Tag Archives: Vanderbilt University

Spooling strips of graphene

An April 18, 2018 news item on phys.org highlights an exciting graphene development at the Massachusetts Institute of Technology (MIT),

MIT engineers have developed a continuous manufacturing process that produces long strips of high-quality graphene.

The team’s results are the first demonstration of an industrial, scalable method for manufacturing high-quality graphene that is tailored for use in membranes that filter a variety of molecules, including salts, larger ions, proteins, or nanoparticles. Such membranes should be useful for desalination, biological separation, and other applications.

A new manufacturing process produces strips of graphene, at large scale, for use in membrane technologies and other applications. Image: Christine Daniloff, MIT

An April 17, 2018 MIT news release (also on EurekAlert) by Jennifer Chu, which originated the news item,. provides more detail,

“For several years, researchers have thought of graphene as a potential route to ultrathin membranes,” says John Hart, associate professor of mechanical engineering and director of the Laboratory for Manufacturing and Productivity at MIT. “We believe this is the first study that has tailored the manufacturing of graphene toward membrane applications, which require the graphene to be seamless, cover the substrate fully, and be of high quality.”

Hart is the senior author on the paper, which appears online in the journal Applied Materials and Interfaces. The study includes first author Piran Kidambi, a former MIT postdoc who is now an assistant professor at Vanderbilt University; MIT graduate students Dhanushkodi Mariappan and Nicholas Dee; Sui Zhang of the National University of Singapore; Andrey Vyatskikh, a former student at the Skolkovo Institute of Science and Technology who is now at Caltech; and Rohit Karnik, an associate professor of mechanical engineering at MIT.

Growing graphene

For many researchers, graphene is ideal for use in filtration membranes. A single sheet of graphene resembles atomically thin chicken wire and is composed of carbon atoms joined in a pattern that makes the material extremely tough and impervious to even the smallest atom, helium.

Researchers, including Karnik’s group, have developed techniques to fabricate graphene membranes and precisely riddle them with tiny holes, or nanopores, the size of which can be tailored to filter out specific molecules. For the most part, scientists synthesize graphene through a process called chemical vapor deposition, in which they first heat a sample of copper foil and then deposit onto it a combination of carbon and other gases.

Graphene-based membranes have mostly been made in small batches in the laboratory, where researchers can carefully control the material’s growth conditions. However, Hart and his colleagues believe that if graphene membranes are ever to be used commercially they will have to be produced in large quantities, at high rates, and with reliable performance.

“We know that for industrialization, it would need to be a continuous process,” Hart says. “You would never be able to make enough by making just pieces. And membranes that are used commercially need to be fairly big – some so big that you would have to send a poster-wide sheet of foil into a furnace to make a membrane.”

A factory roll-out

The researchers set out to build an end-to-end, start-to-finish manufacturing process to make membrane-quality graphene.

The team’s setup combines a roll-to-roll approach – a common industrial approach for continuous processing of thin foils – with the common graphene-fabrication technique of chemical vapor deposition, to manufacture high-quality graphene in large quantities and at a high rate. The system consists of two spools, connected by a conveyor belt that runs through a small furnace. The first spool unfurls a long strip of copper foil, less than 1 centimeter wide. When it enters the furnace, the foil is fed through first one tube and then another, in a “split-zone” design.

While the foil rolls through the first tube, it heats up to a certain ideal temperature, at which point it is ready to roll through the second tube, where the scientists pump in a specified ratio of methane and hydrogen gas, which are deposited onto the heated foil to produce graphene.

“Graphene starts forming in little islands, and then those islands grow together to form a continuous sheet,” Hart says. “By the time it’s out of the oven, the graphene should be fully covering the foil in one layer, kind of like a continuous bed of pizza.”

As the graphene exits the furnace, it’s rolled onto the second spool. The researchers found that they were able to feed the foil continuously through the system, producing high-quality graphene at a rate of 5 centimers per minute. Their longest run lasted almost four hours, during which they produced about 10 meters of continuous graphene.

“If this were in a factory, it would be running 24-7,” Hart says. “You would have big spools of foil feeding through, like a printing press.”

Flexible design

Once the researchers produced graphene using their roll-to-roll method, they unwound the foil from the second spool and cut small samples out. They cast the samples with a polymer mesh, or support, using a method developed by scientists at Harvard University, and subsequently etched away the underlying copper.

“If you don’t support graphene adequately, it will just curl up on itself,” Kidambi says. “So you etch copper out from underneath and have graphene directly supported by a porous polymer – which is basically a membrane.”

The polymer covering contains holes that are larger than graphene’s pores, which Hart says act as microscopic “drumheads,” keeping the graphene sturdy and its tiny pores open.

The researchers performed diffusion tests with the graphene membranes, flowing a solution of water, salts, and other molecules across each membrane. They found that overall, the membranes were able to withstand the flow while filtering out molecules. Their performance was comparable to graphene membranes made using conventional, small-batch approaches.

The team also ran the process at different speeds, with different ratios of methane and hydrogen gas, and characterized the quality of the resulting graphene after each run. They drew up plots to show the relationship between graphene’s quality and the speed and gas ratios of the manufacturing process. Kidambi says that if other designers can build similar setups, they can use the team’s plots to identify the settings they would need to produce a certain quality of graphene.

“The system gives you a great degree of flexibility in terms of what you’d like to tune graphene for, all the way from electronic to membrane applications,” Kidambi says.

