Daily Archives: 22 Feb 2021

Engineering

Heat Loss Control Method in Fusion Reactors (Engineering)

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The core of a fusion reactor is incredibly hot. Hydrogen that inevitably escapes from it must be cooled on its way to the wall, as otherwise, the reactor wall would be damaged. Researchers from the Dutch institute DIFFER and EPFL’s Swiss Plasma Center have developed a strict measurement and control method for the cooling of very hot particles escaping from fusion plasmas.

Fusion energy is a promising sustainable energy source. In a fusion reactor, extremely hot hydrogen plasma is kept suspended by magnetic fields. However, there is always a fraction that escapes. To prevent it from damaging the reactor vessel, the escaped hydrogen must be cooled down on its way to the wall. 

Cooling can be achieved in various ways, such as by injecting a gas. “But if you inject too much additional gas, the plasma is cooled too strongly, which reduces the performance,” says Christian Theiler (Swiss Plasma Center, EPFL), co-author of a study published in Nature Communications. It is therefore necessary to constantly manage the cooling to the point that the reactor can adequately cope. Matthijs van Berkel (DIFFER): “The ability to control the cooling precisely is explicitly stated in the European fusion program (EUROfusion) as a necessary step towards fusion energy. It is fantastic that we can contribute to this now.” In Nature Communications the authors describe how to cool the escaping particles in a quick and controlled manner with an innovative feedback control system. The experiments has been carried out in the TCV tokamak, a fusion research machine at the EPFL’s Swiss Plasma Center.

“We are going from studying to controlling. This is vital for the future of fusion reactors,” says first author Timo Ravensbergen (DIFFER). “We measure, calculate, and control with incredible speed.”

A closed system

Escaping hydrogen is carried away via the reactor’s ‘exhaust’. That exhaust is called the divertor, where the plasma heat losses are captured. The process of strong cooling in the vicinity of the divertor is called divertor detachment. It reduces plasma temperature and pressure near the wall. Fusion physicists already have a lot of experience with this process, but this is partly based on intuition and on experiences from previous measurements. Now things will be done differently. “We have developed a closed system,” says Van Berkel, group leader Energy Systems & Control. “We have combined many different techniques, that is what makes it unique. Our systems engineering approach can be applied to other fusion reactors.” The experiments are a proof-of-principle. Van Berkel thinks that the method will be – with adjustments – applicable in the large fusion reactors ITER and DEMO. 

The closed loop of measuring, calculating, and controlling to prevent the tokamak wall from being destroyed © Julia van Leeuwen

Step-by-step

The researchers made use of the camera system MANTIS at the TCV tokamak for this research. This Multispectral Advanced Narrowband Tokamak Imaging System was developed by DIFFER, EPFL and MIT. The researchers adapted the system in such a way that camera images were converted into data from which a computer model could then calculate in real-time the optimum cooling under varying conditions. This all took place with considerable precision: the status of the plasma is determined 800 times per second.

A new real-time image-processing algorithm, developed at DIFFER, analyzes the MANTIS images. The algorithm calculates how much you need to cool by, and subsequently controls the gas valves automatically. Finally, the researchers produced a model of the system by analyzing, once again with the camera, how the plasma responds to the gas introduced. “With this model, we determine the dynamic relationship between the control of the gas valve and the heat front,” says Van Berkel. 

Fast result: tested on EPFL’s TCV tokamak

The system was tested on the TCV tokamak. “It is a very flexible device, where ideas can be developed and tested rather quickly,” emphases Theiler. Van Berkel agrees: “TCV is a fantastic machine for testing control techniques, with a hypermodern real-time control system.” Van Berkel tells results came fast: “Within just four experiments, we managed to achieve feed-back control of the plasma near the divertor. This demonstrates that our systematic approach works.” 

Future research

A proposal for follow-up research has already been prepared. The researchers made use of just one MANTIS camera, whereas the system has ten. The researchers want to use the other cameras as well, so that they can control the process even more accurately, and to control additional key processes in the divertor. 

Fusion: great energy potential

Fusion, the nuclear reaction that powers the Sun, has a high energy potential, is safe and environment-friendly. Research in this field is boosted by the international reactor ITER. While the giant research machine is being assembled in France, scientists from all over the world are working on the next steps: producing large-scale fusion reactions within it. Fusion occurs when nuclei of light atoms are heated to a hundred million degrees, forming a gas of charged particles called plasma.

Partners

This project is a collaboration between DIFFER, EPFL, Eindhoven University of Technology, Vrije Universiteit Brussel, MIT, Institute of Plasma Physics of CAS, CCFE, and the Max Planck Institute for Plasma Physics and is part of the EUROfusion research programme.

