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The DOE Science News Source is a Newswise initiative to promote research news from the Office of Science of the DOE to the public and news media.
  • 2017-10-05 14:00:42
  • Article ID: 682392

International Team Reconstructs Nanoscale Virus Features from Correlations of Scattered X-rays

Team uses Berkeley Lab CAMERA's M-TIP algorithm to enable visualization

  • Credit: Jeff Donatelli, Berkeley Lab

    Reconstructed Viruses: Reconstructions of a rice dwarf virus (top) and a PR772 bacteriophage (bottom) from experimental correlation data using M-TIP. The images on the right show asymmetries in the internal genetic material for each virus reconstruction.

  • Credit: Marilyn Chung, Berkeley Lab

    CAMERA members (from left) Peter Zarat, Jeff Donatelli and Kanupriya Pande, co- authors of a paper describing how the group’s M-TIP framework helped reconstruct a single molecule virus using light refractions. Donatelli holds a 3D-printed model of the virus.

As part of an international research team, Jeff Donatelli, Peter Zwart and Kanupriya Pande of the Center for Advanced Mathematics for Energy Research Applications (CAMERA) at Lawrence Berkeley National Laboratory (Berkeley Lab) contributed key algorithms which helped achieve a goal first proposed more than 40 years ago – using angular correlations of X-ray snapshots from non-crystalline molecules to determine the 3D structure of important biological objects. This technique has the potential to allow scientists to shed light on biological structure and dynamics that were previously impossible to observe with traditional X-ray methods.

The breakthrough resulted from a single-particle diffraction experiment conducted at the Department of Energy’s (DOE’s) Linac Coherent Light Source (LCLS) by the Single-Particle Initiative organized by the SLAC National Accelerator Laboratory. As part of this initiative, the CAMERA team combined efforts with Ruslan Kurta, a physicist at the European XFEL (X-ray free electron laser) facility in Germany, to analyze angular correlations from the experimental data and use CAMERA’s multi-tiered iterative phasing (M-TIP) algorithm to perform the first successful 3D virus reconstructions from experimental correlations. The results were described in a paper recently published in the of Physical Review Letters.

“For the past 40 years, this was considered a problem that could not be solved,” said Peter Zwart, co-author on the paper and a physical bioscientist who is a member of CAMERA based out of the Molecular Biophysics and Integrated Imaging Division at Berkeley Lab. “But it turns out that the mathematical tools that we developed are able to leverage extra information hidden in the problem that had been previously overlooked. It is gratifying to see our theoretical approach lead to a practical tool.”

New Research Opportunities Enabled by XFELs

For much of the last century, the go-to technique for determining high-resolution molecular structure has been X-ray crystallography, where the sample of interest is arranged into a large periodic lattice and exposed to X-rays which scatter off and form diffraction patterns that are collected on a detector. Even though crystallography has been successful at determining many high-resolution structures, it is challenging to use this technique to study structures which are not susceptible to crystallization or structural changes that do not naturally occur within a crystal.

The creation of XFEL facilities, including the Linac Coherent Light Source (LCLS) and the European X-FEL, have created opportunities for conducting new experiments which can overcome the limitations of traditional crystallography. In particular, XFEL beams are several orders of magnitude brighter than and have much shorter pulse lengths than traditional X-ray light sources, which allow them to collect measurable diffraction signal from smaller uncrystallized samples and, more importantly, study fast dynamics. Single-particle diffraction is one such emerging experimental technique enabled by XFELS, where one collects diffraction images from single molecules instead of crystals. These single-particle techniques can be used to study molecular structure and dynamics that have been hard to study with traditional imaging techniques.

Overcoming Limitations in Single-Particle Imaging via Angular Correlations

One major challenge of single-particle imaging is that of orientation determination. “In a single-particle experiment, you don’t have control over rotation of the particles as they are hit by the X-ray beam, so each snapshot from a successful hit will contain information about the sample from a different orientation,” said co-author Jeff Donatelli, an applied mathematician in CAMERA who developed many of the algorithms in the new framework. “Most approaches to single-particle analysis have so far been based on trying to determine these particle orientations from the images; however, the best resolution achievable from these analyses is restricted by how precisely these orientations can be determined from noisy data.”

Instead of trying to directly determine these orientations, the team took a different approach based on idea originally proposed in the 1970s by Zvi Kam. “Rather than examine the individual data intensities in an attempt to find the correct orientation for each measured frame, we eliminate this step altogether by using so-called cross-correlation functions,” Kurta said.

 This approach, known as fluctuation X-ray scattering, is based on analyzing the angular correlations of ultrashort, intense X-ray pulses scattered from non-crystalline biomolecules. ”The beauty of using correlation data is that it contains a comprehensive fingerprint of the 3D structure of an object that extends traditional solution scattering approaches,” Zwart said.