Looking forward, Hart says he would like to find ways to include polymer casting and other steps that currently are performed by hand, in the roll-to-roll system.

“In the end-to-end process, we would need to integrate more operations into the manufacturing line,” Hart says. “For now, we’ve demonstrated that this process can be scaled up, and we hope this increases confidence and interest in graphene-based membrane technologies, and provides a pathway to commercialization.”

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

A Scalable Route to Nanoporous Large-Area Atomically Thin Graphene Membranes by Roll-to-Roll Chemical Vapor Deposition and Polymer Support Casting by Piran R. Kidambi, Dhanushkodi D. Mariappan, Nicholas T. Dee, Andrey Vyatskikh, Sui Zhang, Rohit Karnik, and A. John Hart. ACS Appl. Mater. Interfaces, 2018, 10 (12), pp 10369–10378 DOI: 10.1021/acsami.8b00846 Publication Date (Web): March 19, 2018

Copyright © 2018 American Chemical Society

This paper is behind a paywall.

Finally, there is a video of the ‘graphene spooling out’ process,

Aliens wreak havoc on our personal electronics

The aliens in question are subatomic particles and the havoc they wreak is low-grade according to the scientist who was presenting on the topic at the AAAS (American Association for the Advancement of Science) 2017 Annual Meeting (Feb. 16 – 20, 2017) in Boston, Massachusetts. From a Feb. 17, 2017 news item on ScienceDaily,

You may not realize it but alien subatomic particles raining down from outer space are wreaking low-grade havoc on your smartphones, computers and other personal electronic devices.

When your computer crashes and you get the dreaded blue screen or your smartphone freezes and you have to go through the time-consuming process of a reset, most likely you blame the manufacturer: Microsoft or Apple or Samsung. In many instances, however, these operational failures may be caused by the impact of electrically charged particles generated by cosmic rays that originate outside the solar system.

“This is a really big problem, but it is mostly invisible to the public,” said Bharat Bhuva, professor of electrical engineering at Vanderbilt University, in a presentation on Friday, Feb. 17 at a session titled “Cloudy with a Chance of Solar Flares: Quantifying the Risk of Space Weather” at the annual meeting of the American Association for the Advancement of Science in Boston.

A Feb. 17, 2017 Vanderbilt University news release (also on EurekAlert), which originated the news item, expands on  the theme,

When cosmic rays traveling at fractions of the speed of light strike the Earth’s atmosphere they create cascades of secondary particles including energetic neutrons, muons, pions and alpha particles. Millions of these particles strike your body each second. Despite their numbers, this subatomic torrent is imperceptible and has no known harmful effects on living organisms. However, a fraction of these particles carry enough energy to interfere with the operation of microelectronic circuitry. When they interact with integrated circuits, they may alter individual bits of data stored in memory. This is called a single-event upset or SEU.

Since it is difficult to know when and where these particles will strike and they do not do any physical damage, the malfunctions they cause are very difficult to characterize. As a result, determining the prevalence of SEUs is not easy or straightforward. “When you have a single bit flip, it could have any number of causes. It could be a software bug or a hardware flaw, for example. The only way you can determine that it is a single-event upset is by eliminating all the other possible causes,” Bhuva explained.

There have been a number of incidents that illustrate how serious the problem can be, Bhuva reported. For example, in 2003 in the town of Schaerbeek, Belgium a bit flip in an electronic voting machine added 4,096 extra votes to one candidate. The error was only detected because it gave the candidate more votes than were possible and it was traced to a single bit flip in the machine’s register. In 2008, the avionics system of a Qantus passenger jet flying from Singapore to Perth appeared to suffer from a single-event upset that caused the autopilot to disengage. As a result, the aircraft dove 690 feet in only 23 seconds, injuring about a third of the passengers seriously enough to cause the aircraft to divert to the nearest airstrip. In addition, there have been a number of unexplained glitches in airline computers – some of which experts feel must have been caused by SEUs – that have resulted in cancellation of hundreds of flights resulting in significant economic losses.

An analysis of SEU failure rates for consumer electronic devices performed by Ritesh Mastipuram and Edwin Wee at Cypress Semiconductor on a previous generation of technology shows how prevalent the problem may be. Their results were published in 2004 in Electronic Design News and provided the following estimates:

  • A simple cell phone with 500 kilobytes of memory should only have one potential error every 28 years.
  • A router farm like those used by Internet providers with only 25 gigabytes of memory may experience one potential networking error that interrupts their operation every 17 hours.
  • A person flying in an airplane at 35,000 feet (where radiation levels are considerably higher than they are at sea level) who is working on a laptop with 500 kilobytes of memory may experience one potential error every five hours.

Bhuva is a member of Vanderbilt’s Radiation Effects Research Group, which was established in 1987 and is the largest academic program in the United States that studies the effects of radiation on electronic systems. The group’s primary focus was on military and space applications. Since 2001, the group has also been analyzing radiation effects on consumer electronics in the terrestrial environment. They have studied this phenomenon in the last eight generations of computer chip technology, including the current generation that uses 3D transistors (known as FinFET) that are only 16 nanometers in size. The 16-nanometer study was funded by a group of top microelectronics companies, including Altera, ARM, AMD, Broadcom, Cisco Systems, Marvell, MediaTek, Renesas, Qualcomm, Synopsys, and TSMC

“The semiconductor manufacturers are very concerned about this problem because it is getting more serious as the size of the transistors in computer chips shrink and the power and capacity of our digital systems increase,” Bhuva said. “In addition, microelectronic circuits are everywhere and our society is becoming increasingly dependent on them.”

