Angular measurement goes nano

At Diamond Light Source we have built and developed a state-of-the art optical metrology laboratory which is equipped with instruments to test and inspect extremely precise mirrors used to focus X-rays for Diamond’s beamlines.

To calibrate this measuring equipment we needed a device that can produce very tiny angle changes in a precise and controlled way.

Imagine a 1m long spirit level set on a flat surface, then place a 1mm spacer under one end. That gives an angular change of 1/1,000 of a radian or 1 milliradian. Radians are an alternative way of describing angles instead of degrees.

Now, instead of a 1m spirit level, we use a 1000km long spirit level, with a 1mm spacer under one end. This would create an angular change of  1 nanoradian, which is exactly what Diamond’s Nano-angle generator (NANGO) can accuractely create.

Image: Diamond-NANGO, with its rotation axis pointing in the horizontal direction.

How legionella manipulates the host cell by means of molecular mimics

Using synchrotron light, researchers from CIC bioGUNE have solved the structure of RavN, a protein that Legionella pneumophila uses for stealing functions and resources of the host cell.

Mimicry is the ability of some animals to resemble others in their environment to ensure their survival. A classic example is the stick bug whose shape and colour make him unnoticed to possible predators. Many intracellular pathogens also use molecular mimicry to ensure their survival. A part of a protein of the pathogen resembles another protein totally different from the host and many intracellular microorganisms use this capability to interfere in cellular processes that enable their survival and replication.

The Membrane Trafficking laboratory of the CIC bioGUNE in the Basque Country, led by Aitor Hierro, in collaboration with other groups from the National Institutes of Health in the United States, have been working for several years in understanding how the infectious bacterium Legionella pneumhopila interacts with human cells. During this research, experiments have been carried out at the XALOC beamline of the ALBA Synchrotron and I04 beamline of Diamond Light Source (UK). The results enabled scientists to solve the structure of RavN, a protein of L. pneumophila that uses this molecular mimicry to trick the infected cell.

>Read more on the ALBA website

Figure: (extract) Schematic representation of the structure of RavN1-123 as ribbon diagram displayed in two orientations (rotated by 90° along the x axis). Secondary elements are indicated as spirals (helices) or arrows (beta strands), with the RING/U-box motif colored in orange and the C-terminal structure colored in slate. (Full image here)

Diamond celebrates publication of its 7000th paper

A paper in PNAS by an international scientific collaboration from the UK, Germany and Switzerland is the 7000th to be published as a result of innovative research conducted at Diamond Light Source, the UK’s Synchrotron.

This new paper reveals details of the 3D spin structure of magnetic skyrmions, and will be of key importance for storing digital information in the development of next-generation devices based on spintronics.

Laurent Chapon, Diamond’s Physical Sciences Director, explains the significance of these new findings:  “A skyrmion is similar to a nanoscale magnetic vortex, made from twisted magnetic spins, but with a non-trivial topology that is ‘protecting them’. They are therefore stable, able to move, deform and interact with their environment without breaking up, which makes them very promising candidates for digital information storage in next-generation devices. For years, scientists have been trying to understand the underlying physical mechanisms that stabilise magnetic skyrmions, usually treating them as 2D objects. However, with its unique facilities and ultra-bright light, Diamond has provided researchers the tools to study skyrmions in 3D revealing significant new data.”

As spintronic devices rely on effects that occur in the surface layers of materials, the team was investigating the influence of surfaces on the twisted spin structure. It is commonly assumed that surface effects only modify the properties of stable materials within the top few atomic layers, and investigating 3D magnetic structures is a challenging task. However, using the powerful circularly polarised light produced at Diamond, the researchers were able to use resonant elastic X-ray scattering (REXS) to reconstruct the full 3D spin structure of a skyrmion below the surface of Cu2OSeO3.

