Tag Archives: microscopy

All about Atomic Force Microscopy (AFM) with Gerd Binnig and Christoph Gerber

Gerd Binnig, Christoph Gerber, and Calvin Quate invented the atomic force microscope in the 1980s and an Aug. 16, 2016 news item on Nanotechnology Now announces a discussion with two of the inventors, Binnig and Gerber (Note: Links have been removed),

The inventors of one of the most versatile tools in modern science – the atomic force microscope, or AFM – tell their story in an interview published online this week. The AFM was invented in the mid 1980s by Gerd Binnig, Christoph Gerber and Calvin Quate, three physicists who are sharing the 2016 Kavli Prize in Nanoscience.

Binnig and Gerber discuss their inspiration for the device, how they solved problems through sport, and why their invention continues to propel science at the nanoscale.

This charming Aug. 20, 2016 discussion for the Kavli Foundation focuses on more than the AFM although it is the main topic,

Our roundtable panelists were:

GERD BINNIG –is a physicist and Nobel Laureate for his invention (with Heinrich Rohrer and Christoph Gerber) of the scanning tunneling microscope while at IBM Zurich. He began development of the atomic force microscope in 1986 to overcome the limitations of his previous invention.
CHRISTOPH GERBER –is a physicist and director for scientific communication at the Swiss Nanoscience Institute at the University of Basel. While at IBM, Gerber worked closely with Binnig on bringing both the scanning tunneling microscope and atomic force microscope to fruition.

Calvin Quate was unable to participate in the roundtable. The transcript has been amended and edited by the laureates

THE KAVLI FOUNDATION [TKF]: You filed your first patent for the atomic force microscope (AFM) nearly 30 years ago. How has it changed the way we look at the world since then?

GERD BINNIG: It was like the first time people looked through an optical microscope and saw bacteria. That completely changed how we look at the world. Suddenly, we understood what was really going on in nature, and we used that knowledge to learn how diseases spread. The AFM is the next step. It lets us look at the molecules that make life possible in those bacteria – and everywhere else – and see things we could not see before. It teaches us how to make changes to surfaces or molecules that we attempted blindly in the past. And it has been used in so many different scientific studies, from looking at polymers and chemical reactions to modifying surfaces at the atomic level.

CHRISTOPH GERBER: As Gerd explained, seeing is believing, and now we can do that onthe atomic scale. AFM has turned into the most powerful and most versatile toolkit that we have for doing nanoscience. And it keeps evolving. In just the past few years, researchers have learned to pick up a molecule on the tip of an AFM, which we can think of as the needle on a record player, and reveal chemical bonds while imaging molecules on surfaces. Nobody thought that ever would be possible.

TKF: Has this changed how researchers think about the ways nanoscale interactions affect the things they study?

BINNIG: Very much so. Before AFM, people who wanted to model very small structures –molecules, cell walls, semiconductors – had to make indirect measurements of them. But those structures can be complex and disordered, and indirect measurements do not always capture that, so the models they came up with were often wrong. But now, we can look at those structures and adapt our models to match what we observe. We as scientists always have to connect our theories to reality. Atomic force microscopy lets us do this.

TKF: When you started thinking about the AFM, biology was one of the fields you had inmind. Yet even you must have been surprised at how it has revolutionized biology.

GERBER: Yes. AFM’s capabilities keep evolving, and researchers are always finding new ways to use it. For example, in recent years, researchers have made tremendous progress in taking AFM measurements in real time. It’s like watching a movie. They can now see biological interactions, such as how molecules degrade or how antimicrobials attack bacterial membranes as they occur – something nobody could have foreseen 20 years ago. It took 15 years to get there, but we can now see biology in action and compare that to our theories.

BINNIG: Exactly. In biology, the biggest and most important question is always whether a molecule will bind to another molecule, change it, and by changing it cause something important to happen. This is all about forces, and researchers can use AFM to bring two molecules or even two cells close together, or pull them apart, and measure those forces directly. We can learn how big those forces are and under what conditions they occur. We’re actually looking into the heart of biology when we do that.

GERBER: And atomic force microscopy can tell us about many different types of forces that determine the outcome of chemical reactions at the nanoscale. These range from chemical, mechanical and electrostatic through, most recently, to the very weak interactions between molecules.

BINNIG: A great example of this is how Hermann Gaub, a professor of biophysics at Ludwig Maximilians University of Munich, used AFM to unfold proteins. He actually attached one end of a protein to a surface and the other end to an AFM tip. When he pulled the tip up, the protein straightened out and he could create a fingerprint of the unfolding forces that he could compare with his model.

