How catalysts age

PSI researchers have developed a new tomography method with which they can measure chemical properties inside catalyst materials in 3-D extremely precisely and faster than before. The application is equally important for science and industry. The researchers published their results today in the journal Science Advances.

The material group of vanadium phosphorus oxides (VPOs) is widely used as a catalyst in the chemical industry. VPOs have been used in the production of maleic anhydride since the 1970s. Maleic anhydride in turn is the starting material for the production of various plastics, increasingly including biodegradable ones. In industry, the catalytic materials are typically used for several years, because they play an important role in the chemical reactions but are not consumed in the process. Nevertheless, a VPO catalyst changes over time as a result of this use.

In a collaborative effort, scientists from two research divisions at the Paul Scherrer Institute PSI – the Photon Science Division and the Energy and Environment Division – together with researchers at ETH Zurich and the Swiss company Clariant AG, have now investigated in detail the ageing process of VPO catalysts. In the course of their research, they also developed a new experimental method.

Read more in the PSI website

Image: Zirui Gao, a researcher at PSI, has developed a new algorithm for experimental studies that significantly shortens the duration of certain imaging measurements that would otherwise take too long. The researchers used it to investigate ageing processes in a much-used catalyst material on the nanoscale.

Credit: Paul Scherrer Institute/Markus Fischer

Dramatic impact of crystallographic conflict on material properties

Many material properties are associated with structural disorder that exhibits local periodicity or correlations. A new form of this phenomenon exhibiting strong disorder-phonon coupling has been shown to arise in response to crystallographic conflict, with dramatic phonon lifetime suppression.

In recent years there has been a rapidly growing understanding that, hidden within the globally periodic structures of many crystals, various forms of disorder may exist that could form ‘locally periodic’ states, which the language of classic crystallography fails to describe. Such phenomena are commonly referred to as ‘correlated disorder’ and in many functional materials, from leading ferroelectric and thermoelectric candidates to photovoltaic perovskites and ionic conductors, this correlated deviation from perfect periodicity plays a pivotal role in governing functionality. As such, understanding the role of disorder, and the correlations that exist within it, is one of the defining challenges for the development of future functional materials.

Read more on the ESRF website

Image: Fig. 1: a) Reciprocal space reconstructions of the (hk2)s plane. All three samples investigated are shown with relevant at. % Mo indicated. Reflections are categorised and indexed in the bottom right quadrant, parent Bragg peaks (black) and diffuse superstructure reflections from two different domains (blue/green). b) Orientational relationship between parent (blue) and superstructure (red) unit cells for one of six possible domains. All atoms in the “shear plane” (highlighted red) move collinearly with the direction of motion indicated by arrows on the plane edge. Alternate planes, demarcated by I, I, III, … , move in antiphase. c) Top-down view showing the 45 relationship between the parent and superstructure. d) Schematic of the atomic motions in a “phonon plane.” Blue dashed and red dotted lines refer to interatomic bonding in the parent and superstructure unit cells, respectively.

Physicists uncover secrets of world’s thinnest superconductor

Physicists report the first experimental evidence to explain the unusual electronic behaviour behind the world’s thinnest superconductor, a material with myriad applications because it conducts electricity extremely efficiently. In this case the superconductor is only an atomic layer thick. 

The research, led by Massachusetts Institute of Technology and Brookhaven National Laboratory, was possible thanks to new instrumentation available at Diamond.  

Diamond is one of only a few facilities in the world to use the new experimental technique, Resonant Inelastic X-ray Scattering (RIXS), which is a combination of X-ray Absorption Spectroscopy (XAS) and X-ray Emission Spectroscopy (XES), where both the incident and emitted energies are scanned. This state-of-the-art facility is where the team from three continents conducted their experiment.  

Read more on the Diamond website

Image: Members of the RIXS team at Diamond. Left to right: Jaewon Choi (Postdoc), Abhishek Nag (Postdoc), Mirian Garcia Fernandez (Beamline Scientist), Charles Tam (joint PhD student), Thomas Rice (Beamline technician), Ke-Jin Zhou (Principal Beamline Scientist), Stefano Agrestini (Beamline Scientist).

Structure-guided nanobodies block SARS-CoV-2 infection

Monoclonal antibodies are valuable weapons in the battle against COVID-19 as direct-acting antiviral agents (1). Central to virus replication cycle, the SARS-CoV-2 spike protein binds the host cell receptor and engages in virus-host membrane fusion (2). Conformational flexibility of the spike protein allows each of its receptor binding domains (RBDs) to exist in two major configurations: a “down” conformation that is thought to be less accessible to binding of many neutralizing antibodies and an “up” conformation that binds both the receptor and neutralizing antibodies (3-5). Some neutralizing antibodies bind to the RBD in the “up” conformation and compete with the receptor (6, 7), while some neutralizing antibodies bind and stabilize the “down” confor­mation to prevent the conforma­tional changes required for viral entry, thereby hindering infection (8, 9).

