From SLAC: “High-Speed Movie Aids Scientists Who Design Glowing Molecules”

SLAC Lab

September 20, 2017
Amanda Solliday

Aequorea victoria, also called the crystal jelly, is a bioluminescent jellyfish that lives near the Pacific coast of North America. (Gary Kavanagh/iStockphoto.com)

The Coherent X-Ray Imaging (CXI) instrument makes use of the brilliant hard X-ray pulses from the Linac Coherent Light Source. The equipment is tailored for X-ray crystallography experiments. (SLAC National Accelerator Laboratory)

SLAC/LCLS

With SLAC’s X-ray laser, a research team captured ultrafast changes in fluorescent proteins between “dark” and “light” states. The insights allowed the scientists to design improved markers for biological imaging.

The crystal jellyfish swims off the coast of the Pacific Northwest and can illuminate the waters when disturbed. That glow comes from proteins that absorb energy and then release it as bright flashes.

To track many of life’s activities, biologists took a cue from this same jellyfish.

Scientists collected one of the proteins found in the sea creatures, green fluorescent protein (GFP), and engineered a molecular light switch that would glow or remain dark depending on specific experimental conditions. The glowing labels are attached to molecules in living cells so researchers can highlight them during imaging experiments. They use these fluorescent markers to understand how a cell responds to changes in its environment, identify which molecules interact within a cell and track the effects of genetic mutations.

Researchers have studied GFP and other fluorescent proteins for decades to better understand their glowing action and improve their function in scientific studies, but they have never been able to observe the ultrafast changes that occur between “off” and “on” states until now.

In a recent experiment conducted at the Department of Energy’s SLAC National Accelerator Laboratory, a research team used bright, ultrafast X-ray pulses from SLAC’s X-ray free-electron laser to create a high-speed movie of a fluorescent protein in action. With that information, the scientists began to design a marker that switches more easily, a quality that can improve resolution during biological imaging.

“We think that this approach will open a world of possibilities to tailor fluorescent proteins,” says Martin Weik, scientist at the Institute of Structural Biology in Grenoble, France and one of the authors on the publication. “We not only have the structure of the fluorescent protein, but now we can see what is happening between one static state and the other.”

Nature Chemistry published the study on Sept. 11.

Filming a Molecular Light Switch

To observe these intermediate states, the scientists initiated a photochemical reaction in the fluorescent protein with an optical laser at the Coherent X-ray Imaging instrument at the Linac Coherent Light Source, followed by X-ray snapshots at distinct time delays. The optical laser provides energy in the form of photons, mimicking what happens in nature.

“Atoms move around in the photoactive site of the molecule as a result of absorption of a photon,” says Sebastien Boutet, SLAC scientist and a co-author of the paper. “This structural change turns the protein from a dark state to a light-emitting (fluorescent) state.”

There’s a vast body of literature calculating what might happen between the two states, but no one studying the protein was able to see the structural changes in the switch as the photon is absorbed. The molecular switch was just too fast for traditional X-ray imaging techniques.

In this study, the femtosecond X-ray pulses generated by LCLS—arriving in just millionths of a billionth of a second—allowed the team to create stop-action images of the process at an extremely close interval after the proteins were activated by the optical laser.

A Door Half Open

The high-speed snapshots were used to generate a movie starting from the dark state, and gave the researchers insights that they used to design more efficient switchable light-emitting proteins. They found a clue in the time the molecules spent between fluorescent and non-fluorescent states.

“After a picosecond, and for a very short time, this molecular switch is stuck between on and off,” says Ilme Schlichting, scientist at the Max-Planck Institute in Heidelberg, Germany and one of the authors on the publication. “People have predicted this, but to actually visualize its structure is extremely exciting.”

“It’s as if there’s a door and it’s neither closed nor completely open; it’s half open,” she says. “And now we are learning what can go through the door, what might be blocking it and how it works in real time.”

In this study, the scientists found that an amino acid blocked the door and prevented the switch from flipping as easily as possible.

The researchers shortened the amino acid in a mutated version of the fluorescent protein. This engineered version switched more easily and gave better contrast. These traits will allow scientists to observe cellular activity with greater precision.

“Contrast is essential in imaging. It’s like on a TV screen, where to see the best picture, you want the dark to be extremely dark and the color to be super bright and colorful,” says Jacques-Philippe Colletier, a scientist at the Institute of Structural Biology who contributed to the research.

This new molecular movie featuring the jellyfish-inspired proteins lights the way to capture more of life’s microscopic details. The team will continue to fine-tune the protein for other desired characteristics that make it ideal for “super-resolution microscopy,” a type of light microscopy where scientists are able to see illuminated details of cells not distinguishable with conventional light microscopy methods.

The research collaboration included several French institutions, including the Institute of Structural Biology, University of Lille, University of Paris-Sud and the University of Rennes, as well as Max Planck Institutes in Germany and SLAC.

LCLS is a DOE Office of Science User Facility.

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SLAC is a multi-program laboratory exploring frontier questions in photon science, astrophysics, particle physics and accelerator research. Located in Menlo Park, California, SLAC is operated by Stanford University for the DOE’s Office of Science.

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From XFEL: “First users at European XFEL”

European XFEL

2017/09/20
No writer credit

DESY’s Anton Barty (left) and Henry Chapman (right), seen at the SPB/SFX instrument, were in one of the first two user groups. (Photo: DESY, Lars Berg)

The first users have now started experiments at the new international research facility in Schenefeld.

“This is a very important event, and we are very happy that the first users have now arrived at European XFEL so we can do a full scale test of the facility” said European XFEL Managing Director Prof. Dr. Robert Feidenhans’l. ”The instruments and the supporting teams have made great progress in the recent weeks and months. Together with our first users, we will now do the first real commissioning experiments and collect valuable scientific data. At the same time, we will continue to further advance our facility and concentrate on further improving the integration and stability of the instrumentation” he added.

The first two instruments available for users in the underground experiment hall are the FXE (Femtosecond X-Ray Experiments) instrument, and the SPB/SFX (Single Particles, Clusters, and Biomolecules and Serial Femtosecond Crystallography) instrument.