Reconstructing 3D Structure from Correlations with CAMERA’s M-TIP Algorithm

The team’s breakthrough in reconstructing 3D structure from correlation data was enabled by the multi-tiered iterative phasing (M-TIP) algorithm developed by CAMERA. “Among the prominent advantages of M-TIP is its ability to solve the structure directly from the correlation data without having to rely on any symmetry constraints, and, more importantly, without the need to solve the orientation determination problem,” Donatelli said.

Donatelli, CAMERA leader James Sethian and Zwart developed their M-TIP framework by developing a mathematical generalization of a class of algorithms known as iterative phasing techniques, which are used in determining structure in a simpler problem, known as phase retrieval. A paper describing the original M-TIP framework was published August 2015 in the Proceedings of the National Academy of Sciences.

“Advanced correlation analyses in combination with ab-initio reconstructions by M-TIP clearly define an efficient route for structural analysis of nanoscale objects at XFELs,” Zwart said.

Future Directions for Correlation Analysis and M-TIP

The team notes that methods used in this analysis can also be applied to analyze diffraction data when there is more than one particle per shot.

“Most algorithms for single-particle imaging can only handle one molecule at a time, thus limiting signal and resolution. Our approach, on the other hand, is scalable so that we should also be able to measure more than one particle at a time,” said Kurta. Imaging with more than one particle per shot will allow scientists to achieve much higher hit rates, since it is easier to use a wide beam and hit many particles at a time, and will also avoid the need to separate out single-particle hits from multiple-particle hits and blank shots, which is another challenging requirement in traditional single-particle imaging.

As part of CAMERA’s suite of computational tools, they have also developed a different version of M-TIP which solves the orientation problem and can classify the images into conformational states, and consequently can used to study small biological differences in the measured sample. This alternate version of M-TIP was described in a paper published June 26 2017 in the Proceedings of the National Academy of Sciences. This alternate version of M-TIP is part of new collaboration initiative between SLAC National Accelerator Laboratory, CAMERA, the National Energy Research Scientific Computing Center (NERSC) and Los Alamos National Laboratory as part of DOE’s Exascale Computing Project (ECP).

This work was supported by the offices of Advanced Scientific Computing Research and Basic Energy Sciences in the Department of Energy’s Office of Science and the National Institute of General Medical Sciences at the National Institutes of Health. LCLS and NERSC are both DOE Office of Science User Facilities.

The Office of Science supports Berkeley Lab. The Office of Science is the single largest supporter of basic research in the physical sciences in the United States, and is working to address some of the most pressing challenges of our time. For more information, please visit science.energy.gov.

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Large Outdoor Study Shows Biodiversity Improves Stability of Algal Biofuel Systems

A diverse mix of species improves the stability and fuel-oil yield of algal biofuel systems, as well as their resistance to invasion by outsiders, according to the findings of a federally funded outdoor study by University of Michigan researchers.

SLAC, Stanford Scientists Discover How a Hardy Microbe's Crystalline Shell Helps it Reel in Food

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Critical plant gene takes unexpected detour that could boost biofuel yields

For decades, biologists have believed a key enzyme in plants had one function--produce amino acids, which are vital to plant survival and also essential to human diets. But for Wellington Muchero, Meng Xie and their colleagues, this enzyme does more than advertised. They had run a series of experiments on poplar plants that consistently revealed mutations in a structure of the life-sustaining enzyme that was not previously known to exist.

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In a year-long project, researchers at Sandia and Los Alamos national laboratories teamed up with the City of New Orleans to analyze ways to increase community resilience and improve the availability of critical lifeline services during and after severe weather. The team used historical hurricane scenarios to model how storms cause localized flooding, disrupt the electrical system and cut off parts of the community from lifeline services. Sandia researchers then developed a tool to analyze and identify existing clusters of businesses and community resources in areas less prone to inundation -- such as gas stations, grocery stores and pharmacies that could be outfitted with microgrids to boost resilience.

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PNNL Technology Clears Way for Ethanol-Derived Jet Fuel

News Release RICHLAND, Wash. -- ASTM International recently revised ASTM D7566 Annex A5 -- the Standard Specification for Aviation Turbine Fuel Containing Synthesized Hydrocarbons -- to add ethanol as an approved feedstock for producing alcohol-to-jet synthetic paraffinic kerosene (ATJ-SPK). The revision of ASTM D7566 Annex A5 clears the way for increased adoption of sustainable aviation fuels because ethanol feedstocks can be made from so many different low-cost sources.

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Experiments conducted at the Department of Energy's Lawrence Berkeley National Laboratory helped to confirm that samples of interplanetary particles - collected from Earth's upper atmosphere and believed to originate from comets - contain dust leftover from the initial formation of the solar system.

Designing a better superconductor with geometric frustration

Notre Dame study shows a magnet-controlled "switch" in superconductor configuration provides unprecedented flexibility in managing the location of vortex filaments, altering the properties of the superconductor.