Unfortunately, antibody molecules can be more difficult to produce in large quantities and are relatively costly to produce. Single domain antibodies, also known as nanobod­ies, offer an opportunity to rapidly produce antiviral agents for immun­ization and for therapy. Nanobodies are easier to produce, have high thermal stability and have the potential to be administered by inha­lation.

Read more on the SLAC website

Image: Bivalent nanobodies inducing post-fusion conformation of the SARS-CoV-2 spike protein: SARS-CoV-2 spike proteins are in a fusion inactive configuration when the RBDs are in the down conformation (left). Binding of bivalent nanobody (red and green ribbons joined by yellow tether) stabilizes the spike in an active conformation with all RBDs up (middle), triggering premature induction of the post-fusion conformation, which irreversibly inactivates the spike protein (right).

Magnetic vortices come full circle

The first experimental observation of three-dimensional magnetic ‘vortex rings’ provides fundamental insight into intricate nanoscale structures inside bulk magnets, and offers fresh perspectives for magnetic devices.

Magnets often harbour hidden beauty. Take a simple fridge magnet: Somewhat counterintuitively, it is ‘sticky’ on one side but not the other. The secret lies in the way the magnetisation is arranged in a well-defined pattern within the material. More intricate magnetization textures are at the heart of many modern technologies, such as hard disk drives. Now, an international team of scientists at PSI, ETH Zurich, the University of Cambridge (UK), the Donetsk Institute for Physics and Engineering (Ukraine) and the Institute for Numerical Mathematics RAS in Moscow (Russia) report the discovery of unexpected magnetic structures inside a tiny pillar made of the magnetic material GdCo2. As they write in a paper published today in the journal Nature Physics [1], the researchers observed sub-micrometre loop-shaped configurations, which they identified as magnetic vortex rings. Far beyond their aesthetic appeal, these textures might point the way to further complex three-dimensional structures arising in the bulk of magnets, and could one day form the basis for novel technological applications.

Mesmerising insights

Determining the magnetisation arrangement within a magnet is extraordinarily challenging, in particular for structures at the micro- and nanoscale, for which studies have been typically limited to looking at a shallow layer just below the surface. That changed in 2017 when researchers at PSI and ETH Zurich introduced a novel X‑ray method for the nanotomography of bulk magnets, which they demonstrated in experiments at the Swiss Light Source SLS [2]. That advance opened up a unique window into the inner life of magnets, providing a tool for determining three-dimensional magnetic configurations at the nanoscale within micrometre-sized samples.

Utilizing these capabilities, members of the original team, together with international collaborators, now ventured into new territory. The stunning loop shapes they observed appear in the same GdComicropillar samples in which they had before detected complex magnetic configurations consisting of vortices — the sort of structures seen when water spirals down from a sink — and their topological counterparts, antivortices. That was a first, but the presence of these textures has not been surprising in itself. Unexpectedly, however, the scientists also found loops that consist of pairs of vortices and antivortices. That observation proved to be puzzling initially. With the implementation of novel sophisticated data-analysis techniques they eventually established that these structures are so-called vortex rings — in essence, doughnut-shaped vortices.

Read more on the PSI website

Image: Magnetic beauty within. Reconstructed vortex rings inside a magnetic micropillar.

Credit: Claire Donnelly

Lightsource research on SARS-CoV-2

Coronaviruses are a family which includes the common cold, SARS, MERS and the current outbreak of the disease COVID-19, caused by the SARS-CoV-2 virus.
Several facilities of our collaboration have started research about SARS-CoV-2 virus or launched open calls for rapid access. This post will be updated regularly.

Publications on SARS-CoV-2 Rapid Access




Publications

The Canadian Light Source (Canada) has created a specific page highlighting their COVID-19 research: COVID-19 research at the Canadian Light Source

BESSY II at HZB (Germany) has set up a page where it shows their contributions to the research on SARS-CoV-2 , see here

DESY (Germany) has launched a new page dedicated to Corona Research: https://www.desy.de/news/corona_research/index_eng.html

Diamond Light Source (UK) has created a specific website “Coronavirus Science” with platforms for various audiences: scientific community, general public and the media: https://www.diamond.ac.uk/covid-19.html

ELETTRA (Italy) has launched a new page dedicated to COVID-19 research: https://www.elettra.eu/science/covid-19-research-at-elettra.html

The Photon Division of PSI (Switzerland) have collated many information linked to their institute on coronavirus-relevant research (recent publications, rapid access…): https://www.psi.ch/en/psd/covid-19

ALBA (Spain) has set up a dedicated area on their website for information related to COVID-19 (rapid access, publications etc): https://www.albasynchrotron.es/en/covid-19-information/