The FXE instrument will enable the research of extremely fast processes. It will be possible to create “molecular movies” showing the progression of chemical reactions which, for example, will help improve our understanding of how catalysts work, or how plants convert light into usable chemical energy. The first seven experiments conducted at FXE highlight the range of methods available at the instrument and the diversity of topics of study possible. Experiments will include using different spectroscopy methods to track ultrafast reactions and electron movement in model molecules, probe organic light emitting diodes, or investigate the recombination of nitrogen and oxygen in the muscle tissue protein myoglobin.

The first user group at the FXE instrument. No image credit

The SPB/SFX instrument will be used to gain a better understanding of the shape and function of biomolecules, such as proteins, that are otherwise difficult to study. Several of the seven first experiments at this instrument will focus on method development for these new research opportunities at European XFEL or ways to reduce the amount of precious sample used for the examination of biological processes. Other groups will be studying biological structures and processes such as the Melbourne virus and the water splitting process in photosynthesis.

The first user group at the SPB/SFX instrument. No image credit

In this first round of beamtime a total of 14 groups, of up to 80 users each and travelling to Schenefeld from across the globe, will conduct experiments at European XFEL until March 2018. Each group will have about five days of 12 hours of beamtime.

See the full article here .

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The Hamburg area will soon boast a research facility of superlatives: The European XFEL will generate ultrashort X-ray flashes—27 000 times per second and with a brilliance that is a billion times higher than that of the best conventional X-ray radiation sources.

The outstanding characteristics of the facility are unique worldwide. Starting in 2017, it will open up completely new research opportunities for scientists and industrial users.

From EPFL: “Unexpected facets of Antarctica emerge from the labs”

École Polytechnique Fédérale de Lausanne EPFL

14.09.17
Sarah Perrin

the Akademik Treshnikov Russian icebreaker

Six months after the Antarctic Circumnavigation Expedition ended, the teams that ran the 22 scientific projects are hard at work sorting through the many samples they collected. Some preliminary findings were announced during a conference in Crans Montana organized by the Swiss Polar Institute, who just appointed Konrad Steffen as new scientific director (see the interview below).

Nearly 30,000 samples were taken during the Antarctic Circumnavigation Expedition (ACE). And now, barely six months after the voyage ended, the research teams tasked with analyzing the samples have already produced some initial figures and findings. These were presented in Crans Montana during a conference put together earlier this week by the Swiss Polar Institute (SPI), the EPFL-based entity that ran the expedition. The event, called “High altitudes meet high latitudes,” brought together world-renowned experts in polar and alpine research in an exercise aimed at highlighting the many similarities between these two fields of study.

Over the course of three months – from December 2016 to March 2017 – 160 researchers from 23 different countries sailed around the Great White Continent on board a Russian icebreaker. They ran 22 research projects in an effort to learn more about the impact of climate change on these fragile and little-known regions. The valuable samples, taken from the Southern Ocean, the atmosphere and a handful of remote islands, are now back at the labs of the 73 scientific institutions involved in the expedition.

The route of the ACE expedition.

Most of the teams that ran the 22 projects are still carrying out the preliminary task of sorting through and identifying the samples, which means the initial results are necessarily incomplete and provisional. It is only later that the samples will be analyzed. Some important observations can nevertheless be made at this stage.

A solid database

The sum total of the samples collected represents an impressive and valuable database. The SPI must now come up with ways to organize, group and present the data so that researchers can readily access and make use of it. What’s more, “the large number of potential collaborations and exchanges between projects is becoming clear,” says David Walton, the chief scientist on the expedition. “Some research projects have been found to have links with as much as nine others.” And some startling figures have already been released – here is a look at just a few of them.

For the SubIce project, around 100 meters of ice cores were taken on five subantarctic islands and the Mertz Glacier, which sits on the edge of the Antarctic continent. The chemical composition of the cores will be analyzed in an attempt to trace climate change over recent decades. In some places, like Balleny, Peter 1st or Bouvet Islands, it was the first time an ice sample had ever been taken. “Of all the islands where we were able to take samples, that last one was the farthest from the continent,” says Liz Thomas, from British Antarctic Survey. “It’s also the island where the ice in the samples is the most granular. Our findings confirm significant seasonal variations at this location.”

The air on the continent is so pure that even the hottest cup of tea does not produce any steam. “No particles, no clouds,” explains Julia Schmale, a researcher with the Paul-Scherrer-Institute who measured for aerosols – tiny chemical particles like grains of sand, dust, pollen, soot, sulfuric acid, and so on – throughout the expedition. These particles attach to water molecules and aggregate to form clouds. On Mertz Glacier, her measurements revealed aerosol levels below 100 particles per cm3, which is less than the level found in a cleanroom.

Christel Hassler and her team, from the University of Geneva, studied bacteria and virus populations in the Southern Ocean. The team took some 170 samples from all around the continent. For the time being, their work consists in isolating and culturing the numerous cells found in the samples. “We will then analyze their DNA in order to identify them,” says Marion Fourquez, a marine biologist. “That will show us whether we have come across any new bacterial strains that have yet never been observed in this region.”

Bacteria collected on the sedimental floor beneath Mertz glacier, on the Antarctic continent, as part of Christel Hassler’s project (University of Geneva). ©M.Fourquez.

One of the subsequent lines of research will be to determine their geographical distribution. The researchers will be able to tell if there’s a link between the presence of a given bacterium and that of other microorganisms by comparing their data with data from other projects, like Nicolas Cassar’s. Cassar, from Duke University in the United States, measured concentrations of phytoplankton, which sit at the very bottom of the region’s food chain. “This approach worked out well, and we have nearly continuous samples from along the entire route,” says Walton.

More than 3,000 whales

Brian Miller, from the Australian Antarctic Division, was interested in somewhat larger animals. For his project, he used a piece of sophisticated acoustic equipment to listen for and count the number of whales in the Southern Ocean. Walton notes: “In around 500 hours of recordings, the researchers counted for example over 3,000 individual blue whales, although we actually saw only three or so at the surface.” These cetaceans appear to be particularly plentiful in the depths of the Ross Sea.

Peter Ryan, from the University of Cape Town in South Africa, observed and counted bird populations. He discovered that one of the largest colonies of king penguins, on Pig Island in the Crozet archipelago, had declined drastically – he estimates the numerical loss to be around 75%. “That’s around half a million animals,” says Walton. “We don’t know if they’ve died or migrated to other colonies, like the one in St. Andrews Bay, in South Georgia, which is actually in a growth phase.”

