Page 1

AUGUST

2017

from curiosity to innovation

PL A S T IC IN VA DE S T HE A RC T IC P L A S T IC DE BR I S R E A C HE S T HE F UR T HE S T C OR NE R S OF E A R T H P.10

MOR E T H A N G A MING GR A P HIC S C A R D S M AY S OLV E C OMP L E X M AT HE M AT IC A L P R OBL E M S P.42

C OF F EE R ING S A ND SEMIC ONDUC T OR S A C H A NC E OB S E R VAT ION I S P R ODUC ING FA S T E R S E MIC ONDUC T OR S P.54

DECODING THE QUINOA GENOME THE HIGHE S TQUALITY DNA SEQUENCING OF THE SUPERGRAIN MAY HELP FEED A HUNGRY F U T UR E P.17


“Over a third of our faculty use computing as the main means of driving discovery, so having Shaheen—a top 20 supercomputer in the world—is indispensable to our mission.”

WELCOME LETTER

Dear Friends, The stories of discovery

Professor David Keyes Director of the Extreme Computing Research Center

Discover more about the KAUST supercomputer at CORELABS.KAUST.EDU.SA

KAUST offers facilities and scientific expertise to help strengthen Saudi Arabia’s position as a rising hub for research and innovation. By providing researchers and partners with high performance computing resources, KAUST is becoming a destination for those with a passion to make a global impact in science and technology.

and innovation in this issue highlight the breadth and depth of the scientific work conducted by our researchers and our commitment to serve as a catalyst in addressing grand challenges related to food, water, energy and the environment. Our scientists and engineers have the opportunity to aim high and explore big ideas. For example, our cover story features the KAUST-led research team that produced the highest-quality quinoa gene sequence to date. This new knowledge will accelerate development of sustainable quinoa varieties and could help develop new approaches to feeding the world’s growing population. Another example includes the work conducted by Dr. Ying Sun, who has collaborated with colleagues in the U.S. to develop a statistical technique for automatically eliminating erroneous data from weather-balloon observations in order to improve the accuracy of weather forecasting.

Dr. Jean-Lou Chameau

You will also learn more about our priority to play a significant role in developing Saudi talent for the Kingdom and for the world. Dr. Hind Abdullah Al-Johani, a recent graduate of KAUST, is now a Professor at Tabuk University. Through her research on controlling the structure of gold nanoparticles, and its potential medical applications, she became the first Saudi woman published as a first author in Nature Chemistry. Throughout this issue, there are more examples of the impact and passion of our faculty and researchers. KAUST continues to become a destination for scientific and technological education. Together, we are exploring important scientific questions and the world’s most difficult problems in an environment that motivates us to think big. I hope you enjoy reading our stories of discovery and that our efforts to advance science and technolog y for local and global impact inspire you. Yours in discovery, Jean-Lou Chameau

“KAUST continues to become a destination for scientific and technological education. Together, we are exploring important scientific questions and the world’s most difficult problems in an environment that motivates us to think big.” K AUST DISCOVERY

di sc o ver y.kaust.edu.sa

1


HIGHLIGHTS / AUGUST 2017

A DVA NCING HUM A N HE A LT H

15

20

T HE IN T ER SEC T ION OF DIS CIPL INE S

31

48

14

17

36

Tracking superbugs for antibiotic resistance

Malaria treatment just got a lot harder

An inflammatory inference

Algorithm helps diagnose medical mysteries

Interdisciplinarity helps unravel the protein puzzle

Quinoa—quest to feed the world

Sharing expert experimental knowledge to expedite design

An antibiotic-resistant bacteria strain could have severe implications for public health.

Parasites resistant to firstline antimalaria drug found in Africa.

Researchers identify surface proteins that navigate immune cells to inflammation sites.

A new tool uses genetic and clinical data to find the root cause of unexplained illnesses.

The work of a small group specializing in demystifying proteins is having farreaching effects.

The high-quality sequencing of a quinoa genome brings new potential for global food security.

A repository of metabolic information provides a quick reference tool for designing useful synthetic biological systems.

CL IM AT E S CIENCE

10

NE W T EC HNOL O GY F OR IMPAC T

26

63

45

50

52

Plastic pollution reaches the final frontier

Clownfish adapt for population survival

Reconstructing the Red Sea’s climate patterns

Blind matchmaking for more efficient wireless networks

Electron cameras offer a deeper look inside MOFs

The race for more efficient engines

Atlantic surface circulation transports high loads of plastic debris to remote Arctic waters.

Identification of candidate pathways in clownfish shows they can control responses to population alterations.

An advanced numerical model is helping researchers better understand the variability of the Red Sea’s climate patterns.

Autonomously pairing network users could expand the capability of the next generation of wireless networks.

Highly sensitive cameras allow researchers to see the atomic structure of metal-organic frameworks.

New technique lays the foundation for greener transport fuels and next generation engines.

E X PER IMEN T ING W I T H NE W ME T HOD S

46

53

PRO T EC T ING C OR A L R EEF S

60

24

30

32

Stretching toward energy efficiency

Gold standards for nanoparticles

The power of attraction

Seeking adaptation for corals in times of stress

Potential for Saudi Arabian coral reefs to shine

Gene sequences reveal secrets of symbiosis

Deformable thermoelectric materials add a new twist to the design of energyscavenging devices.

Understanding how small organic ions stabilize gold nanoparticles may allow for better control.

Hybrid organic-inorganic materials can self-assemble into tiny doughnut-like structures.

The Red Sea could help inform future practices to safeguard the world’s coral reef ecosystems.

Careful marine management and stricter fishing laws could enable Saudi Arabia’s coral reefs to thrive.

Genome sequences of dinoflagellate algae indicate how they maintain their symbiotic relationship with corals.

2

AUGUS T 2 017

1 nm

K AUST DISCOVERY

di sc o ver y.kaust.edu.sa

3


“The support and guidance I receive from my advisor are invaluable. Professor Stenchikov is a leading expert in his field and I am grateful to be a part of his team.”

