Tag Archives: University of Washington (state)

University of Washington (state) is accelerating nanoscale research with Institute for Nano-Engineered Systems

A December 5, 2017 news item on Nanowerk announced a new research institute at the University of Washington (state),

The University of Washington [UW} has launched a new institute aimed at accelerating research at the nanoscale: the Institute for Nano-Engineered Systems, or NanoES. Housed in a new, multimillion-dollar facility on the UW’s Seattle campus, the institute will pursue impactful advancements in a variety of disciplines — including energy, materials science, computation and medicine. Yet these advancements will be at a technological scale a thousand times smaller than the width of a human hair.

The institute was launched at a reception Dec. 4 [2017] at its headquarters in the $87.8-million Nano Engineering and Sciences Building. During the event, speakers including UW officials and NanoES partners celebrated the NanoES mission to capitalize on the university’s strong record of research at the nanoscale and engage partners in industry at the onset of new projects.

A December 5, 2017 UW news release, which originated the news item, somewhat clarifies the declarations in the two excerpted paragraphs in the above,

The vision of the NanoES, which is part of the UW’s College of Engineering, is to act as a magnet for researchers in nanoscale science and engineering, with a focus on enabling industry partnership and entrepreneurship at the earliest stages of research projects. According to Karl Böhringer, director of the NanoES and a UW professor of electrical engineering and bioengineering, this unique approach will hasten the development of solutions to the field’s most pressing challenges: the manufacturing of scalable, high-yield nano-engineered systems for applications in information processing, energy, health and interconnected life.

“The University of Washington is well known for its expertise in nanoscale materials, processing, physics and biology — as well as its cutting-edge nanofabrication, characterization and testing facilities,” said Böhringer, who stepped down as director of the UW-based Washington Nanofabrication Facility to lead the NanoES. “NanoES will build on these strengths, bringing together people, tools and opportunities to develop nanoscale devices and systems.”

The centerpiece of the NanoES is its headquarters, the Nano Engineering and Sciences Building. The building houses 90,300 square feet of research and learning space, and was funded largely by the College of Engineering and Sound Transit. It contains an active learning classroom, a teaching laboratory and a 3,000-square-foot common area designed expressly to promote the sharing and exchanging of ideas. The remainder includes “incubator-style” office space and more than 40,000 square feet of flexible multipurpose laboratory and instrumentation space. The building’s location and design elements are intended to limit vibrations and electromagnetic interference so it can house sensitive experiments.

NanoES will house research in nanotechnology fields that hold promise for high impact, such as:

  • Augmented humanity, which includes technology to both aid and replace human capability in a way that joins user and machine as one – and foresees portable, wearable, implantable and networked technology for applications such as personalized medical care, among others.
  • Integrated photonics, which ranges from single-photon sensors for health care diagnostic tests to large-scale, integrated networks of photonic devices.
  • Scalable nanomanufacturing, which aims to develop low-cost, high-volume manufacturing processes. These would translate device prototypes constructed in research laboratories into system- and network-level nanomanufacturing methods for applications ranging from the 3-D printing of cell and tissue scaffolds to ultrathin solar cells.

A ribbon cutting ceremony.

Cutting the ribbon for the NanoES on Dec. 4. Left-to-right: Karl Böhringer, director of the NanoES and a UW professor of electrical engineering and bioengineering; Nena Golubovic, physical sciences director for IP Group; Mike Bragg, Dean of the UW College of Engineering; Jevne Micheau-Cunningham, deputy director of the NanoES.Kathryn Sauber/University of Washington

Collaborations with other UW-based institutions will provide additional resources for the NanoES. Endeavors in scalable nanomanufacturing, for example, will rely on the roll-to-roll processing facility at the UW Clean Energy Institute‘s Washington Clean Energy Testbeds or on advanced surface characterization capabilities at the Molecular Analysis Facility. In addition, the Washington Nanofabrication Facility recently completed a three-year, $37 million upgrade to raise it to an ISO Class 5 nanofabrication facility.

UW faculty and outside collaborators will build new research programs in the Nano Engineering and Sciences Building. Eric Klavins, a UW professor of electrical engineering, recently moved part of his synthetic biology research team to the building, adjacent to his collaborators in the Molecular Engineering & Sciences Institute and the Institute for Protein Design.

“We are extremely excited about the interdisciplinary and collaborative potential of the new space,” said Klavins.

The NanoES also has already produced its first spin-out company, Tunoptix, which was co-founded by Böhringer and recently received startup funding from IP Group, a U.K.-based venture capital firm.

“IP Group is very excited to work with the University of Washington,” said Nena Golubovic, physical sciences director for IP Group. “We are looking forward to the new collaborations and developments in science and technology that will grow from this new partnership.”

A woman speaking at a podium.

Nena Golubovic, physical sciences director for IP Group, delivering remarks at the Dec. 4 opening of NanoES.Kathryn Sauber/University of Washington

“We are eager to work with our partners at the IP Group to bring our technology to the market, and we appreciate their vision and investment in the NanoES Integrated Photonics Initiative,” said Tunoptix entrepreneurial lead Mike Robinson. “NanoES was the ideal environment in which to start our company.”

The NanoES leaders hope to forge similar partnerships with researchers, investors and industry leaders to develop technologies for portable, wearable, implantable and networked nanotechnologies for personalized medical care, a more efficient interconnected life and interconnected mobility. In addition to expertise, personnel and state-of-the-art research space and equipment, the NanoES will provide training, research support and key connections to capital and corporate partners.

“We believe this unique approach is the best way to drive innovations from idea to fabrication to scale-up and testing,” said Böhringer. “Some of the most promising solutions to these huge challenges are rooted in nanotechnology.”

The NanoES is supported by funds from the College of Engineering and the National Science Foundation, as well as capital investments from investors and industry partners.

You can find out more about Nano ES here.

World heritage music stored in DNA

It seems a Swiss team from the École Polytechnique de Lausanne (EPFL) have collaborated with American companies Twist Bioscience and Microsoft, as well as, the University of Washington (state) to preserve two iconic jazz pieces on DNA (deoxyribonucleic acid) according to a Sept. 29, 2017 news item on phys.org,,

Thanks to an innovative technology for encoding data in DNA strands, two items of world heritage – songs recorded at the Montreux Jazz Festival [held in Switzerland] and digitized by EPFL – have been safeguarded for eternity. This marks the first time that cultural artifacts granted UNESCO heritage status have been saved in such a manner, ensuring they are preserved for thousands of years. The method was developed by US company Twist Bioscience and is being unveiled today in a demonstrator created at the EPFL+ECAL Lab.

“Tutu” by Miles Davis and “Smoke on the Water” by Deep Purple have already made their mark on music history. Now they have entered the annals of science, for eternity. Recordings of these two legendary songs were digitized by the Ecole Polytechnique Fédérale de Lausanne (EPFL) as part of the Montreux Jazz Digital Project, and they are the first to be stored in the form of a DNA sequence that can be subsequently decoded and listened to without any reduction in quality.

A Sept. 29, 2017 EPFL press release by Emmanuel Barraud, which originated the news item, provides more details,

This feat was achieved by US company Twist Bioscience working in association with Microsoft Research and the University of Washington. The pioneering technology is actually based on a mechanism that has been at work on Earth for billions of years: storing information in the form of DNA strands. This fundamental process is what has allowed all living species, plants and animals alike, to live on from generation to generation.

The entire world wide web in a shoe box

All electronic data storage involves encoding data in binary format – a series of zeros and ones – and then recording it on a physical medium. DNA works in a similar way, but is composed of long strands of series of four nucleotides (A, T, C and G) that make up a “code.” While the basic principle may be the same, the two methods differ greatly in terms of efficiency: if all the information currently on the internet was stored in the form of DNA, it would fit in a shoe box!

