Researchers create most complete high-res atomic movie of photosynthesis to date

In a major step forward, SLAC’s X-ray laser captures all four stable states of the process that produces the oxygen we breathe, as well as fleeting steps in between. The work opens doors to understanding the past and creating a greener future.

Despite its role in shaping life as we know it, many aspects of photosynthesis remain a mystery. An international collaboration between scientists at SLAC National Accelerator Laboratory, Lawrence Berkeley National Laboratory and several other institutions is working to change that. The researchers used SLAC’s Linac Coherent Light Source (LCLS) X-ray laser to capture the most complete and highest-resolution picture to date of Photosystem II, a key protein complex in plants, algae and cyanobacteria responsible for splitting water and producing the oxygen we breathe. The results were published in Nature today.

Explosion of life

When Earth formed about 4.5 billion years ago, the planet’s landscape was almost nothing like what it is today. Junko Yano, one of the authors of the study and a senior scientist at Berkeley Lab, describes it as “hellish.” Meteors sizzled through a carbon dioxide-rich atmosphere and volcanoes flooded the surface with magmatic seas.
Over the next 2.5 billion years, water vapor accumulating in the air started to rain down and form oceans where the very first life appeared in the form of single-celled organisms. But it wasn’t until one of those specks of life mutated and developed the ability to harness light from the sun and turn it into energy, releasing oxygen molecules from water in the process, that Earth started to evolve into the planet it is today. This process, oxygenic photosynthesis, is considered one of nature’s crown jewels and has remained relatively unchanged in the more than 2 billion years since it emerged.

>Read more on the SLAC website (for LCLS)
>Read also the article on the Berkeley website (for ALS)

Image: Using SLAC’s X-ray laser, researchers have captured the most complete high-res atomic movie to date of Photosystem II, a key protein complex in plants, algae and cyanobacteria responsible for splitting water and producing the oxygen we breathe.
Credit: Gregory Stewart, SLAC National Accelerator Laboratory)

Insight into catalysis through novel study of X-ray absorption spectroscopy

An international team has made a breakthrough at BESSY II.

For the first time, they succeeded in investigating electronic states of a transition metal in detail and drawing reliable conclusions on their catalytic effect from the data. These results are helpful for the development of future applications of catalytic transition-metal systems. The work has now been published in Chemical Science, the Open Access journal of the Royal Society of Chemistry.

Many important processes in nature depend on catalysts, which are atoms or molecules that facilitate a reaction, but emerge from it themselves unchanged. One example is photosynthesis in plants, which is only possible with the help of a protein complex comprising four manganese atom sites at its centre. Redox reactions, as they are referred to, often play a pivotal role in these types of processes. The reactants are reduced through uptake of electrons, or oxidized through their release. Catalytic redox processes in nature and industry often only succeed thanks to suitable catalysts, where transition metals supply an important function.

>Read more about on the BESSY II at HZB website

Image: Manganese compounds also play a role as catalysts in photosynthesis.
Credit: HZB

Biological light sensor filmed in action

Film shows one of the fastest processes in biology

Using X-ray laser technology, a team led by researchers of the Paul Scherrer Institute PSI has recorded one of the fastest processes in biology. In doing so, they produced a molecular movie that reveals how the light sensor retinal is activated in a protein molecule. Such reactions occur in numerous organisms that use the information or energy content of light – they enable certain bacteria to produce energy through photosynthesis, initiate the process of vision in humans and animals, and regulate adaptations to the circadian rhythm. The movie shows for the first time how a protein efficiently controls the reaction of the embedded light sensor. The images, now published in the journal Science, were captured at the free-electron X-ray laser LCLS at Stanford University in California. Further investigations are planned at SwissFEL, the new free-electron X-ray laser at PSI. Besides the scientists from Switzerland, researchers from Japan, the USA, Germany, Israel, and Sweden took part in this study.

>Read more on the SwissFEL at Paul Scherrer Institute website

Image: Jörg Standfuss at the injector with which protein crystals for the experiments at the Californian X-ray laser LCLS were tested. In the near future, this technology will also be available at PSI’s X-ray laser SwissFEL, for scientists from all over the world.
Credit: Paul Scherrer Institute/Mahir DzaAmbegovic

World’s fastest water heater

Scientists explore exotic state of liquid with X-ray laser

Scientists have used a powerful X-ray laser to heat water from room temperature to 100,000 degrees Celsius in less than a tenth of a picosecond (millionth of a millionth of a second). The experimental set-up, that can be seen as the world’s fastest water heater, produced an exotic state of water, from which researchers hope to learn more about the peculiar characteristics of Earth’s most important liquid. The observations also have practical use for the probing biological and many other samples with X-ray lasers. The team of Carl Caleman from the Center for Free-Electron Laser Science (CFEL) at DESY and Uppsala University (Sweden) reports its findings in the journal Proceedings of the National Academy of Sciences (PNAS).