B E S E

B I O L O G I C A L A N D E N V I R O N M E N TA L S C I E N C E A N D E N G I N E E R I N G D I V I S I O N / A U G U S T 2 0 1 7

20 22

MALARIA TREATMENT JUST GOT A LOT HARDER Africa now joins Southeast Asia in hosting parasites partially resistant to the first-line antimalaria drug.

THE CARPENTER ENZYME GIVES DNA THE SNIP Enzyme follows a two-step verification system before cutting and repairing DNA damage.

24

SEEKING ADAPTATION FOR CORALS IN TIMES OF STRESS The Red Sea could help inform future practices to safeguard the world’s coral reef ecosystems.

26 28

10 Learn more about becoming a KAUST student at WWW.KAUST.EDU.SA

Evgeniya is interested in large-scale volcanic eruptions and their impact on global climate. With her advisor, Professor Georgiy Stenchikov, she investigates atmospheric and ocean circulation changes in the tropical Pacific. With a student-faculty ratio of 6 to 1, students like Evgeniya receive individual attention and mentorship to help advance their academic careers. Learn more about becoming a KAUST student at www.kaust.edu.sa

12

PLASTIC POLLUTION REACHES THE FINAL FRONTIER

15

THE TIPPING POINT FOR MARINE AGRICULTURE

INTERDISCIPLINARITY HELPS UNRAVEL THE PROTEIN PUZZLE The work of a small group specializing in demystifying proteins is having farreaching effects.

TRACKING SUPERBUGS FOR ANTIBIOTIC

RESISTANCE

30

TWEAKING THE TRANSCRIPTOME TO TACKLE STRESS

16

SHORT REGULATORY GENE SPOTTED Two proteins produced by a single gene interact to keep the genome in check.

17

31 32

QUINOA—QUEST TO FEED THE WORLD The high-quality sequencing of a quinoa genome brings new potential for global food security.

POTENTIAL FOR SAUDI ARABIAN CORAL REEFS TO SHINE Careful marine management and stricter fishing laws could enable Saudi Arabia’s coral reefs to thrive.

An antibiotic-resistant bacteria strain could have severe implications for public health.

Carlos Duarte is looking at how oceans can help provide food and fresh water security.

14

Candidate pathways in clown fish show how they respond to population alterations.

Stressed dinoflagellates rewrite their genes during transcription.

Atlantic surface circulation transports high loads of plastic debris to remote Arctic waters.

Evgeniya Predybaylo Ph.D. student, Earth Science and Engineering

CLOWNFISH ADAPT FOR POPULATION SURVIVAL

AN INFLAMMATORY INFERENCE The surface proteins responsible for navigating immune cells to sites of inflammation are identified.

GENE SEQUENCES REVEAL SECRETS OF SYMBIOSIS Genome sequences of dinoflagellate algae indicate how they maintain their symbiotic relationship with corals.

K AUST DISCOVERY

di sc o ver y.kaust.edu.sa

5


“The remarkably well-equipped laboratories and generous funding at KAUST create an environment of academic freedom that I’ve never experienced before. Having these sustained and flexible resources allows me to dedicate more time to doing research with my students in the lab.”

C E M S E

34

COMPUTER, ELEC TRICAL AND M ATHEM ATICAL SCIENCE AND ENGINEERING DIVISION / AUGUS T 2017

COLOR-CHANGING COATINGS READY FOR THE BIG TIME Wafer-thin, scratch-proof films can generate a rainbow of colors using random metallic nanostructures.

36

SHARING EXPERT EXPERIMENTAL KNOWLEDGE TO EXPEDITE DESIGN A repository of metabolic information provides a quick reference tool for designing useful synthetic biological systems.

37

A SAFE SWEEP OF WEATHER DATA

40

DIVIDE AND CONQUER PATTERN SEARCHING

41 Professor Charlotte Hauser National Academy of Inventors Fellow, 2015

Learn more about Charlotte and her work at WWW.KAUST.EDU.SA

Charlotte’s research interests lie at the interfaces of chemistry, biomedicine, bioengineering and nanotechnology. She uses smart nanomaterials to advance discoveries through regenerative, biomedical and environmental applications, which have led to several patents. At KAUST, she explores her passion for scientific discovery and breakthroughs along with the next generation of scientific leaders.

A statistical technique for automatically cleaning erroneous data from weatherballoon observations will improve the accuracy of weather forecasting.

A new data-mining strategy that offers unprecedented pattern search speed could glean new insights from massive datasets.

IMPROVING CONNECTIONS FOR SPATIAL ANALYSIS A statistical model that accounts for common dependencies in spatial data yields more realistic results.

42

43

COVER CREDITS: AMR RAHMA / PARTNERSHIPS & CUSTOM MEDIA NATURE RESEARCH IMAGES: (QUINOA): ANJO KAN / ALAMY STOCK PHOTO (DNA STRAND): PHOTODISC/ GETTYIMAGES

47

45

THE CREST OF WAVEFORMS FOR NEXT-GEN RADAR A new method for shaping the waveform generated by multiantenna radar systems is inexpensive and practical.

An international, multidisciplinary collaboration that led to the world’s first underwater robotic avatar.

TAKING GRAPHICS CARDS BEYOND GAMING A highly efficient mathematical solver designed to run on graphics processors gives scientists and engineers a powerful new tool for a common computational problem.

DEEP THINKING BRINGS UNDERWATER ROBOT TO LIFE

BLIND MATCHMAKING FOR MORE EFFICIENT WIRELESS NETWORKS Autonomously pairing network users could expand the capability of the next generation of wireless networks.

46

STRETCHING TOWARD ENERGY EFFICIENCY Deformable thermoelectric materials add a new twist to the design of energyscavenging devices.

48

ALGORITHM SCOURS DATASETS TO DIAGNOSE MEDICAL MYSTERIES A new tool uses genetic and clinical information to find the root cause of unexplained illnesses.