To determine the rate of SEUs in 16-nanometer chips, the Vanderbilt researchers took samples of the integrated circuits to the Irradiation of Chips and Electronics (ICE) House at Los Alamos National Laboratory. There they exposed them to a neutron beam and analyzed how many SEUs the chips experienced. Experts measure the failure rate of microelectronic circuits in a unit called a FIT, which stands for failure in time. One FIT is one failure per transistor in one billion hours of operation. That may seem infinitesimal but it adds up extremely quickly with billions of transistors in many of our devices and billions of electronic systems in use today (the number of smartphones alone is in the billions). Most electronic components have failure rates measured in 100’s and 1,000’s of FITs.

chart

Trends in single event upset failure rates at the individual transistor, integrated circuit and system or device level for the three most recent manufacturing technologies. (Bharat Bhuva, Radiation Effects Research Group, Vanderbilt University)

“Our study confirms that this is a serious and growing problem,” said Bhuva.“This did not come as a surprise. Through our research on radiation effects on electronic circuits developed for military and space applications, we have been anticipating such effects on electronic systems operating in the terrestrial environment.”

Although the details of the Vanderbilt studies are proprietary, Bhuva described the general trend that they have found in the last three generations of integrated circuit technology: 28-nanometer, 20-nanometer and 16-nanometer.

As transistor sizes have shrunk, they have required less and less electrical charge to represent a logical bit. So the likelihood that one bit will “flip” from 0 to 1 (or 1 to 0) when struck by an energetic particle has been increasing. This has been partially offset by the fact that as the transistors have gotten smaller they have become smaller targets so the rate at which they are struck has decreased.

More significantly, the current generation of 16-nanometer circuits have a 3D architecture that replaced the previous 2D architecture and has proven to be significantly less susceptible to SEUs. Although this improvement has been offset by the increase in the number of transistors in each chip, the failure rate at the chip level has also dropped slightly. However, the increase in the total number of transistors being used in new electronic systems has meant that the SEU failure rate at the device level has continued to rise.

Unfortunately, it is not practical to simply shield microelectronics from these energetic particles. For example, it would take more than 10 feet of concrete to keep a circuit from being zapped by energetic neutrons. However, there are ways to design computer chips to dramatically reduce their vulnerability.

For cases where reliability is absolutely critical, you can simply design the processors in triplicate and have them vote. Bhuva pointed out: “The probability that SEUs will occur in two of the circuits at the same time is vanishingly small. So if two circuits produce the same result it should be correct.” This is the approach that NASA used to maximize the reliability of spacecraft computer systems.

The good news, Bhuva said, is that the aviation, medical equipment, IT, transportation, communications, financial and power industries are all aware of the problem and are taking steps to address it. “It is only the consumer electronics sector that has been lagging behind in addressing this problem.”

The engineer’s bottom line: “This is a major problem for industry and engineers, but it isn’t something that members of the general public need to worry much about.”

That’s fascinating and I hope the consumer electronics industry catches up with this ‘alien invasion’ issue. Finally, the ‘bit flips’ made me think of the 1956 movie ‘Invasion of the Body Snatchers‘.

Getting your brain cells to glow in the dark

The extraordinary effort to colonize our brains continues apace with a new sensor from Vanderbilt University. From an Oct. 27, 2016 news item on ScienceDaily,

A new kind of bioluminescent sensor causes individual brain cells to imitate fireflies and glow in the dark.

The probe, which was developed by a team of Vanderbilt scientists, is a genetically modified form of luciferase, the enzyme that a number of other species including fireflies use to produce light. …

The scientists created the technique as a new and improved method for tracking the interactions within large neural networks in the brain.

“For a long time neuroscientists relied on electrical techniques for recording the activity of neurons. These are very good at monitoring individual neurons but are limited to small numbers of neurons. The new wave is to use optical techniques to record the activity of hundreds of neurons at the same time,” said Carl Johnson, Stevenson Professor of Biological Sciences, who headed the effort.

Individual neuron glowing with bioluminescent light produced by a new genetically engineered sensor. (Johnson Lab / Vanderbilt University)

Individual neuron glowing with bioluminescent light produced by a new genetically engineered sensor. (Johnson Lab / Vanderbilt University)

An Oct. 27, 2016 Vanderbilt University news release (also on EurekAlert) by David Salisbury, which originated the news item, explains the work in more detail,

“Most of the efforts in optical recording use fluorescence, but this requires a strong external light source which can cause the tissue to heat up and can interfere with some biological processes, particularly those that are light sensitive,” he [Carl Johnson] said.

Based on their research on bioluminescence in “a scummy little organism, the green alga Chlamydomonas, that nobody cares much about” Johnson and his colleagues realized that if they could combine luminescence with optogenetics – a new biological technique that uses light to control cells, particularly neurons, in living tissue – they could create a powerful new tool for studying brain activity.

“There is an inherent conflict between fluorescent techniques and optogenetics. The light required to produce the fluorescence interferes with the light required to control the cells,” said Johnson. “Luminescence, on the other hand, works in the dark!”