Featured image: The TCV Tokamak at EPFL’s Swiss Plasma Center © A. Herzog / EPFL

References: T. Ravensbergen, M. van Berkel, A. Perek, C. Galperti, B.P. Duval, O. Février, R.J.R. van Kampen, F. Felici, J.T. Lammers, C. Theiler, J. Schoukens, B. Linehan, M. Komm, S. Henderson, D. Brida, M.R. de Baar, The EUROfusion MST1 Team, and the TCV Team. Real-time feedback control of the impurity emission front in tokamak divertor plasmas. Nature Communications, 17 Feb 2021. DOI 10.1038/s41467-021-21268-3

Provided by EPFL

Medicine

Absence of Natural Killer Cell Receptor Associated With Severe COVID-19 (Medicine)

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The course and severity of COVID-19 in individual patients is largely influenced by the interaction between the SARS-CoV-2 coronavirus and the human immune system. Normally, the antiviral immune response of natural killer cells (NK cells) is an important step in combating viral replication in the early phase of the infection. On their surface, these killer cells have special, activating receptors, including the NKG2C receptor, which communicates with an infected cell via one of its specialised surface structures, HLA-E. This interaction results in the destruction of virus-infected cells. However, due to a genetic variation, approximately 4% of the population naturally lack the activation receptor NKG2C, and in 30% of the population this receptor is only partially available.

A research group from the Center for Virology at the Medical University of Vienna, led by Elisabeth Puchhammer-Stöckl, has now shown, in collaboration with doctors from Klinik Favoriten, that people with a partial or total absence of the NKG2C receptor are most likely to develop severe COVID-19.

In their study, which was recently published  in the journal “Genetics in Medicine”, the authors showed that people who required hospitalisation with COVID-19 were significantly more likely to exhibit the genetic variation underlying the lack of the receptor than people who only experienced mild disease. Puchhammer-Stöckl explains: “Absence of the receptor was particularly prevalent in COVID-19 patients being treated in intensive care units,  irrespective of age or gender. Genetic variations on the HLA-E of the infected cell were also associated with disease severity, albeit to a lesser extent.”  

The current study therefore shows the major importance of NK-cell response in the battle against SARS-CoV-2 infection: “This part of the immune response could therefore also represent an important target for drugs that could help to prevent severe COVID-19 disease,” explains the MedUni Vienna expert.

Service: Genetics in Medicine
Deletion of the NKG2C receptor encoding KLRC2 gene and HLA-E variants are risk factors for severe COVID-19. Vietzen H, Zoufaly A, Traugott M, Aberle J, Aberle SW, Puchhammer-Stöckl E. Genet Med. 2021 Jan 26:1-5. doi: 10.1038/s41436-020-01077-7. Online ahead of print. PMID: 33500568 Free PMC article. LINK: www.nature.com/articles/s41436-020-01077-7

Provided by Medical University of Vienna

Archaeology

New Dating Techniques Reveal Australia’s Oldest Known Rock Painting, and It’s a Kangaroo (Archeology)

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Two-meter kangaroo painting thought to be 17,300 years old

A two-metre-long painting of a kangaroo in Western Australia’s Kimberley region has been identified as Australia’s oldest intact rock painting.

Using the radiocarbon dating of 27 mud wasp nests, collected from over and under 16 similar paintings, a University of Melbourne collaboration has put the painting at 17,500 and 17,100 years old.

“This makes the painting Australia’s oldest known in-situ painting,” said Postdoctoral Researcher Dr Damien Finch who pioneered the exciting new radiocarbon technique.

“This is a significant find as through these initial estimates, we can understand something of the world these ancient artists lived in. We can never know what was in the mind of the artist when he/she painted this piece of work more than 600 generations ago, but we do know that the Naturalistic period extended back into the Last Ice Age, so the environment was cooler and dryer than today.”

The Kimberley-based research is part of Australia’s largest rock art dating project, led by Professor Andy Gleadow from the University of Melbourne. It involves the Balanggarra Aboriginal Corporation, the Universities of Western Australia, Wollongong, and Manchester, the Australian National Science and Technology Organisation, and partners Rock Art Australia and Dunkeld Pastoral.

Published today in Nature Human Behaviour, Dr Finch and his colleagues detail how rock shelters have preserved the Kimberley galleries of rock paintings, many of them painted over by younger artists, for millennia – and how they managed to date the kangaroo rock painting as Australia’s oldest known in-situ painting.

The kangaroo is painted on the sloping ceiling of a rock shelter on the Unghango clan estate in Balanggarra country, above the Drysdale River in the north-eastern Kimberley region of Western Australia.

Earlier researchers looked at the stylistic features of the paintings and the order in which they were painted when they overlapped, and were able to work out from there that the oldest style of painting is what’s known as the Irregular Infill Animal or the Naturalistic period, which often features life-size animals. This kangaroo is a typical example of paintings in this style.

Dr Finch said it was rare to find mud wasp nests both overlying and underlying a single painting. For this painting they were able to sample both types to establish the minimum and maximum age for the artwork.

“We radiocarbon dated three wasp nests underlying the painting and three nests built over it to determine, confidently, that the painting is between 17,500 and 17,100 years old; most likely 17,300 years old.”