TKF: What about applications you could not have foreseen?

BINNIG: I could not have foreseen that we can image molecules with such a high resolution. It’s unbelievable. We can see the bonds between molecules. We can watch them change during a chemical reaction, and sometimes there are surprises. Some researchers have observed an intermediate state in a chemical reaction that should not have lasted long enough to see. So they have had to rethink their theories to take into account why this intermediate state lasted so long. That’s what happens when we can observe such high-resolution details.

GERBER: Another example is high-speed AFM, which biologists use to see the cellular machinery in action. No other technique can do that. It works by tapping a very, very thin cantilever up and down, taking one quick measurement after another.

BINNIG: It is amazing how many people use the AFM in so many different fields. We first thought, well, maybe biology or semiconductor research. But it was picked up everywhere, from studying friction to cosmetics.

GERBER: I recently looked it up, and AFM was mentioned in 353,000 peer-reviewed papers. Our original article was published in Physical Review Letters, the top journal in the field in which all the important theoretical work is published. Ours is the only experimental paper on its list of most-cited papers.

TKF: Amazing. And yet AFM was actually a follow-up to another technology you worked on, the scanning tunneling microscope, or STM. It was probably the first instrument to achieve nanoscale resolution without using electrons or other high-energy beams that can damage what you are observing, right?

BINNIG: Yes.

TKF: And where did that idea come from?

BINNIG: We were trying to solve a problem. IBM was working on a new type of semiconductor chip, and the insulator, which keeps the electric current from escaping the semiconductor, was leaking. But no one knew why. So Heinrich Rohrer, who was working at IBM Zurich, hired me. I looked to all the available instruments, and none of them could study materials on such a fine scale to find out.

So the two of us thought, well, okay, we’ll invent something. We thought we could take advantage of something called quantum tunneling. Quantum tunneling is when an electron tunnels through a conducting material and come out the other side. We developed STM to map the surface of the material by measuring where electrons emerged on the other side. Only later did we realize that we could move our probe from one spot to cover the entire surface.

TKF: Dr. Gerber, you quickly became part of the STM team. What convinced you to join?

GERBER: I felt this was such a crazy idea, and I’m always very fond of this sort of thing. I thought this was fantastic.

BINNIG: I can confirm this. Christoph always likes crazy things. That runs through his life.

GERBER: Actually, the development of STM was kind of an undercover project at the beginning, because Gerd and Heinrich were involved in other projects. I worked for a year or so on my own. When we started overcoming problems and we could see features on the surface of a material that were one-tenth of a nanometer, then it really took off.

I leave you to discover the discussion in its entirety: Aug. 20, 2016 discussion.

Spider silk as a bio super-lens

Bangor University (Wales, UK) is making quite the impact these days. I’d never heard of the institution until their breakthrough with nanobeads (Sept. 7, 2016 posting) to break through a resolution barrier and now there’s a second breakthrough with their partners at Oxford University (England, UK). From an Aug. 19, 2016 news item on ScienceDaily (Note: A link has been removed),

Scientists at the UK’s Bangor and Oxford universities have achieved a world first: using spider-silk as a superlens to increase the microscope’s potential.

Extending the limit of classical microscope’s resolution has been the ‘El Dorado’ or ‘Holy Grail’ of microscopy for over a century. Physical laws of light make it impossible to view objects smaller than 200 nm — the smallest size of bacteria, using a normal microscope alone. However, superlenses which enable us to see beyond the current magnification have been the goal since the turn of the millennium.

Hot on the heels of a paper (Sci. Adv. 2 e1600901,2016) revealing that a team at Bangor University’s School of Electronic Engineering has used a nanobead-derived superlens to break the perceived resolution barrier, the same team has achieved another world first.

Now the team, led by Dr Zengbo Wang and in colloboration with Prof. Fritz Vollrath’s silk group at Oxford University’s Department of Zoology, has used a naturally occurring material — dragline silk of the golden web spider, as an additional superlens, applied to the surface of the material to be viewed, to provide an additional 2-3 times magnification.

This is the first time that a naturally occurring biological material has been used as a superlens.

An Aug. 19, 2016 Bangor University press release (also on EurekAlert), which originated the news item, provides more information about the new work,

In the paper in Nano Letters (DOI: 10.1021/acs.nanolett.6b02641, Aug 17 2016), the joint team reveals how they used a cylindrical piece of spider silk from the thumb sized Nephila spider as a lens.