Recent advances in biotechnology now make it possible for humans to do what Mother Nature has always done. Today’s scientists can create artificial DNA strands, “record” any kind of genetic code on them and then analyze them using a sequencer to reconstruct the original data. What’s more, DNA is extraordinarily stable, as evidenced by prehistoric fragments that have been preserved in amber. Artificial strands created by scientists and carefully encapsulated should likewise last for millennia.

To help demonstrate the feasibility of this new method, EPFL’s Metamedia Center provided recordings of two famous songs played at the Montreux Jazz Festival: “Tutu” by Miles Davis, and “Smoke on the Water” by Deep Purple. Twist Bioscience and its research partners encoded the recordings, transformed them into DNA strands and then sequenced and decoded them and played them again – without any reduction in quality.

The amount of artificial DNA strands needed to record the two songs is invisible to the naked eye, and the amount needed to record all 50 years of the Festival’s archives, which have been included in UNESCO’s [United Nations Educational, Scientific and Cultural Organization] Memory of the World Register, would be equal in size to a grain of sand. “Our partnership with EPFL in digitizing our archives aims not only at their positive exploration, but also at their preservation for the next generations,” says Thierry Amsallem, president of the Claude Nobs Foundation. “By taking part in this pioneering experiment which writes the songs into DNA strands, we can be certain that they will be saved on a medium that will never become obsolete!”

A new concept of time

At EPFL’s first-ever ArtTech forum, attendees got to hear the two songs played after being stored in DNA, using a demonstrator developed at the EPFL+ECAL Lab. The system shows that being able to store data for thousands of years is a revolutionary breakthrough that can completely change our relationship with data, memory and time. “For us, it means looking into radically new ways of interacting with cultural heritage that can potentially cut across civilizations,” says Nicolas Henchoz, head of the EPFL+ECAL Lab.

Quincy Jones, a longstanding Festival supporter, is particularly enthusiastic about this technological breakthrough: “With advancements in nanotechnology, I believe we can expect to see people living prolonged lives, and with that, we can also expect to see more developments in the enhancement of how we live. For me, life is all about learning where you came from in order to get where you want to go, but in order to do so, you need access to history! And with the unreliability of how archives are often stored, I sometimes worry that our future generations will be left without such access… So, it absolutely makes my soul smile to know that EPFL, Twist Bioscience and their partners are coming together to preserve the beauty and history of the Montreux Jazz Festival for our future generations, on DNA! I’ve been a part of this festival for decades and it truly is a magnificent representation of what happens when different cultures unite for the sake of music. Absolute magic. And I’m proud to know that the memory of this special place will never be lost.

A Sept. 29, 2017 Twist Bioscience news release is repetitive in some ways but interesting nonetheless,

Twist Bioscience, a company accelerating science and innovation through rapid, high-quality DNA synthesis, today announced that, working with Microsoft and University of Washington researchers, they have successfully stored archival-quality audio recordings of two important music performances from the archives of the world-renowned Montreux Jazz Festival.
These selections are encoded and stored in nature’s preferred storage medium, DNA, for the first time. These tiny specks of DNA will preserve a part of UNESCO’s Memory of the World Archive, where valuable cultural heritage collections are recorded. This is the first time DNA has been used as a long-term archival-quality storage medium.
Quincy Jones, world-renowned Entertainment Executive, Music Composer and Arranger, Musician and Music Producer said, “With advancements in nanotechnology, I believe we can expect to see people living prolonged lives, and with that, we can also expect to see more developments in the enhancement of how we live. For me, life is all about learning where you came from in order to get where you want to go, but in order to do so, you need access to history! And with the unreliability of how archives are often stored, I sometimes worry that our future generations will be left without such access…So, it absolutely makes my soul smile to know that EPFL, Twist Bioscience and others are coming together to preserve the beauty and history of the Montreux Jazz Festival for our future generations, on DNA!…I’ve been a part of this festival for decades and it truly is a magnificent representation of what happens when different cultures unite for the sake of music. Absolute magic. And I’m proud to know that the memory of this special place will never be lost.”
“Our partnership with EPFL in digitizing our archives aims not only at their positive exploration, but also at their preservation for the next generations,” says Thierry Amsallem, president of the Claude Nobs Foundation. “By taking part in this pioneering experiment which writes the songs into DNA strands, we can be certain that they will be saved on a medium that will never become obsolete!”
The Montreux Jazz Digital Project is a collaboration between the Claude Nobs Foundation, curator of the Montreux Jazz Festival audio-visual collection and the École Polytechnique Fédérale de Lausanne (EPFL) to digitize, enrich, store, show, and preserve this notable legacy created by Claude Nobs, the Festival’s founder.
In this proof-of-principle project, two quintessential music performances from the Montreux Jazz Festival – Smoke on the Water, performed by Deep Purple and Tutu, performed by Miles Davis – have been encoded onto DNA and read back with 100 percent accuracy. After being decoded, the songs were played on September 29th [2017] at the ArtTech Forum (see below) in Lausanne, Switzerland. Smoke on the Water was selected as a tribute to Claude Nobs, the Montreux Jazz Festival’s founder. The song memorializes a fire and Funky Claude’s rescue efforts at the Casino Barrière de Montreux during a Frank Zappa concert promoted by Claude Nobs. Miles Davis’ Tutu was selected for the role he played in music history and the Montreux Jazz Festival’s success. Miles Davis died in 1991.
“We archived two magical musical pieces on DNA of this historic collection, equating to 140MB of stored data in DNA,” said Karin Strauss, Ph.D., a Senior Researcher at Microsoft, and one of the project’s leaders.  “The amount of DNA used to store these songs is much smaller than one grain of sand. Amazingly, storing the entire six petabyte Montreux Jazz Festival’s collection would result in DNA smaller than one grain of rice.”
Luis Ceze, Ph.D., a professor in the Paul G. Allen School of Computer Science & Engineering at the University of Washington, said, “DNA, nature’s preferred information storage medium, is an ideal fit for digital archives because of its durability, density and eternal relevance. Storing items from the Montreux Jazz Festival is a perfect way to show how fast DNA digital data storage is becoming real.”
Nature’s Preferred Storage Medium
Nature selected DNA as its hard drive billions of years ago to encode all the genetic instructions necessary for life. These instructions include all the information necessary for survival. DNA molecules encode information with sequences of discrete units. In computers, these discrete units are the 0s and 1s of “binary code,” whereas in DNA molecules, the units are the four distinct nucleotide bases: adenine (A), cytosine (C), guanine (G) and thymine (T).
“DNA is a remarkably efficient molecule that can remain stable for millennia,” said Bill Peck, Ph.D., chief technology officer of Twist Bioscience.  “This is a very exciting project: we are now in an age where we can use the remarkable efficiencies of nature to archive master copies of our cultural heritage in DNA.   As we develop the economies of this process new performances can be added any time.  Unlike current storage technologies, nature’s media will not change and will remain readable through time. There will be no new technology to replace DNA, nature has already optimized the format.”
DNA: Far More Efficient Than a Computer 
Each cell within the human body contains approximately three billion base pairs of DNA. With 75 trillion cells in the human body, this equates to the storage of 150 zettabytes (1021) of information within each body. By comparison, the largest data centers can be hundreds of thousands to even millions of square feet to hold a comparable amount of stored data.
The Elegance of DNA as a Storage Medium
Like music, which can be widely varied with a finite number of notes, DNA encodes individuality with only four different letters in varied combinations. When using DNA as a storage medium, there are several advantages in addition to the universality of the format and incredible storage density. DNA can be stable for thousands of years when stored in a cool dry place and is easy to copy using polymerase chain reaction to create back-up copies of archived material. In addition, because of PCR, small data sets can be targeted and recovered quickly from a large dataset without needing to read the entire file.
How to Store Digital Data in DNA
To encode the music performances into archival storage copies in DNA, Twist Bioscience worked with Microsoft and University of Washington researchers to complete four steps: Coding, synthesis/storage, retrieval and decoding. First, the digital files were converted from the binary code using 0s and 1s into sequences of A, C, T and G. For purposes of the example, 00 represents A, 10 represents C, 01 represents G and 11 represents T. Twist Bioscience then synthesizes the DNA in short segments in the sequence order provided. The short DNA segments each contain about 12 bytes of data as well as a sequence number to indicate their place within the overall sequence. This is the process of storage. And finally, to ensure that the file is stored accurately, the sequence is read back to ensure 100 percent accuracy, and then decoded from A, C, T or G into a two-digit binary representation.
Importantly, to encapsulate and preserve encoded DNA, the collaborators are working with Professor Dr. Robert Grass of ETH Zurich. Grass has developed an innovative technology inspired by preservation of DNA within prehistoric fossils.  With this technology, digital data encoded in DNA remains preserved for millennia.
About UNESCO’s Memory of the World Register
UNESCO established the Memory of the World Register in 1992 in response to a growing awareness of the perilous state of preservation of, and access to, documentary heritage in various parts of the world.  Through its National Commissions, UNESCO prepared a list of endangered library and archive holdings and a world list of national cinematic heritage.
A range of pilot projects employing contemporary technology to reproduce original documentary heritage on other media began. These included, for example, a CD-ROM of the 13th Century Radzivill Chronicle, tracing the origins of the peoples of Europe, and Memoria de Iberoamerica, a joint newspaper microfilming project involving seven Latin American countries. These projects enhanced access to this documentary heritage and contributed to its preservation.
“We are incredibly proud to be a part of this momentous event, with the first archived songs placed into the UNESCO Memory of the World Register,” said Emily Leproust, Ph.D., CEO of Twist Bioscience.
About ArtTech
The ArtTech Foundation, created by renowned scientists and dignitaries from Crans-Montana, Switzerland, wishes to stimulate reflection and support pioneering and innovative projects beyond the known boundaries of culture and science.
Benefitting from the establishment of a favorable environment for the creation of technology companies, the Foundation aims to position itself as key promoter of ideas and innovative endeavors within a landscape of “Culture and Science” that is still being shaped.
Several initiatives, including our annual global platform launched in the spring of 2017, are helping to create a community that brings together researchers, celebrities in the world of culture and the arts, as well as investors and entrepreneurs from Switzerland and across the globe.
 
