Tag: X-ray diffraction

Deciphering the sugar transport in plants

Deciphering the sugar transport in plants

Synchrotron studies to understand sucrose highway

In most plant species, sucrose is the main form of assimilated carbon produced during photosynthesis. Sucrose is essential for plant growth, as it provides a source of carbon to produce new molecules, but also energy for the plant cells. Sucrose has also an associated role as a signalling molecule, by regulating the growth of new organs, accumulation of storage proteins, and flowering in plants. Long-distance sucrose distribution from the green source tissues, generally leaves, to energy-demanding sink tissues (flowers, fruits, new organ in formation) is mediated by a specific and highly modified vascular tissue called phloem. The transport of sucrose in the phloem is an active transport, as sucrose is loaded in the conductive tissue by specific proteins from the SUC/SUT family. The SUC1 transporter from A. thaliana is located on the membrane of cells and use the proto-motive force to drive the loading of sucrose. Despite their key role in plants, the working mechanism of these SUCs transporters is not yet well understood.

A team of researchers from the Aarhus University recently published a new study in Nature Plants to understand the precise mechanism of action of the SUC1 transporter. They used X-ray diffraction data collected at I04 and I24 beamlines at Diamond to determine the 3D structure of this transmembrane protein. They wanted to understand how SUCs protein recognise sucrose, and how transport is proton coupled. As sugar transport is a key feature in plants, understanding how proteins can fine-tune the sugar concentration in conductive tissue is fundamental. Lead author of this study, Dr Bjørn Panyella Pedersen explained:

Active sucrose transport and loading into the phloem determines the turgor pressure. This pressure creates the vascular flow of nutrients (sucrose and all other components of the sap), and determines which parts of the plant will grow in response to environmental signals. Ultimately, we hope our research will help to augment control of growth and morphology in plants.

For their study, the team used a well-known plant model, Arabidopsis thaliana. This plant is widely used as model because it has a sequenced and annotated genome, and huge collections of mutant lines exists, allowing characterisation of plants where a specific gene is not expressed. Furthermore, this plant has a fast life cycle and produces numerous seeds.

In this study, the researchers present the structure of SUC1, and key elements to explain both the recognition of sucrose by the transporter, and the active transport by proton coupling. They produced SUC1 transporters and performed in-vivo assays to determine if the protein was functioning, and then proceed to solving the structure at the microfocus beamline I24. Dr Bjørn Panyella Pedersen says:

We have used Diamond’s beamlines I24 and I04 for our research since 2014, both in person and by remote data collection. We have always been very happy with the support and quality of the beamlines at Diamond. Brexit and the Corona years have made our access to the facility more challenging at times but with the help from the support staff we have been able to maintain our work at Diamond.

Read more on the Diamond website

Image: The 2.7 Å electron density map of SUC1 (2mFo-DFc map contoured at 1σ). Density corresponding to the N and C domain are coloured cyan and orange, respectively. EHR and IHR domains are coloured pale yellow. 

X-ray diffraction reveals ancient Egyptian illustration methods

X-ray diffraction reveals ancient Egyptian illustration methods

The ancient Egyptians used papyrus as a medium for communication and illustration, with the first illustrations appearing in the fifth and sixth dynasties (2500 – 2100 B.C.). Funerary documents, such as the Book of the Dead, flourished during the New Kingdom period as they were considered essential for entering the afterlife.

The Champollion Museum in Vif, France, holds a collection of 280 papyrus fragments, many of which show scenes from the Book of the Dead. The colours used in these illustrations are typical of the Egyptian palette and include blue, green, red, pink, yellow and white, with different characters and elements of the illustrations outlined with a black line.

Researchers from the ESRF and the Néel Institute CNRS/UGA in Grenoble, France, with collaborators from the Champollion Museum, worked together to gain a deeper understanding of the illustration processs used in ancient Egypt. A combination of optical microscopy, synchrotron X-ray powder diffraction, X-ray fluorescence and Raman spectroscopy was used to identify the pigments and their overall distribution.

Two of the papyrus fragments of the collection (PAP-6 and PAP-12) were examined on beamline ID22, where X-ray fluorescence and X-ray diffraction experiments were carried out. Mixed Rietveld and Pawley refinement was carried out against the XRD data to quantify the fine fraction and to consider the heterogeneous microstructure of the pigments.