K AUST DISCOVERY

di sc o ver y.kaust.edu.sa

7


“At KAUST, I was encouraged to work on both fundamental and goal-driven science. I learned how to apply science and show its impact on improving daily life. Now as a research scientist, I have been committed to giving back and I find the greatest opportunity to do so at the interface between industry and academia.”

P S E

50

PHYSICAL SCIENCE AND ENGINEERING DIVISION / AUGUST 2017

HIGH-SENSITIVITY CAMERAS REVEAL THE ATOMIC STRUCTURE OF METAL-ORGANIC FRAMEWORKS Highly sensitive electron cameras allow researchers to see the atomic structure of metal-organic frameworks.

52

THE RACE FOR MORE EFFICIENT ENGINES

53

GOLD STANDARDS FOR NANOPARTICLES

54

New technique lays the foundation for greener transport fuels and next generation engines.

Understanding how small organic ions stabilize gold nanoparticles may allow for better control.

COFFEE-RING EFFECT LEADS TO CRYSTALLIZATION CONTROL IN SEMICONDUCTORS

58

Standardized reporting of energy conversion efficiency could help to develop photocatalysts to produce renewable fuels.

Varying the thickness of crystallizing materials facilitates control over the patterns and properties of crystals.

55

Noura Shehab ’11 M.S., ’14 Ph.D. Research Scientist at RPD Innovations Learn more about how KAUST is making an impact at WWW.KAUST.EDU.SA

While a student at KAUST, Noura developed technologies to produce freshwater from wastewater using microbial fuel cells. Presently, she works for a joint venture that is committed to accelerating the creation of technology-driven industries in Saudi Arabia. Through the spirit of discovery, KAUST scientists, engineers and entrepreneurs have a passion for doing things that matter.

56

LEVITATION TRICK GIVES DRAG THE SLIP Plunging hot spheres into viscous liquids reveals a way to reduce fluid resistance without complex engineering procedures.

AUGMENTED REALITY AT YOUR FINGERTIPS A flexible, carbon-based device that responds to humidity in two ways can sense 3D objects without touching them.

62

AN INTERNATIONAL LANGUAGE FOR SOLAR ENERGY FIELDS

60

ANDERSON’S MODEL HOLDS FOR 2D MATERIALS A simple model is shown to accurately predict the electronic properties of a combination of 2D semiconductors.

60

THE POWER OF ATTRACTION Hybrid organic-inorganic materials can self-assemble into tiny doughnut-like structures.

63

SETTING REGENERABLE POLYMER TRAPS Stable and recyclable materials synthesized using intrinsically porous polymers selectively retain CO2 from exhaust emissions and natural gas.

RECONSTRUCTING THE RED SEA’S CLIMATE PATTERNS An advanced numerical model is helping researchers better understand the variability of the Red Sea’s climate patterns.

64

INFORMATION STORAGE WITH A NANOSCALE TWIST Discovery of a novel rotational force inside magnetic vortices makes it easier to design ultrahigh capacity disk drives.

KAUST DISCOVERY IS PUBLISHED FOR THE KING ABDULLAH UNIVERSITY OF SCIENCE AND TECHNOLOGY (KAUST) THROUGH THE PARTNERSHIP AND CUSTOM MEDIA UNIT OF NATURE RESEARCH, PART OF SPRINGER NATURE. KAUST THUWAL 23955-6900 – KINGDOM OF SAUDI ARABIA EMAIL: DISCOVERY@KAUST.EDU.SA WEB: WWW.KAUST.EDU.SA NATURE RESEARCH THE CAMPUS – 4 CRINAN STREET – LONDON, N1 9XY, UK EMAIL: NATURE@NATURE.COM WEB: WWW.NATURE.COM K AUST DISCOVERY

di sc o ver y.kaust.edu.sa

9


Biological and Environmental Science and Engineering Division

B E S E

PLASTIC POLLUTION REACHES THE FINAL FRONTIER

Atlantic surface circulation transports high loads of plastic debris to remote Arctic waters.

10

AUGUST 2 017

ANNA DENIAUD

The plastic particles were meticulously sorted by size and shape.

W

ith few nearby settlements as sources of pollution, the Arctic was presumed relatively free of marine plastic debris. An international collaboration has now found that discarded

The expedition traveled from the Greenland Sea to the Labrador Sea and collected samples of plastic of different sizes and shapes to analyze.

plastic has colonized even Earth’s furthest reaches — parts of the remote Arctic Ocean. Ocean circulation models had predicted a potential plastic accumulation zone in the Arctic Polar Circle, similar to those found in the ocean gyres in the subtropics, but there had been no specific studies. Professors Carlos Duarte and Xavier Irigoien from the KAUST Red Sea Research Center were part of an international team that sampled extensively for floating plastic debris in the Arctic waters. The KAUST researchers catalyzed this research as an opportunity through the collaboration of the global projects Malaspina 2010 Expedition and Tara Oceans, where KAUST is a partner. The aim was to analyze the magnitude, distribution and sources of the plastic pollution on the surface waters of the Arctic Ocean. As the expedition traveled from the Greenland Sea to the Labrador Sea, samples were collected between 60o to 80o latitude north. Floating plastic was collected by a fine mesh, wide-mouthed

manta net towed just below the sea surface. The plastic particles were meticulously hand-picked from the nets and sorted by size, shape and possible origin before being washed and weighed. The concentration and plastic load was also calculated to consider possible sources of the pollution. The research team found relatively scant plastic rubbish across much of the area, however, they identified large pockets of plastics in the northern- and easternmost areas of the Greenland and Barents Seas. The median values of floating plastic rubbish were quite similar to those found in the notorious subtropical accumulation zones; however, the maximum concentrations in this polar area were considerably lower. Much of the plastic is aged which suggests that it has floated in from distant sources, explained Duarte. “These results are concerning because they show that plastic pollution is reaching every corner of the Earth.” said Duarte. “The sustained plastic use—and the long time it takes for plastic to be redistributed across

K AUST DISCOVERY

di sc o ver y.kaust.edu.sa

11


Biological and Environmental Science and Engineering Division

B E S E

THE TIPPING POINT FOR MARINE AGRICULTURE

the ocean—also indicates that this pollution is increasing”. “The Barents Sea supports much of the world’s fisheries and is a hotspot for seabirds,” explained Duarte. “The concern is that plastic pollution may be infiltrating the Arctic food web.” One hypothesis that emerged from this study is that plastics may be accumulating on the sea floor. Duarte said that KAUST researchers will seek to test this assumption when they take part in the future expeditions of the Arctic Research Center at the Aarhus University, Denmark. Cozar, A., Marti, E., Duarte, C., García-de-Lomas , J., van Sebille, E…& Irigoien, X. The Arctic Ocean as a dead-end for floating plastics in the North Atlantic branch of the thermohaline circulation. Science Advances, 3 e1600582 (2017).