Dr Zengbo Wang said:

“We have proved that the resolution barrier of microscope can be broken using a superlens, but production of manufactured superlenses invovles some complex engineering processes which are not widely accessible to other reserchers. This is why we have been interested in looking for naturally occurring superlenses provided by ‘Mother Nature’, which may exist around us, so that everyone can access superlenses.”

Prof Fritz Vollrath adds:

“It is very exciting to find yet another cutting edge and totally novel use for a spider silk, which we have been studying for over two decades in my laboratory.”

These lenses could be used for seeing and viewing previously ‘invisible’ structures, including engineered nano-structures and biological micro-structures as well as, potentially, native germs and viruses.

The natural cylindrical structure at a micron- and submicron-scale make silks ideal candidates, in this case, the individual filaments had diameters of one tenth of a thin human hair.

The spider filament enabled the group to view details on a micro-chip and a blue- ray disk which would be invisible using the unmodified optical microscope.

In much the same was as when you look through a cylindrical glass or bottle, the clearest image only runs along the narrow strip directly opposite your line of vision, or resting on the surface being viewed, the single filament provides a one dimensional viewing image along its length.

Wang explains:

“The cylindrical silk lens has advantages in the larger field-of-view when compared to a microsphere superlens. Importantly for potential commercial applications, a spider silk nanoscope would be robust and economical, which in turn could provide excellent manufacturing platforms for a wide range of applications.”

James Monks, a co-author on the paper comments: “it has been an exciting time to be able to develop this project as part of my honours degree in electronic engineering at Bangor University and I am now very much looking forward to joining Dr Wang’s team as a PhD student in nano-photonics.”

The researchers have provided a close up image with details,

Caption: (a) Nephila edulis spider in its web. (b) Schematic drawing of reflection mode silk biosuperlens imaging. The spider silk was placed directly on top of the sample surface by using a soft tape, which magnify underlying nano objects 2-3 times (c) SEM image of Blu-ray disk with 200/100 nm groove and lines (d) Clear magnified image (2.1x) of Blu-ray disk under spider silk superlens. Credit: Bangor University/ University of Oxford

Caption: (a) Nephila edulis spider in its web. (b) Schematic drawing of reflection mode silk biosuperlens imaging. The spider silk was placed directly on top of the sample surface by using a soft tape, which magnify underlying nano objects 2-3 times (c) SEM image of Blu-ray disk with 200/100 nm groove and lines (d) Clear magnified image (2.1x) of Blu-ray disk under spider silk superlens. Credit: Bangor University/ University of Oxford

Here’s a link to and a citation for the ‘spider silk’ superlens paper,

Spider Silk: Mother Nature’s Bio-Superlens by James N. Monks, Bing Yan, Nicholas Hawkins, Fritz Vollrath, and Zengbo Wang. Nano Lett., Article ASAP DOI: 10.1021/acs.nanolett.6b02641 Publication Date (Web): August 17, 2016

Copyright © 2016 American Chemical Society

This paper is behind a paywall.

A new lens (made from nanobeads) for seeing subwavelength images at visible frequencies

The image which illustrates the research is quite intriguing but I don’t think it makes much sense until you read about the research. From an Aug. 12, 2016 news item on ScienceDaily,

Nanobeads are all around us- and are, some might argue, used too frequently in everything from sun-screen to white paint, but a new ground-breaking application is revealing hidden worlds.

A paper in Science Advances provides proof of a new concept, using new solid 3D superlenses to break through the scale of things previously visible through a microscope.

Illustrating the strength of the new superlens, the scientists describe seeing for the first time, the actual information on the surface of a Blue Ray DVD. That shiny surface is not as smooth as we think. Current microscopes cannot see the grooves containing the data- but now even the data itself is revealed.

Now the image,

(a) Conceptual drawing of nanoparticle-based metamaterial solid immersion lens (mSIL) (b) Lab made mSIL (c) SEM image of 60 nm sized imaging sample (d) corresponding superlens imaging of the 60 nm samples by the developed mSIL. Courtesy: Bangor University

(a) Conceptual drawing of nanoparticle-based metamaterial solid immersion lens (mSIL) (b) Lab made mSIL (c) SEM image of 60 nm sized imaging sample (d) corresponding superlens imaging of the 60 nm samples by the developed mSIL. Credit: ©BangorUniversity Fudan University

An Aug. 13, 2016 Bangor University press release (also on EurekAlert with an Aug. 12, 2016 publication date), which originated the news item, describes the work in more detail,

Led by Dr Zengbo Wang at Bangor University UK and Prof Limin Wu at Fudan University, China, the team created minute droplet-like lens structures on the surface to be examined. These act as an additional lens to magnify the surface features previously invisible to a normal lens.

