New detector accelerates protein crystallography

In Feburary a new detector was installed at one of the three MX beamlines at HZB.

Compared to the old detector the new one is better, faster and more sensitive. It allows to acquire complete data sets of complex proteins within a very short time.

Proteins consist of thousands of building blocks that can form complex architectures with folded or entangled regions. However, their shape plays a decisive role in the function of the protein in the organism. Using macromolecular crystallography at BESSY II, it is possible to decipher the architecture of protein molecules. For this purpose, tiny protein crystals are irradiated with X-ray light from the synchrotron source BESSY II. From the obtained diffraction patterns, the morphology of the molecules can be calculated.

>Read more on the BESSY II at HZB website

Image: 60s on the new detector were sufficient to obtain the electron density of the PETase enzyme.
Credit: HZB

X-ray microscopy at BESSY II: Nanoparticles can change cells

Nanoparticles easily enter into cells. New insights about how they are distributed and what they do there are shown for the first time by high-resolution 3D microscopy images from BESSY II.

For example, certain nanoparticles accumulate preferentially in certain organelles of the cell. This can increase the energy costs in the cell. “The cell looks like it has just run a marathon, apparently, the cell requires energy to absorb such nanoparticles” says lead author James McNally.
Today, nanoparticles are not only in cosmetic products, but everywhere, in the air, in water, in the soil and in food. Because they are so tiny, they easily enter into the cells in our body. This is also of interest for medical applications: Nanoparticles coated with active ingredients could be specifically introduced into cells, for example to destroy cancer cells. However, there is still much to be learned about how nanoparticles are distributed in the cells, what they do there, and how these effects depend on their size and coating.

>Read more on the BESSY II at Helmholtz-Zentrum Berlin website

Image: 3D architecture of the cell with different organelles:  mitochondria (green), lysosomes (purple), multivesicular bodies (red), endoplasmic reticulum (cream).
Credit: Burcu Kepsutlu/HZB

Five U.S. light sources form data solution task force

New collaboration between scientists at the five U.S. Department of Energy light source facilities will develop flexible software to easily process big data.

Light source facilities are tackling some of today’s biggest scientific challenges, from designing new quantum materials to revealing protein structures. But as these facilities continue to become more technologically advanced, processing the wealth of data they produce has become a challenge of its own. By 2028, the five U.S. Department of Energy (DOE) Office of Science light sources, will produce data at the exabyte scale, or on the order of billions of gigabytes, each year. Now, scientists have come together to develop synergistic software to solve that challenge.
With funding from DOE for a two-year pilot program, scientists from the five light sources have formed a Data Solution Task Force that will demonstrate, build, and implement software, cyberinfrastructure, and algorithms that address universal needs between all five facilities. These needs range from real-time data analysis capabilities to data storage and archival resources.
“It is exciting to see the progress that is being made by all the light sources working together to produce solutions that will be deployed across the whole DOE complex,” said Stuart Campbell, leader of the data acquisition, management and analysis group at the National Synchrotron Light Source II (NSLS-II), a DOE Office of Science user facility at DOE’s Brookhaven National Laboratory.

>Read more on the NSLS-II at Brookhaven National Lab

>Explore the other member facilities of the task force and read about their latest science news: Advanced Light Source (ALS), Advanced Photon Source (APS), Stanford Synchrotron Radiation Lightsource (SSRL), Linac Coherent Light Source (LCLS).

Image: Members of the task force met at NSLS-II for a project kickoff meeting in August of 2019.

SESAME facilities in ever-increasing demand

No less than 151 proposals have been submitted in response to SESAME’s third call (Call “2”) for experiments on its three beamlines that closed on 27 January, thus confirming the ever-increasing demand for use of its facilities.