More complete and detailed results will be published in the coming months.

Detailed information on SPI and ACE can be found on http://spi-ace-expedition.ch

__________________________________________________________________________

“We urgently need to coordinate our efforts.”

Konrad Steffen, a glaciologist and the new scientific director of the Swiss Polar Institute (SPI), has been involved in polar research for the past 40 years. His work has focused primarily on the Arctic, particularly the changes taking place within Greenland’s ice sheet. He is also a professor at ETH Zurich and director of the Swiss Federal Institute for Forest, Snow and Landscape Research WSL.

Professor Steffen, why is the Swiss Polar Institute so necessary today?

Research in this field tended to be conducted by small groups that organized their own expeditions and ran their own projects. In Switzerland, there had never been any kind of initiative aimed at coordinating all this work. The effects of climate change on polar and alpine regions are now so evident that we urgently need to coordinate our efforts and conduct cross-disciplinary research. This is what we did with the ACE project, where researchers from fields like oceanography, glaciology and biology came together in an attempt to improve our understanding of the climate-change process in a region.

What for you is the top priority when it comes to the polar regions?

At the SPI, one of our aims is to devise a strategic plan within the scientific community. More personally, I think that we urgently need to assess the mass balance of ice sheets across the globe. That’s what will have the greatest and swiftest impact in terms of rising sea levels and changes to our coastlines. Instead of studying individual glaciers in the Alps, we need to look at the bigger picture and observe in detail how the atmosphere interacts with large ice sheets, such as those in Greenland and the Antarctic. We need to connect the dots to see how the system as a whole is affected.

What made the ACE such an innovative expedition?

There have been many scientific expeditions to the Antarctic, but they usually only cover part of the continent. This was the first time that an expedition went all the way around the continent in one three-month period, studying all the oceans during the same season. That provides a fuller picture of the issues, such as microplastics – during the trip, we really saw that they were everywhere! The expedition also served up attractive career opportunities for budding young scientists and enabled several research groups to establish long-term partnerships.

Are any other expeditions in the pipeline?

Yes, the next one is planned for 2019. The aim is to sail around Greenland. We are in the process of looking for a vessel and determining what sort of research will be undertaken during the trip.

__________________________________________________________________________

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EPFL 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.

From UCLA: “In step toward ‘controlling chemistry,’ physicists create a new type of molecule, atom by atom”

UCLA Newsrooom

September 13, 2017
Stuart Wolpert

By working in extremely controlled conditions, Eric Hudson and his colleagues could observe properties of atoms and molecules that have previously been hidden from view. Stuart Wolpert/UCLA

UCLA physicists have pioneered a method for creating a unique new molecule that could eventually have applications in medicine, food science and other fields. Their research, which also shows how chemical reactions can be studied on a microscopic scale using tools of physics, is reported in the journal Science.

For the past 200 years, scientists have developed rules to describe chemical reactions that they’ve observed, including reactions in food, vitamins, medications and living organisms. One of the most ubiquitous is the “octet rule,” which states that each atom in a molecule that is produced by a chemical reaction will have eight outer orbiting electrons. (Scientists have found exceptions to the rule, but those exceptions are rare.)

But the molecule created by UCLA professor Eric Hudson and colleagues violates that rule. Barium-oxygen-calcium, or BaOCa+, is the first molecule ever observed by scientists that is composed of an oxygen atom bonded to two different metal atoms.

Normally, one metal atom (either barium or calcium) can react with an oxygen atom to produce a stable molecule. However, when the UCLA scientists added a second metal atom to the mix, a new molecule, BaOCa+, which no longer satisfied the octet rule, had been formed.

Michael Mills, Prateek Puri, Eric Hudson and Christian Schneider. Stuart Wolpert/UCLA

Other molecules that violate the octet rule have been observed before, but the UCLA study is among the first to observe such a molecule using tools from physics — namely lasers, ion traps and ultra-cold atom traps.

Hudson’s laboratory used laser light to cool tiny amounts of the reactant atoms and molecules to an extremely low temperature — one one-thousandth of a degree above absolute zero — and then levitate them in a space smaller than the width of a human hair, inside of a vacuum chamber. Under these highly controlled conditions, the scientists could observe properties of the atoms and molecules that are otherwise hidden from view, and the “physics tools” they used enabled them to hold a sample of atoms and observe chemical reactions one molecule at a time.

The ultra-cold temperatures used in the experiment can also be used to simulate the reaction as it would occur in outer space. That could help scientists understand how certain complex molecules, including some that could be precursors to life, came to exist in space, Hudson said.

The researchers found that when they brought together calcium and barium methoxide inside of their system under normal conditions, they would not react because the atoms could not find a way to rearrange themselves to form a stable molecule. However, when the scientists used a laser to change the distribution of the electrons in the calcium atom, the reaction quickly proceeded, producing a new molecule, CaOBa+.

The approach is part of a new physics-inspired subfield of chemistry that uses the tools of ultra-cold physics, such as lasers and electromagnetism, to observe and control how and when single-particle reactions occur.

UCLA graduate student Prateek Puri, the project’s lead researcher, said the experiment demonstrates not only how these techniques can be used to create exotic molecules, but also how they can be used to engineer important reactions. The discovery could ultimately be used to create new methods for preserving food (by preventing unwanted chemical reactions between food and the environment) or developing safer medications (by eliminating the chemical reactions that cause negative side effects).

“Experiments like these pave the way for developing new methods for controlling chemistry,” Puri said. “We’re essentially creating ‘on buttons’ for reactions.”

Hudson said he hopes the work will encourage other scientists to further narrow the gap between physics and chemistry, and to demonstrate that increasingly complex molecules can be studied and controlled. He added that one key to the success of the new study was the involvement of experts from various fields: experimental physicists, theoretical physicists and a physical chemist.

A key player in the research is already making a name for itself in Hollywood. A device called the integrated ion-trap-time-of-flight mass spectrometer, which was invented by Hudson’s lab and which was used to discover the reaction — was featured on a recent episode of the sitcom “The Big Bang Theory.”

“The device enables us to detect and identify the products of reactions on the single-particle level, and for us, it has really been a bridge between chemistry and physics,” said Michael Mills, a UCLA graduate student who worked on the project. “We were delighted to see it picked up by the show.”