Made of millions of nanobeads, the spheres break up the light beam. Each bead refracts the light, acting as individual torch-like minute beam. It is the very small size of each beam of light which illuminate the surface, extending the resolving ability of the microscope to record-breaking levels. The new superlens adds 5x magnification on top of existing microscopes.

Extending the limit of classical microscope’s resolution has been the ‘El Dorado’ or ‘Holy Grail’ of microscopy for over a century. Physical laws of light make it impossible to view objects smaller than 200 nm – the smallest size of bacteria, using a normal microscope alone. However, superlenses have been the new goal since the turn of the millennium, with various labs and teams researching different models and materials.

“We’ve used high-index titanium dioxide (TiO2) nanoparticles as the building element of the lens. These nanoparticles are able to bend light to a higher degree than water. To explain, when putting a spoon into a cup of this material, if it were possible, you’d see a larger bend where you spoon enters the material than you would looking at the same spoon in a glass of water,” Dr Wang says.

Nanoparticles splitting single incident beam into multiple=Nanoparticles splitting single incident beam into multiple beams which provides optical super-resolution in imaging.“Each sphere bends the light to a high magnitude and splits the light beam, creating millions of individual beams of light. It is these tiny light beams which enable us to view previously unseen detail.”

Wang believes that the results will be easily replicable and that other labs will soon be adopting the technology and using it for themselves.

The advantages of the technology is that the material, titanium dioxide, is cheap and readily available, and rather than buying a new microscope, the lenses are applied to the material to be viewed, rather than to the microscope.

“We have already viewed details to a far greater level than was previously possible. The next challenge is to adapt the technology for use in biology and medicine. This would not require the current use of a combination of dyes and stains and laser light- which change the samples being viewed. The new lens will be used to see germs and viruses not previously visible.”

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

Three-dimensional all-dielectric metamaterial solid immersion lens for subwavelength imaging at visible frequencies by Wen Fan, Bing Yan, Zengbo Wang, and Limin Wu. Science Advances  12 Aug 2016: Vol. 2, no. 8, e1600901 DOI: 10.1126/sciadv.1600901

This paper is open access.

Nuclear magnetic resonance microscope breaks records

Dutch researchers have found a way to apply the principles underlying magnetic resonance imaging (MRI) to a microscope designed *for* examining matter and life at the nanoscale. From a July 15, 2016 news item on phys.org,

A new nuclear magnetic resonance (NMR) microscope gives researchers an improved instrument to study fundamental physical processes. It also offers new possibilities for medical science—for example, to better study proteins in Alzheimer’s patients’ brains. …

A Leiden Institute of Physics press release, which originated the news item, expands on the theme,

If you get a knee injury, physicians use an MRI machine to look right through the skin and see what exactly is the problem. For this trick, doctors make use of the fact that our body’s atomic nuclei are electrically charged and spin around their axis. Just like small electromagnets they induce their own magnetic field. By placing the knee in a uniform magnetic field, the nuclei line up with their axis pointing in the same direction. The MRI machine then sends a specific type of radio waves through the knee, causing some axes to flip. After turning off this signal, those nuclei flip back after some time, under excitation of a small radio wave. Those waves give away the atoms’ location, and provide physicians with an accurate image of the knee.

NMR

MRI is the medical application of Nuclear Magnetic Resonance (NMR), which is based on the same principle and was invented by physicists to conduct fundamental research on materials. One of the things they study with NMR is the so-called relaxation time. This is the time scale at which the nuclei flip back and it gives a lot of information about a material’s properties.

Microscope

To study materials on the smallest of scales as well, physicists go one step further and develop NMR microscopes, with which they study the mechanics behind physical processes at the level of a group of atoms. Now Leiden PhD students Jelmer Wagenaar and Arthur de Haan have built an NMR microscope, together with principal investigator Tjerk Oosterkamp, that operates at a record temperature of 42 milliKelvin—close to absolute zero. In their article in Physical Review Applied they prove it works by measuring the relaxation time of copper. They achieved a thousand times higher sensitivity than existing NMR microscopes—also a world record.