>Read more on the Diamond Light Source website

Image: (extract) Illustration of a ‘Skyrmion tornado’. The skyrmion order changes from Néel-type at the surface to Bloch-type deeper in the sample. On the right hand side, the corresponding stereographic projections of these two boundary skyrmion patterns are shown. Full image and detailed article here.

Probing the complex dielectric properties of MOFs

Gaining fundamental insights into the full dielectric behaviour of MOFs across the infrared and THz.

An international team of researchers from Oxford, Diamond, and Turin, has demonstrated the novel use of synchrotron radiation infrared (SRIR) reflectivity experiments, to measure the complex and broadband dielectric properties of metal-organic framework (MOFs) materials. Open framework compounds like MOFs have the potential to revolutionise the field of low-k dielectrics, because of their tuneable porosity coupled with an enormous combination of physicochemical properties not found in conventional systems. Furthermore, next generation IR optical sensors and high-speed terahertz (THz) communication technologies will stand to benefit from an improved understanding of the fundamental structure-property relations underpinning novel THz dielectric materials.

>Read more on the Diamond Light Source website

Image: (extract) The high-resolution reflectivity data obtained were subsequently used to determine the real and imaginary components of the complex dielectric function by adopting the Kramers−Kronig Transformation theory.
Credit: ACS

Probing tumour interiors

X-ray fluorescence mapping to measure tumour penetration by a novel anticancer agent.

A new anticancer agent developed by the University of Warwick has been studied using microfocus synchrotron X-ray fluorescence (SXRF) at I18 at Diamond Light Source. As described in The Journal of Inorganic Biochemistry, researchers saw that the drug penetrated ovarian cancer cell spheroids and the distribution of zinc and calcium was perturbed.  

Platinum-based chemotherapy agents are used to treat many cancer patients, but some can develop resistance to them. To address this issue, scientists from the University of Warwick sought to employ alternative precious metals. They developed an osmium-based agent, known as FY26, which exhibits high potency against a range of cancer cell lines. To unlock the potential of this novel agent and to test its efficacy and safety in clinical trials, the team need to fully understand its mechanism of action.

To explore how FY26 behaves in tumours, the team grew ovarian cancer spheroids and used SXRF at I18 to probe the depth of penetration of the drug. They noted that FY26 could enter the cores of the spheroids, which is critical for its activity and very encouraging for the future of the drug. SXRF also enabled them to probe other metals within the cells, which showed that the distribution of zinc and calcium was altered, providing new insights into the mechanism of FY26-induced cell death.

>Read more on the Diamond Light Source website

Figure: (extract) A) Structure of FY26and related complexes, [(ŋ6-p-cym)Os(Azpy-NMe2)X]+. B) Bright field images and SXRF elemental maps of Os, Ca and Zn in A2780 human ovarian carcinoma spheroid sections (500 nm thick) treated with 0.7 µM FY26(½ IC50) for 0 or 48 h. Raster scan: 2×2 µm2 step size, 1 s dwell time. Scale bar 100 µm. Calibration bar in ng mm-2. Yellow squares in bright field images indicate areas of the spheroid studied using SXRF. Red areas in SXRF elemental maps indicate the limits of the spheroids. C) Average Os content (in ng mm-2) as a function of distance from A2780 3D spheroid surface, after treatment for 16 h (green), 24 h (blue) or 48 h (red) with 0.7 µM FY26. 

The power of radio!

A century after the invention of radio, the oscillating electric fields initially generated for communication now perform a fundamental function in all accelerators.

Instead of being broadcast to the world, radiofrequency (RF) energy at Diamond is trapped in resonating metal cavities to generate the electric fields that bring Diamond’s electrons up to speed.

The journey of an electron from source to storage ring is a tale of high power, split-second timing and frankly terrifying voltages. It begins in the linac gun where energetic, hot electrons are sucked away from a metal cathode by 90,000 volts and directed into the linear accelerator, or linac. The electrons travel down the linac together with precisely timed 16 megawatt blasts of microwaves generated by klystron amplifiers that themselves operate at pulsed voltages in excess of 200,000 volts. Electrons are accelerated towards the speed of light in the linac and then injected into the booster synchrotron where they complete many orbits over a tenth of a second.