Read more on the ESRF website 

High pressure synthesis in gallium sulphide chalcogenide

High pressure synthesis in gallium sulphide chalcogenide

Researchers from Universitat Politècnica de València, Universidad de La Laguna, Universidad de Cantabria and the ALBA Synchrotron have published a new work on high pressure chemistry in gallium (III) sulphide chalcogenide. In this work, relevant fingerprints (vibrational and structural) of a pressure-induced paralectric to ferroelectric phase transition are shown. This is the first time when a tetradymite-like (R3m) phase has been synthesized and observed experimentally in gallium-based sequichalcogenides. High pressure X-ray diffraction measurements were carried out at MSPD beamline of ALBA.

Gallium (III) sulphide (Ga2S3) is a compound of sulphur and gallium, that is a semiconductor that has a wide variety of applications in electronics and photonics: nano optoelectronics, photonic chips, electro-catalysis, energy conversion and storage, solar energy devices, gas sensors, laser-radiation detection, second harmonic generation, phase change memories or photocatalytic water splitting systems.

In this work published in Chemistry of Materials,scientists have shown relevant vibrational and structural fingerprints of a pressure-induced paraelectric to ferroelectric R-3m-to-R3m (β’-to-φ) phase transition under decompression on Ga2S3 chalcogenide.

This transition was theoretically predicted in several III−VI B2X3 compounds at high temperature (where B can be aluminium, gallium or indium and X, sulphur, selenium or tellurium). The novelty of this research stems from the synthesis of both phases: β-(R-3m) and α-In2Se3 (R3m)-like structures on Ga2S3 and tuning them via decreasing pressure. Within the III−VI B2X3 compounds, this R-3m-to-R3m (β’-to-φ-Ga2S3) phase transition had been observed experimentally only in the indium (III) selenide (In2Se3)compound, under varying temperature or pressure, to date.

This finding leads the way for designing cheap, nontoxic, nonrare-earth, and abundant element-based devices for second harmonic generation, photocatalytic splitting, ferroelectric, pyroelectric, and piezoelectric applications based on Ga2S3.

Read more on the ALBA website

Image: Samuel Gallego and Catalin Popescu at the MSPD beamline of ALBA.

Discovered: An easier way to create “Flexible Diamonds”

Discovered: An easier way to create “Flexible Diamonds”

As hard as diamond and as flexible as plastic, highly sought-after diamond nanothreads would be poised to revolutionize our world—if they weren’t so difficult to make. A team of scientists led by Samuel Dunning and Timothy Strobel of the Carnegie Institution for Science using high-brightness x-rays from the U.S. Department of Energy’s (DOE’s) Advanced Photon Source developed an original technique that predicts and guides the ordered creation of strong, yet flexible, diamond nanothreads, surmounting several existing challenges.  The innovation will make it easier for scientists to synthesize the nanothreads—an important step toward applying the material to practical problems in the future. The work was published in the Journal of the American Chemical Society.

Diamond nanothreads are ultra-thin, one-dimensional carbon chains, tens of thousands of times thinner than a human hair. They are often created by compressing smaller carbon-based rings together to form the same type of bond that makes diamonds the hardest mineral on our planet. However, instead of the three-dimensional carbon lattice found in a normal diamond, the edges of these threads are “capped” with carbon-hydrogen bonds, which make the whole structure flexible.

Dunning explains: “Because the nanothreads only have these bonds in one direction, they can bend and flex in ways that normal diamonds can’t.”

Scientists predict that the unique properties of carbon nanothreads will have a range of useful applications from providing sci-fi-like scaffolding on space elevators to creating ultra-strong fabrics. However, scientists have had a hard time creating enough nanothread material to actually test their proposed superpowers.

Read more on the APS website

Image: The starting sample of pyridazine—a six atom ring made up of four carbons and two nitrogens—changes under pressure as diamond nanothread formation progresses. The first and last images show that there has been a permanent color change between the samples after thread formation. The images don’t show individual threads, but “bulk” samples of pyridazine during compression, each around 40 microns thick with a 180-micron diameter.

Credit: Samuel Dunning

Unveiling the secrets of biofilms

Unveiling the secrets of biofilms

Most bacteria have the ability to form communities, biofilms, that adhere to a wide variety of surfaces and are difficult to remove. This can lead to major problems, for example in hospitals or in the food industry. Now, an international team led by Hebrew University, Jerusalem, and the Technical University Dresden, has studied a model system for biofilms at the synchrotron radiation facilities BESSY II at HZB and the ESRF and found out what role the structures within the biofilm play in the distribution of nutrients and water.