Alzheimer

With their microscope, they give physicists an instrument to conduct fundamental research on many physical phenomena, like systems displaying strange behavior in extreme cold. And like NMR eventually led to MRI machines in hospitals, NMR microscopes have great potential too. Wagenaar: ‘One example is that you might be able to use our technique to study Alzheimer patients’ brains at the molecular level, in order to find out how iron is locked up in proteins.’

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

Probing the Nuclear Spin-Lattice Relaxation Time at the Nanoscale by J. J. T. Wagenaar, A. M. J. den Haan, J. M. de Voogd, L. Bossoni, T. A. de Jong, M. de Wit, K. M. Bastiaans, D. J. Thoen, A. Endo, T. M. Klapwijk, J. Zaanen, and T. H. Oosterkamp. Phys. Rev. Applied 6, 014007 DOI:http://dx.doi.org/10.1103/PhysRevApplied.6.014007 Published 15 July 2016

This paper is open access.

*’fro’ changed to ‘for’ on Aug. 3, 2016.

Making ordinary microscopes image objects at the nanoscale

The researchers believe this technique for making ordinary microscopes capable of nanoscale imaging will make research into diseases easier, especially in developing countries. A July 20, 2016 news item on phys.org announces the new technique,

Research completed through a collaboration with University of Missouri [MU] engineers, biologists, and chemists could transform how scientists study molecules and cells at sub-microscopic (nanoscale) levels. Shubra Gangopadhyay, an electrical and computer engineer and her team at MU recently published studies outlining a new, relatively inexpensive imaging platform that enables single molecule imaging. This patented method highlights Gangopadhyay’s more than 30 years of nanoscale research that has proven invaluable in biological research and battling diseases.

This diagram shows the difference between regular and plasmonic gratings in terms of fluorescent intensity. Credit: Shubhra Gangopadhyay/Nanoscale.

This diagram shows the difference between regular and plasmonic gratings in terms of fluorescent intensity. Credit: Shubhra Gangopadhyay/Nanoscale.

A July 19, 2016 University of Missouri news release (also received via email), which originated the news item, explains further,

“Usually, scientists have to use very expensive microscopes to image at the sub-microscopic level,” said Gangopadhyay, the C.W. LaPierre Endowed Chair of electrical and computer engineering in the MU College of Engineering. “The techniques we’ve established help to produce enhanced imaging results with ordinary microscopes. The relatively low production cost for the platform also means it could be used to detect a wide variety of diseases, particularly in developing countries.”

The team’s custom platform uses an interaction between light and the surface of the metal grating to generate surface plasmon resonance (SPR), a rapidly developing imaging technique that enables super-resolution imaging down to 65 nanometers—a resolution normally reserved for electron microscopes. Using HD-DVD and Blu-Ray discs as starting templates, a repeating grating pattern is transferred onto the microscope slides where the specimen will be placed. Since the patterns originate from a widely used technology, the manufacturing process remains relatively inexpensive.

“In previous studies, we’ve used plasmonic gratings to detect cortisol and even tuberculosis,” Gangopadhyay said. “Additionally, the relatively low production cost for the platform also means it could be used to further detect a wide variety of diseases, particularly in developing countries. Eventually, we might even be able to use smartphones to detect disease in the field.”

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

Plasmonic gratings with nano-protrusions made by glancing angle deposition for single-molecule super-resolution imaging by B. Chen, A. Wood, A. Pathak, J. Mathai, S. Bok, H. Zheng, S. Hamm, S. Basuray, S. Grant, K. Gangopadhyay, P. V. Cornish, and S. Gangopadhyay. Nanoscale, 2016,8, 12189-12201 DOI: 10.1039/C5NR09165A First published online 24 May 2016

This paper is behind a paywall.

ETA July 22, 2016: Dexter Johnson’s July 21, 2016 posting provides both a neat summary and added detail from an engineer’s perspective.

Nano and a Unified Microbiome Initiative (UMI)

A Jan. 6, 2015 news item on Nanowerk features a proposal by US scientists for a Unified Microbiome Initiative (UMI),

In October [2015], an interdisciplinary group of scientists proposed forming a Unified Microbiome Initiative (UMI) to explore the world of microorganisms that are central to life on Earth and yet largely remain a mystery.

An article in the journal ACS Nano (“Tools for the Microbiome: Nano and Beyond”) describes the tools scientists will need to understand how microbes interact with each other and with us.