The ALS (CA/USA) has created a page listing all COVID-19 related research: https://als.lbl.gov/tag/covid-19/

Published articles

2021.05.11 Swiss Light Source at PSI (Switzerland) article on their website: How remdesivir works against the coronavirus

2021.05.28 SLAC (CA / USA) article from the Stanford Synchrotron Radiation Lightsource (SSRL): Structure-guided Nanobodies Block SARS-CoV-2 Infection | Stanford Synchrotron Radiation Lightsource

2021.05.21 ALS (USA) article on their website: Guiding Target Selection for COVID-19 Antibody Therapeutics

2021.05.21 ESRF (France) article on their website: Combatting COVID-19 with crystallography and cryo-EM (esrf.fr)

2021.05.18 ALS (USA) article on their website: How X-Rays Could Make Reliable, Rapid COVID-19 Tests a Reality | Berkeley Lab (lbl.gov)

2021.04.27 Canadian Light Source (Canada), video on their website Investigating the long-term health impacts of COVID-19 (lightsource.ca)

2021.04.22 Synchrotron Light Research Institute (Thailand), article on their website: SLRI Presented Innovations Against COVID-19 Outbreak to MHESI Minister on His Visit to a Field Hospital at SUT

2021.04.16 Diamond Light Source (UK) article on their website: Massive fragment screen points way to new SARS-CoV-2 inhibitors

2021.04.14 SLAC (CA / USA), article also with news about research at Stanford Synchrotron Radiation Lightsource (SSRL):Researchers search for clues to COVID-19 treatment with help from synchrotron X-rays

2021.04.07 Diamond Light Source (UK), article on their website: First images of cells exposed to COVID-19 vaccine – – Diamond Light Source

2021.04.05 ALS (CA/USA) blog post on Berkeley Lab Biosciences website: New COVID-19 Antibody Supersite Discovered

2021.04.02 PETRA III at DESY (Germany), article and animation on their website DESY X-ray lightsource identifies promising candidate for COVID drugs

2021.03.26 Diamond Light Source (UK), article on their website: New targets for antibodies in the fight against SARS-CoV-2

2021.02.23 Australian Light Source (ANSTO) Australia, article on their website: Progress on understanding what makes COVID-19 more infectious than SARS

2020.12.02 ESRF (France), article and video on their website: ESRF and UCL scientists awarded Chan Zuckerberg Initiative grant for human organ imaging project

2020.11.10 Diamond Light Source (UK), article and video on their website: From nought to sixty in six months… the unmasking of the virus behind COVID-19

2020.10.29 Canadian Light Source (Canada) video on their website: Studying how to damage the COVID-19 virus

2020.10.07 National Synchrotron Light Source II (NSLS-II) at Brookhaven Lab (NY / USA) article on their website: Steady Progress in the Battle Against COVID-19

2020.10.07 Diamond Light Source (UK), article on their website: Structural Biology identifies new information to accelerate structure-based drug design against COVID-19

2020.10.06 MAX IV (Sweden), article on their website: Tackling SARS CoV-2 viral genome replication machinery using X-rays

2020.08.31 SLAC (CA / USA), article also with news about research at Stanford Synchrotron Radiation Lightsource (SSRL): SARS-CoV-2 Spike Protein Targeted for Vaccine

2020.08.27 Diamond Light Source (UK), article on their website: Structural Biology reveals new target to neutralise COVID-19

2020.08.27 Canadian Light Source (Canada) video on their website: Developing more effective drugs

2020.08.25 Australian Synchrotron (ANSTO) (Australia) article on their website: More progress on understanding COVID-19

2020.08.24 DESY (Germany) article on their website: PETRA III provides new insights into COVID-19 lung tissue

2020.08.11 Australian Synchrotron (ANSTO) (Australia) article on their website: Unique immune system of the alpaca being used in COVID-19 research

2020.07.30 Swiss Light Source at PSI (Switzerland) article on their website: COVID-19 research: Anti-viral strategy with double effect

2020.07.29 National Synchrotron Light Source II (NSLS-II) at Brookhaven Lab (NY / USA) article on their website: Ready to join the fight against COVID-19.

2020.07.20 ALBA (Spain) article on their website: A research team from Centro de Investigaciones Biológicas Margarita Salas (CIB-CSIC) uses synchrotron light to study the possible effect of an antitumoral drug of clinical use over the viral cycle of SARS-CoV-2 coronavirus. 