Bacterial biofilms can thrive on almost all types of surfaces: We find them on rocks and plants, on teeth and mucous membranes, but also on contact lenses, medical implants or catheters, in the hoses of the dairy industry or drinking water pipes, where they can pose a serious threat to human health. Some biofilms are also useful, for example, in the production of cheese, where specific types of biofilms not only produce the many tiny holes, but also provide its delicious taste.

Tissue with special structures

“Biofilms are not just a collection of very many bacteria, but a tissue with special structures,” explains Prof. Liraz Chai from the Hebrew University in Jerusalem. Together, the bacteria form a protective layer of carbohydrates and proteins, the so-called extracellular matrix. This matrix protects the from disinfectants, UV radiation or desiccation and ensures that biofilms are really difficult to remove mechanically or eradicate chemically. However, the matrix is not a homogeneous sludge: “It’s a bit like in a leaf of plants, there are specialized structures, for example water channels residing in tiny wrinkles,” says Chai. But what role these structures play and what happens at the molecular level in a biofilm was not known until now. Together with Prof. Yael Politi, TU Dresden, an expert in the characterization of biological materials, Chai therefore applied for measurement time at the synchrotron radiation source BESSY II at HZB.

“The good thing about BESSY II is that we can map quite large areas. By combining X-ray diffraction with fluorescence, not only can we analyze the molecular structures across the biofilm very precisely, but we can also simultaneously track the accumulation of certain metal ions that are transported in the biofilm and learn about some of their biological roles” Yael Politi points out.

Read more on the HZB website

Image: When bacteria join together to form communities, they may build complex structures. The photo shows wild-type Bacillus subtilis biofilms.

Credit: © Liraz Chai/HUJI

Probing the Structure of a Promising NASICON Material

Probing the Structure of a Promising NASICON Material

As physicists, materials scientists, and engineers continue striving to enhance and improve batteries and other energy storage technologies, a key focus is on finding or designing new ways to make electrodes and electrolytes.  One promising avenue of research involves solid-state materials, making possible batteries free of liquid electrolytes, which can pose fire and corrosion hazards.  An international group of researchers joined with scientists at Argonne National Laboratory to investigate the structure of crystalline and amorphous compounds based on the NASICON system, or sodium super-ion conductors. The work (using research carried out at the U.S. Department of Energy’s Advanced Photon Source [APS] and published in the Journal of Chemical Physics) reveals some substantial differences between the crystalline and glass phases of the NAGP system, which affect the ionic conductivity of the various materials.  The investigators note that the fraction of non-bridging oxygen (NBO) atoms appears to play a significant role, possibly altering the Na+ ion mobility, and suggest this as an area of further study.  The work provides fresh insights into the process of homogeneous nucleation and identifying superstructural units in glass ― a necessary step in engineering effective solid-state electrolytes with enhanced ionic conductivity. 

Because of their high ionic conductivity, materials with a NASICON structure are prime candidates for a solid electrolyte in sodium-ion batteries.  They can be prepared by a glass-ceramic route, which involves the crystallization of a precursor glass, giving them the usefulness of moldable bulk materials.  In this work, the research team specifically studied the NAGP system [Na1+xAlxGe2-x(PO4)3] with x = 0, 0.4 and 0.8 in both crystalline and glassy forms. Working at several different facilities, they used a combination of techniques, including neutron and x-ray diffraction, along with 27Al and 31P magic angle spinning and 31P/23Na double-resonance nuclear magnetic resonance spectroscopy.  The glassy form of NAGP materials was examined both in its as-prepared state and after thermal annealing, so that the changes on crystal nucleation could be studied.

Neutron powder diffraction measurements were performed at the BER II reactor source, Helmholtz-Zentrum Berlin, using the fine resolution powder diffractometer E9 (FIREPOD), followed by Rietveld analysis.  Further neutron diffraction observations were conducted at the Institut Laue-Langevin using the D4c diffractometer and at the ISIS pulsed neutron source using the GEM diffractometer.  X-ray diffraction studies were performed at X-ray Science Division Magnetic Materials Group’s beamline 6-ID-D of the APS, an Office of Science user facility at Argonne National Laboratory. 

Read more on the APS website

Image: Fig. 1. NASICON crystal structure showing the tetrahedral P(4) phosphate motifs (purple), octahedral GeO6 motifs (cyan) and Na+ ions (green). Oxygen atoms are depicted in red.

Analysing asteroid Ryugu samples

Analysing asteroid Ryugu samples

The asteroid Ryugu samples brought back by JAXA’s asteroid explorer “Hayabusa2” in December 2020 are analyzed by six initial analysis teams for one year from June 2021. Among the initial analysis teams, the “Stone Material Analysis Team” and the “Organic Macromolecule Analysis Team” conducts their analysis at the Photon Factory, KEK.