A Jan. 6, 2016 American Chemical Society (ACS) news release, which originated the news item, expands on the theme,

Microbes live just about everywhere: in the oceans, in the soil, in the atmosphere, in forests and in and on our bodies. Research has demonstrated that their influence ranges widely and profoundly, from affecting human health to the climate. But scientists don’t have the necessary tools to characterize communities of microbes, called microbiomes, and how they function. Rob Knight, Jeff F. Miller, Paul S. Weiss and colleagues detail what these technological needs are.

The researchers are seeking the development of advanced tools in bioinformatics, high-resolution imaging, and the sequencing of microbial macromolecules and metabolites. They say that such technology would enable scientists to gain a deeper understanding of microbiomes. Armed with new knowledge, they could then tackle related medical and other challenges with greater agility than what is possible today.

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

Tools for the Microbiome: Nano and Beyond by Julie S. Biteen, Paul C. Blainey, Zoe G. Cardon, Miyoung Chun, George M. Church, Pieter C. Dorrestein, Scott E. Fraser, Jack A. Gilbert, Janet K. Jansson, Rob Knight, Jeff F. Miller, Aydogan Ozcan, Kimberly A. Prather, Stephen R. Quake, Edward G. Ruby, Pamela A. Silver, Sharif Taha, Ger van den Engh, Paul S. Weiss, Gerard C. L. Wong, Aaron T. Wright, and Thomas D. Young. ACS Nano, Article ASAP DOI: 10.1021/acsnano.5b07826 Publication Date (Web): December 22, 2015

Copyright © 2015 American Chemical Society

This is an open access paper.

I sped through very quickly and found a couple of references to ‘nano’,

Ocean Microbiomes and Nanobiomes

Life in the oceans is supported by a community of extremely small organisms that can be called a “nanobiome.” These nanoplankton particles, many of which measure less than 0.001× the volume of a white blood cell, harvest solar and chemical energy and channel essential elements into the food chain. A deep network of larger life forms (humans included) depends on these tiny microbes for its energy and chemical building blocks.

The importance of the oceanic nanobiome has only recently begun to be fully appreciated. Two dominant forms, Synechococcus and Prochlorococcus, were not discovered until the 1980s and 1990s.(32-34) Prochloroccus has now been demonstrated to be so abundant that it may account for as much as 10% of the world’s living organic carbon. The organism divides on a diel cycle while maintaining constant numbers, suggesting that about 5% of the world’s biomass flows through this species on a daily basis.(35-37)

Metagenomic studies show that many other less abundant life forms must exist but elude direct observation because they can neither be isolated nor grown in culture.

The small sizes of these organisms (and their genomes) indicate that they are highly specialized and optimized. Metagenome data indicate a large metabolic heterogeneity within the nanobiome. Rather than combining all life functions into a single organism, the nanobiome works as a network of specialists that can only exist as a community, therein explaining their resistance to being cultured. The detailed composition of the network is the result of interactions between the organisms themselves and the local physical and chemical environment. There is thus far little insight into how these networks are formed and how they maintain steady-state conditions in the turbulent natural ocean environment.

Rather than combining all life functions into a single organism, the nanobiome works as a network of specialists that can only exist as a community

The serendipitous discovery of Prochlorococcus happened by applying flow cytometry (developed as a medical technique for counting blood cells) to seawater.(34) With these medical instruments, the faint signals from nanoplankton can only be seen with great difficulty against noisy backgrounds. Currently, a small team is adapting flow cytometric technology to improve the capabilities for analyzing individual nanoplankton particles. The latest generation of flow cytometers enables researchers to count and to make quantitative observations of most of the small life forms (including some viruses) that comprise the nanobiome. To our knowledge, there are only two well-equipped mobile flow cytometry laboratories that are regularly taken to sea for real-time observations of the nanobiome. The laboratories include equipment for (meta)genome analysis and equipment to correlate the observations with the local physical parameters and (nutrient) chemistry in the ocean. Ultimately, integration of these measurements will be essential for understanding the complexity of the oceanic microbiome.

The ocean is tremendously undersampled. Ship time is costly and limited. Ultimately, inexpensive, automated, mobile biome observatories will require methods that integrate microbiome and nanobiome measurements, with (meta-) genomics analyses, with local geophysical and geochemical parameters.(38-42) To appreciate how the individual components of the ocean biome are related and work together, a more complete picture must be established.

