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Science snapshots from Berkeley Lab

Posted By Graphene Council, The Graphene Council, Monday, December 2, 2019
A Matchmaker for Microbiomes

Microbiomes play essential roles in the natural processes that keep the planet and our bodies healthy, so it's not surprising that scientists' investigations into these diverse microbial communities are leading to advances in medicine, sustainable agriculture, cheap water purification methods, and environmental cleanup technology, just to name a few. However, trying to determine which microbes contribute to an important geochemical or physiological reaction is both incredibly challenging and slow-going, because the task involves analyzing enormous datasets of genetic and metabolic information to match the compounds mediating a process to the microbes that produced them.

But now, researchers have devised a new way to sort through the information overload.

Writing in Nature Methods, a team led by UC San Diego describes a neural network-based approach called microbe-metabolite vectors (mmvec), which uses probabilities to identify the most likely relationship of co-occurring microbes and metabolites. The team demonstrates how mmvec can outperform traditional correlation-based approaches by applying mmvec to datasets from two well-studied microbiomes types - those found in desert soils and cystic fibrosis patients' lungs - and gives a taste of how the approach could be used in the future by revealing relationships between microbially-produced metabolites and inflammatory bowel disease.

"Previous statistical tools used to estimate microbe-metabolite correlations performed comparably to random chance," said Marc Van Goethem, a postdoctoral researcher who is one of three study authors from Berkeley Lab. "Their poor performance led to the detection of spurious relationships and missed many true relationships. Mmvec is a powerful new tool that accurately links metabolite and microbial abundances to solve this problem. There could be wide-ranging applications from clinical trials to environmental engineering. Ultimately, mmvec will allow us to begin moving away from simple pattern recognition towards unravelling mechanisms."

When Solids and Liquids Meet: In Nanoscale Detail

How a liquid interacts with the surface of a solid is important in batteries and fuel cells, chemical production, corrosion phenomena, and many biological processes.

To better understand this solid-liquid interface, researchers at Berkeley Lab developed a platform to explore these interactions under real conditions ("in situ") at the nanoscale using a technique that combines infrared light with an atomic force microscopy (AFM) probe. The results were published in the journal Nano Letters.

The team explored the interaction of graphene with several liquids, including water and a common battery electrolyte fluid. Graphene is an atomically thin form of carbon. Its single-layer atomic structure gives the material some unique properties, including incredible mechanical strength and high electrical conductivity.

Researchers used a beam of infrared light produced at Berkeley Lab's Advanced Light Source and they focused it at the tip of an AFM probe that scanned across a section of graphene in contact with the liquids. The infrared technique provides a nondestructive way to explore the active nanoscale chemistry of the solid-liquid interface.

By measuring the infrared light scattered from the probe's tip, researchers collected details about the chemical compounds and the concentration of charged particles along the solid-liquid interface. The same technique, which revealed hidden features at this interface that were not seen using conventional methods, can be used to explore a range of materials and liquids.

Researchers from the Lab's Materials Sciences Division, Molecular Foundry, and Energy Storage and Distributed Resources Division participated in the study. The Molecular Foundry and Advanced Light Source are DOE Office of Science user facilities.

Underwater telecom cables make superb seismic network

Fiber-optic cables that constitute a global undersea telecommunications network could one day help scientists study offshore earthquakes and the geologic structures hidden deep beneath the ocean surface.

In a recent paper in the journal Science, researchers UC Berkeley, Lawrence Berkeley National Laboratory (Berkeley Lab), Monterey Bay Aquarium Research Institute (MBARI), and Rice University describe an experiment that turned 20 kilometers of undersea fiber-optic cable into the equivalent of 10,000 seismic stations along the ocean floor. During their four-day experiment in Monterey Bay, they recorded a 3.5 magnitude quake and seismic scattering from underwater fault zones.

Their technique, which they had previously tested with fiber-optic cables on land, could provide much-needed data on quakes that occur under the sea, where few seismic stations exist, leaving 70% of Earth's surface without earthquake detectors.

"This is really a study on the frontier of seismology, the first time anyone has used offshore fiber-optic cables for looking at these types of oceanographic signals or for imaging fault structures," said Jonathan Ajo-Franklin, a geophysics professor at Rice University in Houston and a faculty scientist at Berkeley Lab. "One of the blank spots in the seismographic network worldwide is in the oceans."