Dr Sven Ouzman, from University Western Australia’s School of Social Sciences and one of the project’s chief investigators, said the rock painting would unlock further understanding of Indigenous cultural history.

“This iconic kangaroo image is visually similar to rock paintings from islands in South East Asia dated to more than 40,000 years ago, suggesting a cultural link – and hinting at still older rock art in Australia,” Dr Ouzman said.

Cissy Gore-Birch, Chair of the Balanggarra Aboriginal Corporation, said partnerships were important to integrate traditional knowledge with western science, to preserve Australia’s history and cultural identity.

“It’s important that Indigenous knowledge and stories are not lost and continue to be shared for generations to come,” Ms Gore-Birch said. “The dating of this oldest known painting in an Australian rock shelter holds a great deal of significance for Aboriginal people and Australians and is an important part of Australia’s history.”

The next step for the researchers, who are aiming to develop a time scale for Aboriginal rock art in the Kimberley, is to date further wasp nests in contact with this and other styles of Kimberley rock art to establish, more accurately, when each art period began and ended.

Featured image: Traditional Owner Ian Waina inspecting a Naturalistic painting of a kangaroo, determined to be more than 12,700 years old based on the age of overlying mud wasp nests. The inset is an illustration of the painting above it. © Photo: Peter Veth and the Balanggarra Aboriginal Corporation, Illustration: Pauline Heaney

Reference: Finch, D., Gleadow, A., Hergt, J. et al. Ages for Australia’s oldest rock paintings. Nat Hum Behav (2021). https://www.nature.com/articles/s41562-020-01041-0 https://doi.org/10.1038/s41562-020-01041-0

Provided by University of Melbourne

Medicine

Oncotarget: MEK is a Promising Target in the Basal Subtype of Bladder Cancer (Medicine)

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Oncotarget recently published in “MEK is a promising target in the basal subtype of bladder cancer” by Merrill, et al. which reported that while many resources exist for the drug screening of bladder cancer cell lines in 2D culture, it is widely recognized that screening in 3D culture is more representative of in vivo response.

To address the need for 3D drug screening of bladder cancer cell lines, the authors screened 17 bladder cancer cell lines using a library of 652 investigational small-molecules and 3 clinically relevant drug combinations in 3D cell culture.

Their goal was to identify compounds and classes of compounds with efficacy in bladder cancer.

Utilizing established genomic and transcriptomic data for these bladder cancer cell lines, they correlated the genomic molecular parameters with drug response, to identify potentially novel groups of tumors that are vulnerable to specific drugs or classes of drugs.

Importantly, the Oncotarget authors demonstrate that MEK inhibitors are a promising targeted therapy for the basal subtype of bladder cancer, and their data indicate that drug screening of 3D cultures provides an important resource for hypothesis generation.

“The Oncotarget authors demonstrate that MEK inhibitors are a promising targeted therapy for the basal subtype of bladder cancer, and their data indicate that drug screening of 3D cultures provides an important resource for hypothesis generation”

Dr. Matthew B. Soellner and Dr. Sofia D. Merajver from The University of Michigan said, “Bladder cancer is the most frequent cancer of the urinary system in the United States with nearly 82,000 new cases each year and 18,000 deaths, affecting men more often, in a 3:1 ratio.“

Bladder cancer can be divided broadly into non-muscle-invasive bladder cancer and muscle-invasive bladder cancer.

The Genomics of Drug Sensitivity in Cancer represents one of the largest efforts in total drugs, screening 19 bladder cancer cell lines against 518 drugs.

Indeed, screening in 3D using ultra-low attachment plates is ideal for bladder cancer cell culture, and this method has been utilized in seminal studies for screening patient-derived organoids to predict patient response to drug treatments.

Therefore, there is a utility in screening bladder cancer cell lines in large drug screens in 3D cultures to identify novel therapeutic options for future testing in PDOs and, ultimately, patients.

Then, utilizing established genomic and transcriptomic data for these bladder cancer cell lines, including prioritized mutations, copy number variants, and RNA-based molecular subtyping, they correlated these molecular parameters with drug response identifying potentially novel groups of tumors that are vulnerable to specific drugs or classes of drugs.