Co-authors of the study are Christian Schneider, a UCLA research scientist; Ionel Simbotin, a University of Connecticut physics postdoctoral scholar; John Montgomery Jr., a University of Connecticut research professor of physics; Robin Côté, a University of Connecticut professor of physics; and Arthur Suits, a University of Missouri professor of chemistry.

The research was funded by the National Science Foundation and Army Research Office.

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For nearly 100 years, UCLA has been a pioneer, persevering through impossibility, turning the futile into the attainable.

We doubt the critics, reject the status quo and see opportunity in dissatisfaction. Our campus, faculty and students are driven by optimism. It is not naïve; it is essential. And it has fueled every accomplishment, allowing us to redefine what’s possible, time after time.

This can-do perspective has brought us 12 Nobel Prizes, 12 Rhodes Scholarships, more NCAA titles than any university and more Olympic medals than most nations. Our faculty and alumni helped create the Internet and pioneered reverse osmosis. And more than 100 companies have been created based on technology developed at UCLA.

From Cardiff: “Scientists make methanol using air around us”

Cardiff University

7 September 2017

Scientists at Cardiff University have created methanol from methane using oxygen from the air.

Methanol is currently produced by breaking down natural gas at high temperatures into hydrogen gas and carbon monoxide before reassembling them – expensive and energy-intensive processes known as ‘steam reforming’ and ‘methanol synthesis.’

But researchers at Cardiff Catalysis Institute have discovered they can produce methanol from methane through simple catalysis that allows methanol production at low temperatures using oxygen and hydrogen peroxide.

The breakthrough, published today in Science, has major implications for cleaner, greener industrial processes worldwide.

Professor Graham Hutchings, Director of Cardiff Catalysis Institute, said: “The quest to find a more efficient way of producing methanol is a hundred years old. Our process uses oxygen – effectively a ‘free’ product in the air around us – and combines it with hydrogen peroxide at mild temperatures which require less energy.

“We have already shown that gold nanoparticles supported by titanium oxide could convert methane to methanol, but we simplified the chemistry further and took away the titanium oxide powder. The results have been outstanding…”

“At present global natural gas production is ca. 2.4 billion tons per annum and 4% of this is flared into the atmosphere – roughly 100 million tons. Cardiff Catalysis Institute’s approach to using natural gas could use this “waste” gas saving CO2 emissions. In the US there is now a switch to shale gas, and our approach is well suited to using this gas as it can enable it to be liquefied so it can be readily transported.”

Research of significant value

Dr. James J. Spivey, Professor of Chemical Engineering at Louisiana State University and Editor-in-Chief of Catalysis Today, said: “This research is of significant value to the scientific and industrial communities. The conversion of our shale resources into higher value intermediates like methanol provide new routes for chemical intermediates.”

Cardiff Catalysis Institute has a world-wide reputation for outstanding science. The Institute works with industry to develop new catalytic processes and promote the use of catalysis as a sustainable 21st century technology.

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We are an ambitious and innovative university with a bold and strategic vision located in a beautiful and thriving capital city. Our research is world-leading and we provide an educationally outstanding experience for our students.

Driven by creativity and curiosity, we strive to fulfil our social, cultural and economic obligations to Cardiff, Wales, and the world.

From LBNL: “New Results Reveal High Tunability of 2-D Material”

Berkeley Lab

August 25, 2017
Glenn Roberts Jr
geroberts@lbl.gov
(510) 486-5582

From left: Kaiyuan Yao, Nick Borys, and P. James Schuck, seen here at Berkeley Lab’s Molecular Foundry, measured a property in a 2-D material that could help realize new applications. (Credit: Marilyn Chung/Berkeley Lab)

Two-dimensional materials are a sort of a rookie phenom in the scientific community. They are atomically thin and can exhibit radically different electronic and light-based properties than their thicker, more conventional forms, so researchers are flocking to this fledgling field to find ways to tap these exotic traits.

Applications for 2-D materials range from microchip components to superthin and flexible solar panels and display screens, among a growing list of possible uses. But because their fundamental structure is inherently tiny, they can be tricky to manufacture and measure, and to match with other materials. So while 2-D materials R&D is on the rise, there are still many unknowns about how to isolate, enhance, and manipulate their most desirable qualities.

Now, a science team at the Department of Energy’s Lawrence Berkeley National Laboratory (Berkeley Lab) has precisely measured some previously obscured properties of moly sulfide, a 2-D semiconducting material also known as molybdenum disulfide or MoS2. The team also revealed a powerful tuning mechanism and an interrelationship between its electronic and optical, or light-related, properties.

To best incorporate such monolayer materials into electronic devices, engineers want to know the “band gap,” which is the minimum energy level it takes to jolt electrons away from the atoms they are coupled to, so that they flow freely through the material as electric current flows through a copper wire. Supplying sufficient energy to the electrons by absorbing light, for example, converts the material into an electrically conducting state.

As reported in the Aug. 25 issue of Physical Review Letters, researchers measured the band gap for a monolayer of moly sulfide, which has proved difficult to accurately predict theoretically, and found it to be about 30 percent higher than expected based on previous experiments. They also quantified how the band gap changes with electron density – a phenomenon known as “band gap renormalization.”

“The most critical significance of this work was in finding the band gap,” said Kaiyuan Yao, a graduate student researcher at Berkeley Lab and the University of California, Berkeley, who served as the lead author of the research paper.

This diagram shows a triangular sample of monolayer moly sulfide (dark blue) on silicon-based layers (light blue and green) during an experimental technique known as photoluminescence excitation spectroscopy. (Credit: Berkeley Lab)

“That provides very important guidance to all of the optoelectronic device engineers. They need to know what the band gap is” in orderly to properly connect the 2-D material with other materials and components in a device, Yao said.

Obtaining the direct band gap measurement is challenged by the so-called “exciton effect” in 2-D materials that is produced by a strong pairing between electrons and electron “holes” ­– vacant positions around an atom where an electron can exist. The strength of this effect can mask measurements of the band gap.

Nicholas Borys, a project scientist at Berkeley Lab’s Molecular Foundry who also participated in the study, said the study also resolves how to tune optical and electronic properties in a 2-D material.

“The real power of our technique, and an important milestone for the physics community, is to discern between these optical and electronic properties,” Borys said.