Tags:  atomic force microscopy  Berkeley Lab  disease  fuel cells  Graphene  Healthcare  Jonathan Ajo-Franklin  journal Science  Marc Van Goethem  microbiomes  Molecular Foundry  Monterey Bay Aquarium Research Institute  Nano Letters  nanoscale  Rice University  UC San Diego 

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Step right up for bigger 2D sheets

Posted By Graphene Council, The Graphene Council, Thursday, March 7, 2019
Rice University researchers determined complementarity between growing hexagonal boron nitride crystals and a stepped substrate mimics the complementarity found in strands of DNA. The Rice theory supports experiments that have produced large, oriented wafers.

Very small steps make a big difference to researchers who want to create large wafers of two-dimensional material. Atom-sized steps in a substrate provide the means for 2D crystals growing in a chemical vapor furnace to come together in perfect rank. Scientists have recently observed this phenomenon, and now a Rice University group has an idea why it works.

Rice materials theorist Boris Yakobson and researcher Ksenia Bets led the construction of simulations that show atom-sized steps on a growth surface, or substrate, have the remarkable ability to keep monolayer crystal islands in alignment as they grow. If the conditions are right, the islands join into a larger crystal without the grain boundaries so characteristic of 2D materials like graphene grown via chemical vapor deposition (CVD). That preserves their electronic perfection and characteristics, which differ depending on the material.

Atom-sized steps in a substrate provide the means for 2D crystals growing in a chemical vapor furnace to come together in perfect rank. Scientists have recently observed this phenomenon, and now a Rice University group has an idea why it works.

Rice materials theorist Boris Yakobson and researcher Ksenia Bets led the construction of simulations that show atom-sized steps on a growth surface, or substrate, have the remarkable ability to keep monolayer crystal islands in alignment as they grow.

If the conditions are right, the islands join into a larger crystal without the grain boundaries so characteristic of 2D materials like graphene grown via chemical vapor deposition (CVD). That preserves their electronic perfection and characteristics, which differ depending on the material.

The Rice theory appears in the American Chemical Society journal Nano Letters.The investigation focused on hexagonal boron nitride (h-BN), aka white graphene, a crystal often grown via CVD. Crystals nucleate at various places on a perfectly flat substrate material and not necessarily in alignment with each other.

However, recent experiments have demonstrated that growth on vicinal substrates -- surfaces that appear flat but actually have sparse, atomically small steps -- can align the crystals and help them merge into a single, uniform structure, as reported on arXiv. A co-author of that report and leader of the Korean team, Feng Ding, is an alumnus of the Yakobson lab and a current adjunct professor at Rice.

But the experimentalists do not show how it works as, Yakobson said, the steps are known to meander and be somewhat misaligned.

"I like to compare the mechanism to a 'digital filter,' here offered by the discrete nature of atomic lattices," he said. "The analog curve that, with its slopes, describes a meandering step is 'sampled and digitized' by the very grid of constituent atomic rows, breaking the curve into straight 1D-terrace segments. The slope doesn't help, but it doesn't hurt. Surprisingly, the match can be good; like a well-designed house on a hill, it stands straight.

"The theory is simple, though it took a lot of hard work to calculate and confirm the complementarity matching between the metal template and the h-BN, almost like for A-G-T-C pairs in strands of DNA," Yakobson said.

It was unclear why the crystals merged into one so well until simulations by Bets, with the help of co-author and Rice graduate student Nitant Gupta, showed how h-BN "islands" remain aligned while nucleating along visibly curved steps.

"A vicinal surface has steps that are slightly misaligned within the flat area," Bets said. "It has large terraces, but on occasion there will be one-atom-high steps. The trick by the experimentalists was to align these vicinal steps in one direction."

In chemical vapor deposition, a hot gas of the atoms that will form the material are flowed into the chamber, where they settle on the substrate and nucleate crystals. h-BN atoms on a vicinal surface prefer to settle in the crook of the steps.

"They have this nice corner where the atoms will have more neighbors, which makes them happier," Bets said. "They try to align to the steps and grow from there.

"But from a physics point of view, it's impossible to have a perfect, atomically flat step," she said. "Sooner or later, there will be small indentations, or kinks. We found that at the atomic scale, these kinks in the steps don't prevent h-BN from aligning if their dimensions are complementary to the h-BN structure. In fact, they help to ensure co-orientation of the islands."