2020.07.15 ALS (USA) article on their website: Antibody from SARS Survivor Neutralizes SARS-CoV-2

2020.07.14 Diamond Light Source (UK), article on their website: Engineered llama antibodies neutralise Covid-19 virus

2020.06.17 European XFEL (Germany) article on their website: Pulling Together: A collaborative research approach to study COVID-19

2020.06.15 European XFEL (Germany) article on their website: Open Science COVID19 analysis platform online

2020.06.09 APS at Argonne National Laboratory (USA) article on their website: Novel Coronavirus Research at the Advanced Photon Source

2020.05. Società Italiana di Fisica publishes an article about research done at Elettra Sincrotrone Trieste (Italy) and the Advanced Light Source (CA / USA): Accelerator facilities support COVID-19-related research

2020.05.27 Diamond Light Source (UK), new animation video demonstrating the work that has been done at Diamond’s XChem facilities.

2020.05.19 Advanced Light Source (CA / USA), article about their latest results: X-ray Experiments Zero in on COVID-19 Antibodies

2020.05.15 Swiss Light Source (Switzerland), article about their first MX results: First MX results of the priority COVID-19 call

2020.05.14 MAX VI (Sweden), article about their research: Tackling SARS CoV-2 viral genome replication machinery using X-rays

2020.05.14 CHESS (NY/USA), article: CHESS to restart in June for COVID-19 research

2020.05.14 the LEAPS initiative brings together many of our European members. The initative published this brochure: Research at LEAPS facilities fighting COVID-19

2020.05.12 Diamond Light Source (UK), article about their collaboration in a consortium: UK consortium launches COVID-19 Protein Portal to provide essential reagents for SARS-CoV-2 research

2020.05.11 Advanced Photon Source (IL/USA), article: Studying Elements from the SARS-CoV-2 Virus at the Bio-CAT Beamline

2020.05.07 European XFEL (Germany), article: European XFEL open for COVID-19 related research

2020.05.06 ESRF (France), article: World X-ray science facilities are contributing to overcoming COVID-19

2020.04.29. BESSY II at HZB (Germany), article: Corona research: Consortium of Berlin research and industry seeks active ingredients

2020.04.29. Swiss Light Source and SwissFEL at PSI (Switzerland), interview series on the PSI website: Research on Covid-19

2020.04.23. PETRA III at DESY (Germany), article: X-ray screening identifies potential candidates for corona drugs

2020.04.21. MAX IV (Sweden), article: BioMAX switches to remote operations in times of COVID-19

2020.04.16. SLAC (CA / USA), article also with news about research at Stanford Synchrotron Radiation Lightsource (SSRL): SLAC joins the global fight against COVID-19

2020.04.15 Berkeley National Lab (CA/ USA), article with a focus on the research at the Advanced Light Source (ALS):
Staff at Berkeley Lab’s X-Ray Facility Mobilize to Support COVID-19-Related Research

2020.04.07 Diamond Light Source (UK), article: Call for Chemists to contribute to the fight against COVID-19
Crowdfunding: COVID-19 Moonshot

2020.04.07. ANSTO’s Australian Synchrotron (Victoria), article: Aiding the global research effort on COVID-19

2020.04.06. National Synchrotron Light Source II (NSLS-II) at Brookhaven Lab (NY / USA), article: Brookhaven Lab Mobilizes Resources in Fight Against COVID-19

2020.04.02. BESSY II at HZB (Germany), article: Corona research: Two days of measuring operation to find the right key

2020.03.31 Diamond Light Source (UK), article: Jointly with Exscientia and Scripps Research, Diamond aims to accelerate the search for drugs to treat COVID-19

2020.03.27 Argonne National Laboratory with the Advanced Photon Source (APS) and other facilities on-site (IL / USA), article: Argonne’s researchers and facilities playing a key role in the fight against COVID-19

2020.03.27 ANSTO’s Australian Synchrotron (Victoria), article and video: Helping in the fight against COVID-19

2020.03.25 PETRA III at DESY (Germany), article: Research team will X-ray coronavirus proteins

2020.03.23 Diamond Light Source (UK) releases its first animation explaining: SARS-CoV-2 Mpro Single Crystal Crystallography

2020.03.25 CERN Courrier (Switzerland) article about synchrotron research on SARS-CoV-2, written by Tessa Charles (accelerator physicist at the University of Melbourne currently based at CERN, completed her PhD at the Australian Synchrotron): Synchrotrons on the coronavirus frontline

2020.03.19 BESSY II at Helmholtz-Zentrum Berlin (Germany), research publication: Coronavirus SARS-CoV2: BESSY II data accelerate drug development

2020.03.19 BESSY II at Helmholtz-Zentrum Berlin (Germany), technique explanation webpage: Protein crystallography at BESSY II: A mighty tool for the search of anti-viral agents

2020.03.16 Diamond Light Source (UK), article on their “Coronavirus Science” website: Main protease structure and XChem fragment screen

2020.03.12. Elettra Sincrotrone (Italy), article on their website: New project to fight the spread of Coronavirus has been approved

2020.03.05. Advanced Photon Source (IL / USA), article on their website: APS Coronavirus Research in the Media Spotlight

2020.03.05. Advanced Photon Source (IL / USA), research publication: “Crystal structure of Nsp15 endoribonuclease NendoU from SARS-CoV-2,” bioRXiv preprint  DOI: 10.1101/2020.03.02.968388, Article on their website (source: Northwestern University): New Coronavirus Protein Reveals Drug Target




Rapid access

Scientists can apply for rapid access at following facilities (only member facilities of Lightsources.org are referenced, the most recent published (or updated) call is mentioned first).