The team used several tools at the Molecular Foundry, a facility that is open to the scientific community and specializes in the creation and exploration of nanoscale materials.

The Molecular Foundry technique that researchers adapted for use in studying monolayer moly sulfide, known as photoluminescence excitation (PLE) spectroscopy, promises to bring new applications for the material within reach, such as ultrasensitive biosensors and tinier transistors, and also shows promise for similarly pinpointing and manipulating properties in other 2-D materials, researchers said.

The research team measured both the exciton and band gap signals, and then detangled these separate signals. Scientists observed how light was absorbed by electrons in the moly sulfide sample as they adjusted the density of electrons crammed into the sample by changing the electrical voltage on a layer of charged silicon that sat below the moly sulfide monolayer.

This image shows a slight “bump” (red arrow) in charted experimental data that reveals the band gap measurement in a 2-D material known as moly sulfide. (Credit: Berkeley Lab)

Researchers noticed a slight “bump” in their measurements that they realized was a direct measurement of the band gap, and through a slew of other experiments used their discovery to study how the band gap was readily tunable by simply adjusting the density of electrons in the material.

“The large degree of tunability really opens people’s eyes,” said P. James Schuck, who was director of the Imaging and Manipulation of Nanostructures facility at the Molecular Foundry during this study.

“And because we could see both the band gap’s edge and the excitons simultaneously, we could understand each independently and also understand the relationship between them,” said Schuck, who is now at Columbia University. “It turns out all of these properties are dependent on one another.”

Kaiyuan Yao works with equipment at Berkeley Lab’s Molecular Foundry that was used to help measure a property in a 2-D material. (Credit: Marilyn Chung/Berkeley Lab)

Moly sulfide, Schuck also noted, is “extremely sensitive to its local environment,” which makes it a prime candidate for use in a range of sensors. Because it is highly sensitive to both optical and electronic effects, it could translate incoming light into electronic signals and vice versa.

Schuck said the team hopes to use a suite of techniques at the Molecular Foundry to create other types of monolayer materials and samples of stacked 2-D layers, and to obtain definitive band gap measurements for these, too. “It turns out no one yet knows the band gaps for some of these other materials,” he said.

The team also has expertise in the use of a nanoscale probe to map the electronic behavior across a given sample.

Borys added, “We certainly hope this work seeds further studies on other 2-D semiconductor systems.”

The Molecular Foundry is a DOE Office of Science User Facility that provides free access to state-of-the-art equipment and multidisciplinary expertise in nanoscale science to visiting scientists.

Researchers from the Kavli Energy NanoSciences Institute at UC Berkeley and Berkeley Lab, and from Arizona State University also participated in this study, which was supported by the National Science Foundation.

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A U.S. Department of Energy National Laboratory Operated by the University of California

From Princeton: “‘Acidic patch’ regulates access to genetic information”

Princeton University Research Blog

August 14, 2017
Pooja Makhijani

Chromatin remodelers — protein machines that pack and unpack chromatin, the tightly wound DNA-protein complex in cell nuclei — are essential and powerful regulators for critical cellular processes, such as replication, recombination and gene transcription and repression. In a new study published Aug. 2 in the journal Nature, a team led by researchers from Princeton University unravels more details on how a class of ATP-dependent chromatin remodelers, called ISWI, regulate access to genetic information.

The researchers reported that ISWI remodelers use a structural feature of the nucleosome, known as the “acidic patch,” to remodel chromatin. The nucleosome is the fundamental structural subunit of chromatin, and is often compared to thread wrapped around a spool.

“The acidic patch is a negatively charged surface, presented on each face of the nucleosome disc, that is formed by amino acids contributed by two different histone proteins, H2A and H2B,” said Geoffrey Dann, a graduate student in the Department of Molecular Biology at Princeton and the study’s lead author. “Histone proteins are overall very positively charged, which makes the negatively charged acidic patch region of the nucleosome very unique. Recognition of the acidic patch has never before been implicated in chromatin remodeling.”

The research was conducted in the laboratory of Tom Muir, the Van Zandt Williams Jr. Class of 1965 Professor of Chemistry and chair of the Department of Chemistry. Research in the Muir group centers on elucidating the physiochemical basis of protein functions in biomedically relevant systems.

Because ISWI remodelers are known to interact extensively with nucleosomes, the researchers hypothesized that signals, in the form of chemical modifications on histone proteins embedded within nucleosomes, communicate to the remodelers on which nucleosome to act. Using high throughput screening technology, an assay process often used in drug discovery, allowed the researchers to quickly conduct tens of thousands of biochemical measurements to test their assumptions. “The number of chromatin modifications known to exist in vivo is astronomical,” Dann said.

Not only did the experiments reveal that ISWI remodelers use the “acidic patch” to remodel chromatin, but also determined that remodeling enzymes outside the family of ISWI remodelers also use this structural feature, “suggesting that this feature may be a general requirement for chromatin remodeling to occur,” Dann said.

Geoffrey Dann. Photo by Jeffrey Bos.

Certain chemical modifications that act on histone proteins that are adjacent to the acidic patch also have the ability to enhance or inhibit ISWI remodeling activity, he explained. “A handful of other proteins are known to engage the acidic patch in their interaction with chromatin as well, and we also found that the biochemistry of several of these proteins was affected by such modifications. Interestingly, each protein tested had its own signature response to this collection of modifications.”

The high throughput screening technology method also generated a vast library of data to drive the design of future studies geared toward further understanding ISWI regulation. “This study generated an immense amount of data pointing to many other novel regulatory inputs, in the form of chromatin modifications, into ISWI remodeling activity,” Dann said. “A long-term goal in our lab is to use this data resource as a launch pad for additional studies investigating how chromatin modifications affect ISWI remodeling, and how this plays into the various roles ISWI remodelers assume in the cell.”

Their findings may also identify a new instrument in cells’ molecular repertoire of chromatin-remodeling tools and spur investigations into potential cancer therapeutic targets. “Mutations in the acidic patch are known to occur in certain types of human cancers, which underscores the emerging importance of the acidic patch in chromatin biology,” Dann said.

See the full article here .

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About Princeton: Overview

Princeton University is a vibrant community of scholarship and learning that stands in the nation’s service and in the service of all nations. Chartered in 1746, Princeton is the fourth-oldest college in the United States. Princeton is an independent, coeducational, nondenominational institution that provides undergraduate and graduate instruction in the humanities, social sciences, natural sciences and engineering.