Because the steps the Rice lab modeled are 1.27 angstroms deep (an angstrom is one-billionth of a meter), the growing crystals have little trouble surmounting the boundary. "Those steps are smaller than the bond distance between the atoms," Bets said. "If they were larger, like two angstroms or higher, it would be more of a natural barrier, so the parameters have to be adjusted carefully."

Two growing islands that approach each other zip together seamlessly, according to the simulations. Similarly, cracks that appear along steps easily heal because the bonds between the atoms are strong enough to overcome the small distance.

Any path toward large-scale growth of 2D materials is worth pursuing for an army of applications, according to the researchers. 2D materials like conductive graphene, insulating h-BN and semiconducting transition metal dichalcogenides are all the focus of intense scrutiny by researchers around the world. The Rice researchers hope their theoretical models will point the way toward large crystals of many kinds.

The U.S. Department of Energy (DOE) supported the research. Computer resources were provided by the National Energy Research Scientific Computing Center, supported by the DOE Office of Science, and the National Science Foundation-supported DAVinCI cluster at Rice, administered by the Center for Research Computing and procured in partnership with Rice's Ken Kennedy Institute for Information Technology.

Tags:  Boris Yakobson  CVD  Graphene  Ksenia Bets  Rice University  U.S. Department of Energy (DOE) 

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Laser-induced graphene gets tough

Posted By Graphene Council, The Graphene Council, Monday, February 18, 2019
Updated: Monday, February 18, 2019
Laser-induced graphene (LIG), a flaky foam of the atom-thick carbon, has many interesting properties on its own but gains new powers as part of a composite.

The labs of Rice University chemist James Tour and Christopher Arnusch, a professor at Ben-Gurion University of the Negev in Israel, introduced a batch of LIG composites in the American Chemical Society journal ACS Nano that put the material’s capabilities into more robust packages.

By infusing LIG with plastic, rubber, cement, wax or other materials, the lab made composites with a wide range of possible applications. These new composites could be used in wearable electronics, in heat therapy, in water treatment, in anti-icing and deicing work, in creating antimicrobial surfaces and even in making resistive random-access memory devices.

The Tour lab first made LIG in 2014 when it used a commercial laser to burn the surface of a thin sheet of common plastic, polyimide. The laser’s heat turned a sliver of the material into flakes of interconnected graphene. The one-step process made much more of the material, and at far less expense, than through traditional chemical vapor deposition.

Since then, the Rice lab and others have expanded their investigation of LIG. Last year, the Rice researchers created graphene foam for sculpting 3D objects.

“LIG is a great material, but it’s not mechanically robust,” said Tour, who co-authored an overview of laser-induced graphene developments in the Accounts of Chemical Research journal last year. “You can bend it and flex it, but you can’t rub your hand across it. It’ll shear off. If you do what’s called a Scotch tape test on it, lots of it gets removed. But when you put it into a composite structure, it really toughens up.”

To make the composites, the researchers poured or hot-pressed a thin layer of the second material over LIG attached to polyimide. When the liquid hardened, they pulled the polyimide away from the back for reuse, leaving the embedded, connected graphene flakes behind.

Soft composites can be used for active electronics in flexible clothing, Tour said, while harder composites make excellent superhydrophobic (water-avoiding) materials. When a voltage is applied, the 20-micron-thick layer of LIG kills bacteria on the surface, making toughened versions of the material suitable for antibacterial applications.

Composites made with liquid additives are best at preserving LIG flakes’ connectivity. In the lab, they heated quickly and reliably when voltage was applied. That should give the material potential use as a deicing or anti-icing coating, as a flexible heating pad for treating injuries or in garments that heat up on demand.

“You just pour it in, and now you transfer all the beautiful aspects of LIG into a material that’s highly robust,” Tour said.

Rice graduate students Duy Xuan Luong and Kaichun Yang and former postdoctoral researcher Jongwon Yoon, now a senior researcher at the Korea Basic Science Institute, are co-lead authors of the paper. Co-authors are former Rice postdoctoral researcher Swatantra Singh, now at the Indian Institute of Technology Bombay, and Rice graduate student Tuo Wang. Tour is the T.T. and W.F. Chao Chair in Chemistry as well as a professor of computer science and of materials science and nanoengineering at Rice.

The Air Force Office of Scientific Research and the United States-Israel Binational Science Foundation supported the research.