>Read more on the Diamond Light Source website

Image: The linac, with the gun at the far end and the accelerating structures coming towards us.

A surprising twist on skyrmions

Magnetic tomography has been used to reconstruct a tornado-like 3D magnetic skyrmion structure.

Vortex structures are common in nature, reaching from swirls in our morning coffee to spiral galaxies in the universe. Vortices are been best known from fluid dynamics. Take the example of a tornado. Air circulates around an axis, forming a swirl, and once formed, the twisted air parcels can move, deform, and interact with their environment without disintegrating. A skyrmion is the magnetic version of a tornado which is obtained by replacing the air parcels that make up the tornado by magnetic spins, and by scaling the system down to the nanometre scale. Once formed, the ensemble of twisted spins can also move, deform, and interact with their environment without breaking up ‒ the ideal property for information carriers for memory and logic devices.

What makes a tornado stable is not only coming from its twist, but also due to its three-dimensional properties, i.e., the wind current has extra twist along the column of turbulent flow. This leads to a tight bundling of the vortex sheets at different heights along the tornado column. Similarly, such a 3D structure can also occur in magnetic skyrmions, guaranteeing their topological stability. Up to now, skyrmions have been most commonly treated as two-dimensional objects, and their exciting tornado-like structure remained unexplored. In fact, the 3D characterization of magnetic structures is a rather challenging task. A team of researchers, led by the University of Oxford and Diamond Light Source, have used the energy-dependence of resonant elastic X-ray scattering (REXS) on beamline I10 at Diamond to measure the microscopic depth dependence of ‘skyrmion tornados’ in Cu2OSeO3. In their work, published in Proceedings of the National Academy of Sciences, they reveal a continuous change from Néel-type winding at the surface to Bloch-type winding in the bulk with increasing depth. This not only demonstrates the power of REXS for microscopic studies of surface-induced reconstructions of magnetic order, but also reveals the hidden energetics that makes magnetic skyrmions such a stable state – a crucial finding for skyrmion device engineering.

>Read more on the Diamond Light Source website

Figure: Illustration of a ‘Skyrmion tornado’. The skyrmion order changes from Néel-type at the surface to Bloch-type deeper in the sample. On the right hand side, the corresponding stereographic projections of these two boundary skyrmion patterns are shown.

New forensic DNA profiling technique on the horizon

A study recently conducted at the Circular Dichroism beamline (B23) here at Diamond Light Source could pave the way to a new forensic DNA profiling technique. Researchers hailing from the Ivanovo State University of Chemistry and Technology, Russia, The University of Southampton and Diamond investigated the application of specially designed DNA building blocks.

DNA is a versatile template that can be used for a variety of applications. It is made up of building blocks known as nucleotides (labelled A, C, G and T) which form long strands that bind to complementary sequences and give the familiar double helix. The nucleotides can be tailor made to build new functional molecules for biotechnology, analytics, or even materials science.

>Read more on the Diamond Light Source website


The power supplies giving Diamond a boost

The electrons that produce Diamond’s ultra-bright light whizz round the storage ring fast enough to travel around the entire world 7.5 times in a single second. But they don’t start out life super speedy, and they need a huge energy boost to get them ready for work!

Diamond’s electrons are generated in the injection system, where they are produced by a glowing filament (just like a dim light bulb) and accelerated to ninety thousand electron volts (90 keV). From there, a linear accelerator (linac) takes over, accelerating the electrons to a hundred million electron volts (100 MeV, or 0.1 GeV).

That’s not fast enough though, so the electrons from the linac are fed into the booster ring, where they’re are accelerated to 3 GeV by passing through an RF cavity millions of times. It’s like microwaving the electrons to get them to accelerate, which is not an easy task. The electrons want to travel in a straight line, and have to be forced to bend around the ring by dipole bending magnets. As the energy of the electrons increases, it gets harder to keep them moving around the booster ring, and the bending magnets need more power.