As a world-renowned research university, Princeton seeks to achieve the highest levels of distinction in the discovery and transmission of knowledge and understanding. At the same time, Princeton is distinctive among research universities in its commitment to undergraduate teaching.

Today, more than 1,100 faculty members instruct approximately 5,200 undergraduate students and 2,600 graduate students. The University’s generous financial aid program ensures that talented students from all economic backgrounds can afford a Princeton education.

From Stanford: “How do you make ethanol without growing corn?”

Stanford University

June 20, 2017 [Delayed waiting for a link to the science paper.]
Mark Shwartz

SLAC scientist Christopher Hahn sees his reflection in a copper catalyst that converts carbon dioxide into ethanol. | Image credit: Mark Shwartz.

Most cars and trucks in the United States run on a blend of 90 percent gasoline and 10 percent ethanol, a renewable fuel made primarily from fermented corn. But producing the 14 billion gallons of ethanol consumed annually by American drivers requires millions of acres of farmland.

A recent discovery by Stanford University scientists could lead to a new, more sustainable way to make ethanol without corn or other crops. This technology has three basic components: water, carbon dioxide and electricity delivered through a copper catalyst. The results are published in Proceedings of the National Academy of Sciences.

“One of our long-range goals is to produce renewable ethanol in a way that doesn’t impact the global food supply,” said study principal investigator Thomas Jaramillo, an associate professor of chemical engineering at Stanford and of photon science at the SLAC National Accelerator Laboratory.

“Copper is one of the few catalysts that can produce ethanol at room temperature,” he said. “You just feed it electricity, water and carbon dioxide, and it makes ethanol. The problem is that it also makes 15 other compounds simultaneously, including lower-value products like methane and carbon monoxide. Separating those products would be an expensive process and require a lot of energy.”

Scientists would like to design copper catalysts that selectively convert carbon dioxide into higher-value chemicals and fuels, like ethanol and propanol, with few or no byproducts. But first they need a clear understanding of how these catalysts actually work. That’s where the recent findings come in.

Copper crystals

For the PNAS study, the Stanford team chose three samples of crystalline copper, known as copper (100), copper (111) and copper (751). Scientists use these numbers to describe the surface geometries of single crystals.

“Copper (100), (111) and (751) look virtually identical but have major differences in the way their atoms are arranged on the surface,” said Christopher Hahn, an associate staff scientist at SLAC and co-lead lead author of the study. “The essence of our work is to understand how these different facets of copper affect electrocatalytic performance.”

In previous studies, scientists had created single-crystal copper electrodes just 1-square millimeter in size. For this study, Hahn and his co-workers at SLAC developed a novel way to grow single crystal-like copper on top of large wafers of silicon and sapphire. This approach resulted in films of each form of copper with a 6-square centimeter surface, 600 times bigger than typical single crystals.

Catalytic performance

To compare electrocatalytic performance, the researchers placed the three large electrodes in water, exposed them to carbon dioxide gas and applied a potential to generate an electric current.

The results were clear. When the team applied a specific voltage, the electrodes made of copper (751) were far more selective to liquid products, such as ethanol and propanol, than those made of copper (100) or (111).

Ultimately, the Stanford team would like to develop a technology capable of selectively producing carbon-neutral fuels and chemicals at an industrial scale.

“The eye on the prize is to create better catalysts that have game-changing potential by taking carbon dioxide as a feedstock and converting it into much more valuable products using renewable electricity or sunlight directly,” Jaramillo said. “We plan to use this method on nickel and other metals to further understand the chemistry at the surface. We think this study is an important piece of the puzzle and will open up whole new avenues of research for the community.”

See the full article here .

Please help promote STEM in your local schools.

Stem Education Coalition

Leland and Jane Stanford founded the University to “promote the public welfare by exercising an influence on behalf of humanity and civilization.” Stanford opened its doors in 1891, and more than a century later, it remains dedicated to finding solutions to the great challenges of the day and to preparing our students for leadership in today’s complex world. Stanford, is an American private research university located in Stanford, California on an 8,180-acre (3,310 ha) campus near Palo Alto. Since 1952, more than 54 Stanford faculty, staff, and alumni have won the Nobel Prize, including 19 current faculty members

From Princeton: “Researchers find path to discovering new topological materials, holding promise for technological applications”

Princeton University

July 20, 2017
No writer credit

Researchers have discovered how to identify new examples of topological materials, which have unique and desirable electronic properties. The technique involves finding the connection between band theory, which describes the energy levels of electrons in a solid, with a material’s topological nature. The disconnected bands indicate the material is a topological insulator. Image courtesy of Nature.

Researchers find path to discovering new topological materials, holding promise for technological applications.

An international team of researchers has found a way to determine whether a crystal is a topological insulator — and to predict crystal structures and chemical compositions in which new ones can arise. The results, published July 20 in the journal Nature, show that topological insulators are much more common in nature than currently believed.

Topological materials, which hold promise for a wide range of technological applications due to their exotic electronic properties, have attracted a great deal of theoretical and experimental interest over the past decade, culminating in the 2016 Nobel Prize in physics. The materials’ electronic properties include the ability of current to flow without resistance and to respond in unconventional ways to electric and magnetic fields.

Until now, however, the discovery of new topological materials occurred mainly by trial and error. The new approach described this week [see above reference to the Nature article] allows researchers to identify a large series of potential new topological insulators. The research represents a fundamental advance in the physics of topological materials and changes the way topological properties are understood.

The team included: at Princeton University, Barry Bradlyn and Jennifer Cano, both associate research scholars at the Princeton Center for Theoretical Science, Zhijun Wang, a postdoctoral research associate, and B. Andrei Bernevig, professor of physics; professors Luis Elcoro and Mois Aroyo at the University of the Basque Country in Bilbao; assistant professor Maia Garcia Vergniory of University of the Basque Country and Donostia International Physics Center (DIPC) in Spain; and Claudia Felser, professor at the Max Planck Institute for Chemical Physics of Solids in Germany.

“Our approach allows for a much easier way to find topological materials, avoiding the need for detailed calculations,” Felser said. “For some special lattices, we can say that, regardless of whether a material is an insulator or a metal, something topological will be going on,” Bradlyn added.