It is thought that asteroids such as Ryugu may have brought water and organic matter to the Earth in the past. By integrating the results of each team’s analysis, we will be closer to solving the great mystery of how life came to be on the Earth.

Read more on the HAYABUSA2-IMSS website

Image : Primordial solar system. 

AI Agent Helps Identify Material Properties Faster

AI Agent Helps Identify Material Properties Faster

High-throughput X-ray diffraction measurements generate huge amounts of data. The agent renders them usable more quickly.

Artificial intelligence (AI) can analyse large amounts of data, such as those generated when analysing the properties of potential new materials, faster than humans. However, such systems often tend to make definitive decisions even in the face of uncertainty; they overestimate themselves. An international research team has stopped AI from doing this: the researchers have refined an algorithm so that it works together with humans and supports decision-making processes. As a result, promising new materials can be identified more quickly.

A team headed by Dr. Phillip M. Maffettone (currently at National Synchrotron Light Source II in Upton, USA) and Professor Andrew Cooper from the Department of Chemistry and Materials Innovation Factory at the University of Liverpool joined forces with the Bochum-based group headed by Lars Banko and Professor Alfred Ludwig from the Chair of Materials Discovery and Interfaces and Yury Lysogorskiy from the Interdisciplinary Centre for Advanced Materials Simulation. The international team published their report in the journal Nature Computational Science from 19 April 2021.

Read more on the BNL website

Image: Daniel Olds (left) and Phillip M. Maffettone working at the beamline.

Credit: BNL

Building knowledge of changes in uranium chemistry

Building knowledge of changes in uranium chemistry

ANSTO’s considerable expertise in characterising uranium-containing compounds has contributed to a new systematic investigation of the origins of atomic structural distortions in a family of actinide compounds.

These compounds are known as rutile-related mixed metal ternary (three-part) uranium oxides. Rutile refers to mineral compounds composed primarily of titanium dioxide.

In research published in Inorganic Chemistry, a large team of researchers used both neutron and synchrotron radiation and theoretical calculations to establish systematically precise and accurate crystal structures and uranium oxidation states in the rutile-related mixed metal ternary uranium oxide systems.

Read more on the ANSTO website

Image:  Dr Zhaoming Zhang, Principal Research Scientist, Nuclear Fuel Cycle, ANSTO

Credit: ANSTO

Perfect recipe for efficient perovskite solar cells

Perfect recipe for efficient perovskite solar cells

A long-cherished dream of materials researchers is a solar cell that converts sunlight into electrical energy as efficiently as silicon, but that can be easily and inexpensively fabricated from abundant materials. Scientists at the Helmholtz-Zentrum Berlin have now come a step closer to achieving this. They have improved a process for vertically depositing a solution made from an inexpensive perovskite solute onto a moving substrate below. Not only have they discovered the crucial role played by one of the solvents used, but they have also taken a closer look at the aging and storage properties of the solution.

Solar cells made of crystalline silicon still account for the lion’s share of roof installations and solar farms. But other technologies have long since become established as well – such as those that convert sunlight into electrical energy through use of extremely thin layers of solar-cell material deposited upon a substrate. The perovskite solar cells that Prof. Eva Unger and her team at the Helmholtz-Zentrum Berlin (HZB) are researching belong to this group. “These are the best solar cells to date that can be made using a 2D ink”, the researcher explains. “And now their efficiencies are approaching those for cells made of crystalline silicon.”

Read more on the HZB website

Image: The liquid solution of perovskite precursor, solvent, and additive flows from a slit-shaped nozzle onto the glass substrate being conveyed below.

Credit: © Jinzhao Li / HZB

Surviving the deep freeze

Surviving the deep freeze

Key proteins protect wildlife when the temperature drops

It is hard to imagine what some fish, carrots and tiny snow fleas might have in common, but it turns out it is something key to their survival when the temperature drops below freezing.

The common trait, also shared by insects, bacteria and other microorganisms, is antifreeze proteins (AFP). As the name suggests, AFPs work “to prevent organisms from freezing or to help them survive in a frozen state,” explained Dr. Peter Davies, a professor at Queen’s University and Canada Research Chair in Protein Engineering.

Davies has been studying these unique proteins for about 40 years. His latest research, aided by X-ray diffraction techniques at the Canadian Light Source (CLS) at the University of Saskatchewan was recently published in The FEBS Journal. This study continues to build knowledge about AFP structures, their function and evolution.