About EPFL
EPFL, one of the two Swiss Federal Institutes of Technology, based in Lausanne, is Europe’s most cosmopolitan technical university with students, professors and staff from over 120 nations. A dynamic environment, open to Switzerland and the world, EPFL is centered on its three missions: teaching, research and technology transfer. EPFL works together with an extensive network of partners including other universities and institutes of technology, developing and emerging countries, secondary schools and colleges, industry and economy, political circles and the general public, to bring about real impact for society.
About Twist Bioscience
At Twist Bioscience, our expertise is accelerating science and innovation by leveraging the power of scale. We have developed a proprietary semiconductor-based synthetic DNA manufacturing process featuring a high throughput silicon platform capable of producing synthetic biology tools, including genes, oligonucleotide pools and variant libraries. By synthesizing DNA on silicon instead of on traditional 96-well plastic plates, our platform overcomes the current inefficiencies of synthetic DNA production, and enables cost-effective, rapid, high-quality and high throughput synthetic gene production, which in turn, expedites the design, build and test cycle to enable personalized medicines, pharmaceuticals, sustainable chemical production, improved agriculture production, diagnostics and biodetection. We are also developing new technologies to address large scale data storage. For more information, please visit www.twistbioscience.com. Twist Bioscience is on Twitter. Sign up to follow our Twitter feed @TwistBioscience at https://twitter.com/TwistBioscience.

If you hadn’t read the EPFL press release first, it might have taken a minute to figure out why EPFL is being mentioned in the Twist Bioscience news release. Presumably someone was rushing to make a deadline. Ah well, I’ve seen and written worse.

I haven’t been able to find any video or audio recordings of the DNA-preserved performances but there is an informational video (originally published July 7, 2016) from Microsoft and the University of Washington describing the DNA-based technology,

I also found this description of listening to the DNA-preserved music in an Oct. 6, 2017 blog posting for the Canadian Broadcasting Corporation’s (CBC) Day 6 radio programme,

To listen to them, one must first suspend the DNA holding the songs in a solution. Next, one can use a DNA sequencer to read the letters of the bases forming the molecules. Then, algorithms can determine the digital code those letters form. From that code, comes the music.

It’s complicated but Ceze says his team performed this process without error.

You can find out more about UNESCO’s Memory of the World and its register here , more about the EPFL+ECAL Lab here, and more about Twist Bioscience here.

Growing shells atom-by-atom

The University of California at Davis (UC Davis) and the University of Washington (state) collaborated in research into fundamental questions on how aquatic animals grow. From an Oct. 24, 2016 news item on ScienceDaily,

For the first time scientists can see how the shells of tiny marine organisms grow atom-by-atom, a new study reports. The advance provides new insights into the mechanisms of biomineralization and will improve our understanding of environmental change in Earth’s past.

An Oct. 24, 2016 UC Davis news release by Becky Oskin, which originated the news item, provides more detail,

Led by researchers from the University of California, Davis and the University of Washington, with key support from the U.S. Department of Energy’s Pacific Northwest National Laboratory, the team examined an organic-mineral interface where the first calcium carbonate crystals start to appear in the shells of foraminifera, a type of plankton.

“We’ve gotten the first glimpse of the biological event horizon,” said Howard Spero, a study co-author and UC Davis geochemistry professor. …

Foraminifera’s Final Frontier

The researchers zoomed into shells at the atomic level to better understand how growth processes may influence the levels of trace impurities in shells. The team looked at a key stage — the interaction between the biological ‘template’ and the initiation of shell growth. The scientists produced an atom-scale map of the chemistry at this crucial interface in the foraminifera Orbulina universa. This is the first-ever measurement of the chemistry of a calcium carbonate biomineralization template, Spero said.

Among the new findings are elevated levels of sodium and magnesium in the organic layer. This is surprising because the two elements are not considered important architects in building shells, said lead study author Oscar Branson, a former postdoctoral researcher at UC Davis who is now at the Australian National University in Canberra. Also, the greater concentrations of magnesium and sodium in the organic template may need to be considered when investigating past climate with foraminifera shells.

Calibrating Earth’s Climate

Most of what we know about past climate (beyond ice core records) comes from chemical analyses of shells made by the tiny, one-celled creatures called foraminifera, or “forams.” When forams die, their shells sink and are preserved in seafloor mud. The chemistry preserved in ancient shells chronicles climate change on Earth, an archive that stretches back nearly 200 million years.

The calcium carbonate shells incorporate elements from seawater — such as calcium, magnesium and sodium — as the shells grow. The amount of trace impurities in a shell depends on both the surrounding environmental conditions and how the shells are made. For example, the more magnesium a shell has, the warmer the ocean was where that shell grew.

“Finding out how much magnesium there is in a shell can allow us to find out the temperature of seawater going back up to 150 million years,” Branson said.

But magnesium levels also vary within a shell, because of nanometer-scale growth bands. Each band is one day’s growth (similar to the seasonal variations in tree rings). Branson said considerable gaps persist in understanding what exactly causes the daily bands in the shells.

“We know that shell formation processes are important for shell chemistry, but we don’t know much about these processes or how they might have changed through time,” he said. “This adds considerable uncertainty to climate reconstructions.”