Robust MOF Material Exhibits Selective, Fully Reversible and Repeatable Capture of Toxic Atmospheric Gas

Scientists have developed a metal-organic framework material offering selective, reversible and repeatable capture of nitrogen dioxide from ambient air. This could lead to cost-effective capture of greenhouse gases, to facilitate sequestration and help mitigate air pollution and global warming.

Diamond Dust Shimmering Around Distant Stars

Some of the tiniest diamonds in the universe - bits of crystalline carbon hundreds of thousands of times smaller than a grain of sand - have been detected swirling around three infant star systems in the Milky Way. These microscopic gemstones are neither rare nor precious; they are, however, exciting for astronomers who identified them as the source of a mysterious cosmic microwave "glow" emanating from several protoplanetary disks in our galaxy.


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Professor Emily Liu Receives $1.8 Million DoE Award for Solar Power Systems Research

Li (Emily) Liu, associate professor of nuclear engineering and engineering physics in the Department of Mechanical, Aerospace, and Nuclear Engineering at Rensselaer Polytechnic Institute, has been selected by the U.S. Department of Energy Solar Energy Technologies Office (SETO) to receive a $1.8 million award to study high-temperature molten-salt properties and corrosion mechanisms.

Vasilis Fthenakis Receives IEEE's William R. Cherry Award

UPTON, NY; Vasilis Fthenakis, a Senior Scientist Emeritus at the U.S. Department of Energy's (DOE) Brookhaven National Laboratory and Founder and Director of the Center for Life Cycle Analysis at Columbia University, will receive the 2018 William R. Cherry Award from the Institute of Electrical & Electronics Engineers (IEEE).

New PPPL director Steve Cowley is honored with knighthood by Queen Elizabeth II

Steven Cowley, newly named director of the U.S. Department of Energy's (DOE) Princeton Plasma Physics Laboratory (PPPL) effective July 1, has received a knighthood from Queen Elizabeth "for services to science and the development of nuclear fusion."

UVA Darden Releases Policy Playbook Identifying Six Actions to Catalyze Clean-Tech Innovation

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Work Begins on New SLAC Facility for Revolutionary Accelerator Science

The Department of Energy's SLAC National Accelerator Laboratory has started to assemble a new facility for revolutionary accelerator technologies that could make future accelerators 100 to 1,000 times smaller and boost their capabilities.

Oak Ridge National Laboratory Launches America's New Top Supercomputer for Science

The U.S. Department of Energy's Oak Ridge National Laboratory unveiled Summit as the world's most powerful and smartest scientific supercomputer.

Takeuchi Receives European Inventor Award 2018 in the Non-EPO Countries Category

Prolific patent-holder won for inventing battery that increases the lifespan of implantable defibrillators fivefold, greatly reducing need for reoccurring surgery

Steve Kevan Named Next Director of Berkeley Lab's Advanced Light Source

After an international search, Stephen D. "Steve" Kevan has been named the new director of the Advanced Light Source (ALS) at the U.S. Department of Energy's Lawrence Berkeley National Laboratory.

International corrosion society elects first Sandia fellow

Sandia National Laboratories materials scientist David Enos has been elected a fellow of NACE International, the chief professional society for corrosion engineering. He is the first Sandia employee to receive the honor.

Power to the People

The University of Utah College of Engineering has received a $2 million grant to create a laboratory and develop new technology for communities with backup power sources, known as microgrids, so they can quickly and more securely operate in the event of a massive power outage due to a natural disaster or cyberattack.


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Simulations of Magnetically Confined Plasmas Reveal a Self-Regulating Stabilizing Mechanism

A mysterious mechanism that prevents instabilities may be similar to the process that maintains the Earth's magnetic field.

Seeing All the Colors of the Plasma Wind

2-D velocity imaging helps fusion researchers understand the role of ion winds (aka flows) in the boundary of tokamak plasmas.

Renewable Solvents Derived From Lignin Lowers Waste in Biofuel Production

New class of solvents breaks down plant biomass into sugars for biofuels and bioproducts in a closed-loop biorefinery concept.

Scientists Studying Nuclear Spin Make a Surprising Discovery

The size of a nucleus appears to influence the direction of certain particles emitted from collisions with spinning protons.

Simulating Turbulent Bubbly Flows in Nuclear Reactors

With a better understanding of bubbly flows, researchers can improve the safety and operation of our nuclear reactors.

Solving a Magnesium Mystery in Rechargeable Battery Performance

Study reveals surprising, bad chemical reactivity in battery components previously considered compatible.

Changing the Surroundings Improves Catalysis

Water changes how cobalt-based molecule turns carbon dioxide into chemical feedstock.

How to Draw a Line Narrower Than a Cold Virus

Scientists use ion beams to write high-purity metal structures, enabling nanofabrication opportunities.

Powering Up With a Smart Window

Window material repeatedly switches from being see-through to blocking the heat and converting sunlight into electricity.

Remnant Superconductivity From Invisible Stripes

Scientists used an intense light to unveil hidden rivers that transport electricity with no loss.


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