This time, it has been 64 proposals for experiments on its XAFS/XRF beamline that have been received, and 63 proposals for experiments on its IR beamline, as opposed to 60 and 43 proposals respectively in the second call, and 36 and 19 respectively in the first call. Added to this there have been 24 proposals for use of its MS beamline that comes into operation this year.
As in the first two calls in which there were not only proposals from the Members of SESAME but also from countries further afield (Colombia, France, Germany, Italy, Kenya, Mexico and Sweden), this time again they have not only originated from the Members of SESAME. There have again been proposals from Italy and Kenya, but also from Belgium, Malta, Qatar, South Africa and the U.K.
The large number of proposals and the variety of places from where they originate are excellent by any standards, and SESAME is greatly encouraged by the continuous upward trend in the number being received whether from users having already utilized SESAME’s facilities who are seeking to return to carry out further measurements, or new users from both the SESAME Members and beyond. In the case of the first group, this demonstrates that SESAME’s facilities are fully meeting users’ expectations, while in the second, this is evidence of the sound reputation SESAME is gaining on the world stage as a state-of-the-art synchrotron light source.

>Read more on the SESAME website

Growing an international community for agricultural synchrotron research

Dr. Chithra Karunakaran’s passion for agriculture has taken her around the world and helped her to grow an international agricultural imaging research community from Saskatoon. 

Given that the Canadian Light Source (CLS) is situated on the University of Saskatchewan (USask) campus, renowned for agriculture, and surrounded by some of the finest farm land in the country, it’s little wonder it has developed a reputation for outstanding agriculture-related research. Location is only part of the story though; some credit has to go to an engineer determined to apply advanced synchrotron techniques to the study of what we grow and what we eat.

The view from Agriculture Science Manager Dr. Chithra Karunakaran’s office window is dominated by the USask College of Agriculture and Bioresources, which also owns the research greenhouse located across the street from the CLS. Both are part of what she termed “the right ecosystem” needed to expand ag research at the facility, a project she has devoted herself to since she arrived in Saskatoon. The key has been adapting beamline techniques to serve the needs of plant, soil and food scientists.

>Read more on the Canadian Light Source website

Image: Karunakaran working with synchrotron science equipment. 

The role of synthesis gas in tomorrow’s sustainable fuels

In a new publication in Nature Communications, a team from the Dutch company Syngaschem BV and the Dutch Institute for Fundamental Energy Research elucidates for the first time some aspects of the Fischer-Tropsch reaction, used for converting synthesis gas into synthetic fuels.

Analysis performed at HIPPIE beamline at MAX IV were instrumental to achieve these results. The adoption of sustainable and renewable energy sources to permanently move beyond the dependence from fossil fuels constitutes one of the great challenges of our time. One that is made more urgent by the effects of climate change we witness on a daily basis. Electrification, such as we see in the development of electric vehicles, seems a promising strategy, but it cannot be the solution for all applications. In many cases liquid fuels are still considered the best and most efficient option. Is there a way to produce liquid fuels in an efficient and sustainable manner, one that does not rely on fossil sources?

>Read more on the MAX IV website

Cathode ‘defects’ improve battery performance

A counterintuitive finding revealed by high-precision powder diffraction analyses suggests a new strategy for building better batteries

UPTON, NY—Engineers strive to design smartphones with longer-lasting batteries, electric vehicles that can drive for hundreds of miles on a single charge, and a reliable power grid that can store renewable energy for future use. Each of these technologies is within reach—that is, if scientists can build better cathode materials.

To date, the typical strategy for enhancing cathode materials has been to alter their chemical composition. But now, chemists at the U.S. Department of Energy’s (DOE) Brookhaven National Laboratory have made a new finding about battery performance that points to a different strategy for optimizing cathode materials. Their research, published in Chemistry of Materials and featured in ACS Editors’ Choice, focuses on controlling the amount of structural defects in the cathode material.

“Instead of changing the chemical composition of the cathode, we can alter the arrangement of its atoms,” said corresponding author Peter Khalifah, a chemist at Brookhaven Lab and Stony Brook University.

>Read more on the NSLS-II at Brookhaven Lab website

Image: Corresponding author Peter Khalifah (left) with his students/co-authors Gerard Mattei (center) and Zhuo Li (right) at one of Brookhaven’s chemistry labs.

Learning how breast cancer cells evade the immune system

Cancer cells have ways to evade the human immune system, but research at UK’s Synchrotron, Diamond could leave them with nowhere to hide.