Atomic Maps

The researchers used two cutting-edge techniques: Time-of-Flight Secondary Ionization Mass Spectrometry (ToF-SIMS) and Laser-Assisted Atom Probe Tomography (APT). ToF-SIMS is a two-dimensional chemical mapping technique which shows the elemental composition of the surface of a polished sample. The technique was developed for the elemental analysis of complex polymer materials, and is just starting to be applied to natural samples like shells.

APT is an atomic-scale three-dimensional mapping technique, developed for looking at internal structures in advanced alloys, silicon chips and superconductors. The APT imaging was performed at the Environmental Molecular Sciences Laboratory, a U.S. Department of Energy Office of Science User Facility at the Pacific Northwest National Laboratory.

This foraminifera is just starting to form its adult spherical shell. The calcium carbonate spherical shell first forms on a thin organic template, shown here in white, around the dark juvenile skeleton. Calcium carbonate spines then extend from the juvenile skeleton through the new sphere and outward. The bright flecks are algae that the foraminifera “farm” for sustenance.Howard Spero/University of California, Davis

This foraminifera is just starting to form its adult spherical shell. The calcium carbonate spherical shell first forms on a thin organic template, shown here in white, around the dark juvenile skeleton. Calcium carbonate spines then extend from the juvenile skeleton through the new sphere and outward. The bright flecks are algae that the foraminifera “farm” for sustenance.Howard Spero/University of California, Davis

An Oct. 24, 2016 University of Washington (state) news release (also on EurekAlert) adds more information (there is a little repetition),

Unseen out in the ocean, countless single-celled organisms grow protective shells to keep them safe as they drift along, living off other tiny marine plants and animals. Taken together, the shells are so plentiful that when they sink they provide one of the best records for the history of ocean chemistry.

Oceanographers at the University of Washington and the University of California, Davis, have used modern tools to provide an atomic-scale look at how that shell first forms. Results could help answer fundamental questions about how these creatures grow under different ocean conditions, in the past and in the future. …

“There’s this debate among scientists about whether shelled organisms are slaves to the chemistry of the ocean, or whether they have the physiological capacity to adapt to changing environmental conditions,” said senior author Alex Gagnon, a UW assistant professor of oceanography.

The new work shows, he said, that they do exert some biologically-based control over shell formation.

“I think it’s just incredible that we were able to peer into the intricate details of those first moments that set how a seashell forms,” Gagnon said. “And that’s what sets how much of the rest of the skeleton will grow.”

The results could eventually help understand how organisms at the base of the marine food chain will respond to more acidic waters. And while the study looked at one organism, Orbulina universa, which is important for understanding past climate, the same method could be used for other plankton, corals and shellfish.

The study used tools developed for materials science and semiconductor research to view the shell formation in the most detail yet to see how the organisms turn seawater into solid mineral.

“We’re interested more broadly in the question ‘How do organisms make shells?'” said first author Oscar Branson, a former postdoctoral researcher at the University of California, Davis who is now at Australian National University in Canberra. “We’ve focused on a key stage in mineral formation — the interaction between biological template materials and the initiation of shell growth by an organism.”

These tiny single-celled animals, called foraminifera, can’t reproduce anywhere but in their natural surroundings, which prevents breeding them in captivity. The researchers caught juvenile foraminifera by diving in deep water off Southern California. Then they then raised them in the lab, using tiny pipettes to feed them brine shrimp during their weeklong lives.

Marine shells are made from calcium carbonate, drawing the calcium and carbon from surrounding seawater. But the animal first grows a soft template for the mineral to grow over. Because this template is trapped within the growing skeleton, it acts as a snapshot of the chemical conditions during the first part of skeletal growth.

To see this chemical picture, the authors analyzed tiny sections of foraminifera template with a technique called atom probe tomography at the Pacific Northwest National Laboratory. This tool creates an atom-by-atom picture of the organic template, which was located using a chemical tag.

Results show that the template contains more magnesium and sodium atoms than expected, and that this could influence how the mineral in the shell begins to grow around it.

“One of the key stages in growing a skeleton is when you make that first bit, when you build that first bit of structure. Anything that changes that process is a key control point,” Gagnon said.

The clumping suggests that magnesium and sodium play a role in the first stages of shell growth. If their availability changes for any reason, that could influence how the shell grows beyond what simple chemistry would predict.

“We can say who the players are — further experiments will have to tell us exactly how important each of them is,” Gagnon said.

Follow-up work will try to grow the shells and create models of their formation to see how the template affects growth under different conditions, such as more acidic water.

“Translating that into, ‘Can these forams survive ocean acidification?’ is still many steps down the line,” Gagnon cautioned. “But you can’t do that until you have a picture of what that surface actually looks like.”

The researchers also hope that by better understanding the exact mechanism of shell growth they could tease apart different aspects of seafloor remains so the shells can be used to reconstruct more than just the ocean’s past temperature. In the study, they showed that the template was responsible for causing fine lines in the shells — one example of the rich chemical information encoded in fossil shells.

“There are ways that you could separate the effects of temperature from other things and learn much more about the past ocean,” Gagnon said.

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

Nanometer-Scale Chemistry of a Calcite Biomineralization Template: Implications for Skeletal Composition and Nucleation, Proceedings of the National Academy of Sciences, www.pnas.org/cgi/doi/10.1073/pnas.1522864113

This paper is behind a paywall.

‘Seamless’ bioeletronics made possible with protein bridge

For some years now I’ve been tagging certain posts with ‘machine/flesh’ as more bioelectronic devices are being invented for use as implants of various kinds.

Researchers at the University of Washington (state) have found a means of making bioelectronics implants a more comfortable fit in the body according to an Oct. 4, 2016 news item on phys.org,

Life has always played by its own set of molecular rules. From the biochemistry behind the first cells, evolution has constructed wonders like hard bone, rough bark and plant enzymes that harvest light to make food.

But our tools for manipulating life—to treat disease, repair damaged tissue and replace lost limbs—come from the nonliving realm: metals, plastics and the like. Though these save and preserve lives, our synthetic treatments are rooted in a chemical language ill-suited to our organic elegance. Implanted electrodes scar, wires overheat and our bodies struggle against ill-fitting pumps, pipes or valves.

A solution lies in bridging this gap where artificial meets biological—harnessing biological rules to exchange information between the biochemistry of our bodies and the chemistry of our devices. In a paper published Sept. 22 [2016] in Scientific Reports, engineers at the University of Washington unveiled peptides—small proteins which carry out countless essential tasks in our cells—that can provide just such a link.

An Oct. 3, 2016 University of Washington (state) news release (also on EurekAlert), which originated the news item, expands on the theme,

The team, led by UW professor Mehmet Sarikaya in the Departments of Materials Science & Engineering, shows how a genetically engineered peptide can assemble into nanowires atop 2-D, solid surfaces that are just a single layer of atoms thick. These nanowire assemblages are critical because the peptides relay information across the bio/nano interface through molecular recognition — the same principles that underlie biochemical interactions such as an antibody binding to its specific antigen or protein binding to DNA.

Since this communication is two-way, with peptides understanding the “language” of technology and vice versa, their approach essentially enables a coherent bioelectronic interface.

“Bridging this divide would be the key to building the genetically engineered biomolecular solid-state devices of the future,” said Sarikaya, who is also a professor of chemical engineering and oral health sciences.

His team in the UW Genetically Engineered Materials Science and Engineering Center studies how to coopt the chemistry of life to synthesize materials with technologically significant physical, electronic and photonic properties. To Sarikaya, the biochemical “language” of life is a logical emulation.

“Nature must constantly make materials to do many of the same tasks we seek,” he said.

The UW team wants to find genetically engineered peptides with specific chemical and structural properties. They sought out a peptide that could interact with materials such as gold, titanium and even a mineral in bone and teeth. These could all form the basis of future biomedical and electro-optical devices. Their ideal peptide should also change the physical properties of synthetic materials and respond to that change. That way, it would transmit “information” from the synthetic material to other biomolecules — bridging the chemical divide between biology and technology.