Tags:  Christopher Arnusch  Graphene  James Tour  Lasers  Rice University 

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Graphene used as toxic free MRI biomarker

Posted By Terrance Barkan, Saturday, November 12, 2016

This image from a high-resolution transmission electron microscope shows one of Rice University’s graphene-based MRI contrast agents, nanoparticles measuring about 10-nanometers in diameter that are so thin that they are difficult to distinguish. Credit: C.S. Tiwari/Rice University

Graphene, the atomically thin sheets of carbon that materials scientists are hoping to use for everything from nanoelectronics and aircraft de-icers to batteries and bone implants, may also find use as contrast agents for magnetic resonance imaging (MRI), according to new research from Rice University.

"They have a lot of advantages compared with conventionally available contrast agents," Rice researcher Sruthi Radhakrishnan said of the graphene-based quantum dots she has studied for the past two years. "Virtually all of the widely used contrast agents contain toxic metals, but our material has no metal. It's just carbon, hydrogen, oxygen and fluorine, and in all of our tests so far it has shown no signs of toxicity."

The initial findings for Rice's nanoparticles—disks of graphene that are decorated with fluorine atoms and simply organic molecules that make them magnetic—are described in a new paper in the journal Particle and Particle Systems Characterization.

Pulickel Ajayan, the Rice materials scientist who is directing the work, said the fluorinated graphene oxide quantum dots could be particularly useful as MRI contrast agents because they could be targeted to specific kinds of tissues.

"There are tried-and-true methods for attaching biomarkers to carbon nanoparticles, so one could easily envision using these quantum dots to develop tissue-specific contrast agents," Ajayan said. "For example, this method could be used to selectively target specific types of cancer or brain lesions caused by Alzheimer's disease. That kind of specificity isn't available with today's contrast agents."

Rice University graduate student Sruthi Radhakrishnan spent two years developing a process to make graphene-based quantum dots that could be used as MRI contrast agents. Credit: Jeff Fitlow/Rice University

MRI scanners make images of the body's internal structures using strong magnetic fields and radio waves. As diagnostic tests, MRIs often provide greater detail than X-rays without the harmful radiation, and as a result, MRI usage has risen sharply over the past decade. More than 30 million MRIs are performed annually in the U.S.

Radhakrishnan said her work began in 2014 after Ajayan's research team found that adding fluorine to either graphite or graphene caused the materials to show up well on MRI scans.
All materials are influenced by magnetic fields, including animal tissues. In MRI scanners, a powerful magnetic field causes individual atoms throughout the body to become magnetically aligned. A pulse of radio energy is used to disrupt this alignment, and the machine measures how long it takes for the atoms in different parts of the body to become realigned. Based on these measures, the scanner can build up a detailed image of the body's internal structures.

MRI contrast agents shorten the amount of time it takes for tissues to realign and significantly improve the resolution of MRI scans. Almost all commercially available contrast agents are made from toxic metals like gadolinium, iron or manganese.

"We worked with a team from MD Anderson Cancer Center to assess the cytocompatibility of fluorinated graphene oxide quantum dots," Radhakrishnan said. "We used a test that measures the metabolic activity of cell cultures and detects toxicity as a drop in metabolic activity. We incubated quantum dots in kidney cell cultures for up to three days and found no significant cell death in the cultures, even at the highest concentrations."

Unlike most currently used MRI contrast agents, Rice University’s fluorinated graphene oxide quantum dots contain no toxic metals and could potentially be targeted to specific kinds of tissues. Credit: Jeff Fitlow/Rice University

The fluorinated graphene oxide quantum dots Radhakrishnan studies can be made in less than a day, but she spent two years perfecting the recipe for them. She begins with micron-sized sheets of graphene that have been fluorinated and oxidized. When these are added to a solvent and stirred for several hours, they break into smaller pieces. Making the material smaller is not difficult, but the process for making small particles with the appropriate magnetic properties is exacting.

Radhakrishnan said there was no "eureka moment" in which she suddenly achieved the right results by stumbling on the best formula. Rather, the project was marked by incremental improvements through dozens of minor alterations.

"It required a lot of optimization," she said. "The recipe matters a lot."

Radhakrishnan said she plans to continue studying the material and hopes to eventually have a hand in proving that it is safe and effective for clinical MRI tests.
"I would like to see it applied commercially in clinical ways because it has a lot of advantages compared with conventionally available agents," she said.



Tags:  contrast agents  GNP  magnetic resonance imaging  MD Anderson Cancer Center  MRI  Pulickel Ajayan  Rice University  Sruthi Radhakrishnan 

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