The Soellner/Merajver Research Team concluded in their Oncotarget Research Paper, “this work is a valuable resource for the identification of experimental therapeutics in bladder cancer, having screened 652 investigational therapeutics and 3 drug combinations in 17 bladder cancer cell lines, using a 3D cell culture format. As next steps, we pose that this work be used to further test additional therapeutic options for patients with bladder cancer. Moreover, this work highlights a need for biomarkers of drug response, beyond mutational data. Lastly, using these methods, we identify MEK inhibitors as a promising therapeutic in the basal bladder cancer subtype. Important future work will investigate the specific molecular features of the basal subtype that make these cells more sensitive to MEK inhibition, and if this MEK sensitivity signature is applicable to other cancer subtypes.“

Featured image: MEK inhibitor response correlates with basal subtype. Average and standard deviation for DSS3 response to (A) Trametinib, (B) TAK-733, (C) Normalized MEK inhibitors, and (D) Average drug response, grouped by cell line subtype. Each point represents an individual cell line. Center line is average and brackets are standard deviation. Significance determined using Mann-Whitney test, *p < 0.05, or Kruskal-Wallis with Dunn test for multiple comparisons, ***p < 0.001. © Oncotarget

Reference: Merrill N. M., Vandecan N. M., Day K. C., Palmbos P. L., Day M. L., Udager A. M., Merajver S. D., Soellner M. B. MEK is a promising target in the basal subtype of bladder cancer. Oncotarget. 2020; 11: 3921-3932. Retrieved from https://www.oncotarget.com/article/27767/text/

Provided by Impact Journals

PHYSICS

New “Metalens” Shifts Focus Without Tilting or Moving (Physics)

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The design may enable miniature zoom lenses for drones, cellphones, or night-vision goggles.

Polished glass has been at the center of imaging systems for centuries. Their precise curvature enables lenses to focus light and produce sharp images, whether the object in view is a single cell, the page of a book, or a far-off galaxy.

Changing focus to see clearly at all these scales typically requires physically moving a lens, by tilting, sliding, or otherwise shifting the lens, usually with the help of mechanical parts that add to the bulk of microscopes and telescopes.

Now MIT engineers have fabricated a tunable “metalens” that can focus on objects at multiple depths, without changes to its physical position or shape. The lens is made not of solid glass but of a transparent “phase-changing” material that, after heating, can rearrange its atomic structure and thereby change the way the material interacts with light.

The researchers etched the material’s surface with tiny, precisely patterned structures that work together as a “metasurface” to refract or reflect light in unique ways. As the material’s property changes, the optical function of the metasurface varies accordingly. In this case, when the material is at room temperature, the metasurface focuses light to generate a sharp image of an object at a certain distance away. After the material is heated, its atomic structure changes, and in response, the metasurface redirects light to focus on a more distant object.

In this way, the new active “metalens” can tune its focus without the need for bulky mechanical elements. The novel design, which currently images within the infrared band, may enable more nimble optical devices, such as miniature heat scopes for drones, ultracompact thermal cameras for cellphones, and low-profile night-vision goggles.

“Our result shows that our ultrathin tunable lens, without moving parts, can achieve aberration-free imaging of overlapping objects positioned at different depths, rivaling traditional, bulky optical systems,” says Tian Gu, a research scientist in MIT’s Materials Research Laboratory.

Gu and his colleagues have published their results today in the journal Nature Communications. His co-authors include Juejun Hu, Mikhail Shalaginov, Yifei Zhang, Fan Yang, Peter Su, Carlos Rios, Qingyang Du, and Anuradha Agarwal at MIT; Vladimir Liberman, Jeffrey Chou, and Christopher Roberts of MIT Lincoln Laboratory; and collaborators at the University of Massachusetts at Lowell, the University of Central Florida, and Lockheed Martin Corporation.

A material tweak

The new lens is made of a phase-changing material that the team fabricated by tweaking a material commonly used in rewritable CDs and DVDs. Called GST, it comprises germanium, antimony, and tellurium, and its internal structure changes when heated with laser pulses. This allows the material to switch between transparent and opaque states — the mechanism that enables data stored in CDs to be written, wiped away, and rewritten.

Earlier this year, the researchers reported adding another element, selenium, to GST to make a new phase-changing material: GSST. When they heated the new material, its atomic structure shifted from an amorphous, random tangle of atoms to a more ordered, crystalline structure. This phase shift also changed the way infrared light traveled through the material, affecting refracting power but with minimal impact on  transparency.

The team wondered whether GSST’s switching ability could be tailored to direct and focus light at specific points depending on its phase. The material then could serve as an active lens, without the need for mechanical parts to shift its focus.

“In general when one makes an optical device, it’s very challenging to tune its characteristics postfabrication,” Shalaginov says. “That’s why having this kind of platform is like a holy grail for optical engineers, that allows [the metalens] to switch focus efficiently and over a large range.”

In the hot seat

In conventional lenses, glass is precisely curved so that incoming light beam refracts off the lens at various angles, converging at a point a certain distance away, known as the lens’ focal length. The lenses can then produce a sharp image of any objects at that particular distance. To image objects at a different depth, the lens must physically be moved.

Rather than relying on a material’s fixed curvature to direct light, the researchers looked to modify GSST-based metalens in a way that the focal length changes with the material’s phase.

In their new study, they fabricated a 1-micron-thick layer of GSST and created a “metasurface” by etching the GSST layer into microscopic structures of various shapes that refract light in different ways.