Johnson and his collaborators – Associate Professor Donna Webb, Research Assistant Professor Shuqun Shi, post-doctoral student Jie Yang and doctoral student Derrick Cumberbatch in biological sciences and Professor Danny Winder and postdoctoral student Samuel Centanni in molecular physiology and biophysics – genetically modified a type of luciferase obtained from a luminescent species of shrimp so that it would light up when exposed to calcium ions. Then they hijacked a virus that infects neurons and attached it to their sensor molecule so that the sensors are inserted into the cell interior.

The researchers picked calcium ions because they are involved in neuron activation. Although calcium levels are high in the surrounding area, normally they are very low inside the neurons. However, the internal calcium level spikes briefly when a neuron receives an impulse from one of its neighbors.

They tested their new calcium sensor with one of the optogenetic probes (channelrhodopsin) that causes the calcium ion channels in the neuron’s outer membrane to open, flooding the cell with calcium. Using neurons grown in culture they found that the luminescent enzyme reacted visibly to the influx of calcium produced when the probe was stimulated by brief light flashes of visible light.

To determine how well their sensor works with larger numbers of neurons, they inserted it into brain slices from the mouse hippocampus that contain thousands of neurons. In this case they flooded the slices with an increased concentration of potassium ions, which causes the cell’s ion channels to open. Again, they found that the sensor responded to the variations in calcium concentrations by brightening and dimming.

“We’ve shown that the approach works,” Johnson said. “Now we have to determine how sensitive it is. We have some indications that it is sensitive enough to detect the firing of individual neurons, but we have to run more tests to determine if it actually has this capability.”

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

Coupling optogenetic stimulation with NanoLuc-based luminescence (BRET) Ca++ sensing by Jie Yang, Derrick Cumberbatch, Samuel Centanni, Shu-qun Shi, Danny Winder, Donna Webb, & Carl Hirschie Johnson. Nature Communications 7, Article number: 13268 (2016)  doi:10.1038/ncomms13268 Published online: 27 October 2016

This paper is open access.

New elements named (provisionally)

They say it’s provisionally but I suspect it would take an act of god for a change in the proposed names. From a June 8, 2016 blog posting (scroll down about 25% of the way) on the International Union of Pure and Applied Chemistry (IUPAC) website,

IUPAC is naming the four new elements nihonium, moscovium, tennessine, and oganesson

Following earlier reports that the claims for discovery of these elements have been fulfilled [1, 2], the discoverers have been invited to propose names and the following are now disclosed for public review:

  • Nihonium and symbol Nh, for the element 113,
  • Moscovium and symbol Mc, for the element 115,
  • Tennessine and symbol Ts, for the element 117, and
  • Oganesson and symbol Og, for the element 118.

The IUPAC Inorganic Chemistry Division has reviewed and considered these proposals and recommends these for acceptance. A five-month public review is now set, expiring 8 November 2016, prior to the formal approval by the IUPAC Council.

I can’t figure out how someone from the public might offer a comment about the names.

There’s more from the posting about what kinds of names are acceptable and how the names in this set of four were arrived at,

The guidelines for the naming the elements were recently revised [3] and shared with the discoverers to assist in their proposals. Keeping with tradition, newly discovered elements can be named after:
(a) a mythological concept or character (including an astronomical object),
(b) a mineral or similar substance,
(c) a place, or geographical region,
(d) a property of the element, or
(e) a scientist.
The names of all new elements in general would have an ending that reflects and maintains historical and chemical consistency. This would be in general “-ium” for elements belonging to groups 1-16, “-ine” for elements of group 17 and “-on” for elements of group 18. Finally, the names for new chemical elements in English should allow proper translation into other major languages.

For the element with atomic number 113 the discoverers at RIKEN Nishina Center for Accelerator-Based Science (Japan) proposed the name nihonium and the symbol Nh. Nihon is one of the two ways to say “Japan” in Japanese, and literally mean “the Land of Rising Sun”. The name is proposed to make a direct connection to the nation where the element was discovered. Element 113 is the first element to have been discovered in an Asian country. While presenting this proposal, the team headed by Professor Kosuke Morita pays homage to the trailblazing work by Masataka Ogawa done in 1908 surrounding the discovery of element 43. The team also hopes that pride and faith in science will displace the lost trust of those who suffered from the 2011 Fukushima nuclear disaster.

For the element with atomic number 115 the name proposed is moscovium with the symbol Mc and for element with atomic number 117, the name proposed is tennessine with the symbol Ts. These are in line with tradition honoring a place or geographical region and are proposed jointly by the discoverers at the Joint Institute for Nuclear Research, Dubna (Russia), Oak Ridge National Laboratory (USA), Vanderbilt University (USA) and Lawrence Livermore National Laboratory (USA).

Moscovium is in recognition of the Moscow region and honors the ancient Russian land that is the home of the Joint Institute for Nuclear Research, where the discovery experiments were conducted using the Dubna Gas-Filled Recoil Separator in combination with the heavy ion accelerator capabilities of the Flerov Laboratory of Nuclear Reactions.

Tennessine is in recognition of the contribution of the Tennessee region, including Oak Ridge National Laboratory, Vanderbilt University, and the University of Tennessee at Knoxville, to superheavy element research, including the production and chemical separation of unique actinide target materials for superheavy element synthesis at ORNL’s High Flux Isotope Reactor (HFIR) and Radiochemical Engineering Development Center (REDC).