  • The National Synchrotron Light Source II (NSLS-II) in NY / USA is offering a streamlined and expedited rapid access proposal process for groups that require beam time for structural biology projects directly related to COVID-19. The Center for Biomolecular Structure team is supporting remote macromolecular crystallography experiments at Beamlines 17-ID-1 (AMX) and 17-ID-2 (FMX) in this research area. To submit a macromolecular crystallography proposal for COVID-19 related research, use the following form:
    https://surveys.external.bnl.gov/n/RapidAccessProposal.aspx
  • The Advanced Photon Source (APS) at Argonne National Laboratory in IL / USA  user program is operational to support:

·         Research on SARS-CoV-2 or other COVID-19-related research that addresses the current pandemic.

·         Critical, proprietary pharmaceutical research.

·         Mail-in/remote access work for any research involving low-risk samples and most medium-risk samples (as defined on the APS ESAF form).

·         Limited in situ research (set-up with one person, and ability to carry out majority of experiment safely remotely)
https://www.aps.anl.gov/Users-Information/About-Proposals/Apply-for-Time

PETRA III at DESY in Germany offers also Fast Track Access for Corona-related research:
https://photon-science.desy.de/users_area/fast_track_access_for_covid_19/index_eng.html

Australian Synchrotron at ANSTO makes its macromolecular crystallography beamlines available to structural biologists in response to the COVID-19 pandemic: https://www.ansto.gov.au/user-access

North American DOE lightsource facilities have created a platform to enable COVID-19 research. There you can find ressources and points of contact to request priority access:
Structural Biology Resources at DOE Light Sources

Elettra Sincrotrone Trieste in Italy opens to remote acces following beamlines: XRD1, XRD2, SISSI-BIO and MCX thanks to an CERIC-ERIC initiative:
https://www.ceric-eric.eu/2020/03/10/covid-19-fast-track-access/
http://www.elettra.eu/userarea/user-area.html

The Advanced Light Source (ALS) at LBNL in California / USA has capabilities relevant to COVID-19 and researchers can apply through their RAPIDD mechanism:
https://als.lbl.gov/apply-for-beamtime/

ALBA Synchrotron in Spain offers a COVID-19 RAPID ACCESS on all beamlines:
https://www.albasynchrotron.es/en/en/users/call-information

SOLARIS Synchrotron in Poland gives acces to its Cryo Electron Microscope thanks to an CERIC-ERIC initiative: https://www.ceric-eric.eu/2020/03/10/covid-19-fast-track-access/

Swiss Light Source and Swiss FEL at PSI in Switzerland offer priority access to combating COVID-19:
https://www.psi.ch/en/sls/scientific-highlights/priority-access-call-for-work-on-combating-covid-19

Diamond Light Source in the United Kingdom opened also a call for rapid access:
https://www.diamond.ac.uk/Users.html

Image: Electron density at the active site of the SARS-CoV-2 protease, revealing a fragment bound
Credit: Diamond Light Source

Report reveals impact of over £1.8bn on UK science & economy by Diamond

A recent study by Technopolis and Diamond estimates a cumulative monetised impact of at least £1.8 billion from the UK’s synchrotron, reflecting very favourably with the £1.2 billion investment made in the facility to date.  And it costs less than a cup of coffee as each taxpayer contributes only £2.45 a year towards it.  The study, published today (26 May), set out to measure and demonstrate Diamond’s scientific, technological, societal, and economic benefits.  The report summarises the findings and highlights the significant impact it has achieved to date.  

Diamond’s mission is to keep the UK at the forefront of scientific research. We do this by providing our users in academia and industry access to our state-of-the-art facilities enabling them to fulfil their research goals across a wide variety of scientific disciplines. This report illustrates the fantastic benefits the facility has delivered and brilliant science being achieved by our 14,000-strong user community, who are tackling some of the most challenging scientific questions of the 21st century.  We are so grateful to our funding agencies UKRI’s STFC and the Wellcome for their trust and ongoing support.Chief Executive of Diamond, Professor Andrew Harrison OBE

Read more on the Diamond website

Image: Break down of impact area mapped as part of this report with trend data (where available) showing the steady growth over time.