In exploring the properties of 80 genetically selected peptides — which are not found in nature but have the same chemical components of all proteins — they discovered that one, GrBP5, showed promising interactions with the semimetal graphene. They then tested GrBP5’s interactions with several 2-D nanomaterials which, Sarikaya said, “could serve as the metals or semiconductors of the future.”

“We needed to know the specific molecular interactions between this peptide and these inorganic solid surfaces,” he added.

Their experiments revealed that GrBP5 spontaneously organized into ordered nanowire patterns on graphene. With a few mutations, GrBP5 also altered the electrical conductivity of a graphene-based device, the first step toward transmitting electrical information from graphene to cells via peptides.

In parallel, Sarikaya’s team modified GrBP5 to produce similar results on a semiconductor material — molybdenum disulfide — by converting a chemical signal to an optical signal. They also computationally predicted how different arrangements of GrBP5 nanowires would affect the electrical conduction or optical signal of each material, showing additional potential within GrBP5’s physical properties.

“In a way, we’re at the flood gates,” said Sarikaya. “Now we need to explore the basic properties of this bridge and how we can modify it to permit the flow of ‘information’ from electronic and photonic devices to biological systems.”

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

Bioelectronic interfaces by spontaneously organized peptides on 2D atomic single layer materials by Yuhei Hayamizu, Christopher R. So, Sefa Dag, Tamon S. Page, David Starkebaum, & Mehmet Sarikaya. Scientific Reports 6, Article number: 33778 (2016) doi:10.1038/srep33778 Published online: 22 September 2016

This paper is open access.

This image illustrates the GrBP5 nanowires,

A top view image of GrBP5 nanowires on a 2-D surface of molybdenum disulfide.Mehmet Sarikaya/Scientific Reports

A top view image of GrBP5 nanowires on a 2-D surface of molybdenum disulfide.Mehmet Sarikaya/Scientific Reports

Ferroelectric switching in the lung, heart, and arteries

A June 23, 2014 University of Washington (state) news release (also on EurekAlert) describes how the human body (and other biological tissue) is capable of generating ferroelectricity,

University of Washington researchers have shown that a favorable electrical property is present in a type of protein found in organs that repeatedly stretch and retract, such as the lungs, heart and arteries. These findings are the first that clearly track this phenomenon, called ferroelectricity, occurring at the molecular level in biological tissues.

The news release gives a brief description of ferroelectricity and describes the research team’s latest work with biological tissues,

Ferroelectricity is a response to an electric field in which a molecule switches from having a positive to a negative charge. This switching process in synthetic materials serves as a way to power computer memory chips, display screens and sensors. This property only recently has been discovered in animal tissues and researchers think it may help build and support healthy connective tissues in mammals.

A research team led by Li first discovered ferroelectric properties in biological tissues in 2012, then in 2013 found that glucose can suppress this property in the body’s connective tissues, wherever the protein elastin is present. But while ferroelectricity is a proven entity in synthetic materials and has long been thought to be important in biological functions, its actual existence in biology hasn’t been firmly established.

This study proves that ferroelectric switching happens in the biological protein elastin. When the researchers looked at the base structures within the protein, they saw similar behavior to the unit cells of solid-state materials, where ferroelectricity is well understood.

“When we looked at the smallest structural unit of the biological tissue and how it was organized into a larger protein fiber, we then were able to see similarities to the classic ferroelectric model found in solids,” Li said.

The researchers wanted to establish a more concrete, precise way of verifying ferroelectricity in biological tissues. They used small samples of elastin taken from a pig’s aorta and poled the tissues using an electric field at high temperatures. They then measured the current with the poling field removed and found that the current switched direction when the poling electric field was switched, a sign of ferroelectricity.

They did the same thing at room temperature using a laser as the heat source, and the current also switched directions.

Then, the researchers tested for this behavior on the smallest-possible unit of elastin, called tropoelastin, and again observed the phenomenon. They concluded that this switching property is “intrinsic” to the molecular make-up of elastin.

The next step is to understand the biological and physiological significance of this property, Li said. One hypothesis is that if ferroelectricity helps elastin stay flexible and functional in the body, a lack of it could directly affect the hardening of arteries.

“We may be able to use this as a very sensitive technique to detect the initiation of the hardening process at a very early stage when no other imaging technique will be able to see it,” Li said.

The team also is looking at whether this property plays a role in normal biological functions, perhaps in regulating the growth of tissue.

Co-authors are Pradeep Sharma at the University of Houston, Yanhang Zhang at Boston University, and collaborators at Nanjing University and the Chinese Academy of Sciences.

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

Ferroelectric switching of elastin by Yuanming Liu, Hong-Ling Cai, Matthew Zelisko, Yunjie Wang, Jinglan Sun, Fei Yan, Feiyue Ma, Peiqi Wang, Qian Nataly Chen, Hairong Zheng, Xiangjian Meng, Pradeep Sharma, Yanhang Zhang, and Jiangyu Li. Proceedings of the National Academy of Sciences (PNAS) doi: 10.1073/pnas.1402909111

This paper is behind a paywall.

I think this is a new practice. There is a paragraph on the significance of this work (follow the link to the paper),

Ferroelectricity has long been speculated to have important biological functions, although its very existence in biology has never been firmly established. Here, we present, to our knowledge, the first macroscopic observation of ferroelectric switching in a biological system, and we elucidate the origin and mechanism underpinning ferroelectric switching of elastin. It is discovered that the polarization in elastin is intrinsic at the monomer level, analogous to the unit cell level polarization in classical perovskite ferroelectrics. Our findings settle a long-standing question on ferroelectric switching in biology and establish ferroelectricity as an important biophysical property of proteins. We believe this is a critical first step toward resolving its physiological significance and pathological implications.

Protein nanomachines at the University of Washington

Scouring pad or protein nanomachine?

Caption: This is a computational model of a successfully designed two-component protein nanocage with tetrahedral symmetry. Credit: Dr. Vikram Mulligan

Caption: This is a computational model of a successfully designed two-component protein nanocage with tetrahedral symmetry.
Credit: Dr. Vikram Mulligan

This illustration of a protein nanocage reminded me of a type of scouring pad, which come to think of it, I haven’t seen in any stores for some years. Getting back on topic, this nanocage is a first step to building nanomachines according to a June 5, 2014 news item on Nanowerk,

A route for constructing protein nanomachines engineered for specific applications may be closer to reality.

Biological systems produce an incredible array of self-assembling, functional protein tools. Some examples of these nanoscale protein materials are scaffolds to anchor cellular activities, molecular motors to drive physiological events, and capsules for delivering viruses into host cells.

Scientists inspired by these sophisticated molecular machines want to build their own, with forms and functions customized to tackle modern-day challenges. The ability to design new protein nanostructures could have useful implications in targeted delivery of drugs, in vaccine development and in plasmonics, which is manipulating electromagnetic signals to guide light diffraction for information technologies, energy production or other uses.

A recently developed computational method may be an important step toward that goal. The project was led by the University of Washington’s [Washington state] Neil King, translational investigator; Jacob Bale, graduate student in Molecular and Cellular Biology; and William Sheffler in David Baker’s laboratory at the University of Washington Institute for Protein Design, in collaboration with colleagues at UCLA [University of California at Los Angeles] and Janelia Farm.

The work is based in the Rosetta macromolecular modeling package developed by Baker and his colleagues. The program was originally created to predict natural protein structures from amino acid sequences. Researchers in the Baker lab and around the world are increasingly using Rosetta to design new protein structures and sequences aimed at solving real-world problems.