The marine environment consists of stratified zones, each with a unique, characteristic biome.(43) The sunlit waters near the surface are mixed by wind action. Deeper waters may be mixed only occasionally by passing storms. The dark deepest layers are stabilized by temperature/salinity density gradients. Organic material from the photosynthetically active surface descends into the deep zone, where it decomposes into nutrients that are mixed with compounds that are released by volcanic and seismic action. These nutrients diffuse upward to replenish the depleted surface waters. The biome is stratified accordingly, sometimes with sudden transitions on small scales. Photo-autotrophs dominate near the surface. Chemo-heterotrophs populate the deep. The makeup of the microbial assemblages is dictated by the local nutrient and oxygen concentrations. The spatiotemporal interplay of these systems is highly relevant to such issues as the carbon budget of the planet but remains little understood.

And then, there was this,

Nanoscience and Nanotechnology Opportunities

The great advantage of nanoscience and nanotechnology in studying microbiomes is that the nanoscale is the scale of function in biology. It is this convergence of scales at which we can “see” and at which we can fabricate that heralds the contributions that can be made by developing new nanoscale analysis tools.(159-168) Microbiomes operate from the nanoscale up to much larger scales, even kilometers, so crossing these scales will pose significant challenges to the field, in terms of measurement, stimulation/response, informatics, and ultimately understanding.

Some progress has been made in creating model systems(143-145, 169-173) that can be used to develop tools and methods. In these cases, the tools can be brought to bear on more complex and real systems. Just as nanoscience began with the ability to image atoms and progressed to the ability to manipulate structures both directly and through guided interactions,(162, 163, 174-176) it has now become possible to control structure, materials, and chemical functionality from the submolecular to the centimeter scales simultaneously. Whereas substrates and surface functionalization have often been tailored to be resistant to bioadhesion, deliberate placement of chemical patterns can also be used for the growth and patterning of systems, such as biofilms, to be put into contact with nanoscale probes.(177-180) Such methods in combination with the tools of other fields (vide infra) will provide the means to probe and to understand microbiomes.

Key tools for the microbiome will need to be miniaturized and made parallel. These developments will leverage decades of work in nanotechnology in the areas of nanofabrication,(181) imaging systems,(182, 183) lab-on-a-chip systems,(184) control of biological interfaces,(185) and more. Commercialized and commoditized tools, such as smart phone cameras, can also be adapted for use (vide infra). By guiding the development and parallelization of these tools, increasingly complex microbiomes will be opened for study.(167)

Imaging and sensing, in general, have been enjoying a Renaissance over the past decades, and there are various powerful measurement techniques that are currently available, making the Microbiome Initiative timely and exciting from the broad perspective of advanced analysis techniques. Recent advances in various -omics technologies, electron microscopy, optical microscopy/nanoscopy and spectroscopy, cytometry, mass spectroscopy, atomic force microscopy, nuclear imaging, and other techniques, create unique opportunities for researchers to investigate a wide range of questions related to microbiome interactions, function, and diversity. We anticipate that some of these advanced imaging, spectroscopy, and sensing techniques, coupled with big data analytics, will be used to create multimodal and integrated smart systems that can shed light onto some of the most important needs in microbiome research, including (1) analyzing microbial interactions specifically and sensitively at the relevant spatial and temporal scales; (2) determining and analyzing the diversity covered by the microbial genome, transcriptome, proteome, and metabolome; (3) managing and manipulating microbiomes to probe their function, evaluating the impact of interventions and ultimately harnessing their activities; and (4) helping us identify and track microbial dark matter (referring to 99% of micro-organisms that cannot be cultured).

In this broad quest for creating next-generation imaging and sensing instrumentation to address the needs and challenges of microbiome-related research activities comprehensively, there are important issues that need to be considered, as discussed below.

The piece is extensive and quite interesting, if you have the time.

Developing optical microscopes that measure features down to 10 nanometer level on computer chips

The US National Institute of Standards and Technology (NIST) issued a Dec. 2, 2015 news release (also on EurekAlert) announcing a new kind of optical microscope and its possible impact on the semiconductor industry,

National Institute of Standards and Technology (NIST) researchers are seeing the light, but in an altogether different way. And how they are doing it just might be the semiconductor industry’s ticket for extending its use of optical microscopes to measure computer chip features that are approaching 10 nanometers, tiny fractions of the wavelength of light.

The news release goes on to provide details and an explanation of scatterfield imaging,

Using a novel microscope that combines standard through-the-lens viewing with a technique called scatterfield imaging, the NIST team accurately measured patterned features on a silicon wafer that were 30 times smaller than the wavelength of light (450 nanometers) used to examine them. They report* that measurements of the etched lines–as thin as 16 nanometers wide–on the SEMATECH-fabricated wafer were accurate to one nanometer. With the technique, they spotted variations in feature dimensions amounting to differences of a few atoms.