12

AUGUST 2 017

Professor of Marine Science, Director of the Red Sea Research Center and the Tarek Ahmed Juffali Research Chair in Red Sea Ecology, Carlos Duarte, is widely recognized as one of the world’s leading voices on the impacts of climate change on marine ecosystems. He is currently leading a multidisciplinary research team that is looking at how the world’s oceans can help us provide food and fresh water security for current and future generations. Tell me about your role at KAUST. I joined KAUST at the start of 2015 as a Professor in Marine Science. I have since then been appointed Director of the Red Sea Research Center. My role’s changed— I’m now spanning the bridge between research and education here and moving into a leadership position. I’m enjoying developing a strategy to take the Center in a new direction—I want to engage with my colleagues from across KAUST to address problems in marine environments.

“The sustained plastic use—and the long time it takes for plastic to be redistributed across the ocean— also indicates that this pollution is increasing.”

What were you doing before KAUST? I had a dual appointment and I split my time 50/50 between a research professorship in Spain with the Spanish National Research Council working on Marine Ecology and Oceanography and in Australia working as the Director of a new research institute at the University of Western Australia in Perth.

Why is your research area so important?

BOTTOM IMAGE: 2016 K AUST, TOP IMAGE: ANNA DENIAUD

The scientists used nets towed behind the boat to collect plastic debris.

answer. As part of this, I’ve transitioned from just working on my own discipline to a more multidisciplinary approach. I found that in many of the previous environments where I’d worked, there were obstacles that slowed down interdisciplinary research. KAUST emerged as a destination that would alleviate those concerns and as one that provides researchers with the necessary time and environment to be able to collaborate across disciplines.

We’re exhausting the resources that are available to us on land and are no longer able to sustain the production levels we need. The key bottlenecks we’re facing are the availability of both fresh water and arable land. The oceans have plenty of water, and every single square meter of the ocean is productive. The development of a sustainable and ethical marine agriculture model that meets our needs for food and water security is achievable. The industry is only 30 years old but I think this is an area of development that history will look back on as a turning point.

What specifically are you working on at the moment? KAUST has a strong program in ocean genomics, and we’ve cataloged about 55

million genes from the ocean’s microbes. We’re currently developing systems to stream through this large pool of genes. Our aim is to identify the genes and proteins that will give us a better understanding of the impact we’re having on the environment and how we can utilize these resources responsibly. We want to ensure that marine life will continue to be healthy, that marine environments will continue to be well preserved and that we meet the future needs of humanity. As an example, we’re looking at how marine environments, such as mangroves, sea grass and salt marshes, adapt to the impacts of climate change. How marine environments react to a rapid change to their environment has been grossly underappreciated. We can drive change in our societies by delivering messages around the opportunities we have on our planet as opposed to bombarding them with negative news.

Where do you see KAUST’s research in this area going in future? An institution’s reputation is based on having a strong fundamental research program and we have built that at KAUST. We also have strong partnerships with industry so our aim is to continue to ensure we have strong applied research outcomes too. We also need to be looking at how we can support the need for scientific and technological progress in Saudi Arabia and the region in general. We strive to do the best research, whether it focuses on fundamental science or applied outcomes.

What made you choose KAUST? My main research focus is on how oceanbased solutions can help to solve the challenges facing humanity as a whole. Food supply for a growing population and being able to reduce our footprint are the two big questions that I think I can help

Carlos Duarte believes we are on the verge of an ethical and sustainable agricultural revolution.

What has being at KAUST enabled you to do that you couldn’t do elsewhere? I am currently working with colleagues from nanotechnology, electrical engineering, imaging, machine learning, genomics, big data and biology. My expectations for interdisciplinary research collaborations have been met and exceeded. The absence of the administration and funding constraints I’ve experienced at other institutions has allowed me to spend more time on my research and to build strong internal collaborations. KAUST is a community that we live and work in—it doesn’t close at 5:00 pm. Many of the colleagues I’m working with I’ve met at social events or even at the supermarket. I’ve built social networks that I haven’t seen before in my career.

What would you say to anyone who was thinking of coming to KAUST? I often find that it is difficult to explain KAUST because I’m so passionate about my experience—I worry that people will think I’m overselling it. If someone’s interested in knowing something about KAUST, I invite them to come and join us to experience it for themselves. This usually works a lot better than trying to explain it to somebody because it just doesn’t work—the best advice is to come and experience it for yourself.

What is the best thing about being at KAUST? It’s the time to reflect, to talk, to conceive of new ideas. For the first time in my career I don’t have to work 24/7. The KAUST environment encourages you to do things other than just work. There are a number of activities that also feed our intellects and our spirits in terms of arts and opportunities to learn about other topics. Time is a luxury that I had forgotten about. I have the time to think in a stimulated environment, similar to when I was a graduate student, and I haven’t experienced that for maybe thirty years or so.