Until now, of the roughly 200,000 materials catalogued in materials databases, only around a few hundred are known to host topological behavior, according to the researchers. “This raised the question for the team: Are topological materials really that scarce, or does this merely reflect an incomplete understanding of solids?” Cano said.

To find out, the researchers turned to the nearly century-old band theory of solids, considered one of the early landmark achievements of quantum mechanics. Pioneered by Swiss-born physicist Felix Bloch and others, the theory describes the electrons in crystals as residing in specific energy levels known as bands. If all the states in a group of bands are filled with electrons, then the electrons cannot move and the material is an insulator. If some of the states are unoccupied, then electrons can move from atom to atom and the material is capable of conducting an electrical current.

Because of the symmetry properties of crystals, however, the quantum states of electrons in solids have special properties. These states can be described as a set of interconnected bands characterized by their momentum, energy and shape. The connections between these bands, which on a graph resemble tangled spaghetti strands, give rise to topological behaviors such as those of electrons that can travel on surfaces or edges without resistance.

The team used a systematic search to identify many previously undiscovered families of candidate topological materials. The approach combined tools from such disparate fields as chemistry, mathematics, physics and materials science.

First, the team characterized all the possible electronic band structures arising from electronic orbitals at all the possible atomic positions for all possible crystal patterns, or symmetry groups, that exist in nature, with the exception of magnetic crystals. To search for topological bands, the team first found a way to enumerate all allowed non-topological bands, with the understanding that anything left out of the list must be topological. Using tools from group theory, the team organized into classes all the possible non-topological band structures that can arise in nature.

Next, by employing a branch of mathematics known as graph theory — the same approach used by search engines to determine links between websites — the team determined the allowed connectivity patterns for all of the band structures. The bands can either separate or connect together. The mathematical tools determine all the possible band structures in nature — both topological and non-topological. But having already enumerated the non-topological ones, the team was able to show which band structures are topological.

By looking at the symmetry and connectivity properties of different crystals, the team identified several crystal structures that, by virtue of their band connectivity, must host topological bands. The team has made all of the data about non-topological bands and band connectivity available to the public through the Bilbao Crystallographic Server. “Using these tools, along with our results, researchers from around the world can quickly determine if a material of interest can potentially be topological,” Elcoro said.

The research shows that symmetry, topology, chemistry and physics all have a fundamental role to play in our understanding of materials, Bernevig said. “The new theory embeds two previously missing ingredients, band topology and orbital hybridization, into Bloch’s theory and provides a prescriptive path for the discovery and characterization of metals and insulators with topological properties.”

David Vanderbilt, a professor of physics and astronomy at Rutgers University who was not involved in the study, called the work remarkable. “Most of us thought it would be many years before the topological possibilities could be catalogued exhaustively in this enormous space of crystal classes,” Vanderbilt said. “This is why the work of Bradlyn and co-workers comes as such a surprise. They have developed a remarkable set of principles and algorithms that allow them to construct this catalogue at a single stroke. Moreover, they have combined their theoretical approach with materials database search methods to make concrete predictions of a wealth of new topological insulator materials.”

The theoretical underpinnings for these materials, called “topological” because they are described by properties that remain intact when an object is stretched, twisted or deformed, led to the awarding of the Nobel Prize in physics in 2016 to F. Duncan M. Haldane, Princeton’s Sherman Fairchild University Professor of Physics; J. Michael Kosterlitz of Brown University; and David J. Thouless of the University of Washington.

Chemistry and physics take different approaches to describing crystalline materials, in which atoms occur in regularly ordered patterns or symmetries. Chemists tend to focus on the atoms and their surrounding clouds of electrons, known as orbitals. Physicists tend to focus on the electrons themselves, which can carry electric current when they hop from atom to atom and are described by their momentum.

“This simple fact — that the physics of electrons is usually described in terms of momentum, while the chemistry of electrons is usually described in terms of electronic orbitals — has left material discovery in this field at the mercy of chance,” Wang said.

“We initially set out to better understand the chemistry of topological materials — to understand why some materials have to be topological,” Vergniory said.

Aroyo added, “What came out was, however, much more interesting: a way to marry chemistry, physics and mathematics that adds the last missing ingredient in a century-old theory of electronics, and in the present-day search for topological materials.”

Funding for the study was provided by the U.S. Department of Energy (DE-SC0016239), the U.S. National Science Foundation (EAGER DMR-1643312 and MRSEC DMR-1420541), and the U.S. Office of Naval Research (N00014-14-1-0330). Additional funding came from a Simons Investigator Award, the David & Lucile Packard Foundation, and Princeton University’s Eric and Wendy Schmidt Transformative Technology Fund. Funding was also provided by the Spanish Ministry of Economy and Competitiveness (FIS2016-75862-P and FIS2013-48286-C2-1-P), the Government of the Basque Country (project IT779-13), and the Spanish Ministry of Economy and Competitiveness and European Federation for Regional Development (MAT2015-66441-P).

The study, Topological quantum chemistry, by Barry Bradlyn, Luis Elcoro, Jennifer Cano, Maia Garcia Vergniory, Zhijun Wang, Claudia Felser, Mois Aroyo and B. Andrei Bernevig, was published in the journal Nature on July 20, 2017.

See the full article here .

Please help promote STEM in your local schools.

Stem Education Coalition

About Princeton: Overview

Princeton University is a vibrant community of scholarship and learning that stands in the nation’s service and in the service of all nations. Chartered in 1746, Princeton is the fourth-oldest college in the United States. Princeton is an independent, coeducational, nondenominational institution that provides undergraduate and graduate instruction in the humanities, social sciences, natural sciences and engineering.

As a world-renowned research university, Princeton seeks to achieve the highest levels of distinction in the discovery and transmission of knowledge and understanding. At the same time, Princeton is distinctive among research universities in its commitment to undergraduate teaching.

Today, more than 1,100 faculty members instruct approximately 5,200 undergraduate students and 2,600 graduate students. The University’s generous financial aid program ensures that talented students from all economic backgrounds can afford a Princeton education.