Announced on World Cancer Day, the latest research (published in Frontiers in Immunology) by Dr Vadim Sumbayev, together with an international team of researchers, working in collaboration with Dr Rohanah Hussain and Prof Giuliano Siligardi at Diamond Light Source.  They have been investigating the complex defence mechanisms of the human immune system and how cancer cells in breast tumours avoid it. In particular, they sought to understand one of the biochemical pathways leading to production of a protein called galectin-9, which cancer cells use to avoid immune surveillance. Dr Vadim Sumbayev explains, The human immune system has cells that can attack invading pathogens, protecting us from bacteria and viruses. These cells are also capable of killing cancer cells, but they don’t. Cancer cells have evolved defence mechanisms that protect them from our immune system, allowing them to survive and replicate, growing into tumours that may then spread across the body. Unfortunately, the molecular mechanisms that allow cancer cells to escape host immune surveillance remain poorly understood.  So, with a growing body of evidence suggesting that some solid tumours also use proteins called Tim-3 and galectin-9 and to evade host immune attack, we chose to study the activity of this pathway in breast and other solid and liquid tumours. 

>Read more on the Diamond Light Source website

Image: Breast cancer cell-based pathobiochemical pathways showing LPHN-induced activation of PKCα, which triggers the translocation of Tim-3 and galectin-9 onto the cell surface which is required for immune escape.

Double X-ray vision helps tuberculosis and osteoporosis research

Combination measurement shows distribution of metals in biological samples

With an advanced X-ray combination technique, scientists have traced nanocarriers for tuberculosis drugs within cells with very high precision. The method combines two sophisticated scanning X-ray measurements and can locate minute amounts of various metals in biological samples at very high resolution, as a team around DESY scientist Karolina Stachnik reports in the journal Scientific Reports. To illustrate its versatility, the researchers have also used the combination method to map the calcium content in human bone, an analysis that can benefit osteoporosis research.“Metals play key roles in numerous biological processes, from the oxygen transport in our red blood cells and the mineralisation of bones to the detrimental accumulation of metals in nerve cells as seen in diseases like Alzheimer’s,” explains Stachnik who works in the Center for Free-Electron Laser Science CFEL at DESY. High-energy X-rays make metals light up in fluorescence, a method that is very sensitive even to tiny amounts. “However, the X-ray fluorescence measurements usually do not show the ultrastructure of a cell, for example,” says DESY scientist Alke Meents who led the research. “If you want to exactly locate the metals within your sample, you have to combine the measurements with an imaging technique.” The ultrastructure comprises the details of the cell morphology that are not visible under an optical microscope.

>Read More on the DESY Website

Image: Two agglomerates of antibiotic-loaded iron nanocontainers (red) in a macrophage. Credit: Stachnik et al., „Scientific Reports“, CC BY 4.0

Toward better motors with X-ray light

Making Switzerland’s road traffic fit for the future calls for research, first and foremost. In the large-scale research facilities of PSI, chemists and engineers are investigating how to improve the efficiency of motors and reduce their emissions.

“The overall transportation system of Switzerland in 2040 is efficient in all aspects.” The primary strategic goal of the Federal Department of the Environment, Transport, Energy and Communications (DETEC) sounds good. The subordinate Swiss Federal Office of Energy (SFOE) specifies that vehicular traffic should pollute the environment less and become more energy-efficient and climate-friendly. Switzerland has set an ambitious goal for itself: to be climate-neutral by 2050.
This is a major challenge. According to the most recent “microcensus” on mobility from 2015, every person living in Switzerland travels around 24,850 kilometres per year. A high number, which also includes trips abroad. In everyday life and within Switzerland, the average per person is nearly 37 kilometres per day – and rising.
According to the Federal Office for the Environment (FOEN), cars, trucks, and buses produce three-fourths of the greenhouse gas emissions in the transportation sector. From this it follows: Whether or not the nation achieves its goal depends heavily on the motors used in these modes of transportation. Their CO2 emissions must be radically reduced. This is precisely the starting point for researchers at PSI and other institutions.