The researchers used the X-ray free-electron laser Linac Coherent Light Source LCLS at the SLAC National Accelerator Laboratory in the U.S. to shoot extremely intense and ultra-short flashes of X-rays at a jet of water. “It is certainly not the usual way to boil your water,” said Caleman. “Normally, when you heat water, the molecules will just be shaken stronger and stronger.” On the molecular level, heat is motion – the hotter, the faster the motion of the molecules. This can be achieved, for example, via heat transfer from a stove, or more directly with microwaves that make the water molecules swing back and forth ever faster in step with the electromagnetic field.

> Read more on on the DESY website and on the LCLS website

Image: After about 70 femtoseconds (quadrillionths of a second) most water molecules have already split into hydrogen (white) and oxygen (red).
Credit: Carl Caleman, DESY/Uppsala University

X-ray laser opens new view on Alzheimer proteins

Graphene enables structural analysis of naturally occurring amyloids

A new experimental method permits the X-ray analysis of amyloids, a class of large, filamentous biomolecules which are an important hallmark of diseases such as Alzheimer’s and Parkinson’s. An international team of researchers headed by DESY scientists has used a powerful X-ray laser to gain insights into the structure of different amyloid samples. The X-ray scattering from amyloid fibrils give patterns somewhat similar to those obtained by Rosalind Franklin from DNA in 1952, which led to the discovery of the well-known structure, the double helix. The X-ray laser, trillions of times more intense than Franklin’s X-ray tube, opens up the ability to examine individual amyloid fibrils, the constituents of amyloid filaments. With such powerful X-ray beams any extraneous material can overwhelm the signal from the invisibly small fibril sample. Ultrathin carbon film – graphene – solved this problem to allow extremely sensitive patterns to be recorded. This marks an important step towards studying individual molecules using X-ray lasers, a goal that structural biologists have long been pursuing. The scientists present their new technique in the journal Nature Communications.

Amyloids are long, ordered strands of proteins which consist of thousands of identical subunits. While amyloids are believed to play a major role in the development of neurodegenerative diseases, recently more and more functional amyloid forms have been identified. “The ‘feel-good hormone’ endorphin, for example, can form amyloid fibrils in the pituitary gland. They dissolve into individual molecules when the acidity of their surroundings changes, after which these molecules can fulfil their purpose in the body,” explains DESY’s Carolin Seuring, a scientist at the Center for Free-Electron Laser Science (CFEL) and the principal author of the paper. “Other amyloid proteins, such as those found in post-mortem brains of patients suffering from Alzheimer’s, accumulate as amyloid fibrils in the brain, and cannot be broken down and therefore impair brain function in the long term.”

Image: On the ultra-thin, extremely regular layer of graphene, the fibrils align themselves in parallel in large domains. The intense X-ray light from the X-rax free-electron laser LCLS at the SLAC National Accelerator Center enabled the researchers to gain partial information about the fibril structure from ensembles of just a few fibrils.
Credit: Greg Stewart/SLAC National Accelerator Laboratory

Freeze-framing nanosecond movements of nanoparticles

New method allows to monitor fast movements at hard X-ray lasers.

A team of scientists from DESY, the Advanced Photon Source APS and National Accelerator Laboratory SLAC, both in the USA, have developed and integrated a new method for monitoring ultrafast movements of nanoscopic systems. With the light of the X-ray laser LCLS at the research center SLAC in California, they took images of the movements of nanoparticles taking only the billionth of a second (0,000 000 001 s). In their experiments now published in the journal Nature Communications they overcame the slowness of present-day two-dimensional X-ray detectors by splitting individual laser flashes of LCLS, delaying one half of it by a nanosecond and recording a single picture of the nanoparticle with these pairs of X-ray pulses. The tunable light splitter for hard X-rays which the scientists developed for these experiments enables this new technique to monitor movements of nanometer size fluctuations down to femtoseconds and at atomic resolution. For comparison: modern synchrotron radiation light sources like PETRA III at DESY can typically measure movements on millisecond timescales.

The intense light flashes of X-ray lasers are coherent which means that the waves of the monochromatic laser light propagate in phase to each other. Diffracting coherent light by a sample usually results in a so-called speckle diffraction pattern showing apparently randomly ordered light spots. However, this speckle is also a map of the sample arrangement, and movements of the sample constituents result in a different speckle pattern.

>Read more on the DESY website

Image: Scheme of the experiment: An autocorrelator developed at DESY splits the ultrashort X-ray laser pulses into two equal intensity pulses which arrive with a tunable delay at the sample. The speckle pattern of the sample is collected in a single exposure of the 2-D detector
Credit: W. Roseker/DESY

Magnetic trick triples the power of SLAC’s X-ray laser

The new technique will allow researchers to observe ultrafast chemical processes previously undetectable at the atomic scale.