“It’s a sophisticated process to build the metasurface that switches between different functionalities, and requires judicious engineering of what kind of shapes and patterns to use,” Gu says. “By knowing how the material will behave, we can design a specific pattern which will focus at one point in the amorphous state, and change to another point in the crystalline phase.”

They tested the new metalens by placing it on a stage and illuminating it with a laser beam tuned to the infrared band of light. At certain distances in front of the lens, they placed transparent objects composed of double-sided patterns of horizontal and vertical bars, known as resolution charts, that are typically used to test optical systems.

The lens, in its initial, amorphous state, produced a sharp image of the first pattern. The team then heated the lens to transform the material to a crystalline phase. After the transition, and with the heating source removed, the lens produced an equally sharp image, this time of the second, farther set of bars.

“We demonstrate imaging at two different depths, without any mechanical movement,” Shalaginov says.

The experiments show that a metalens can actively change focus without any mechanical motions. The researchers say that a metalens could be potentially fabricated with integrated microheaters to quickly heat the material with short millisecond pulses. By varying the heating conditions, they can also tune to other material’s intermediate states, enabling continuous focal tuning.

“It’s like cooking a steak — one starts from a raw steak, and can go up to well done, or could do medium rare, and anything else in between,” Shalaginov says. “In the future this unique platform will allow us to arbitrarily control the focal length of the metalens.”

Featured image: A new MIT-fabricated metalens shifts focus without tilting, shifting, or otherwise moving. The design may enable miniature zoom lenses for drones, cellphones, or night-vision goggles. Credits: Courtesy of the researchers

Reference: Shalaginov, M.Y., An, S., Zhang, Y. et al. Reconfigurable all-dielectric metalens with diffraction-limited performance. Nat Commun 12, 1225 (2021). https://www.nature.com/articles/s41467-021-21440-9 https://doi.org/10.1038/s41467-021-21440-9

Provided by MIT

Psychology

NYU Abu Dhabi Researcher Sheds New Light on the Psychology of Radicalization

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The paper explores how to reverse this potentially violent form of addiction by restoring an individual’s psychological needs and how challenging their ideology is counterproductive

Learning more about what motivates people to join violent ideological groups and engage in acts of cruelty against others is of great social and societal importance. New research from Assistant Professor of Psychology at NYUAD Jocelyn Bélanger explores the idea of ideological obsession as a form of addictive behavior that is central to understanding why people ultimately engage in ideological violence, and how best to help them break this addiction.

In the new study, The Sociocognitive Processes of Ideological Obsession: Review and Policy Implications which appears in the journal Philosophical Transactions of the Royal Society B, Bélanger draws from evidence collected across cultures and ideologies to describe four processes through which ideological obsession puts individuals on a path toward violence.

The first is moral disengagement: ideological obsession deactivates moral self-regulation processes, which allows unethical behaviors to happen without self-recrimination. The second is hatred: ideologically obsessed individuals are ego-defensive and easily threatened by information that criticizes their beliefs, which leads to greater hatred and potentially violent retaliation. Third, ideological obsession changes people’s social interactions, causing them to gravitate toward like-minded people – networks — who support their violent thinking. And finally, these individuals are prone to psychological reactance, which makes them immune to communications that attempt to dissuade them from violence.

“As we seek ways to prevent and combat violent radicalization, we must understand this behavior as an addiction to an ideology, rooted in a feeling of absence of personal significance,” said Belanger. “Common approaches, like trying to provide information that counters someone’s hateful ideology, are not only futile, but often counterproductive. To steer people away from ideologically-motivated violence, we must focus on their psychological needs, such as meaning and belonging, and helping them attain richer, more satisfying, and better-balanced lives.”

Reference: Jocelyn J. Bélanger, “The sociocognitive processes of ideological obsession: review and policy implications”, Royal Society Publishing, 22 February 2021. https://doi.org/10.1098/rstb.2020.0144

Provided by New York University

About NYU Abu Dhabi

NYU Abu Dhabi is the first comprehensive liberal arts and science campus in the Middle East to be operated abroad by a major American research university. NYU Abu Dhabi has integrated a highly-selective liberal arts, engineering and science curriculum with a world center for advanced research and scholarship enabling its students to succeed in an increasingly interdependent world and advance cooperation and progress on humanity’s shared challenges. NYU Abu Dhabi’s high-achieving students have come from more than 115 nations and speak over 115 languages. Together, NYU’s campuses in New York, Abu Dhabi, and Shanghai form the backbone of a unique global university, giving faculty and students opportunities to experience varied learning environments and immersion in other cultures at one or more of the numerous study-abroad sites NYU maintains on six continents.

Computer Science, Engineering

Researchers Develop Speedier Network Analysis For a Range of Computer Hardware (Engineering / Computer Science)

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The advance could boost recommendation algorithms and internet search.

Graphs — data structures that show the relationship among objects — are highly versatile. It’s easy to imagine a graph depicting a social media network’s web of connections. But graphs are also used in programs as diverse as content recommendation (what to watch next on Netflix?) and navigation (what’s the quickest route to the beach?). As Ajay Brahmakshatriya summarizes: “graphs are basically everywhere.”