Scientists uncover a different facet of fuel-cell chemistry

Solid oxide fuel cells (SOFCs) are a promising technology for cleanly converting chemical energy to electrical energy. But their efficiency depends on the rate at which solids and gases interact at the devices’ electrode surfaces. Thus, to explore ways to improve SOFC efficiency, an international team led by researchers from Berkeley Lab studied a model electrode material in a new way—by exposing a different facet of its crystal structure to oxygen gas at operating pressures and temperatures.

“We began by asking questions like, could different reaction rates be achieved from the same material, just by changing which surface the oxygen reacts with?” said Lane Martin, a faculty scientist in Berkeley Lab’s Materials Sciences Division. “We wanted to examine how the atomic configuration at specific surfaces of these materials makes a difference when it comes to reacting with the oxygen gas.”

Thin films of a common SOFC cathode material, La0.8Sr0.2Co0.2Fe0.8O3 (LSCF), were epitaxially grown to expose a surface that was oriented along a diagonal crystallographic plane. Electrochemical measurements on this atypical surface yielded oxygen reaction rates up to three times faster than those measured on the usual horizontal plane.

To better understand the mechanisms underlying this improvement, the researchers used Advanced Light Source (ALS) Beamline 9.3.2 to perform ambient-pressure spectroscopy experiments at high temperatures and in varying pressures of oxygen. The results, combined with first-principles calculations, revealed that different crystallographic planes stabilize different surface chemistries, even though the bulk chemistry of the films is identical.

Read more on the ALS website

Image: A model SOFC cathode material adsorbs oxygen molecules (purple spheres) at vacancy sites, an important step in the electrochemical reaction taking place in fuel cells. Ambient-pressure experiments at the ALS allowed measurement of the surface chemical and electronic interactions at high temperature so that researchers could “see” the adsorption of oxygen at it happens. Light blue = La, dark blue = Sr, red = lattice O or O2 molecules, purple = adsorbed O2 molecules.

Credit: Abel Fernandez/UC Berkeley

Ultrafast lasers protect a DNA building block from destruction

An international research team led by DESY researcher Francesca Calegari and with the key participation of the Max Planck Institute for the Structure and Dynamics of Matter (MPSD) has demonstrated that ultrashort laser pulses can be used to protect one of the DNA building blocks against destruction induced by vacuum ultraviolet (VUV) radiation. The research group unveiled that a second laser flash in the infrared, timed shortly (only a few millionths of billions of a second) after the first VUV flash, prevented the adenine molecule to disintegrate, therefore stabilising it. The group presents their work in the journal Communications Chemistry published by Nature publishing group.

High energy radiation can cause irreparable damage to our own biological molecules – such as DNA – leading to mutations and potentially cell death. Damage is often occurring as a consequence of the molecular ionisation, inducing the fragmentation of the DNA subunits. So far, protection against radiation damage has hardly been achieved, as the photo-induced dissociation process could not be stopped. In their ultra-short-time experiments, Francesca Calegari´s research group and collaborators have discovered that, by taking advantage of mechanisms that take place on extremely fast time scales, it is indeed possible to protect the molecule.

Read more on the DESY website

image: Artist´s impression of the ultrafast stabilisation of adenine against dissociation: When the molecule is ionised by VUV radiation it undergoes dissociation, however, by taking advantage of a charge migration mechanism and by properly timing a second infrared laser pulse it is possible to stabilise it via a second ionisation event.

Credit: U. De Giovannini MPSD

Unravelling the history of 15th Century Chinese porcelains

Researchers from French and Spanish Institutions used the combination of two synchrotron light characterization techniques to study Chinese blue-and-white Ming porcelains. They were able to identify the firing temperature by determining the porcelain’s pigments and the reduction-oxidation media conditions during their production. The approach they used can also be applied on a broad range of modern and archaeological ceramics to elucidate their production technology.

Pottery is found at the majority of archaeological sites dating from the Neolithic period, when first human settings appear, onwards. Which makes it a major focus of study in archaeological science.  The study of style and production of ceramics is central to the historical reconstruction of a site, region and period.

More specifically, ceramic technological studies look to reconstruct the production technology of ceramics, by determining the selection and preparation of the raw materials, the formation of ceramics, treatment and decoration of the ware’s surface and the firing atmosphere. All of this is possible thanks to the scientific techniques available nowadays.

In a recent publication, researchers from French and Spanish Institutions used the combination of two synchrotron light characterization techniques to study Chinese blue-and-white Ming porcelains. These characteristic porcelains, whose production flourished around the 14th century, are decorated under the glaze with Cobalt-based blue pigments that provided their distinctive blue decorations and produced during a one-step firing at high temperatures.

They were able to identify the firing temperature by determining the porcelain’s pigments and the reduction-oxidation media conditions during their production. The approach they used can also be applied on a broad range of modern and archaeological ceramics to elucidate their production technology.