A June 4 (?), 2014 University of Washington news release by Leila Gray (also on EurekAlert), which originated the news item, provides more detail about the models and what the scientists hope to accomplish,

“Proteins are amazing structures that can do remarkable things,” King said, “they can respond to changes in their environment. Exposure to a particular metabolite or a rise in temperature, for example, can trigger an alteration in a particular protein’s shape and function.” People often call proteins the building blocks of life.

“But unlike, say, a PVC pipe,” King said, “they are not simply construction material.” They are also construction (and demolition) workers — speeding up chemical reactions, breaking down food, carrying messages, interacting with each other, and performing countless other duties vital to life.

With the new software the scientists were able to create five novel, 24-subunit cage-like protein nanomaterials. Importantly, the actual structures, the researchers observed, were in very close agreement with their computer modeling.

Their method depends on encoding pairs of protein amino acid sequences with the information needed to direct molecular assembly through protein-protein interfaces. The interfaces not only provide the energetic forces that drive the assembly process, they also precisely orient the pairs of protein building blocks with the geometry required to yield the desired cage-like symmetric architectures.

Creating this cage-shaped protein, the scientists said, may be a first step towards building nano-scale containers. [emphasis mine] King said he looks forward to a time when cancer-drug molecules will be packaged inside of designed nanocages and delivered directly to tumor cells, sparing healthy cells.

“The problem today with cancer chemotherapy is that it hits every cell and makes the patient feel sick,” King said. Packaging the drugs inside customized nanovehicles with parking options restricted to cancer sites might circumvent the side effects.

The scientists note that combining just two types of symmetry elements, as in this study, can in theory give rise to a range of symmetrical shapes, such as cubic point groups, helices, layers, and crystals.

King explained that the immune system responds to repetitive, symmetric patterns, such as those on the surface of a virus or disease bacteria. Building nano-decoys may be a way train the immune system to attack certain types of pathogens.

“This concept may become the foundation for vaccines based on engineered nanomaterials,” King said. Further down the road, he and Bale anticipate that these design methods might also be useful for developing new clean energy technologies.

The scientists added in their report, “The precise control over interface geometry offered by our method enables the design of two-component protein nanomaterials with diverse nanoscale features, such as surfaces, pores, and internal volumes, with high accuracy.”

They went on to say that the combinations possible with two-component materials greatly expand the number and variety of potential nanomaterials that could be designed.

It may be possible to produce nanomaterials in a variety of sizes, shapes and arrangements, and also move on to construct increasingly more complex materials from more than two components.

The researchers emphasized that the long-term goal of such structures is not to be static. The hope is that they will mimic or go beyond the dynamic performance of naturally occurring protein assemblies, and that eventually novel molecular protein machines could be manufactured with programmable functions. [emphasis mine]

The researchers pointed out that although designing proteins and protein-based nanomaterials is very challenging due to the relative complexity of protein structures and interactions, there are now more than a handful of laboratories around the world making major strides in this field. Each of the leading contributors have key strengths, they said. The strengths of the UW team is in the accuracy of the match of the designed proteins to the computational models and the predictability of the results.

It seems like it’s going to be several years before we have protein nanomachines. Here’s a link to and a citation for the research paper,

Accurate design of co-assembling multi-component protein nanomaterials by Neil P. King, Jacob B. Bale, William Sheffler, Dan E. McNamara, Shane Gonen, Tamir Gonen, Todd O. Yeates, & David Baker. Nature 510, 103–108 (05 June 2014) doi:10.1038/nature13404 Published online 25 May 2014

This paper is behind a paywall but there is a free preview via ReadCube Access.

For anyone curious about the Rosetta macromolecular modeling package used in this work, you can find out more here at the Rosetta Commons website.  As for Janelia Farm, it is a research center in Virginia and is part of the Howard Hughes Medical Institute.

Saving the frogs (and other amphibians)

Given this blog’s name, I couldn’t pass up this May 1, 2014 news release from Simon Fraser University (located in Vancouver, Canada),

An ecological strategy developed by four researchers, including two from Simon Fraser University, aims to abate the grim future that the combination of two factors could inflict on many amphibians, including frogs and salamanders.

A warming climate and the introduction of non-native fish in the American West’s mountainous areas are combining to threaten the habitat that this ecologically critical group of species needs to thrive.

Previous studies predict the combined effect of climate change and non-native fish could cause amphibian populations to decline and even become locally extinct.

In their newly published study in the journal Frontiers in Ecology and the Environment, researchers examine this challenge and propose several new climate adaptation tools to reduce threats to amphibians.

The researchers say the novel suite of tools could help prioritize the restoration of amphibian habitats in Western North America’s mountainous regions.

Wendy Palen, an SFU ecologist, Maureen Ryan, a postdoctoral fellow at SFU and the University of Washington (UW), Michael Adams, a research ecologist at the U.S. Geological Survey and Regina Rochefort, a science advisor at Washington State’s North Cascades National Park, co-authored the paper.

Many amphibians in the American West’s mountainous areas need predator-free wetlands and lakes during their aquatic life stages. “Amphibians predominantly use mountainous areas’ small, shallow ponds to breed and feed,” explains Ryan, the study’s lead author.

“These kinds of wetlands are at the highest risk of drying up under climate change due to reduced snowpack and longer summer droughts. Non-native fish, such as brook and rainbow trout, were introduced for recreational fishing almost a century ago. They remove amphibians from the biggest and most stable lakes in the environment. Fish eat most amphibians and even at low densities can devour a lake’s whole amphibian population.”

Mindful of an opportunity to help amphibians, the researchers collaborated with UW colleagues to develop new maps and hydrological models of climate impacts specific to mountainous regions.

They are using these tools along with biological survey data to identify regions where native species are most threatened by the combined effects of climate change and fish. They then hope to work with area managers who would implement fish removals.

“Our work suggests that removing fish from strategic sites may restore resilience to landscapes where inaction might lead to tipping points of species loss,” says Palen.

The SFU Earth to Ocean Research Group member has been collaborating with Adams since 1999 to evaluate threats to amphibians in mountainous regions.

“We hope newly developed wetland modeling tools can improve climate adaptation action plans so that intact ecosystems persist in the face of a changing climate,” says Palen.

Hydrologists and remote sensors helped the researchers develop models that project a substantial loss of wetlands in America’s western mountains over the next 40 to 80 years.

They note the combined threat of climate change and fish to amphibian survival also exists in B.C. but records of where fish have been introduced are scarce.

The researchers remind us that 95 per cent of the American West’s lakes are currently stocked with non-native fish, so removing them from a few sites doesn’t threaten recreational fishing opportunities.

Let’s save some frogs

Sing a song of science literacy

Let’s applaud the American Educational Research Association for its plan to livestream part of its 2014 conference being held April 3 – 6, 2014 for free (you do have to register; pause for applause). Unfortunately, the one session I’d really like to hear is not one of the chosen ones. It’s the “Sing about Science: Leveraging the Power of Music to Improve Science Education” session being delivered by two researchers from the University of Washington (UW; state). From the April 2, 2014 UW news release (also on EurekAlert),

As the United States puts ever-greater emphasis on science, technology, engineering and mathematics education to keep competitive in the global economy, schools are trying to figure out how to improve student learning in science.

University of Washington researchers Katie Davis and Greg Crowther think music may be the answer for some kids. They studied the ability of music videos to enhance students’ understanding of scientific concepts.

Davis will present “Sing about Science: Leveraging the Power of Music to Improve Science Education” on Friday (April 4) at the American Educational Research Association’s annual conference.

Davis and Crowther aren’t just talking about music as a mnemonic device to help students memorize facts. Previous research has shown that music can reduce stress and increase student engagement in the learning process, so the researchers theorized that music videos could help some students process and retain information better.

“It makes sense that we shouldn’t teach all kids in the same way; we should individualize,” said Davis, an assistant professor in the UW’s Information School. “We need to provide multiple entry points in all subject matters. Music is a different entry point into scientific concepts.”