Scientists at the Department of Energy’s SLAC National Accelerator Laboratory have discovered a way to triple the amount of power generated by the world’s most powerful X-ray laser. The new technique, developed at SLAC’s Linac Coherent Light Source (LCLS), will enable researchers to observe the atomic structure of molecules and ultrafast chemical processes that were previously undetectable at the atomic scale.

The results, published in a Jan. 3 study in Physical Review Letters (PRL), will help address long-standing mysteries about photosynthesis and other fundamental chemical processes in biology, medicine and materials science, according to the researchers.

“LCLS produces the world’s most powerful X-ray pulses, which scientists use to create movies of atoms and molecules in action,” said Marc Guetg, a research associate at SLAC and lead author of the PRL study. “Our new technique triples the power of these short pulses, enabling higher contrast.”

>Read more on the LCSL website

Picture: The research team, from left: back row, Yuantao Ding, Matt Gibbs, Nora Norvell, Alex Saad, Uwe Bergmann, Zhirong Huang; front row, Marc Guetg and Timothy Maxwell.
Credit: Dawn Harmer/SLAC

 

Berkeley Lab delivers injector that will drive X-Ray laser upgrade

Unique device will create bunches of electrons to stimulate million-per-second X-ray pulses

 

Every powerful X-ray pulse produced for experiments at a next-generation laser project, now under construction, will start with a “spark” – a burst of electrons emitted when a pulse of ultraviolet light strikes a 1-millimeter-wide spot on a specially coated surface.

A team at the U.S. Department of Energy’s Lawrence Berkeley National Laboratory (Berkeley Lab) designed and built a unique version of a device, called an injector gun, that can produce a steady stream of these electron bunches that will ultimately be used to produce brilliant X-ray laser pulses at a rapid-fire rate of up to 1 million per second.

The injector arrived Jan. 22 at SLAC National Accelerator Laboratory (SLAC) in Menlo Park, California, the site of the Linac Coherent Light Source II (LCLS-II), an X-ray free-electron laser project.

Getting up to speed

The injector will be one of the first operating pieces of the new X-ray laser. Initial testing of the injector will begin shortly after its installation.

The injector will feed electron bunches into a superconducting particle accelerator that must be supercooled to extremely low temperatures to conduct electricity with nearly zero loss. The accelerated electron bunches will then be used to produce X-ray laser pulses.

>Read more on the Advanced Light Source website

 Image: Joe Wallig, left, a mechanical engineering associate, and Brian Reynolds, a mechanical technician, work on the final assembly of the LCLS-II injector gun in a specially designed clean room at Berkeley Lab in August.
Credit: Marilyn Chung/Berkeley Lab

Superconducting X-Ray laser takes shape in Silicon Valley

The first cryomodule has arrived at SLAC

Linked together and chilled to nearly absolute zero, 37 of these segments will accelerate electrons to almost the speed of light and power an upgrade to the nation’s only X-ray free-electron laser facility.

An area known for high-tech gadgets and innovation will soon be home to an advanced superconducting X-ray laser that stretches 3 miles in length, built by a collaboration of national laboratories. On January 19, the first section of the machine’s new accelerator arrived by truck at SLAC National Accelerator Laboratory in Menlo Park after a cross-country journey that began in Batavia, Illinois, at Fermi National Accelerator Laboratory.

These 40-foot-long sections, called cryomodules, are building blocks for a major upgrade called LCLS-II that will amplify the performance of the lab’s X-ray free-electron laser, the Linac Coherent Light Source (LCLS).

 

>Read more on the Linac Coherent Light Source website

Photo credit: Fermilab / Jefferson Lab

 

 

Kasper Kjaer Wins First LCLS Young Investigator Award

The early career award from SLAC’s X-ray laser

Kasper Kjaer is the winner of the inaugural LCLS Young Investigator Award given by the Users Executive Committee of the Linac Coherent Light Source (LCLS). The prize recognizes scientists in the early stages of their career for exceptional research performed with the LCLS X-ray free-electron laser at the Department of Energy’s SLAC National Accelerator Laboratory.

“With this award, we’re supporting the new ideas, new insights and new talent at our young facility,” said Mike Dunne, the director of LCLS.

>Read More

 

High-Speed Movie Aids Scientists Who Design Glowing Molecules

A research team captured ultrafast changes in fluorescent proteins between “dark” and “light” states.

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

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

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

>Read More

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

 

Molecular Movie

Researchers Create Molecular Movie of Virus Preparing to Infect Healthy Cells

With SLAC’s X-ray laser, scientists captured a virus changing shape and rearranging its genome to invade a cell.

A research team has created for the first time a movie with nanoscale resolution of the three-dimensional changes a virus undergoes as it prepares to infect a healthy cell. The scientists analyzed thousands of individual snapshots from intense X-ray flashes, capturing the process in an experiment at the Department of Energy’s SLAC National Accelerator Laboratory.

>Read More