Read more on the ALBA website

Image: Porcelain Jar with cobalt blue under a transparent glaze (Jingdezhen ware). Mid-15th century

Credit: Metropolitan Museum of Art.

How ventilation might impact blood flow in ventilated preterm babies

A large international collaboration led by researchers from the Hudson Institute for Medical Research and Monash University has revealed that the ventilation of preterm babies to prevent lung collapse could create a risk of brain injury.  

A/Prof Flora Wong, a researcher at Hudson Institute and Monash University, and consultant neonatologist at Monash Children’s Hospital, and a team of physiologists used the Imaging and Medical beamline (IMBL) at the Australian Synchrotron to acquire extremely clear and detailed images of blood vessels in large, preterm clinical models, in an investigation to determine if the pressure of lung ventilation affected blood vessels and blood flow.

A/Prof Wong said the group have shown that higher lung pressure causes engorgement and stretching of the brain blood vessels, which could slow down blood flow in the brain. 

 “This may play a role in preterm brain injury,” she said.

Because of the findings, A/Prof Wong alerted hospitals to carefully monitor their ventilation of preterm babies, who now survive after as few as 23 weeks gestation.

IMBL Principal Scientist Dr Daniel Hausermann, a co-author on the paper published in The Journal of Physiology, said that in vivo CT imaging of dynamic physiological processes, such as blood flow, can be captured quickly in real-time video on the IMBL beamline.

Read more on the Australian synchrotron website

Image: Micro-angiography showing micro-vessels

Artificial spin ice toggles twist in X-ray beams on demand

SCIENTIFIC ACHIEVEMENT

Advanced Light Source (ALS) studies helped scientists understand how a nanoscale magnetic lattice (an artifical spin ice) acts as a toggle switch for x-ray beams with spiral character.

SIGNIFICANCE AND IMPACT

The findings represent an important step toward the development of a versatile new tool for probing or controlling exotic phenomena in electronic and magnetic systems.

A curious singularity

Artificial spin ices (ASIs) are engineered arrays of nanomagnets that are often “frustrated,” meaning that the magnets, constrained by geometry, cannot align themselves to minimize their interaction energy. Water ice exhibits a similar property with regard to the positioning of hydrogen atoms.

While studying ASIs, a collaboration between scientists from the University of Kentucky and the ALS (see related feature article) made an interesting observation: light scattered from certain ASIs produced diffraction patterns in which spots of constructive interference were shaped like donuts instead of dots. The donuts were indicative of a phase singularity—a hallmark of light with a property known as orbital angular momentum (OAM).

Read more on the ALS website

Image: When x-rays are scattered from a patterned array of nanoscale magnets with a lattice defect, the beams acquire a spiral character (orbital angular momentum, or OAM) that produces diffraction patterns with donut-shaped spots. Researchers have found that these OAM beams can be switched on and off by adjusting the temperature or applying an external magnetic field.

Target selection for COVID-19 antibody therapeutics

SCIENTIFIC ACHIEVEMENT

Protein-structure studies at the Advanced Light Source (ALS) helped demonstrate that the primary target of antibody-based COVID-19 immunity is the part of the virus’s spike protein that can most easily mutate.

SIGNIFICANCE AND IMPACT

This work anticipated the rise of SARS-CoV-2 variants and guides the selection of antibody therapeutics that are likely to be more resistant to immune escape.

A better understanding of immunity

To better predict the course of the COVID-19 pandemic and to develop the best new therapeutics, researchers need to understand what regions of the SARS-CoV-2 virus are most critical to the immune response and how likely these regions are to mutate and evade immunity.

Two recent papers, relying in part on protein-structure studies at the ALS, have provided detailed information about the SARS-CoV-2 virus that causes COVID-19 and the human immune response to it. The results reveal where the virus surface protein is most likely to mutate, what the consequences of those mutations may be, and which types of antibodies may be the most effective therapeutics.

Read more on the ALS website

Image: Left: Composite model of the SARS-CoV-2 spike protein trimer with six mAbs shown bound to one RBD (Piccoli et al.). Right: The first RBD–ACE2 complex structure where the RBD is a variant, in this case N439K; the figure highlights a new interaction between the N439K residue and ACE2 (Thomson et al.).

Combatting COVID-19 with crystallography and cryo-EM

Crystallography and cryo-electron microscopy are vital tools in the fight against COVID-19, allowing researchers to reveal the molecular structures and functions of the SARS-CoV-2 virus, paving the way for new drugs and vaccines. Since the start of the pandemic, the ESRF has mobilised its crystallography and cryo-electron microscopy expertise and made its new Extremely Brilliant Source available as part of the collective effort to address this critical global health challenge.