>Read more on the Diamond Light Source website

Image: Members of the Power Supply team working in the Booster Supply Hall.

Metallic drivers of Alzheimer’s disease

The detection of iron and calcium compounds in amyloid plaque cores

X-ray spectromicroscopy at the Scanning X-ray Microscopy beamline (I08), here at Diamond, has been utilised to pinpoint chemically reduced iron and calcium compounds within protein plaques derived from brains of Alzheimer’s disease patients. The study, published in Nanoscale, has shed light on the way in which metallic species contribute to the pathogenesis of Alzheimer’s disease and could help direct future therapies.

Alzheimer’s disease is a neurodegenerative disease that is associated with dementia and shortened life expectancy. The disease is characterised by the formation of protein plaques and tangles in the brain that impair function. As well as protein plaques, perturbed metal ion homeostasis is also linked with pathogenesis, and iron levels in particular are elevated in certain regions of the brain.

A team of scientists with a long history in exploring biomineralisation in Alzheimer’s brains set out to characterise the iron species that are associated with the amyloid protein plaques. They extracted samples from the brains of two deceased patients who had Alzheimer’s and applied synchrotron X-ray spectromicroscopy to differentiate the iron oxide phases in the samples.

They noted evidence that the chemical reduction of iron, and indeed the formation of a magnetic iron oxide called magnetite, which is not commonly found in the human brain, had occurred during amyloid plaque formation, a finding that could help inform the outcomes of future Alzheimer’s therapies.

>Read more on the Diamond Light Source website

Image: Synchrotron soft X-ray nano-imaging and spectromicroscopy reveals iron and calcium biomineralisation in Alzheimer’s disease amyloid plaques.

Understanding how alkaline treatment affects bamboo

In China, bamboo is a symbol of longevity and vitality, able to survive the hardest natural conditions and remain green all year round. In a storm, bamboo stems bend but do not break, representing the qualities of durability, strength, flexibility and resilience1.

Bamboo is a traditional construction material in Asia. Its strength and flexibility arise from its hollow stems (‘culms’) made from distinct material components. The solid outer shell of the culm is made primarily from longitudinal fibres. A higher density at the outer wall makes it stronger than the inner regions, and results in remarkable stiffness and flexural strength. Running through the centre of bamboo stem are parenchyma cells that store and channel the plant’s nutrients.

At the micro-/nano-scale both the fibres and the matrix contain cellulose nano-fibrils of the same type. However, the structural arrangement of the two materials result in contrasting mechanical properties. Individual fibres may reach a strength of 900 MPa, whilst the matrix can only resist about 50 MPa. There is also a considerable difference in their elastic properties, with the fibres being much stiffer than the matrix.

Bamboo is often treated with alkaline solutions, to modify these properties. Alkaline treatments can turn this rapidly renewable and low-cost resource into soft textiles, and extract fibres to be used in composite materials or as biomass for fuel.

>Read more on the Diamond Light Source website

Image: Dr Enrico Salvati on the B16 beamline at Diamond.

The proteins that bind

Researchers reveal the structure of a protein that helps bacteria aggregate

Serine-rich repeat proteins (SRRPs), which help bacteria attach to surfaces, have been structurally characterised in pathogenic bacteria but not in beneficial bacteria such as those present in the gut. Dr Nathalie Juge’s team at the Quadram Institute Bioscience has previously identified SRRP as a main adhesin in Lactobacillus reuteri strains from pigs and mice. Now, together with colleagues at the University of East Anglia, they have described the structure and activity of the binding region of L. reuteri SRRPs in a paper published in PNAS. Using the Macromolecular Crystallography beamlines (I03 and I04) at Diamond Light Source, they discovered that the structure of these proteins is unique among characterised SRRPs and is surprisingly similar to pectin degrading enzymes. Molecular simulations and binding experiments revealed a pH-dependent binding to pectin and to proteins from the epithelium known as mucins. Altogether, these findings shed light on the activity of a key protein in these bacteria and may help guide the development of more targeted probiotic interventions.