From MIT: “Preventing severe blood loss on the battlefield or in the clinic” Reginald Avery

MIT News

July 11, 2017
Dara Farhadi

At MIT graduate student Reginald Avery has been conducting research on a biomaterial that could stop wounded soldiers from dying from shock due to severe blood loss. “I wanted to do something related to the military because I grew up around that environment,” he says. “The people, the uniformed soldiers, and the well-controlled atmosphere created a good environment to grow up in, and I wanted to still contribute in some way to that community.” Photo: Ian MacLellan

PhD student Reginald Avery is developing an injectable material that patches ruptured blood vessels.

In a tiny room in the sub-basement of MIT’s Building 66 sits a customized, super-resolution microscope that makes it possible to see nanoscale features of a red blood cell. Here, Reginald Avery, a fifth-year graduate student in the Department of Biological Engineering, can be found conducting research with quiet discipline, occasionally fidgeting with his silver watch.

He spends most of his days either at the microscope, taking high-resolution images of blood clots forming over time, or at the computer, reading literature about super-resolution microscopy. Without windows to approximate the time of day, Avery’s watch comes in handy. Not surprisingly for those who know him, it’s set to military time.

Avery describes his father as a hard-working inspector general for the U.S. Army Test and Evaluation Command. Avery and his fraternal twin brother, Jeff, a graduate student in computer science at Purdue University, were born in Germany and lived for a portion of their childhoods on military bases in Hawaii and Alabama. Eventually the family moved to Maryland and entered civilian life, but Avery’s experiences on a military base never left him. At MIT he’s been conducting research on a biomaterial that could stop wounded soldiers from dying from shock due to severe blood loss.

“I wanted to do something related to the military because I grew up around that environment,” he says. “The people, the uniformed soldiers, and the well-controlled atmosphere created a good environment to grow up in, and I wanted to still contribute in some way to that community.”

Blocking blood loss

Avery is one of the first graduate students to join the Program in Polymers and Soft Matter (PPSM) from the Department of Biological Engineering. When he first joined the lab of Associate Professor Bradley Olsen in the Department of Chemical Engineering, his focus was on optimizing and testing a material that could be topically applied to wounded soldiers.

The biomaterial is a hydrogel — a material consisting largely of water — with a viscosity similar to toothpaste. Gelatin proteins and inorganic silica nanoparticles are incorporated into the material and function as a substrate that helps to accelerate coagulation rates and reduce clotting times.

Co-advised by Ali Khademhosseini at Brigham and Women’s Hospital and in collaboration with others at Massachusetts General Hospital, Avery further developed the material so that it could be injected into ruptured blood vessels. Like a cork on a wine bottle, the biomaterial forms a plug in the leaky vessel and stops any blood loss. Avery’s research was published in Science Translational Medicine and featured on the front cover of the November 2016 issue.

The current standard for patching blood vessels is imperfect. Surgeons typically use metallic coils, special plastic beads, or compounds also found in super glue. Each technology has limitations that the nanocomposite hydrogel attempts to address.

“The old techniques don’t take advantage of tissue engineering. It can be difficult for a surgeon to deliver metallic coils and beads to the targeted site, and blood may sometimes still find a path through and result in re-bleeding. It’s also expensive, and some techniques have a finite time period to place the material where it needs to be,” Avery says. “We wanted to use a hydrogel that could completely fill a vessel and not allow any leakage to occur through that injury site.”

The nanocomposite, which can be injected easily with a syringe or catheter, has been tested in animal models without causing inflammatory side-effects or the formation of clots elsewhere in the animal’s circulatory system. Some in vitro experiments also indicate that the material could be useful for treating aneurysms.

For the past six months Avery has concentrated on uncovering the physical mechanism by which the nanocomposite material interacts with blood. A super-resolution microscope can achieve a resolution of 250 nanometers; a single red blood cell, for a comparison, is about 8,000 nanometers wide. Avery says the ability to visualize how the physiological molecules and proteins interact with the nanocomposite and other surgical tools may also help him design a better material. Obtaining a comprehensive view of the process, however, can be time-consuming.

“It’s taking snapshots every 10 or 20 seconds for approximately 30 minutes, and putting all of those pictures together,” he says. “What I want to do is visualize these gels and clots forming over time.”

Found in translation

While he is eager to see his material put to use to save lives, Avery is glad to be contributing to the work at the basic and translational research stages. He says he’s driven to appropriately characterize a treatment or biomaterial, ask the right questions, and make sure it functions just as well as, or better than, what is currently used in the clinic.

“I’m comfortable doing a thorough study in vitro to characterize materials or design some synthetic tests prior to in vivo testing,” he says. “You must be very confident in [the biomaterial] before getting to that step so that you’re effectively utilizing the animals, or even more important, you’re not putting a person at risk if something finally does get to that point.”

Avery also finds meaning in collaborating and helping others with their research. He has worked on projects using neutron scattering to elucidate the network structure of a homo-polypeptide, performed cell culture on thermoresponsive hydrogels, and developed highly elastic polypeptides, projects that Avery says aren’t directly applicable to his thesis work of treating internal bleeding. However, he was happy to have simply had the experience of learning something new.

“If I can help somebody with something then I’m going to try to do the best that I can. Whether it’s a homework assignment or something in lab, my goal is not to leave somebody worse off,” Avery says. “If there’s something I’ve done in the past that could help you now, I’m excited to show you and hopefully have it work out well for you. If it doesn’t, we can talk even longer to try to figure out what we could do to make it work better.”

Of the seven papers that Avery has been involved in over the past three years, almost half were collaborative projects outside the area of his thesis work.

Avery hopes to finish his PhD thesis by the summer of next year. Afterward, he envisions working for a research institute that is devoted to a single disease or condition, or perhaps for a research center associated with a hospital within the military health system so that he could continue developing biomaterials, diagnostics, or other approaches to help soldiers.

“I’m usually excited to help somebody get something done or get something done for my project. It’s always exciting to get closer to determining the optimum concentration that you need, seeing that one data point that’s higher than the others, or getting that nice image that shows the effect that you have hypothesized,” Avery says. “That’s still a motivating aspect of coming to lab, to eventually get those results. It can take a long time to get there but once you do, you appreciate the journey.”

See the full article here .

Please help promote STEM in your local schools.

Stem Education Coalition

The mission of MIT is to advance knowledge and educate students in science, technology, and other areas of scholarship that will best serve the nation and the world in the twenty-first century. We seek to develop in each member of the MIT community the ability and passion to work wisely, creatively, and effectively for the betterment of humankind.