For the element with atomic number 118 the collaborating teams of discoverers at the Joint Institute for Nuclear Research, Dubna (Russia) and Lawrence Livermore National Laboratory (USA) proposed the name oganesson and symbol Og. The proposal is in line with the tradition of honoring a scientist and recognizes Professor Yuri Oganessian (born 1933) for his pioneering contributions to transactinoid elements research. His many achievements include the discovery of superheavy elements and significant advances in the nuclear physics of superheavy nuclei including experimental evidence for the “island of stability”.

“It is a pleasure to see that specific places and names (country, state, city, and scientist) related to the new elements is recognized in these four names. Although these choices may perhaps be viewed by some as slightly self-indulgent, the names are completely in accordance with IUPAC rules”, commented Jan Reedijk, who corresponded with the various laboratories and invited the discoverers to make proposals. “In fact, I see it as thrilling to recognize that international collaborations were at the core of these discoveries and that these new names also make the discoveries somewhat tangible.”

So, let’s welcome Tennessine, Muscovium, Nihonium, and Oganesson to the table of periodic elements. I imagine Don Lehrer’s Elements Song will be updated soon. In the meantime we have this from ASAP Science, which includes the new elements under their placeholder names (when the addition was first publicized in January 2016. All of the placeholder names start with U,

Enjoy!

ISEA (International Symposium on Electronic Arts) 2015 and the pronoun ‘I’

The 2015 International Symposium on Electronic Arts (or ISEA 2015) held  in Vancouver ended yesterday, Aug. 19, 2015. It was quite an experience both as a participant and as a presenter (mentioned in my Aug. 14, 2015 posting, Sneak peek: Steep (1): a digital poetry of gold nanoparticles). Both this ISEA and the one I attended previously in 2009 (Belfast, Northern Ireland, and Dublin, Ireland) were jampacked with sessions, keynote addresses, special events, and exhibitions of various artworks. Exhilarating and exhausting, that is the ISEA experience for me and just about anyone else I talked to here in Vancouver (Canada). In terms of organization, I have to give props to the Irish. Unfortunately, the Vancouver team didn’t seem to have given their volunteers any training and technical difficulties abounded. Basics such as having a poster outside a room noting what session was taking place, signage indicating which artist’s work was being featured, and good technical support (my guy managed to plug in a few things but seemed disinclined or perhaps didn’t have the technical expertise (?) to troubleshoot prior to the presentation) seemed elusive (a keynote presentation had to be moved due to technical requirements [!] plus no one told the volunteer staff who consequently misdirected people). Ooops.

Despite the difficulties, people remained enthusiastic and that’s a tribute to both the participants and, importantly, the organizers. The Vancouver ISEA was a huge undertaking with over 1000 presentation submissions made and over 1800 art work submissions. They had 900+ register and were the first ISEA able to offer payment to artists for their installations. Bravo to Philippe Pasquier, Thecla Schiphorst, Kate Armstrong, Malcolm Levy, and all the others who worked hard to pull this off.

Moving on to ‘I’, while the theme for ISEA 2015 was Disruption, I noticed a number of presentations focused on biology and on networks (in particular, generative networks). In some ways this parallels what’s happening in the sciences where more notice is being given to networks and network communications of all sorts.  For example, there’s an Aug. 19, 2015 news item on ScienceDaily suggesting that our use of the pronoun ‘I’ may become outdated.  What we consider to be an individual may be better understood as a host for a number of communities or networks,

Recent microbiological research has shown that thinking of plants and animals, including humans, as autonomous individuals is a serious over-simplification.

A series of groundbreaking studies have revealed that what we have always thought of as individuals are actually “biomolecular networks” that consist of visible hosts plus millions of invisible microbes that have a significant effect on how the host develops, the diseases it catches, how it behaves and possibly even its social interactions.

“It’s a case of the whole being greater than the sum of its parts,” said Seth Bordenstein, associate professor of biological sciences at Vanderbilt University, who has contributed to the body of scientific knowledge that is pointing to the conclusion that symbiotic microbes play a fundamental role in virtually all aspects of plant and animal biology, including the origin of new species.

In this case, the parts are the host and its genome plus the thousands of different species of bacteria living in or on the host, along with all their genomes, collectively known as the microbiome. (The host is something like the tip of the iceberg while the bacteria are like the part of the iceberg that is underwater: Nine out of every 10 cells in plant and animal bodies are bacterial. But bacterial cells are so much smaller than host cells that they have generally gone unnoticed.)

An Aug. 19, 2015 Vanderbilt University news release, which originated the news item, describes this provocative idea (no more ‘I’)  further,

Microbiologists have coined new terms for these collective entities — holobiont — and for their genomes — hologenome. “These terms are needed to define the assemblage of organisms that makes up the so-called individual,” said Bordenstein.

In the article “Host Biology in Light of the Microbiome: Ten Principles of Holobionts and Hologenomes” published online Aug. 18 [2015] in the open access journal PLOS Biology, Bordenstein and his colleague Kevin Theis from the University of Michigan take the general concepts involved in this new paradigm and break them down into underlying principles that apply to the entire field of biology.

They make specific and refutable predictions based on these principles and call for other biologists to test them theoretically and experimentally.

“One of the basic expectations from this conceptual framework is that animal and plant experiments that do not account for what is happening at the microbiological level will be incomplete and, in some cases, will be misleading as well,” said Bordenstein.