Measurements were confirmed by those made with an atomic force microscope, which achieves sub-nanometer resolution, but is considered too slow for online quality-control measurements. Combined with earlier results, the NIST researchers write, the new proof-of-concept study* suggests that the innovative optical approach could be a “realistic solution to a very challenging problem” facing chip makers and others aiming to harness advances in nanotechnology. All need the means for “nondestructive measurement of nanometer-scale structures with sub-nanometer sensitivity while still having high throughput.

“Light-based, or optical, microscopes can’t “see” features smaller than the wavelength of light, at least not in the crisp detail necessary for making accurate measurements. However, light does scatter when it strikes so-called subwavelength features and patterned arrangements of such features. “Historically, we would ignore this scattered light because it did not yield sufficient resolution,” explains Richard Silver, the physicist who initiated NIST’s scatterfield imaging effort. “Now we know it contains helpful information that provides signatures telling us something about where the light came from.”

With scatterfield imaging, Silver and colleagues methodically illuminate a sample with polarized light from different angles. From this collection of scattered light–nothing more than a sea of wiggly lines to the untrained eye–the NIST team can extract characteristics of the bounced lightwaves that, together, reveal the geometry of features on the specimen.

Light-scattering data are gathered in slices, which together image the volume of scattered light above and into the sample. These slices are analyzed and reconstructed to create a three-dimensional representation. The process is akin to a CT scan, except that the slices are collections of interfering waves, not cross-sectional pictures.

“It’s the ensemble of data that tells us what we’re after,” says project leader Bryan Barnes.” We may not be able see the lines on the wafer, but we can tell you what you need to know about them–their size, their shape, their spacing.”

Scatterfield imaging has critical prerequisites that must be met before it can yield useful data for high-accuracy measurements of exceedingly small features. Key steps entail detailed evaluation of the path light takes as it beams through lenses, apertures and other system elements before reaching the sample. The path traversed by light scattering from the specimen undergoes the same level of scrutiny. Fortunately, scatterfield imaging lends itself to thorough characterization of both sequences of optical devices, according to the researchers. These preliminary steps are akin to error mapping so that recognized sources of inaccuracy are factored out of the data.

The method also benefits from a little advance intelligence–the as-designed arrangement of circuit lines on a chip, down to the size of individual features. Knowing what is expected to be the result of the complex chip-making process sets up a classic matchup of theory vs. experiment.

The NIST researchers can use standard equations to simulate light scattering from an ideal, defect-free pattern and, in fact, any variation thereof. Using wave analysis software they developed, the team has assembled an indexed library of light-scattering reference models. So once a specimen is scanned, the team relies on computers to compare their real-world data to models and to find close matches.

From there, succeeding rounds of analysis homes in on the remaining differences, reducing them until the only ones that remain are due to variations in geometry such as irregularities in the height, width, or shape of a line.

Measurement results achieved with the NIST approach might be said to cast light itself in an entirely new light. Their new study, the researchers say, shows that once disregarded scattered light “contains a wealth of accessible optical information.”

Next steps include extending the technique to even shorter wavelengths of light, down to ultraviolet, or 193 nanometers. The aim is to accurately measure features as small as 5 nanometers.

This work is part of a larger NIST effort to supply measurement tools that enable the semiconductor industry to continue doubling the number of devices on a chip about every two years and to help other industries make products with nanoscale features. Recently, NIST and Intel researchers reported using an X-ray technique to accurately measure features on a silicon chip to within fractions of a nanometer.

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

Deep-subwavelength Nanometric Image Reconstruction using Fourier Domain Optical Normalization by Jing  Qin, Richard  M Silver, Bryan  M  Barnes, Hui Zhou, Ronald G Dixson, and Mark Alexander Hen. Light: Science & Applications accepted article preview 5 November 2015; e16038 doi: 10.1038/lsa.2016.38

[Note:] This is a PDF file of an unedited peer-reviewed manuscript that has been accepted for publication. NPG are providing this early version of the manuscript as a service to our customers. The manuscript will undergo copy editing, typesetting and a proof review before it is published in its final form. Please note that during the production process errors may be discovered which could affect the content, and all legal disclaimers apply.

This seems to be an open access paper but it is an early version.

Characterizing anatase titanium dixoide at the nanoscale

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

*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

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.