces of equipment (Titan Themis scanning/transmission electron microscope and Helios NanoLab 600 DualBeam microscope) in Rice University’s 2011 facility, Brockman Hall for Physics. They are very excited about having the most powerful microscope in the US (the Titan) and hope to be holding a two-day workshop on these new microscopes for the research community at Rice and at other institutions.

Nanoscale imaging gets rough

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Smooth is easier than rough when imaging at the nanoscale according to a June 17, 2015 Northwestern University news release by Megan Fellman (also on EurekAlert),

A multi-institutional team of scientists has taken an important step in understanding where atoms are located on the surfaces of rough materials, information that could be very useful in diverse commercial applications, such as developing green energy and understanding how materials rust.

Researchers from Northwestern University, Brookhaven National Laboratory, Lawrence Berkeley National Laboratory and the University of Melbourne, Australia, have developed a new imaging technique that uses atomic resolution secondary electron images in a quantitative way to determine the arrangement of atoms on the surface.

Many important processes take place at surfaces, ranging from the catalysis used to generate energy-dense fuels from sunlight and carbon dioxide to how bridges and airplanes corrode, or rust. Every material interacts with the world through its surface, which is often different in both structure and chemistry from the bulk of the material.

The real focus of the work is on corrosion, according to the news release,

“We are excited by the possibilities of applying our imaging technique to corrosion and catalysis problems,” said Laurence Marks, a co-author of the paper and a professor of materials science and engineering at Northwestern’s McCormick School of Engineering and Applied Science. “The cost of corrosion to industry and the military is enormous, and we do not understand everything that is taking place. We must learn more, so we can produce materials that will last longer.”

To understand these processes and improve material performance, it is vital to know how the atoms are arranged on surfaces. While there are many good methods for obtaining this information for rather flat surfaces, most currently available tools are limited in what they can reveal when the surfaces are rough.

Scanning electron microscopes are widely used to produce images of many different materials, and roughness of the surface is not that important. Until very recently, instruments could not obtain clear atomic images of surfaces until a group at Brookhaven managed in 2011 to get the first images that seemed to show the surfaces very clearly. However, it was not clear to what extent they really were able to image the surface, as there was no theory for the imaging and many uncertainties.

The new work has answered all these questions, Marks said, providing a definitive way of understanding the surfaces in detail. What was needed was to use a carefully controlled sample of strontium titanate and perform a large range of different types of imaging to unravel the precise details of how secondary electron images are produced.

“We started this work by investigating a well-studied material,” said Jim Ciston, a staff scientist at Lawrence Berkeley National Laboratory and the lead author of the paper, who obtained the experimental images. “This new technique is so powerful that we had to revise much of what was already thought to be well-known. This is an exciting prospect because the surface of every material can act as its own nanomaterial coating, which can greatly change the chemistry and behavior.”

“The beauty of the technique is that we can image surface atoms and bulk atoms simultaneously,” said Yimei Zhu, a scientist at Brookhaven National Laboratory. “Currently, no existing methods can achieve that.”

Les Allen, who led the theoretical and modeling aspects of the new imaging technique in Melbourne, said, “We now have a sophisticated understanding of what the images mean. It now will be full steam ahead to apply them to many different types of problems.”

Here’s a link to and citation for the paper,

Surface determination through atomically resolved secondary-electron imaging by J. Ciston, H. G. Brown, A. J. D’Alfonso, P. Koirala, C. Ophus, Y. Lin, Y. Suzuki, H. Inada, Y. Zhu, L. J. Allen, & L. D. Marks. Nature Communications 6, Article number: 7358 doi:10.1038/ncomms8358 Published 17 June 2015

This paper is open access.

Magnetic sensitivity under the microscope

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Humans do not have the sense of magnetoreception (the ability to detect magnetic fields) unless they’ve been enhanced. On the other hand, species of fish, insects, birds, and some mammals (other than human) possess the sense naturally. Scientists at the University of Tokyo (Japan) have developed a microscope capable of observing magnetoreception according to a June 4, 2015 news item on Nanowerk (Note: A link has been removed),

Researchers at the University of Tokyo have succeeded in developing a new microscope capable of observing the magnetic sensitivity of photochemical reactions believed to be responsible for the ability of some animals to navigate in the Earth’s magnetic field, on a scale small enough to follow these reactions taking place inside sub-cellular structures (Angewandte Chemie International Edition, “Optical Absorption and Magnetic Field Effect Based Imaging of Transient Radicals”).

A June 4, 2015 University of Tokyo news release on EurekAlert, which originated the news item, describes the research in more detail,

Several species of insects, fish, birds and mammals are believed to be able to detect magnetic fields – an ability known as magnetoreception. For example, birds are able to sense the Earth’s magnetic field and use it to help navigate when migrating. Recent research suggests that a group of proteins called cryptochromes and particularly the molecule flavin adenine dinucleotide (FAD) that forms part of the cryptochrome, are implicated in magnetoreception. When cryptochromes absorb blue light, they can form what are known as radical pairs. The magnetic field around the cryptochromes determines the spins of these radical pairs, altering their reactivity. However, to date there has been no way to measure the effect of magnetic fields on radical pairs in living cells.