The first principle they advance is that holobionts and hologenomes are fundamental units of biological organization.

Another is that evolutionary forces such as natural selection and drift may act on the hologenome not just on the genome. So mutations in the microbiome that affect the fitness of a holobiont are just as important as mutations in the host’s genome. However, they argue that this does not change the basic rules of evolution but simply upgrades the types of biological units that the rules may act upon.

Although it does not change the basic rules of evolution, holobionts do have a way to respond to environmental challenges that is not available to individual organisms: They can alter the composition of their bacterial communities. For example, if a holobiont is attacked by a pathogen that the host cannot defend against, another symbiont may fulfill the job by manufacturing a toxin that can kill the invader. In this light, the microbes are as much part of the holobiont immune system as the host immune genes themselves.

According to Bordenstein, these ideas are gaining acceptance in the microbiology community. At the American Society of Microbiology General Meeting in June [2015], he convened the inaugural session on “Holobionts and Their Hologenomes” and ASM’s flagship journal mBio plans to publish a special issue on the topic in the coming year. [emphases are mine]

However, adoption of these ideas has been slower in other fields.

“Currently, the field of biology has reached an inflection point. The silos of microbiology, zoology and botany are breaking down and we hope that this framework will help further unify these fields,” said Bordenstein.

Not only will this powerful holistic approach affect the basic biological sciences but it also is likely to impact the practice of personalized medicine as well, Bordenstein said.

Take the missing heritability problem, for example. Although genome-wide studies have provided valuable insights into the genetic basis of a number of simple diseases, they have only found a small portion of the genetic causes of a number of more complex conditions such as autoimmune and metabolic diseases.

These may in part be “missing” because the genetic factors that cause them are in the microbiome, he pointed out.

“Instead of being so ‘germophobic,’ we need to accept the fact that we live in and benefit from a microbial world. We are as much an environment for microbes as microbes are for us,” said Bordenstein.

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

Host Biology in Light of the Microbiome: Ten Principles of Holobionts and Hologenomes by Seth R. Bordenstein and Kevin R. Theis. PLOS DOI: 10.1371/journal.pbio.1002226 Published: August 18, 2015

This is an open access paper.

It’s intriguing to see artists and scientists exploring ideas that resonate with each other. In fact, ISEA 2015 hosted a couple of sessions on BioArt, as well as, having sessions devoted to networks. While, I wasn’t thinking about networks or biological systems when I wrote my poem on gold nanoparticles, I did pose this possibility (how we become the sum of our parts) at the end:

Nature’s alchemy
breathing them
eating them
drinking them
we become gold
discovering what we are

As for how Raewyn handled the idea, words fail, please do go here to see the video here.

Tiny gold Archimedes’ spirals and identity theft prevention

There’s more than one way to prevent identity theft and counterfeit currency (there’s more about an approach pioneered in Canada at the end of this post). Scientists at Vanderbilt University and at Pacific Northwest National Laboratory have developed a new technology to achieve those ends, according to a June 3, 2015 news item on Azonano,

Take gold spirals about the size of a dime…and shrink them down about six million times. The result is the world’s smallest continuous spirals: “nano-spirals” with unique optical properties that would be almost impossible to counterfeit if they were added to identity cards, currency and other important objects.

Students and faculty at Vanderbilt University fabricated these tiny Archimedes’ spirals and then used ultrafast lasers at Vanderbilt and the Pacific Northwest National Laboratory in Richland, Washington, to characterize their optical properties. The results are reported in a paper published online by the Journal of Nanophotonics on May 21 [2015].

A June 2, 2015 Vanderbilt University news release, which originated the news item, describes how the research was approached,

“They are certainly smaller than any of the spirals we’ve found reported in the scientific literature,” said Roderick Davidson II, the Vanderbilt doctoral student who figured out how to study their optical behavior. The spirals were designed and made at Vanderbilt by another doctoral student, Jed Ziegler, now at the Naval Research Laboratory.

Most other investigators who have studied the remarkable properties of microscopic spirals have done so by arranging discrete nanoparticles in a spiral pattern: similar to spirals drawn with a series of dots of ink on a piece of paper. By contrast, the new nano-spirals have solid arms and are much smaller: A square array with 100 nano-spirals on a side is less than a hundredth of a millimeter wide.

When these spirals are shrunk to sizes smaller than the wavelength of visible light, they develop unusual optical properties. For example, when they are illuminated with infrared laser light, they emit visible blue light. A number of crystals produce this effect, called frequency doubling or harmonic generation, to various degrees. The strongest frequency doubler previously known is the synthetic crystal beta barium borate, but the nano-spirals produce four times more blue light per unit volume.

When infrared laser light strikes the tiny spirals, it is absorbed by electrons in the gold arms. The arms are so thin that the electrons are forced to move along the spiral. Electrons that are driven toward the center absorb enough energy so that some of them emit blue light at double the frequency of the incoming infrared light.

“This is similar to what happens with a violin string when it is bowed vigorously,” said Stevenson Professor of Physics Richard Haglund, who directed the research. “If you bow a violin string very lightly it produces a single tone. But, if you bow it vigorously, it also begins producing higher harmonics, or overtones. The electrons at the center of the spirals are driven pretty vigorously by the laser’s electric field. The blue light is exactly an octave higher than the infrared – the second harmonic.”