Brahmakshatriya has developed software to more efficiently run graph applications on a wider range of computer hardware. The software extends GraphIt, a state-of-the-art graph programming language, to run on graphics processing units (GPUs), hardware that processes many data streams in parallel. The advance could accelerate graph analysis, especially for applications that benefit from a GPU’s parallelism, such as recommendation algorithms.

Brahmakshatriya, a PhD student in MIT’s Department of Electrical Engineering and Computer Science and the Computer Science and Artificial Intelligence Laboratory, will present the work at this month’s International Symposium on Code Generation and Optimization. Co-authors include Brahmakshatriya’s advisor, Professor Saman Amarasinghe, as well as Douglas T. Ross Career Development Assistant Professor of Software Technology Julian Shun, postdoc Changwan Hong, recent MIT PhD student Yunming Zhang PhD ’20 (now with Google), and Adobe Research’s Shoaib Kamil.

When programmers write code, they don’t talk directly to the computer hardware. The hardware itself operates in binary — 1s and 0s — while the coder writes in a structured, “high-level” language made up of words and symbols. Translating that high-level language into hardware-readable binary requires programs called compilers. “A compiler converts the code to a format that can run on the hardware,” says Brahmakshatriya. One such compiler, specially designed for graph analysis, is GraphIt.

The researchers developed GraphIt in 2018 to optimize the performance of graph-based algorithms regardless of the size and shape of the graph. GraphIt allows the user not only to input an algorithm, but also to schedule how that algorithm runs on the hardware. “The user can provide different options for the scheduling, until they figure out what works best for them,” says Brahmakshatriya. “GraphIt generates very specialized code tailored for each application to run as efficiently as possible.”

A number of startups and established tech firms alike have adopted GraphIt to aid their development of graph applications. But Brahmakshatriya says the first iteration of GraphIt had a shortcoming: It only runs on central processing units or CPUs, the type of processor in a typical laptop.

“Some algorithms are massively parallel,” says Brahmakshatriya, “meaning they can better utilize hardware like a GPU that has 10,000 cores for execution.” He notes that some types of graph analysis, including recommendation algorithms, require a high degree of parallelism. So Brahmakshatriya extended GraphIt to enable graph analysis to flourish on GPUs.

Brahmakshatriya’s team preserved the way GraphIt users input algorithms, but adapted the scheduling component for a wider array of hardware. “Our main design decision in extending GraphIt to GPUs was to keep the algorithm representation exactly the same,” says Brahmakshatriya. “Instead, we added a new scheduling language. So, the user can keep the same algorithms that they had before written before [for CPUs], and just change the scheduling input to get the GPU code.”

This new, optimized scheduling for GPUs gives a boost to graph algorithms that require high parallelism — including recommendation algorithms or internet search functions that sift through millions of websites simultaneously. To confirm the efficacy of GraphIt’s new extension, the team ran 90 experiments pitting GraphIt’s runtime against other state-of-the-art graph compilers on GPUs. The experiments included a range of algorithms and graph types, from road networks to social networks. GraphIt ran fastest in 65 of the 90 cases and was close behind the leading algorithm in the rest of the trials, demonstrating both its speed and versatility.

GraphIt “advances the field by attaining performance and productivity simultaneously,” says Adrian Sampson, a computer scientist at Cornell University who was not involved with the research. “Traditional ways of doing graph analysis have one or the other: Either you can write a simple algorithm with mediocre performance, or you can hire an expert to write an extremely fast implementation — but that kind of performance is rarely accessible to mere mortals. The GraphIt extension is the key to letting ordinary people write high-level, abstract algorithms and nonetheless getting expert-level performance out of GPUs.”

Sampson adds the advance could be particularly useful in rapidly changing fields: “An exciting domain like that is genomics, where algorithms are evolving so quickly that high-performance expert implementations can’t keep up with the rate of change. I’m excited for bioinformatics practitioners to get their hands on GraphIt to expand the kinds of genomic analyses they’re capable of.”

Brahmakshatriya says the new GraphIt extension provides a meaningful advance in graph analysis, enabling users to go between CPUs and GPUs with state-of-the-art performance with ease. “The field these days is tooth-and-nail competition. There are new frameworks coming out every day,” He says. But he emphasizes that the payoff for even slight optimization is worth it. “Companies are spending millions of dollars each day to run graph algorithms. Even if you make it run just 5 percent faster, you’re saving many thousands of dollars.”

This research was funded, in part, by the National Science Foundation, U.S. Department of Energy, the Applications Driving Architectures Center, and the Defense Advanced Research Projects Agency.