K AUST DISCOVERY

di sc o ver y.kaust.edu.sa

13


Biological and Environmental Science and Engineering Division

B E S E contaminant is present, ContaMiner can typically detect it in only 5-15 minutes,” said Arold. Several hundred researchers have used the program since it was first described in late 2016 in the Journal of Applied Crystallography. Many from the crystallography community have helped update ContaBase to now include 71 contaminants. “It’s an ongoing community effort,” said Arold. ContaMiner has also been selected to be included in an online server, called CCP4, which is a highly selective collection of software related to structural biology and is the most widely used resource worldwide, explained Arold. While having international impact, Arold and his team also play a vital role in the local scientific community through their unique set of skills. The KAUST team combines expertise in molecular biology, biochemistry, biophysics, bioinformatics and computation to investigate protein structures and function. It is the only group involved in structural biology in Saudi Arabia but,

Stefan Arold (left) and his team play a vital role in the local scientific community through collaboration with other research groups in the Kingdom.

INTERDISCIPLINARITY HELPS UNRAVEL THE PROTEIN PUZZLE The work of a small group specializing in demystifying proteins is having far-reaching effects.

14

AUGUST 2 017

the identity of the protein contaminant that they had unintentionally crystallized,” said Arold. Arold’s team has worked tirelessly to compile a preliminary database, called ContaBase, of 62 known contaminants. “Contaminants were a known but under appreciated problem because many cases went undetected,” said Arold. Even in cases where contaminants are finally identified, this information often goes unpublished since the experiment was considered a failure. Often researchers report issues of contamination in online forums rather than peer-reviewed publications. “Because of this, nobody had a good idea of how many and which contaminants might occur and crystalize,” he continued. ContaMiner changes this. Now, researchers can submit their X-ray diffraction data to the program, which compares it with an updateable database of known contaminants. “If a

experts in nuclear magnetic resonance spectroscopy, which is highly complementary to X-ray crystallography.” He also advocates that biologists develop more awareness of the importance of structural biology for their research. “Wisely, KAUST has invested heavily in structural biology; and biological imaging in general is clearly an area of priority. We have outstanding resources, such as 700 and 950 megahertz nuclear magnetic resonance imaging spectrometers and the TITAN KRIOS electron microscope. And although I am currently the only structural biologist, I might not be alone for much longer,” Arold said. Negotiations are already underway to bring more talent to the institution. Hungler, A., Momin, A., Diederichs, K. & Arold, S. T. ContaMiner and ContaBase: a webserver and database for early identification of unwantedly crystallized protein contaminants. Journal of Applied Crystallography 49, 2252–2258 (2016).

TRACKING SUPERBUGS FOR ANTIBIOTIC RESISTANCE An antibiotic-resistant strain of bacteria found circulating in municipal wastewater could have severe implications for public health.

2016 K AUST / RAIHAN JUMAT

indication of its structure. Researchers then apply “molecular replacement,” which compares the target protein crystal to the 3D structure of other known similar proteins. But for the researchers to compare their protein with similar ones, first they need to know how its amino acids are arranged. ContaMiner can help researchers determine if they are even looking at the right protein to begin with. “The protein we crystallized might not be the protein we thought it was but instead an unknown contaminant,” explained Arold. Protein-based contaminants can, more often than previously thought, get crystallized instead of, or in addition to, the protein under study. These might come from the organism that originally produced the protein or occur during the purification or crystallization process. “Scientists often waste months of work before they identify the error and

2017 K AUST / ANASTASIA KHRENOVA

C

ontaMiner is a web-based, opensource program developed by a unique interdisciplinary team in KAUST. This program is already saving time for international researchers. “How much can you understand and repair a car if you don’t have a detailed picture of what is going on under the hood?” said KAUST Associate Professor Stefan Arold. “Proteins are life’s workhorses: their function and dysfunction both create life and end it. Each protein’s amino acid sequence folds into a particular 3D structure that is required to support its function. If you want to understand, affect or engineer a protein’s function, you need to know its 3D structure,” he explained. The process to determine that structure begins by purifying and crystallizing the protein under investigation. The protein crystal is then bombarded by extremely powerful X-rays, which diffract in various directions, giving an

under the supervision of structural biologist Arold, it is setting up important local collaborations. Currently they are collaborating with researchers at King Fahd Specialist Hospital and Research Centre to identify gene mutations that cause diseases in the Saudi population. Arold uses his expertise, together with computational modeling, to understand why specific mutations cause protein malfunctions. “It is intriguing how much harm can be caused by a single mutation” he said. “It also gives us a glimpse of the unimaginable sophistication and complexity of our bodies. Arold and his team also recently worked with KAUST plant scientist Mark Tester and a diverse international team to understand the molecular basis for the production of toxic compounds, called saponins, in some but not all quinoa strains (see page 17). “Does the region need more structural biologists?” asked Arold. “In my biased opinion, of course yes. In particular,

The dramatic rise in bacterial superbugs that are resistant to last-resort antibiotics poses a significant global health threat. Recently, KAUST researchers studied incidences of a resistance-conferring gene carried by bacteria in municipal wastewater in Jeddah, Saudi Arabia. The recently discovered New Delhi metallo beta-lactamase enzyme (NDM), which is carried by the blaNDM-1 gene, confers resistance to last-resort antibiotics called carbapenems. Without carbapenems, our ability to tackle potentially lethal

bacterial infections is greatly reduced. The situation is exacerbated by people travelling widely, enabling resistant bacteria to spread further and faster than ever before. “There has been an increase in infections caused by NDM-positive bacteria reported in hospitals across the Gulf,” explained Assistant Professor of Environmental Science and Engineering and member of the University’s Water Desalination and Reuse Center Pei-Ying Hong, who led the project team. “We began to wonder if viable NDM-positive pathogens

were circulating in local communities via presence in Jeddah’s municipal wastewater networks. We were also interested to see if pathogen levels spiked during times of religious pilgrimage, a time

Cross-section of mammalian cell lines (in red) internalized by Escherichia coli strain PI-7 (in green).

when millions of people come to Saudi Arabia from across the world.” In Jeddah, only around 50% of wastewater is treated in centralized sewage plants. The remainder is partially treated in septic tanks and later discharged into the environment. Hong’s team used the state-of-the art equipment in the University’s Bioscience Core Lab to analyze wastewater from a Jeddah treatment plant over the course of a year. Using a molecular technique, they found that up to 104 copies of blaNDM-1