Read more on the CLS website

Image: A snow flea (Granisotoma rainieri) that was collected in Japan by coauthor Dr Sakae Tsuda

Credit: Canadian Light Source (CLS)

Under wraps: X-rays reveal 1,900-year-old mummy’s secrets

Under wraps: X-rays reveal 1,900-year-old mummy’s secrets

Researchers used the powerful X-rays of the Advanced Photon Source to see the preserved remains of an ancient Egyptian girl without disturbing the linen wrappings. The results of those tests point to a new way to study mummified specimens.

The mummified remains of ancient Egyptians hold many secrets, from the condition of the bodies to the artifacts placed within the burial garments. Now a team of researchers has found a way to unwrap those secrets, without unraveling the mummies themselves.

Three years ago, researchers from Northwestern University, in preparation for an exhibit on campus, carefully transported a 1,900-year-old mummy to the Advanced Photon Source (APS), a U.S. Department of Energy (DOE) Office of Science User Facility at DOE’s Argonne National Laboratory. There scientists used powerful X-ray beams to peer inside the layers of linen and resin to examine the 2,000-year-old bones and objects buried within.

Read more on the Argonne National Laboratory website

Image: In 2017, Stuart Stock, center, of Northwestern University, talks with Rachel Sabino, right, of the Art Institute of Chicago while Argonne scientist Ali Mashayekhi, left, makes adjustments to the apparatus holding a 1,900-year-old Egyptian mummy.

Credit: Mark Lopez / Argonne National Laboratory.

Shedding light on the causes of arsenic contamination

Shedding light on the causes of arsenic contamination

An international team has used the Canadian Light Source at the University of Saskatchewan to uncover the elusive structure of two arsenic-containing compounds, information that can be used to prevent and predict arsenic contamination.

Arsenic occurs naturally in the environment, and it is present in ore deposits and the waste left behind by mining for gold, uranium, and other metals. The concern with arsenic-containing compounds, like yukonite and arseniosiderite, is that soil sources can find their way into waterways. Understanding how this happens on a structural level can help scientists — and industry — better understand how the two are formed and better protect the surrounding environment from potential arsenic contamination.

Discovered more than 100 years ago, yukonite and arseniosiderite, which are compounds of arsenic, calcium, iron and oxygen, have concealed their structure from scientists thanks to their low crystallinity. While it’s relatively easy to determine the structure of materials that have a high degree of crystallinity, because of the complexity in the way these minerals’ atoms are arranged, usual methods have come up short in painting a clear picture of their structure.

Using a special technique at the CLS called the pair distribution function (PDF), an international team of researchers from Canada, China, the USA, Italy, and Ireland was able to visualize for the first time how atoms are structured in samples of arseniosiderite, which is classified as semi-crystalline, and yukonite, which is considered a nano-crystalline mineral.

Read more on the CLS website

 Image: Specimen BM.62813 from the collections of the Natural History Museum, London 

Credit: © The Trustees of the Natural History Museum, London

The African fly of death might also save lives

The African fly of death might also save lives

For the first time, an international team of scientists recreated in the lab the molecule that allows the tsetse fly to feed on blood. It’s a powerful yet small anticoagulant with a unique and strong binding to thrombin, the key enzyme of the coagulation pathway. X-ray diffraction measurements at two synchrotron facilities ––ALBA and ESRF–– were instrumental to understand the structure and the mechanism of action of this molecule, which suggests it is also a promising platform for designing improved anticoagulant drugs.

 In the waiting rooms of health care facilities around the world, millions of patients take anticoagulants every day. These are life-saving drugs for the treatment of cardiovascular diseases, which now are also being explored for their benefits to patients with advanced symptoms of COVID-19.

And, as incredible as it may seem, the tsetse fly, responsible for the sleeping sickness disease in humans, is now on the spotlight in the efforts to develop more powerful and safer anticoagulants. 

In a study co-authored by Bárbara Calisto, researcher at the ALBA Synchrotron, an international team of scientists has become the first to recreate in the lab the molecule that the tsetse fly uses to prevent coagulation when it bites to feed. These bites are also the entry channel for the parasite that causes sleeping sickness, a life-threatening disorder, if untreated. And the reason why the tsetse fly has been dubbed as the fly of death in Africa.

Read more on the ALBA website

Image:  Bárbara Calisto at the XALOC beamline of the ALBA Synchrotron

Credit: ALBA