The research group of Associate Professor Jonathan Woodward at the Graduate School of Arts and Sciences are specialists in radical pair chemistry and investigating the magnetic sensitivity of biological systems. In this latest research, PhD student Lewis Antill made measurements using a special microscope to detect radical pairs formed from FAD, and the influence of very weak magnetic fields on their reactivity, in volumes less than 4 millionths of a billionth of a liter (4 femtoliters). This was possible using a technique the group developed called TOAD (transient optical absorption detection) imaging, employing a microscope built by postdoctoral research associate Dr. Joshua Beardmore based on a design by Beardmore and Woodward.

“In the future, using another mode of the new microscope called MIM (magnetic intensity modulation), also introduced in this work, it may be possible to directly image only the magnetically sensitive regions of living cells,” says Woodward. “The new imaging microscope developed in this research will enable the study of the magnetic sensitivity of photochemical reactions in a variety of important biological and other contexts, and hopefully help to unlock the secrets of animals’ miraculous magnetic sense.”

Here’s a link to and a citation for the paper,

Optical Absorption and Magnetic Field Effect Based Imaging of Transient Radicals by Dr. Joshua P. Beardmore, Lewis M. Antill, and Prof. Jonathan R. Woodward. Angewandte Chemie International Edition DOI: 10.1002/anie.201502591 Article first published online: 3 JUN 2015

© 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim

This paper is behind a paywall.

I mentioned human enhancement earlier with regard to magnetoreception. There are people (body hackers) who’ve had implants that give them this extra sense. Dann Berg in a March 21, 2012 post on his website blog (iamdann.com) describes why he implanted a magnet into his finger and his experience with it (at that time, three years and counting),

…

I quickly learned that magnetic surfaces provided almost no sensation at all. Rather, it was movement that caused my finger to perk up. Things like power cord transformers, microwaves, and laptop fans became interactive in a whole new way. Each object has its own unique field, with different strength and “texture.” I started holding my finger over almost everything that I could, getting a feeling for each object’s invisible reach.

Portable electronics proved to be an experience as well. There were two fairly large electronic items that hit the shelves around the same time as I got my implant: the first iPad and the Kindle 2.

…

Something to consider,

Courtesy: iamdann.com (Dann Berg)

Courtesy: iamdann.com (Dann Berg)

Motor proteins have a stiff-legged walk

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An April 23, 2015 news item on Nanowerk calls to mind Monty Python and its Ministry of Silly Walks,

The ‘stiff-legged’ walk of a motor protein along a tightrope-like filament has been captured for the first time.

Because cells are divided in many parts that serve different functions some cellular goodies need to be transported from one part of the cell to another for it to function smoothly. There is an entire class of proteins called ‘molecular motors’, such as myosin 5, that specialise in transporting cargo using chemical energy as fuel.

Remarkably, these proteins not only function like nano-scale lorries, they also look like a two-legged creature that takes very small steps. But exactly how Myosin 5 did this was unclear.

For anyone unfamiliar with The Ministry of Silly Walks (from its Wikipedia entry; Note: Links have been removed),

“The Ministry of Silly Walks” is a sketch from the Monty Python comedy troupe’s television show Monty Python’s Flying Circus, season 2, episode 14, which is entitled “Face the Press”.

Here’s an image from the sketch, which perfectly illustrates a stiff-legged walk,

John Cleese as a Civil Servant in the Ministry of Silly Walks. Screenshot from Monty Python's Flying Circus episode, Dinsdale (Alternate episode title: Face the Press). Ministry_of_Silly_Walks.jpg ‎(300 × 237 pixels, file size: 14 KB, MIME type: image/jpeg) [downloaded from http://en.wikipedia.org/wiki/File:Ministry_of_Silly_Walks.jpg]

John Cleese as a Civil Servant in the Ministry of Silly Walks. Screenshot from Monty Python’s Flying Circus episode, Dinsdale (Alternate episode title: Face the Press). Ministry_of_Silly_Walks.jpg ‎(300 × 237 pixels, file size: 14 KB, MIME type: image/jpeg) [downloaded from http://en.wikipedia.org/wiki/File:Ministry_of_Silly_Walks.jpg]

As far as I can tell, the use of this image would fall under the notion of ‘fair dealing‘ as it’s called in Canada.

Getting back to the Nanowerk news item, it started life as a University of Oxford Science blog April 23, 2015 posting  by Pete Wilton (Note: A link has been removed),

The motion of myosin 5 has now been recorded by a team led by Oxford University scientists using a new microscopy technique that can ‘see’ tiny steps of tens of nanometres captured at up to 1000 frames per second. The findings are of interest for anyone trying to understand the basis of cellular function but could also help efforts aimed at designing efficient nanomachines.