K AUST DISCOVERY

di sc o ver y.kaust.edu.sa

15


Biological and Environmental Science and Engineering Division

B E S E

SHORT REGULATORY GENE SPOTTED Two proteins produced by a single gene interact to keep the genome in check. An epigenetic mechanism regulating gene activity has been revealed by a KAUST -led international team of researchers investigating interactions between the human genome and its environment in adult tissues. Professor Valerio Orlando’s lab at KAUST looks at the role of Ezh1, a gene whose function in mature tissues has remained unclear for 25 years. Like its twin Ezh2, Ezh1, along with a partner protein, encodes a protein involved in tagging genes to repress their activity. However, while Ezh2 mutations have been linked to cancer and developmental defects, mice lacking Ezh1 seem to develop normally. In the past, Orlando’s group observed Ezh1 attached to the promoter of many genes that are normally switched on. “We saw this prototypical epigenetic repressor sitting on active genes, and our interpretation was that it provides the ability to repress them,” said Orlando. Hypothesizing that repression might be useful under stress, the team chemically stressed muscle cells and observed repression only in cells expressing Ezh1. Stress spurred Ezh1 into action, tagging genes with a repressive marker that could later be removed. A turning point in the conception of Ezh1 came when the team discovered a truncated version of the protein. Many Schematic model of cytosolic Ezh1ß function in postmitotic differentiated muscle cells.

human genes encode several slightly different versions of a protein, known as isoforms. “Once our eyes were redirected to the short version, we immediately understood a number of things,” recalled Orlando. The truncated isoform was in the cytoplasm rather than the nucleus, and the team demonstrated that it acts as an environmental sensor regulating the activity of the full-length protein. Ezh1 needs a partner protein in order to tag genes, but the short isoform binds to the partner, trapping it in the cytoplasm, “like keeping that protein on a leash.” In stressed cells, the short isoform is degraded, releasing the partner to join full-length Ezh1 in the nucleus. Once the stress stops, shortEzh1 once again traps the partner, stopping long-Ezh1 from acting. These findings reveal a new landscape of genetic regulation for researchers to explore, where interactions occur between isoforms of a single gene rather than products of different genes. “This offers a new paradigm for gene regulation, linking the genome with the environment,” said Orlando. “It’s a very exciting perspective.” Bodega, B., Marasca, F., Ranzani, V., Cherubini, A., Della Valle, F... Orlando, V. A cytosolic Ezh1 isoform modulates a PRC2-Ezh1 epigenetic adaptive response in postmitotic cells. Nature Structure & Molecular Biology 24, 444–452 (2017).

ATROPHY + H 2 O 2 EED

EED

Mantilla-Calderon, D., Jumat, M.R.,

EZH1ß

Wang, T., Ganesan, P., Al-Jassim,

EZH1ß

N. & Hong, P-Y. Isolation and

EED

EED

characterization of NDM-positive EZH1A

Escherichia coli from municipal

EED

SUZ12

EZH1A SUZ12

wastewater in Jeddah, Saudi Arabia. Antimicrobial Agents and Chemotherapy 60, 5223–5231 (2016). CYTOSOL

CYTOSOL

16

AUGUST 2 017

NUCLEUS NUCLEUS

RECOVERY

M3

BOTTOM IMAGE SOURCE: 2017 K AUST / IVAN GROMICHO - RIGHT IMAGE CREDIT: 2016 K AUST / PHOTO BY DAVID JARVIS, EDITED BY IVAN GROMICHO

were present in every cubic meter of wastewater. While the abundance of the gene fluctuated throughout the year, there was no spike during the Hajj pilgrimage, suggesting that blaNDM-1 was already locally prevalent in bacterial communities. When the team identified that the gene was carried by a strain of Escherichia coli called PI7, they conducted genomic investigations into E. coli PI7 to reveal concerning results. “E.coli PI7 possesses a resistance profile organized in a genetic structure that is similar to one discovered in another bacterium in Taiwan,” said the study’s first author Ph.D. student David MantillaCalderon. “This highlights the global mobility of this genetic structure. Not only this, but E. coli PI7 is resistant to a wide spectrum of antibiotics and its genetic make-up encourages gene transfer to other bacteria.” The results also indicate that E. coli PI7 remains viable even after passing through sewage networks over long distances. This raises questions about its potential environmental persistence. Hong told us that further investigations into the persistence of blaNDM-1 in the environment are vital. She also stressed the importance of improving wastewater treatment infrastructures and of having careful surveillance of pathogens in such networks.

QUI NOA—QUE S T TO FEED

TH E W O RL D The high-quality sequencing of a quinoa genome brings new potential for global food security.


Biological and Environmental Science and Engineering Division

Q Get social with KAUST Follow us on social media KAUSTofficial @kaust_news kaustedu kaustofficial

uinoa could hold the key to feeding the world’s growing population because it can thrive in harsh environments and grows well on poor-quality, marginal land. Researchers have now completed the first high-quality sequence of the Chenopodium quinoa genome, and they have begun pinpointing genes that could be manipulated to change the way the plant matures and produces food. The project brought together 33 researchers from four continents, including 20 people from seven research groups at KAUST, to produce an article that made it to the cover of the Nature February 16 issue. “Quinoa was the staple ‘Mother Grain’ that fueled the ancient Andean civilizations, but the crop was marginalized when the Spanish arrived in South America and has only recently been revived as a new crop of global interest,” said KAUST Professor of Plant Science Mark Tester, who led the project team. “This means quinoa has never been fully domesticated or bred to its full potential even though it provides a more balanced source of nutrients for humans than cereals.” As a first step toward improving our understanding of how quinoa grows, m a t u re s a n d p ro d u c e s seeds, Tester’s team decided to sequence its genome. They used a combination of techniques, including cutting-edge sequencing technologies and genetic mapping, to piece together full chromosomes of C. quinoa. Their resulting genome

18

AU G U S T 2 017

THE SEQUENCING OF THE FIRST HIGHQUALITY QUINOA GENOME BY A KAUST-LED RESEARCH TEAM COULD ONE DAY HELP TRANSFORM OUR ABILITY TO FEED THE WORLD’S GROWING POPULATION.