The nano-spirals also have a distinctive response to polarized laser light. Linearly polarized light, like that produced by a Polaroid filter, vibrates in a single plane. When struck by such a light beam, the amount of blue light the nano-spirals emit varies as the angle of the plane of polarization is rotated through 360 degrees.

The effect is even more dramatic when circularly polarized laser light is used. In circularly polarized light, the polarization plane rotates either clockwise or counterclockwise. When left-handed nano-spirals are illuminated with clockwise polarized light, the amount of blue light produced is maximized because the polarization pushes the electrons toward the center of the spiral. Counterclockwise polarized light, on the other hand, produces a minimal amount of blue light because the polarization tends to push the electrons outward so that the waves from all around the nano-spiral interfere destructively.

The news release goes on to explain how the properties of these gold nanospirals can be applied to identity theft protection and anti-counterfeiting measures,

The combination of the unique characteristics of their frequency doubling and response to polarized light provide the nano-spirals with a unique, customizable signature that would be extremely difficult to counterfeit, the researchers said.

So far, Davidson has experimented with small arrays of gold nano-spirals on a glass substrate made using scanning electron-beam lithography. Silver and platinum nano-spirals could be made in the same way. Because of the tiny quantities of metal actually used, they can be made inexpensively out of precious metals, which resist chemical degradation. They can also be made on plastic, paper and a number of other substrates.

“If nano-spirals were embedded in a credit card or identification card, they could be detected by a device comparable to a barcode reader,” said Haglund.

The frequency doubling effect is strong enough so that arrays that are too small to see with the naked eye can be detected easily. That means they could be placed in a secret location on a card, which would provide an additional barrier to counterfeiters.

The researchers also argue that coded nano-spiral arrays could be encapsulated and placed in explosives, chemicals and drugs – any substance that someone wants to track closely – and then detected using an optical readout device.

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

Eflcient forward second-harmonic generation from planar archimedean nanospirals by Roderick B. Davidson II,  Jed I. Ziegler,Guillermo Vargas, Sergey M. Avanesyan, Yu Gong, Wayne Hess, & Richard F. Haglund Jr. Nanophotonics. Volume 4, Issue 1, ISSN (Online) 2192-8614, DOI: 10.1515/nanoph-2015-0002, May 2015

This paper is open access.

The researchers have provided an image,

Scanning electron microscope image of an individual nano-spiral. (Haglund Lab / Vanderbilt)

Scanning electron microscope image of an individual nano-spiral. (Haglund Lab / Vanderbilt)

This works brings to mind Nanotech Security, a Vancouver (Canada) -based company that provides anti-counterfeiting measures derived from observations made of the Blue Morpho butterfly and the nanostructures on its wings. My latest post about the technology, a June 1, 2015 piece, describes the company’s latest patents and my earliest post, a Jan. 17, 2011 piece, features the first laboratory announcement about the butterfly, the work, and hopes for the technology.

Vaccines that are pure gold give patients breathing space

I exaggerated a little bit, the vaccine isn’t pure gold but it does have gold nanoparticles which mimic a virus. From the June 25, 2013 news item on ScienceDaily,

Scientists in the US have developed a novel vaccination method that uses tiny gold particles to mimic a virus and carry specific proteins to the body’s specialist immune cells.

The technique differs from the traditional approach of using dead or inactive viruses as a vaccine and was demonstrated in the lab using a specific protein that sits on the surface of the respiratory syncytial virus (RSV).

The results have been published today, 26 June [2013], in IOP Publishing’s journal Nanotechnology by a team of researchers from Vanderbilt University.

The June 26, 2013 IOP [Institute of Physics] Publishing news release (perhaps the journal publishers posted their news release after it was published elsewhere?), which originated the news item, provides more details about RSV and the technique,

RSV is the leading viral cause of lower respiration tract infections, causing several hundred thousand deaths and an estimated 65 million infections a year, mainly in children and the elderly.

The detrimental effects of RSV come, in part, from a specific protein, called the F protein, which coats the surface of the virus. The protein enables the virus to enter into the cytoplasm of cells and also causes cells to stick together, making the virus harder to eliminate.

The body’s natural defence to RSV is therefore directed at the F protein; however, up until now, researchers have had difficulty creating a vaccine that delivers the F protein to the specialised immune cells in the body. If successful, the F protein could trigger an immune response which the body could ‘remember’ if a subject became infected with the real virus.

In this study the researchers created exceptionally small gold nanorods, just 21 nanometres wide and 57 nanometres long, which were almost exactly the same shape and size as the virus itself. The gold nanorods were successfully coated with the RSV F proteins and were bonded strongly thanks to the unique physical and chemical properties of the nanorods themselves.

The researchers then tested the ability of the gold nanorods to deliver the F protein to specific immune cells, known as dendritic cells, which were taken from adult blood samples.

Dendritic cells function as processing cells in the immune system, taking the important information from a virus, such as the F protein, and presenting it to cells that can perform an action against them―the T cells are just one example of a cell that can take action.

Once the F protein-coated nanorods were added to a sample of dendritic cells, the researchers analysed the proliferation of T cells as a proxy for an immune response. They found that the protein-coated nanorods caused the T cells to proliferate significantly more compared to non-coated nanorods and just the F protein alone.