Crowther is a biologist but is so interested in music that 10 years ago he created a website with a database of songs about science and math; SingAboutScience.org now has links to more than 7,000 of them (the majority do not have video). Teachers can type in a topic and find music relevant to what they are teaching.

For their current research, they set up laptop computers at five science-related outreach events in Washington state. Most targeted students in K-12, but adults also participated. Participants in the study ranged from 3 to 76 years old, with a median age of 12. Each person sat in front of a laptop and selected a science-based music video to watch.

For instance, one video is titled “Fossil Rock Anthem,” and is a parody of the hip-hop song “Party Rock Anthem.” It shows a dancing archaeologist, graphics of fossils and ground striations and continental plates drifting. It’s a catchy tune with fun, colorful graphics.

Participants took a pre-video quiz of four questions related to information in the video, plus a bonus question not covered by the video. They were also asked to rate their confidence in their answers. They were randomly assigned to watch either a visually-rich music video or a music video that showed only the lyrics on screen. Then they took a post-video quiz that included the same content and confidence questions.

In two-thirds of the music videos (10 out of 15), participants had more correct answers after watching the videos. Quiz scores rose by an average of one more correct answer after watching the videos. The lyrics-only music videos were as beneficial to improving quiz scores as the visually-rich videos.

Participants improved their scores not only on factoid-type questions, but also the more complex comprehension questions, which shows that the videos improved people’s scientific understanding and not just memorization.

Pre- and post-quiz scores were no different for the bonus questions, which did not cover material from the videos. This finding suggests that the boost in quiz scores was due to watching the video, and not by some other variable.

The researchers say everyone learns in different ways, and past research has shown that students learn best with hands-on, personally relevant tools that utilize powers of observation and audio-visuals. They also note that a person’s memories can change based on an emotionally charged atmosphere. Since music is an emotional medium, it makes sense that our educational memory could be enhanced by it.

“We’re not saying this is the only way you should teach science, it’s just a different way,” Davis said. “We’re hoping it can engage a broader array of students, to help them find success and create identities as science learners.”

Added Crowther, “There wasn’t a teacher breathing down students’ necks telling them they had to learn this for a test. People voluntarily watched these videos for fun. This is exactly the type of opportunity we should be creating more of. Students will seek it out just because it’s fun and interesting.”

I went to Crowther’s website, Sing About Science (be careful, you may spend more time on the website than you planned), and picked this video from the listing,

It makes me think of protest songs from the 1960s. Here’s more about the video from its YouTube home,

Uploaded on Feb 25, 2011

NIMBioS Songwriter-in-Residence RB Morris performs his song “Science for the People.” For more information about the Songwriter-in-Residence program at the National Institute for Mathematical and Biological Synthesis (NIMBioS), visit http://www.nimbios.org/songwriter

I most recently mentioned NIMBioS in a November 1, 2013 interview with Canadian rapper and science afficionado, Baba Brinkman who has also been one of their artists-in-residence.

Transition metal dichalcogenides (molybdenum disulfide and tungsten diselenide) rock the graphene boat

Anyone who’s read stories about scientific discovery knows that the early stages are characterized by a number of possibilities so the current race to unseat graphene as the wonder material of the nanoworld is a ‘business as usual’ sign although I imagine it can be confusing for investors and others hoping to make their fortunes. As for the contenders to the ‘wonder nanomaterial throne’, they are transition metal dichalcogenides: molybdenum disulfide and tungsten diselenide both of which have garnered some recent attention.

A March 12, 2014 news item on Nanwerk features research on molybdenum disulfide from Poland,

Will one-atom-thick layers of molybdenum disulfide, a compound that occurs naturally in rocks, prove to be better than graphene for electronic applications? There are many signs that might prove to be the case. But physicists from the Faculty of Physics at the University of Warsaw have shown that the nature of the phenomena occurring in layered materials are still ill-understood and require further research.

….

Researchers at the University of Warsaw, Faculty of Physics (FUW) have shown that the phenomena occurring in the crystal network of molybdenum disulfide sheets are of a slightly different nature than previously thought. A report describing the discovery, achieved in collaboration with Laboratoire National des Champs Magnétiques Intenses in Grenoble, has recently been published in Applied Physics Letters.

“It will not become possible to construct complex electronic systems consisting of individual atomic sheets until we have a sufficiently good understanding of the physics involved in the phenomena occurring within the crystal network of those materials. Our research shows, however, that research still has a long way to go in this field”, says Prof. Adam Babinski at the UW Faculty of Physics.

A March 12, 2014 Dept. of Physics University of Warsaw (FUW) news release, which originated the news item, describes the researchers’ ideas about graphene and alternative materials such as molybdenum disulfide,

“It will not become possible to construct complex electronic systems consisting of individual atomic sheets until we have a sufficiently good understanding of the physics involved in the phenomena occurring within the crystal network of those materials. Our research shows, however, that research still has a long way to go in this field”, says Prof. Adam Babiński at the UW Faculty of Physics.

The simplest method of creating graphene is called exfoliation: a piece of scotch tape is first stuck to a piece of graphite, then peeled off. Among the particles that remain stuck to the tape, one can find microscopic layers of graphene. This is because graphite consists of many graphene sheets adjacent to one another. The carbon atoms within each layer are very strongly bound to one another (by covalent bonds, to which graphene owes its legendary resilience), but the individual layers are held together by significantly weaker bonds (van de Walls [van der Waals] bonds). Ordinary scotch tape is strong enough to break the latter and to tear individual graphene sheets away from the graphite crystal.

A few years ago it was noticed that just as graphene can be obtained from graphite, sheets a single atom thick can similarly be obtained from many other crystals. This has been successfully done, for instance, with transition metals chalcogenides (sulfides, selenides, and tellurides). Layers of molybdenum disulfide (MoS2), in particular, have proven to be a very interesting material. This compound exists in nature as molybdenite, a crystal material found in rocks around the world, frequently taking the characteristic form of silver-colored hexagonal plates. For years molybdenite has been used in the manufacturing of lubricants and metal alloys. Like in the case of graphite, the properties of single-atom sheets of MoS2 long went unnoticed.

From the standpoint of applications in electronics, molybdenum disulfide sheets exhibit a significant advantage over graphene: they have an energy gap, an energy range within which no electron states can exist. By applying electric field, the material can be switched between a state that conducts electricity and one that behaves like an insulator. By current calculations, a switched-off molybdenum disulfide transistor would consume even as little as several hundred thousand times less energy than a silicon transistor. Graphene, on the other hand, has no energy gap and transistors made of graphene cannot be fully switched off.

The news release goes on to describe how the researchers refined their understanding of molybdenum disulfide and its properties,

Valuable information about a crystal’s structure and phenomena occurring within it can be obtained by analyzing how light gets scattered within the material. Photons of a given energy are usually absorbed by the atoms and molecules of the material, then reemitted at the same energy. In the spectrum of the scattered light one can then see a distinctive peak, corresponding to that energy. It turns out, however, that one out of many millions of photons is able to use some of its energy otherwise, for instance to alter the vibration or circulation of a molecule. The reverse situation also sometimes occurs: a photon may take away some of the energy of a molecule, and so its own energy slightly increases. In this situation, known as Raman scattering, two smaller peaks are observed to either side of the main peak.

The scientists at the UW Faculty of Physics analyzed the Raman spectra of molybdenum disulfide carrying on low-temperature microscopic measurements. The higher sensitivity of the equipment and detailed analysis methods enabled the team to propose a more precise model of the phenomena occurring in the crystal network of molybdenum disulfide.

“In the case of single-layer materials, the shape of the Raman lines has previously been explained in terms of phenomena involving certain characteristic vibrations of the crystal network. We have shown for molybdenum disulfide sheets that the effects ascribed to those vibrations must actually, at least in part, be due to other network vibrations not previously taken into account”, explains Katarzyna Gołasa, a doctorate student at the UW Faculty of Physics.