is the highest-quality quinoa sequence to date, and it is already yielding insights into the plant’s traits and growth mechanisms. “One problem with quinoa is that the plant naturally produces bitter-tasting seeds,” said Tester. “This is due to the accumulation of chemical compounds called saponins in the seeds. We’ve pinpointed one of the genes that we believe controls the production of saponins in quinoa, which would facilitate the breeding of plants without saponins to make the seeds taste sweeter.” There is immense potential for the genome sequence to help scientists understand quinoa and therefore modify it for more widespread, commercial use. For example, breeders could use this genetic information to learn how to control plant size to favor shorter, stockier plants that are less likely to fall over. These more stable plants could support bigger seed heads and be grown closer together in large fields. “We already know that the quinoa plant family is incredibly resilient,” said Tester. “It can grow in poor soils, salty soils and at high altitudes. It really is a very tough plant. Quinoa could provide a healthy, nutritious food source for the world using land and water that currently cannot be used, and our new genome takes us one step closer to that goal.” Jarvis, D.E., Ho, Y.S., Lightfoot, D.J., Schmöckel, S.M., Li, B., ... & Tester, M. The genome of Chenopodium quinoa. Nature 542, 307– 312 (2017).

LEFT PAGE: LINDA POLIK , RIGHT PAGE: 2017 K AUST / ANASTASIA KHRENOVA

B E S E

TAKING AGRICULTURE INTO THE FUTURE Passionate plant scientist Mark Tester is out to conduct ground-breaking research into plants that could one day help feed the world.

Left: Several co-authors surrounded by quinoa in the Greenhouse Core Lab. From left to right (back row) Professor Mark Tester, Associate Professor Salim Al-Babili, Dr. David E. Jarvis, Dr. Damien J. Lightfoot, Dr. Hajime Ohyanagi; (middle row) Dr. Sandra M. Schmöckel, Dr. Katsuhiko Mineta, Ge Gao, Dr. Sónia Negrão; (front row) Noha Saber, Afaque A. Momin (Not pictured: Dr. Xiujie Guo, Dr. Najeh M. Kharbatia) Right: Computational Bioscience Research Center faculty and co-authors Associate Professor Stefan T. Arold and Professor Takashi Gojobori. The following co-authors had left KAUST at the time this photo was taken: Professor Christopher Gehring, Dr. Yung Shwen Ho, Dr. Bo Li, Dr. Yong H. Woo, Craig Michell

MEET THE TEAM This extraordinarily collaborative work involved the expertise of 20 KAUST scientists from two of the University’s Divisions, including two Research Centers and the facilities of three of the University’s Core Labs. Although the majority of the authors are affiliated with the Desert Agriculture Initiative, they were supported by specialists in the Greenhouse Core Lab and the Red Sea Research Center, all under the Biological and Environmental Sciences and Engineering Division. In addition, the big data challenge of the project called upon considerable contributions from several individuals in the Computer, Electrical and Mathematical Sciences and Engineering Division, including the Imaging and Characterization Core Lab. However, the work would not have been completed without analyses performed in the University’s Analytical Chemistry Core Lab. Publishing this in Nature involved five KAUST faculty members and several postdocs, research assistants, technical specialists, lab technicians and graduate students representing more than 10 nationalities.

“Ever since I was a child, I’ve had a strong belief that we should leave the world in a better state than we found it,” said Mark Tester, Professor of Plant Science. “This is one of the reasons I’ve chosen this career. As a plant scientist, the most challenging, inspiring and powerful goal is to contribute to helping feed all the people on this Earth.” Tester’s research has already charted a course towards achieving this goal. Originally from Australia, he has worked there and in the United Kingdom since graduating in the 1980s. Before he moved to KAUST in 2013, Tester designed and created the Plant Accelerator at the University of Adelaide in Australia. This unique facility allows scientists to grow and image thousands of plants, all at the same development stage, and monitor how subtle differences in environmental and genetic factors can affect their productivity and health. Tester’s expertise spans a wide, cross-curricular spectrum, from plant physiology and cell biology to research projects that utilize the latest in plant genetics and genomics technologies. At KAUST he is leading research that

aims to pinpoint key genes conferring salinity tolerance. The manipulation of these genes could transform the ability of specific crops to thrive in poor-quality soils or under saline conditions. “My research team is currently focusing on three key areas,” said Tester. “Firstly, we aim to increase the salinity tolerance of common, hardy crops. For example, we recently identified key genetic loci responsible for increased salt tolerance in different strains of barley and rice. Secondly, we aim to domesticate salt-tolerant plants so that they flourish and produce high yields even under extreme conditions. We recently reported on the first high-quality sequencing of the quinoa genome; our results will help us to understand how the plant grows, matures and produces seeds, ultimately allowing us to create highly-productive, resilient quinoa plants.” Complementing these two strands of research, Tester also hopes to facilitate crop irrigation with partially desalinated water. This could be via the desalination of seawater or by using brackish water from estuaries or underground aquifers.

K AUST DISCOVERY

di sc o ver y.kaust.edu.sa

19


Biological and Environmental Science and Engineering Division

B E S E

MALARIA TREATMENT JUST GOT A LOT HARDER Africa now joins Southeast Asia in hosting parasites partially resistant to the first-line antimalaria drug. The first known case of artemisininresistance in Africa has been identified—a finding of great significance for efforts in global malaria control and drug resistance monitoring. A large international team of scientists identified the African origin of drug-resistant malaria parasites detected in a Chinese

20

AUGUST 2 017

patient, who had travelled from Equatorial Guinea to China. Artemisinin-based combination therapy (ACT) is the first-line recommended malaria treatment and comprises artemisinin and another antimalarial drug. Normally ACT clears the parasites from the blood within three days; however,

recently, strains of the malaria-causing agent, Plasmodium falciparum, in Southeast Asia have become relatively tolerant to artemisinin. The resistance is partial and the majority of patients can be cured, albeit with a considerable delay. But, malariologists, including experts from the World Health Organization,

EDWIN REMSBERG / ALAMY

Anopheles gambiae mosquitos are the most important vectors for the transmission of malaria to humans in Africa.

fear that P. falciparum might eventually develop complete resistance to artemisinin, as it has to other antimalarials. The study, led by Jun Cao from the Jiangsu Institute for Parasitic Diseases, China, confirmed that the parasite carried a new mutation in a gene called Kelch13 (K13), the main driver for artemisinin resistance in Asia. Then, Arnab Pain, KAUST Professor of Bioscience, and his Ph.D. student Abhinay Ramaprasad set out to determine whether the parasite originated from Africa or Southeast Asia.