Not only did this prove that the coated-nanorods were capable of mimicking the virus and stimulating an immune response, it also showed that they were not toxic to human cells, offering significant safety advantages and increasing their potential as a real-life human vaccine.

Lead author of the study, Professor James Crowe, said: “A vaccine for RSV, which is the major cause of viral pneumonia in children, is sorely needed. This study shows that we have developed methods for putting RSV F protein into exceptionally small particles and presenting it to immune cells in a format that physically mimics the virus. Furthermore, the particles themselves are not infectious.”

Due to the versatility of the gold nanorods, Professor Crowe believes that their potential use is not limited to RSV.

“This platform could be used to develop experimental vaccines for virtually any virus, and in fact other larger microbes such as bacteria and fungi.

“The studies we performed showed that the candidate vaccines stimulated human immune cells when they were interacted in the lab. The next steps to testing would be to test whether or not the vaccines work in vivo” Professor Crowe continued.

I look forward to hearing more about this new vaccine as they continue with the testing. Meanwhile, here’s a link to and a citation for the latest published work,

Gold nanorod vaccine for respiratory syncytial virus by John W Stone, Natalie J Thornburg, David L Blum, Sam J Kuhn, David W Wright, and James E Crowe Jr. Nanotechnology Volume 24 Number 29 or Nanotechnology 24 295102 doi:10.1088/0957-4484/24/29/295102

The article is open access.

Spinach + Silicon = Green Power

I wouldn’t expect that anyone will be turning their spinach salads into hybrid solar cells anytime soon despite what scientists at Vanderbilt University (Tennessee) have achieved. From the Sept. 4, 2012 news release on EurekAlert,

An interdisciplinary team of researchers at Vanderbilt University have developed a way to combine the photosynthetic protein that converts light into electrochemical energy in spinach with silicon, the material used in solar cells, in a fashion that produces substantially more electrical current than has been reported by previous “biohybrid” solar cells.

Here’s an illustration of the concept provided by Vanderbilt University,

(Julie Turner/Vanderbilt)

According to the Sept. 4, 2012 Vanderbilt University news release , the researchers were trying exploit a feature of a protein found in spinach (and other plants),

More than 40 years ago, scientists discovered that one of the proteins involved in photosynthesis, called Photosystem 1 (PS1), continued to function when it was extracted from plants like spinach. Then they determined PS1 converts sunlight into electrical energy with nearly 100 percent efficiency, compared to conversion efficiencies of less than 40 percent achieved by manmade devices. This prompted various research groups around the world to begin trying to use PS1 to create more efficient solar cells.

When a PS1 protein exposed to light, it absorbs the energy in the photons and uses it to free electrons and transport them to one side of the protein. That creates regions of positive charge, called holes, which move to the opposite side of the protein.

In a leaf, all the PS1 proteins are aligned. But in the protein layer on the device, individual proteins are oriented randomly. Previous modeling work indicated that this was a major problem. When the proteins are deposited on a metallic substrate, those that are oriented in one direction provide electrons that the metal collects while those that are oriented in the opposite direction pull electrons out of the metal in order to fill the holes that they produce. As a result, they produce both positive and negative currents that cancel each other out to leave a very small net current flow.

The problem with using a metallic substrate was addressed by using and ‘doping’ silicon (from the Vanderbilt University news release),

The Vanderbilt researchers report that their PS1/silicon combination produces nearly a milliamp (850 microamps) of current per square centimeter at 0.3 volts. That is nearly two and a half times more current than the best level reported previously from a biohybrid cell. The reason this combo works so well is because the electrical properties of the silicon substrate have been tailored to fit those of the PS1 molecule. This is done by implanting electrically charge atoms in the silicon to alter its electrical properties: a process called “doping.” In this case, the protein worked extremely well with silicon doped with positive charges and worked poorly with negatively doped silicon.

To make the device, the researchers extracted PS1 from spinach into an aqueous solution and poured the mixture on the surface of a p-doped silicon wafer. Then they put the wafer in a vacuum chamber in order to evaporate the water away leaving a film of protein. They found that the optimum thickness was about one micron, about 100 PS1 molecules thick.

Here’s a graph illustrating the improvement (larger version available here),

Graph shows the dramatic increase in electrical current that Vanderbilt researchers have managed to produce from biohybrid solar cells. (Courtesy of Cliffel Lab/Vanderbilt University)

Encouraging news overall but the researchers still have more work to do (from the Vanderbilt University news release),

This combination produces current levels almost 1,000 times higher than we were able to achieve by depositing the protein on various types of metals. It also produces a modest increase in voltage,” said David Cliffel, associate professor of chemistry, who collaborated on the project with Kane Jennings, professor of chemical and biomolecular engineering.

“If we can continue on our current trajectory of increasing voltage and current levels, we could reach the range of mature solar conversion technologies in three years.”

The researchers’ next step is to build a functioning PS1-silicon solar cell using this new design. Jennings has an Environmental Protection Agency award that will allow a group of undergraduate engineering students to build the prototype. The students won the award at the National Sustainable Design Expo in April based on a solar panel that they had created using a two-year old design. With the new design, Jennings estimates that a two-foot panel could put out at least 100 milliamps at one volt – enough to power a number of different types of small electrical devices.

So, our solar cells are going to become more and more plantlike? I can certainly see the appeal if it means minimizing dependency on “rare and expensive materials like platinum or indium” as per the Vanderbilt University news release.