Featured image: MIT researchers developed software to more efficiently run graph applications on a range of computing hardware, including both CPUs and GPUs. Credits: Image: Istockphoto images edited by MIT News

Reference paper: “Compiling Graph Applications for GPUs with GraphIt”

Provided by MIT

Material science

Can Bacteria Make Stronger Cars, Airplanes and Armor? (Material Science)

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USC researchers harness the power of living organisms to make materials that are strong, tolerant and resilient

Biological systems can harness their living cells for growth and regeneration, but engineering systems cannot. Until now.

Qiming Wang and researchers at the USC Viterbi School of Engineering are harnessing living bacteria to create engineering materials that are strong, tolerant, and resilient. The research is published in Advanced Materials.

“The materials we are making are living and self-growing,” said Wang, the Stephen Schrank Early Career Chair in Civil and Environmental Engineering and assistant professor of civil and environmental engineering in the Sonny Astani Department of Civil and Environmental Engineering (CEE). “We have been amazed by the sophisticated microstructures of natural materials for centuries, especially after microscopes were invented to observe these tiny structures. Now we take an important step forward: We use living bacteria as a tool to directly grow amazing structures that cannot be made on our own.”

The researchers work with specific bacteria– S. pasteurii–known for secreting an enzyme called urease. When urease is exposed to urea and calcium ions, it produces calcium carbonate, a fundamental and strong mineral compound found in bones or teeth. “The key innovation in our research,” said Wang, “is that we guide the bacteria to grow calcium carbonate minerals to achieve ordered microstructures which are similar to those in the natural mineralized composites.”

Wang added: “Bacteria know how to save time and energy to do things. They have their own intelligence, and we can harness their smartness to design hybrid materials that are superior to fully synthetic options.

Borrowing inspiration from nature is not new in engineering. As one would suspect, nature has great examples of complex mineralized composites that are strong, fracture resistant, and energy damping–for example nacre or the hard shell surrounding a mollusk.

Wang said: “Although microorganisms such as bacteria, fungi and viri are sometimes detrimental in causing diseases–like COVID-19–they can also be beneficial. We have a long history of using microorganisms as factories–for example, using yeast to make beer. But there is limited research on using microorganisms to manufacture engineering materials.”

Combining living bacteria and synthetic materials, Wang said this new living material demonstrates mechanical properties superior to that of any natural or synthetic material currently in use. This is largely due to the material’s bouligand structure, which is characterized by multiple layers of minerals laid at varying angles from each other to form a sort of “twist” or helicoidal shape. This structure is difficult to create synthetically.

Wang worked in collaboration with USC Viterbi researchers An Xin, Yipin Su, Minliang Yan, Kunhao Yu, Zhangzhengrong Feng, and Kyung Hoon Lee. Additional support was provided by Lizhi Sun, professor of civil engineering at the University of California, Irvine, and his student Shengwei Feng.

What’s in a Shape?

One of the key properties of a mineralized composite, Wang said, is that it can be manipulated to follow different structures or patterns. Researchers long ago observed the ability of a mantis shrimp to use his “hammer” to break open a muscle shell. Looking at his “hammer”–a club-like structure or hand–more closely, they found it was arranged in a bouligand structure. This structure offers superior strength to one arranged at more homogenous angles–for example alternating the lattice structure of the material at 90 degrees with each layer.

“Creating this structure synthetically is very challenging in the field,” Wang said. “So we proposed using bacteria to achieve it instead.”

In order to build the material, the researchers 3-D printed a lattice structure or scaffolding. This structure has empty squares within it and the lattice layers are laid at varying angles to create scaffolding in line with the helicoidal shape.

The bacteria are then introduced to this structure. Bacteria intrinsically like to attach to surfaces and will gravitate to the scaffolding, grabbing on to the material with their “legs.” There the bacteria will secrete urease, the enzyme which triggers formations of calcium carbonate crystals. These grow from the surface up, eventually filling in the tiny squares or voids in the 3-D printed lattice structure. Bacteria like porous surfaces, Wang said, allowing them to create different patterns with the minerals.

The Trifecta

“We did mechanical testing that demonstrated the strength of such structures to be very high. They also were able to resist crack propagation–fractures–and help dampen or dissipate energy within the material,” said An Xin, a CEE doctoral student.

Existing materials have shown exceptional strength, fracture resistance, and energy dissipation but the combination of all three elements has not been demonstrated to work as well as in the living materials Wang and his team created.

“We fabricated something very stiff and strong,” Wang said. “The immediate implications are for use in infrastructures like aerospace panels and vehicle frames.”

The living materials are relatively lightweight, also offering options for defense applications like body armor or vehicle armor. “This material could resist bullet penetration and dissipate energy from its release to avoid damage,” said Yipin Su, a postdoc working with Wang.

There’s even potential for these materials to be reintroduced to bacteria when repairs are needed.

“An interesting vision is that these living materials still possess self-growing properties,” Wang said. “When there is damage to these materials, we can introduce bacteria to grow the materials back. For example, if we use them in a bridge, we can repair damages when needed.”