>Read more on the Diamond Light Source website

Figure: (Left) Cartoon representation of crystal structures of the binding region of SRRP53608. (Right) Cartoon representation of crystal structures of the binding region of SRRP100-23. The N-terminus is shown with blue balls and the C-terminus is shown with red balls.

A new Polarisation Analyser, and the benefits of 3D printing

The I16 beamline at Diamond is dedicated to the study of advanced materials using X-ray diffraction; part of this process is to use a device, known as a polarisation analyser (PA) that can analyse magnetic scattering from samples. Magnetic scattering is different to, and weaker than, normal X-ray scattering and analysis of the polarisation of this scattering can be used to gain insights into the magnetic properties of materials. Researchers can use this information to determine details of the 3D structure of the sample material.

The design of the PA includes an assembly of vacuum chambers, sets of slits to remove unwanted scattering and various detectors, arranged to rotate about different axes. Researchers use data collected from the detectors as they are moved and rotated to build up information on the polarisation of the scattering.

>Read more on the Diamond Light Source website

Image: extract of the polarisation analyser; to watch the video “The motion of the main axes of the polarisation analyser”, please have a look here.


Garnet gemstones contain secrets of our seismic past

Somewhere in the world an earthquake is occurring. In general, it will be a small tremor, an earthquake of magnitude two or lower, which humans cannot even feel. However when a major earthquake occurs, of magnitude 7 or above, it can cause devastating damage, events like tsunamis, and loss of life. These type of quakes, like the 2011 event in Japan and 2015 Nepalese events, happen around 20 times each year worldwide.

Large earthquakes tend to occur in subduction zones, such as the so-called Ring of Fire, where tectonic plates meet and one is bent and forced underneath the other, into the mantle of the earth. As well as leading to earthquakes, subduction also causes the composition and structure of the rock itself to become altered, in a process called high-pressure/low temperature metamorphism.

Metamorphism can take a variety of forms, in a number of different rocks, but one that is of particular interest is a type called rhythmic major-element zoning, in the mineral garnet. If found it can be a sign that subduction has occurred, and it can act as a record of seismicity in the crust of our Earth.

>Read more on the Diamond Light Source website

Solution to plastic pollution on the horizon

Engineering a unique plastic-degrading enzyme

The inner workings of a recently discovered bacterium with a fascinating ability to use plastic as an energy source have been recently revealed in PNAS. The world’s unique Long-Wavelength Macromolecular Crystallography (MX) beamline here at Diamond Light Source was used to successfully solve the structure of the bacterial enzyme responsible for chopping up the plastic. This newly evolved enzyme could be the key to tackling the worldwide problem of plastic waste.

Plastic pollution is a global threat that desperately needs addressing. Plastics are rarely biodegradable and they can remain in the environment for centuries. One of the most abundant plastics that contributes hugely to this dire situation is poly(ethylene terephthalate) (PET).

PET is used largely in textiles, where it is commonly referred to as polyester, but it is also used as packaging for liquids and foodstuffs. In fact, PET’s excellent water-repellent properties led to it being the plastic of choice for soft drink bottles. However, once plastic bottles are discarded in the environment the water resistance of PET means that they are highly resistant to natural biodegradation. PET bottles can linger for hundreds of years and plastic waste like this will accumulate over time unless a solution is found to degrade them.

A recent breakthrough came in the discovery of a unique bacterium, Ideonella sakaiensis 201-F6, which was found feeding on waste from an industrial PET recycling facility. PET has only been widely used since the 1970s, so the bacterium had evolved at breakneck speed to be able to take advantage of the new food source.

The bacterium had the amazing ability to degrade PET and use it to provide carbon for energy. Central to this ability was the production of a PET-digesting enzyme, known as PETase.

>Read more on the Diamond Light Source website