The presence of the new type of vibration in single-sheet materials has an impact on how electrons behave. As a consequence, these materials must have somewhat different electronic properties than previously anticipated.

Here’s what the rocks look like,

Molybdenum disulfide occurs in nature as molybdenite, crystalline material that frequently takes the characteristic form of silver-colored hexagonal plates. (Source: FUW)

Molybdenum disulfide occurs in nature as molybdenite, crystalline material that frequently takes the characteristic form of silver-colored hexagonal plates. (Source: FUW)

I am not able to find the published research at this time (March 13, 2014).

The tungsten diselenide story is specifically application-centric. Dexter Johnson in a March 11, 2014 post on his Nanoclast blog (on the IEEE [Institute of Electrical and Electronics Engineers] website) describes the differing perspectives and potential applications suggested by the three teams that cooperated to produce papers united by a joint theme ,

The three research groups focused on optoelectronics applications of tungsten diselenide, but each with a slightly different emphasis.

The University of Washington scientists highlighted applications of the material for a light emitting diode (LED). The Vienna University of Technology group focused on the material’s photovoltaic applications. And, finally, the MIT [Massachusetts Institute of Technology] group looked at all of the optoelectronic applications for the material that would result from the way it can be switched from being a p-type to a n-type semiconductor.

Here are some details of the research from each of the institutions’ news releases.

A March 10, 2014 University of Washington (state) news release highlights their LED work,

University of Washington [UW] scientists have built the thinnest-known LED that can be used as a source of light energy in electronics. The LED is based off of two-dimensional, flexible semiconductors, making it possible to stack or use in much smaller and more diverse applications than current technology allows.

“We are able to make the thinnest-possible LEDs, only three atoms thick yet mechanically strong. Such thin and foldable LEDs are critical for future portable and integrated electronic devices,” said Xiaodong Xu, a UW assistant professor in materials science and engineering and in physics.

The UW’s LED is made from flat sheets of the molecular semiconductor known as tungsten diselenide, a member of a group of two-dimensional materials that have been recently identified as the thinnest-known semiconductors. Researchers use regular adhesive tape to extract a single sheet of this material from thick, layered pieces in a method inspired by the 2010 Nobel Prize in Physics awarded to the University of Manchester for isolating one-atom-thick flakes of carbon, called graphene, from a piece of graphite.

In addition to light-emitting applications, this technology could open doors for using light as interconnects to run nano-scale computer chips instead of standard devices that operate off the movement of electrons, or electricity. The latter process creates a lot of heat and wastes power, whereas sending light through a chip to achieve the same purpose would be highly efficient.

“A promising solution is to replace the electrical interconnect with optical ones, which will maintain the high bandwidth but consume less energy,” Xu said. “Our work makes it possible to make highly integrated and energy-efficient devices in areas such as lighting, optical communication and nano lasers.”

Here’s a link to and a citation for this team’s paper,

Electrically tunable excitonic light-emitting diodes based on monolayer WSe2 p–n junctions by Jason S. Ross, Philip Klement, Aaron M. Jones, Nirmal J. Ghimire, Jiaqiang Yan, D. G. Mandrus, Takashi Taniguchi, Kenji Watanabe, Kenji Kitamura, Wang Yao, David H. Cobden, & Xiaodong Xu. Nature Nanotechnology (2014) doi:10.1038/nnano.2014.26 Published online 09 March 2014

This paper is behind a paywall.

A March 9, 2014 University of Vienna news release highlights their work on tungsten diselinide and its possible application in solar cells,

… With graphene as a light detector, optical signals can be transformed into electric pulses on extremely short timescales.

For one very similar application, however, graphene is not well suited for building solar cells. “The electronic states in graphene are not very practical for creating photovoltaics”, says Thomas Mueller. Therefore, he and his team started to look for other materials, which, similarly to graphene, can arranged in ultrathin layers, but have even better electronic properties.

The material of choice was tungsten diselenide: It consists of one layer of tungsten atoms, which are connected by selenium atoms above and below the tungsten plane. The material absorbs light, much like graphene, but in tungsten diselenide, this light can be used to create electrical power.

The layer is so thin that 95% of the light just passes through – but a tenth of the remaining five percent, which are absorbed by the material, are converted into electrical power. Therefore, the internal efficiency is quite high. A larger portion of the incident light can be used if several of the ultrathin layers are stacked on top of each other – but sometimes the high transparency can be a useful side effect. “We are envisioning solar cell layers on glass facades, which let part of the light into the building while at the same time creating electricity”, says Thomas Mueller.

Today, standard solar cells are mostly made of silicon, they are rather bulky and inflexible. Organic materials are also used for opto-electronic applications, but they age rather quickly. “A big advantage of two-dimensional structures of single atomic layers is their crystallinity. Crystal structures lend stability”, says Thomas Mueller.

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

Solar-energy conversion and light emission in an atomic monolayer p–n diode by Andreas Pospischil, Marco M. Furchi, & Thomas Mueller. Nature Nanotechnology (2014) doi:10.1038/nnano.2014.14 Published online 09 March 2014

This paper is behind a paywll.

Finally, a March 10, 2014 MIT news release details their work about material able to switch from p-type (p = positive) to a n-type (n = negative) semiconductors,

The material they used, called tungsten diselenide (WSe2), is part of a class of single-molecule-thick materials under investigation for possible use in new optoelectronic devices — ones that can manipulate the interactions of light and electricity. In these experiments, the MIT researchers were able to use the material to produce diodes, the basic building block of modern electronics.

Typically, diodes (which allow electrons to flow in only one direction) are made by “doping,” which is a process of injecting other atoms into the crystal structure of a host material. By using different materials for this irreversible process, it is possible to make either of the two basic kinds of semiconducting materials, p-type or n-type.

But with the new material, either p-type or n-type functions can be obtained just by bringing the vanishingly thin film into very close proximity with an adjacent metal electrode, and tuning the voltage in this electrode from positive to negative. That means the material can easily and instantly be switched from one type to the other, which is rarely the case with conventional semiconductors.

In their experiments, the MIT team produced a device with a sheet of WSe2 material that was electrically doped half n-type and half p-type, creating a working diode that has properties “very close to the ideal,” Jarillo-Herrero says.

By making diodes, it is possible to produce all three basic optoelectronic devices — photodetectors, photovoltaic cells, and LEDs; the MIT team has demonstrated all three, Jarillo-Herrero says. While these are proof-of-concept devices, and not designed for scaling up, the successful demonstration could point the way toward a wide range of potential uses, he says.

“It’s known how to make very large-area materials” of this type, Churchill says. While further work will be required, he says, “there’s no reason you wouldn’t be able to do it on an industrial scale.”

In principle, Jarillo-Herrero says, because this material can be engineered to produce different values of a key property called bandgap, it should be possible to make LEDs that produce any color — something that is difficult to do with conventional materials. And because the material is so thin, transparent, and lightweight, devices such as solar cells or displays could potentially be built into building or vehicle windows, or even incorporated into clothing, he says.

While selenium is not as abundant as silicon or other promising materials for electronics, the thinness of these sheets is a big advantage, Churchill points out: “It’s thousands or tens of thousands of times thinner” than conventional diode materials, “so you’d use thousands of times less material” to make devices of a given size.

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

Optoelectronic devices based on electrically tunable p–n diodes in a monolayer dichalcogenide by Britton W. H. Baugher, Hugh O. H. Churchill, Yafang Yang, & Pablo Jarillo-Herrero. Nature Nanotechnology (2014) doi:10.1038/nnano.2014.25 Published online 09 March 2014

This paper is behind a paywall.

These are very exciting, if not to say, electrifying times. (Couldn’t resist the wordplay.)