> Read more on the Swiss Light Source (PSI) website

Image: Passenger cars powered by hydrogen fuel cells have a greater range than electric cars, but they are less efficient. PSI researchers want to change that.
Credit: Adobe Stock/Graphic: Stefan Schulze-Henrichs

Tuneable self-organisation of liquid crystals in nanopores

Innovative path to novel materials with adaptive electrical and optical properties

A team of researchers has used X-rays from DESY’s research light source PETRA III to explore the amazingly diverse self-organisation of liquid crystals in nanometre-sized pores. The study, led by Patrick Huber from the Hamburg University of Technology (TUHH), shows how liquid crystals arrange themselves in pores of different sizes, exhibiting different electrical and optical properties. These could be of interest for applications such as sensors and novel optical metamaterials, as the group around first author Kathrin Sentker from TUHH reports in the journal Nanoscale. The research, which Huber presented at the annual DESY Users’ Meeting running until this Friday, will be continued within the framework of the planned Centre for Multiscale Materials Systems (CIMMS), in which TUHH, University of Hamburg, Helmholtz-Zentrum Geesthacht and DESY are involved and for which the Hamburg Science Authority has just approved approximately four million euros funding.

The researchers had studied a special liquid crystal material called HAT6 (2,3,6,7,10,11-hexakis(hexyloxy)triphenylene; C54H84O6), whose single molecules are disc-shaped. Below about 70 degrees Celsius, they arrange themselves into a liquid crystal; by heating to about 100 degrees, the order can be broken. The scientists filled this material into pores in an aluminium oxide substrate and cooled it down. The cylindrical pores were 17 to 160 nanometres (millionths of a millimeter) in diameter, 0.1 millimetres long and situated on a regular, hexagonal lattice.

Read more on the PETRA III website

Image: Simulation of the different orders of the liquid crystal, matching the measurements. Simulation: Marco D. Mazza, Max Planck Institute for dynamics and self-organisation and und Loughborough University

X-rays shine again in the Experimental Hall

It’s a great achievement for the EBS project. Beamlines saw first EBS beam one month ahead of schedule.

30 January 2020, after reaching in the last two days stable operation conditions of the EBS storage ring at 100 mA injection current, 65% injection efficiency and stable and rapid vacuum conditioning, 26 out of 27 Insertion Device beamlines opened their front-end with 5 mA stored electron beam current. 

The EBS X-ray beam – on all these beamlines, at distances from the source varying from 45 to 160 m, depending on the specific beamline – was found within fractions of millimetres from its position as measured in December 2018 before the start of the shutdown.

>Read more on the ESRF website

Record participation at user meetings of the Hamburg research light sources

More than 1300 participants from 28 countries have registered

For this year’s users’ meetings of the Hamburg X-ray light sources, more participants have registered than ever before: More than 1300 scientists from 28 countries will come to discuss research with DESY’s X-ray source PETRA III, the free-electron laser in Hamburg FLASH and the X-ray laser European XFEL for three days starting this Wednesday. The jointly organised users’ meetings of DESY and European XFEL are the largest gathering of this kind worldwide.

“The steadily increasing number of participants from Germany and abroad shows the great importance of the Hamburg research light sources for the national and international scientific community,” says DESY’s Director for Photon Science, Edgar Weckert. “Hamburg is one of the X-ray capitals of the world.” The brilliant X-ray light from the powerful particle accelerators provides detailed insights into the structure and dynamics of matter at the atomic level. It can be used, for example, to decipher the structure of biomolecules, illuminate innovative materials, film chemical reactions and simulate and study the conditions inside planets and stars.

At the European X-ray laser European XFEL, all six scientific experiment stations are in operation since June. “Our users’ experiences and expertise are crucial for shaping the future of our science and facility”, says European XFEL managing director Robert Feidenhans’l. “The annual users’ meeting, therefore, is an extremely valuable opportunity for users and scientists who work at our facilities to share their experiences of doing experiments at the instruments, and talk about ideas for further development.” In 2019, 890 scientists from 255 institutes in 28 countries participated in experiments at the facility.