Featured image: The living materials by USC Viterbi Researchers mimics the Bouligand structure found in many strong, fracture-resistant and energy damping materials found in nature. © Qiming Wang, USC Viterbi School of Engineering

Reference: Xin, A., Su, Y., Feng, S., Yan, M., Yu, K., Feng, Z., Lee, K. H., Sun, L., Wang, Q., Growing Living Composites with Ordered Microstructures and Exceptional Mechanical Properties. Adv. Mater. 2021, 2006946. https://doi.org/10.1002/adma.202006946

Provided by University of South California

Planetary Science

SwRI Scientists Image a Bright Meteoroid Explosion in Jupiter’s Atmosphere (Planetary Science)

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From aboard the Juno spacecraft, a Southwest Research Institute-led instrument observing auroras serendipitously spotted a bright flash above Jupiter’s clouds last spring. The Ultraviolet Spectrograph (UVS) team studied the data and determined that they had captured a bolide, an extremely bright meteoroid explosion in the gas giant’s upper atmosphere.

“Jupiter undergoes a huge number of impacts per year, much more than the Earth, so impacts themselves are not rare,” said SwRI’s Dr. Rohini Giles, lead author of a paper outlining these findings in Geophysical Research Letters. “However, they are so short-lived that it is relatively unusual to see them. Only larger impacts can be seen from Earth, and you have to be lucky to be pointing a telescope at Jupiter at exactly the right time. In the last decade, amateur astronomers have managed to capture six impacts on Jupiter.”

Since Juno arrived at Jupiter in 2016, UVS has been used to study the morphology, brightness and spectral characteristics of Jupiter’s auroras as the spacecraft cartwheels close to its surface every 53 days. During the course of a 30-second spin, UVS observes a swath of the planet. The UVS instrument has occasionally observed short-lived, localized ultraviolet emissions outside of the auroral zone, including a singular event on April 10, 2020.

“This observation is from a tiny snapshot in time — Juno is a spinning spacecraft, and our instrument observed that point on the planet for just 17 milliseconds, and we don’t know what happened to the bright flash outside of that time frame,” Giles said, “But we do know that we didn’t see it on an earlier spin or a later spin, so it must have been pretty short-lived.”

Previously, UVS had observed a set of eleven bright transient flashes that lasted 1 to 2 milliseconds. They were identified as Transient Luminous Events (TLEs), an upper atmospheric phenomenon triggered by lightning. The team initially thought this bright flash might be a TLE, however, it was different in two key ways. While it was also short-lived, it lasted at least 17 milliseconds, much longer than a TLE. It also had very different spectral characteristics. Spectra of TLEs and auroras feature emissions of molecular hydrogen, the main component of Jupiter’s atmosphere. This bolide event had a smooth “blackbody’’ curve, which is what is expected from a meteor.

“The flash duration and spectral shape match up well with what we expect from an impact,” Giles said. “This bright flash stood out in the data, as it had very different spectral characteristics than the UV emissions from the Jupiter’s auroras. From the UV spectrum, we can see that the emission came from blackbody with a temperature of 9600 Kelvin, located at an altitude of 140 miles above the planet’s cloud tops. By looking at the brightness of the bright flash, we estimate that it was caused by an impactor with a mass of 550–3,300 pounds.”

Comet Shoemaker-Levy was the largest observed Jupiter impactor. The comet broke apart in July 1992 and collided with Jupiter in July 1994, which was closely observed by astronomers worldwide and the Galileo spacecraft. An SwRI-led team detected impact-related X-ray emissions from Jupiter’s northern hemisphere, and prominent scars from the impacts persisted for many months.  

“Impacts from asteroids and comets can have a significant impact on the planet’s stratospheric chemistry — 15 years after the impact, comet Shoemaker Levy 9 was still responsible for 95% of the stratospheric water on Jupiter,” Giles said. “Continuing to observe impacts and estimating the overall impact rates is therefore an important element of understanding the planet’s composition.”

The Jet Propulsion Laboratory, a division of Caltech in Pasadena, California, manages the Juno mission for the principal investigator, Dr. Scott J. Bolton, of Southwest Research Institute. Juno is part of NASA’s New Frontiers Program, which is managed at NASA’s Marshall Space Flight Center in Huntsville, Alabama, for the agency’s Science Mission Directorate in Washington. Lockheed Martin Space in Denver built and operates the spacecraft.

The new paper “Detection of a bolide in Jupiter’s atmosphere with Juno UVS” can be found at the American Geophysical Union.

Featured image: SwRI scientists studied the area imaged by Juno’s UVS instrument on April 10, 2020, and determined that a large meteoroid had exploded in a bright fireball in Jupiter’s upper atmosphere. The UVS swath includes a segment of Jupiter’s northern auroral oval, appearing purely in green, representing hydrogen emissions. In contrast, the bright spot (see enlargement) appears mostly yellow, indicating significant emissions at longer wavelengths. © SwRI

Provided by Southwest Research Institute