When the WHO declared the outbreak of COVID-19 a public health emergency of international concern in early 2020, it signalled the start of a race against time for scientists to understand how the newly identified SARS-CoV-2 virus functioned and to develop treatments for the disease. Structural biologists around the world pitched in, determining the structures of most of the 28 proteins encoded by the novel coronavirus. This remarkable collective effort resulted in over a thousand 3D structural models of SARS-CoV-1 and SARS-CoV-2 proteins deposited in the Protein Data Bank (PDB) public archive in just one year [1]. Researchers and drug developers rely on these models to design antiviral drugs, therapies and vaccines. However, the speed and urgency with which the SARS-CoV-2 protein structures were solved means that errors could inevitably slip in, with potentially severe consequences for drug designers targeting certain parts of the virus’s structure. 

Enter the Coronavirus Structural Task Force, an international team of 25 structural biologists offering their time and expertise to fix errors in structural models of the virus’s proteins in order to give drug designers the best possible templates to work from. Gianluca Santoni, crystallography data scientist in the ESRF’s structural biology group, is part of the task force, whose work is detailed in an article recently published in Nature Structural & Molecular Biology [2]. “Every week, we check the PDB for any new protein structure related to SARS-CoV-2,” he explains. “We push structural biology tools and methods to the limit to get every last bit of information from the data, to evaluate the quality and improve the models where possible.” 

To read more visit the ESRF website

Image: The coronavirus research project ‘COVNSP3’ is based on the use of the ESRF’s cryo-electron microscope facility, led by Eaazhisai Kandiah (pictured)

Credit: ESRF/S. Cande.

Electrons riding a double wave

Since they are far more compact than today’s accelerators, which can be kilometers long, plasma accelerators are considered as a promising technology for the future. An international research group has now made significant progress in the further development of this approach: With two complementary experiments at the Helmholtz-Zentrum Dresden-Rossendorf (HZDR) and at the Ludwig-Maximilians-Universität Munich (LMU), the team was able to combine two different plasma technologies for the first time and build a novel hybrid accelerator. The concept could advance accelerator development and, in the long term, become the basis of highly brilliant X-ray sources for research and medicine, as the experts describe in the journal Nature Communications (DOI: 10.1038/s41467-021-23000-7).

In conventional particle accelerators, strong radio waves are guided into specially shaped metal tubes called resonators. The particles to be accelerated – which are often electrons – can ride these radio waves like surfers ride an ocean wave. But the potential of the technology is limited: Feeding too much radio wave power into the resonators creates a risk of electrical charges that can damage the component. This means that in order to bring particles to high energy levels, many resonators have to be connected in series, which makes today’s accelerators in many cases kilometers long.

That is why experts are eagerly working on an alternative: plasma acceleration. In principle, short and extremely powerful laser flashes fire into a plasma – an ionized state of matter consisting of negatively charged electrons and positively charged atomic cores. In this plasma, the laser pulse generates a strong alternating electric field, similar to the wake of a ship, which can accelerate electrons enormously over a very short distance. In theory, this means facilities can be built far more compact, shrinking an accelerator that is a hundred meters long today down to just a few meters. “This miniaturization is what makes the concept so attractive,” explains Arie Irman, a researcher at the HZDR Institute of Radiation Physics. “And we hope it will allow even small university laboratories to afford a powerful accelerator in the future.”

Read more on the HZDR website

Image: Numerical rendering of the laser-driven acceleration (left side) and a subsequent electron-driven acceleration (right side), forming together the hybrid plasma accelerator.

Credit: Alberto Martinez de la Ossa, Thomas Heinemann

X-rays get a grip on why erucamide slips

X-Ray Reflectivity measurements offer insights into a slippery industrial additive

Slip additives have a wide range of industrial uses, finding their way into everything from lubricants to healthcare products. Fatty acid amides have been used as slip additives since the 1960s, and erucamide is widely used in polymer manufacturing. Research into erucamide migration and distribution and its nanomechanical properties has shown that the assembly and performance of the slip-additive surface depend on concentration and application method, as well as the substrate surface chemistry. However, questions remain regarding the nanostructure of organised erucamide surface layers, including the molecular orientation of the outermost erucamide layer. In work recently published in the Journal of Colloid and Interface Science, a team of researchers from the University of Bristol and Procter & Gamble used a combination of techniques to investigate the erucamide nanostructure formed in a model system. Their findings will allow the use of rigorous scientific methods in real-world scenarios. 

Essential erucamide

Manufacturers use slip additives to modify the surface structure of a wide range of materials, reducing friction without compromising the material’s other properties (e.g. modulus). Slip additives are included in everything from food packaging and textiles, dyes and lubricants, to hygiene products such as nappies.

Read on the Diamond website

Image:Multiscale characterisation of polypropylene (PP) fibre vs polypropylene fibre + 1.5 % erucamide: (A) Optical microscopy, (B) Scanning Electron Microscopy, (C) Atomic Force Microscopy (height image)