‘Until now, we believed that the sort of movements or steps these proteins made were random and free-flowing because none of the experiments suggested otherwise,’ said Philipp Kukura of Oxford University’s Department of Chemistry who led the research recently reported in the journal eLife. ‘However, what we have shown is that the movements only appeared random; if you have the capability to watch the motion with sufficient speed and precision, a rigid walking pattern emerges.’

One of the key problems for those trying to capture proteins on a walkabout is that not only are these molecules small – with steps much smaller than the wavelength of light and therefore the resolution of most optical microscopes – but they are also move very quickly.

Philipp describes how the team had to move from the microscope equivalent of an iPhone camera to something more like the high speed cameras used to snap speeding bullets. Even with such precise equipment the team had to tag the ‘feet’ of the protein in order to precisely image its gait: one foot was tagged with a quantum dot, the other with a gold particle just 20 nanometres across. (Confusingly, technically speaking, these ‘feet’ are termed the ‘heads’ of the protein because they bind to the actin filament).

I recommend reading Wilton’s post in its entirety. Meanwhile, here’s a 12 secs. video illustrating the motor protein’s stiff-legged walk,

Here’s a link to and a citation for the paper,

Structural dynamics of myosin 5 during processive motion revealed by interferometric scattering microscopy by Joanna Andrecka, Jaime Ortega Arroyo, Yasuharu Takagi, Gabrielle de Wit, Adam Fineberg, Lachlan MacKinnon, Gavin Young, James R Sellers, & Philipp Kukura. eLife 2015;4:e05413 DOI: http://dx.doi.org/10.7554/eLife.05413Published March 6, 2015

This paper is open access.

As for silly walks, there is more than one version of the sketch with John Cleese on YouTube but I was particularly taken with this public homage which took place in Brno (Czech Republic) in Jan. 2013,

Enjoy!

Bipolar disorder at the nanoscale

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In all the talk generated by the various brain projects (BRAIN initiative [US], The Human Brain Project [European Union], Brain Canada), there’s remarkably little discussion about mental illness. So, this news is a little unusual.

Using super-high resolution technique scientists at Northwestern University (Chicago, Illinois, US) believe they’ve made a discovery which explains how bipolar disorder affects the brain according to an Oct. 22, 2014 Northwestern University news release (also on EurekAlert and ScienceDaily) by Erin White,

Scientists used a new super-resolution imaging method — the same method recognized with the 2014 Nobel Prize in chemistry — to peer deep into brain tissue from mice with bipolar-like behaviors. In the synapses (where communication between brain cells occurs), they discovered tiny “nanodomain” structures with concentrated levels of ANK3 — the gene most strongly associated with bipolar disorder risk. ANK3 is coding for the protein ankyrin-G.

“We knew that ankyrin-G played an important role in bipolar disease, but we didn’t know how,” said Northwestern Medicine scientist Peter Penzes, corresponding author of the paper. “Through this imaging method we found the gene formed in nanodomain structures in the synapses, and we determined that these structures control or regulate the behavior of synapses.”

Penzes is a professor in physiology and psychiatry and behavioral sciences at Northwestern University Feinberg School of Medicine. The results were published Oct. 22 in the journal Neuron.

High-profile cases, including actress Catherine Zeta-Jones and politician Jesse Jackson, Jr., have brought attention to bipolar disorder. The illness causes unusual shifts in mood, energy, activity levels and the ability to carry out day-to-day tasks. About 3 percent of Americans experience bipolar disorder symptoms, and there is no cure.

Recent large-scale human genetic studies have shown that genes can contribute to disease risk along with stress and other environmental factors. However, how these risk genes affect the brain is not known.

This is the first time any psychiatric risk gene has been analyzed at such a detailed level of resolution. As explained in the paper, Penzes used the Nikon Structured Illumination Super-resolution Microscope to study a mouse model of bipolar disorder. The microscope realizes resolution of up to 115 nanometers. To put that size in perspective, a nanometer is one-tenth of a micron, and there are 25,400 microns in one inch. Very few of these microscopes exist worldwide.

“There is important information about genes and diseases that can only been seen at this level of resolution,” Penzes said. “We provide a neurobiological explanation of the function of the leading risk gene, and this might provide insight into the abnormalities in bipolar disorder.”

The biological framework presented in this paper could be used in human studies of bipolar disorder in the future, with the goal of developing therapeutic approaches to target these genes.

Here’s a link to and a citation for the paper,

Psychiatric Risk Factor ANK3/Ankyrin-G Nanodomains Regulate the Structure and Function of Glutamatergic Synapses by Katharine R. Smith, Katherine J. Kopeikina, Jessica M. Fawcett-Patel, Katherine Leaderbrand, Ruoqi Gao, Britta Schürmann, Kristoffer Myczek, Jelena Radulovic, Geoffrey T. Swanson, and Peter Penzes. Neuron, Volume 84, Issue 2, p399–415, 22 October 2014 DOI: http://dx.doi.org/10.1016/j.neuron.2014.10.010

This paper is behind a paywall.

You can find more about super-high resolution and nanoscopy in my Oct. 8, 2014 post about the 2014 Nobel Chemistry prize winners.