> Read more on the PETRA III and FLASH website

> Please find here another article on the European XFEL website

Picture: The jointly organised users’ meetings are the largest gathering of this kind worldwide.
Credit: DESY, Marta Mayer

New catalyst resists destructive carbon buildup in electrodes

Key challenges in the transition to sustainable energy include the long-duration storage of cheap, renewable electricity and the electrification of the heavy-freight transportation sector. Both challenges can be met using electrochemical cells. Solid oxide electrolysis cells are capable of highly efficient splitting of steam and CO2 to produce a synthetic H2–CO gas mixture (syngas), which can be converted into synthetic hydrocarbon transportation fuels using conventional industrial reactors. However, the efficiency of the process is limited by the risk of destructive carbon deposition inside the cells’ porous solid electrodes. A nickel catalyst is responsible for the carbon growth, but replacing this long-standing conventional catalyst has turned out to be highly challenging.

Now, researchers have used ambient-pressure x-ray photoelectron spectroscopy (APXPS) at ALS Beamlines 9.3.2 and 11.0.2 to probe the mechanisms by which carbon grows on different catalysts during CO2 electrolysis. Gadolinium-doped cerium oxide (GDC) is known to resist carbon growth, and the ambient-pressure experiments probed the degree and mechanism of this carbon resistance. The experimental data, subsequently confirmed by density functional theory calculations, revealed that the carbon atoms are energetically trapped by various oxygen species on the surface of GDC—a capability entirely lacking for nickel.

>Read more on the Advanced Light Source website

Image: Artistic representation of a nickel-based electrode as a broken down fuel pump and of a cerium-based electrode as a new, productive pump. Credit: Cube3D

Soft X-ray Laminography: 3D imaging with powerful contrast mechanisms

Soft X-ray 3D imaging has already been realized at synchrotron radiation sources using either scanning transmission X-ray microscopy (STXM) schemes or tomography-based concepts. However, the maximum accessible sample volume is severely limited by the reduced penetration depth of the lower-energy soft X-ray radiation. This becomes even more of a drawback in the case of flat and extended specimens, which can be found in various fields of nanoscience.

The generalized geometry of laminography, characterized by a tilted axis of rotation concerning the incident X-ray beam resulting in a constant material thickness during rotation, has proven to be particularly suitable for the investigation of laterally extended and thin objects. The combination of soft X-rays and laminography provides the unique potential of bridging the gap between investigations of elaborate nanostructured thin film samples and taking advantage of the characteristic absorption contrast mechanisms in the soft X-ray range.

>Read more on the Swiss Light Source at PSI website

Image: 3D model constructed from soft X-ray laminography measurements of the front tip of the wing scale from a European peacock butterfly.

NSLS-II achieves design beam current of 500 milliamperes

Accelerator division enables new record current during studies.

The National Synchrotron Light Source II (NSLS-II) at the U.S. Department of Energy’s (DOE) Brookhaven National Laboratory is a gigantic x-ray microscope that allows scientists to study the inner structure of all kinds of material and devices in real time under realistic operating conditions. The scientists using the machine are seeking answers to questions including how can we built longer lasting batteries; when life started on our planet; and what kinds of new materials can be used in quantum computers, along with many other questions in a wide variety of research fields.

The heart of the facility is a particle accelerator that circulates electrons at nearly the speed of light around the roughly half-a-mile-long ring. Steered by special magnets within the ring, the electrons generate ultrabright x-rays that enable scientists to address the broad spectrum of research at NSLS-II.

Now, the accelerator division at NSLS-II has reached a new milestone for machine performance. During recent accelerator studies, the team has been able to ramp up the machine to 500 milliamperes (mA) of current and to keep this current stable for more than six hours. Similar to a current in a river, the current in an accelerator is a measure of the number of electrons that circulate the ring at any given time. In NSLS-II’s case, a higher electron current opens the pathway to more intense x-rays for all the experiments happening at the facility.

>Read more on the NSLS-II at Brookhaven Lab website

Image: The NSLS-II accelerator division proudly gathered to celebrate their recent achievement. The screen above them shows the slow increase of the electron current in the NSLS-II storage ring and its stability.