“We used whole-genome sequencing and bioinformatics tools we had previously developed—like detectives trying to link the culprit parasite to the crime scene,” explained Pain. Sequencing and analysis of P. falciparum DNA unveiled its origin by disclosing the several one-nucleotide differences, called single nucleotide polymorphisms (SNPs) that vary according to the geographical source of the strain. In the same way as merchandise barcodes contain information about the country of a product’s origin, SNP patterns reveal the birthplace of the parasite. For these tests, KAUST scientists used the nuclear DNA, as well as the one present in two organelles of the parasite: the mitochondrion and the apicoplast, a defining organelle of malaria parasites and related species. Both methods independently validated the origin of the parasite as West African, confirming the first case of artemisinin-resistance mediated by a K13 gene mutation on the African continent. “The spread of artemisinin resistance in Africa would be a major setback in the fight against malaria, as ACT is the only effective and widely used antimalarial treatment at the moment. Therefore, it is very important to regularly monitor artemisinin resistance worldwide,” explained Pain. Lu, F., Culleton, R., Zhang, M. Ramaprasad, A., ... & Cao, J. Emergence of indigenous Artemisinin resistant Plasmodium falciparum in Africa. New England Journal of Medicine 376, 991-993 (2017).

GLOWING REPORT ON PLANT HORMONE FUNCTION

THIS RESEARCH CAN HELP OPTIMIZE GROWTH, NUTRIENT UPTAKE, AND COMBAT PARASITIC WEEDS.

AS IN ANY EXCITING RESEARCH PROJECT, THE RESULTS GENERATED MORE QUESTIONS THAN ANSWERS.

A biological sensor can identify and quantify the activity of a little-known class of plant hormones, strigolactones. Strigolactones are an important and diverse class of plant hormones. Now, an international team led by KAUST and the University of Dusseldorf has developed a strigolactone sensor that can be genetically encoded into plant cells to help our understanding of plant development. Strigolactones regulate development within plants and facilitate communication with other organisms, such as parasites and symbiotic fungi. However, we don’t know the functions of the different strigolactones or how they trigger responses. The new strigolactone sensor contains a yellow luminescent version of an enzyme that, when degraded, loses its luminescence. The researchers believe this will help understand regulatory networks in plants and facilitate future manipulation of plant development. CATALYSIS WITH A LIGHT TOUCH Pairing two catalysts in a single, illuminated reaction flask proves to be a lightbulb moment for organic synthesis. The light from a standard electric light bulb is the key to a simple, green version of the C-H activation reaction, and researchers at KAUST have shown this is one of the hottest new reactions for assembling complicated chemical structures. They have shown that light, in combination with a carefully selected pair of catalysts, can drive the aromatic C-H activation reaction. This method has already caught the eye of pharmaceutical industry chemists. An additional advantage of the new protocol is that any lab can use it because no special lamps or other equipment are required. “We are interested in obtaining a deeper understanding of the mechanism at play and in testing the boundaries of the combined photo- and metal-catalysis reactions,” said Professor Magnus Rueping who led the study.

K AUST DISCOVERY

di sc o ver y.kaust.edu.sa

21


Biological and Environmental Science and Engineering Division

B E S E

THE CARPENTER ENZYME GIVES DNA THE SNIP

FEN1 uses a two-step verification mechanism before repairing DNA damage.

Enzyme follows a two-step verification system before cutting and repairing DNA damage.

2017 K AUST / SAMIR HAMDAN

M

22

AUGUS T 2 017

icroscopes that reveal the hidden complexities of life down to the nanoscale level have shown in exquisite detail how an enzyme involved in DNA repair works its molecular magic. This enz yme—known as Flap endonuclease 1, or FEN1—is often highly overexpressed or faulty in cancer and other types of diseases. Now that researchers know how it operates, they plan to use the information to design an inhibitor against it, said Samir Hamdan, KAUST Associate Professor of Bioscience, who led the study into FEN1. As its name suggests, FEN1 removes overhanging “flaps” of single-stranded DNA that dangle off the edge of the double helix during repair or replication of the genome. Scientists have advanced a number of theories for how FEN1 operates, but it’s been unclear how exactly the enzyme recognizes damage in the genome and how then it removes the fault. To get a closer look, Hamdan and his colleagues turned

to a sophisticated microscopy technique known as single-molecule fluorescence resonance energy transfer, or smFRET. This method repeatedly images the same area, each time turning on and off different glowing probes that tag different molecules. Superimposing these images together yields a nanoscale-quality molecular movie with a millisecond to sub-millisecond temporal resolution. In this way, the team— which included first author Fahad Rashid and several other KAUST graduate students—showed that FEN1 first binds to DNA weakly if damage is detected. Only then, if it’s the kind of damage that FEN1 can fix, does the enzyme lock on and get to work. “With this two-step verification mechanism,” Hamdan said, “FEN1 follows the old carpenter rule ‘measure twice and cut once.’” Given how critical FEN1 is for replication and repair, Hamdan said it’s no surprise that FEN1 is highly

“By understanding the molecular mechanisms of how FEN1 works, we will understand better how defects in FEN1 cause human diseases and result in genomic instability.”

overexpressed in several types of cancer or that functional mutations associated with the enzyme are linked to cancer and various diseases. Finding a drug that blocks FEN1’s function could thus provide a highly effective anticancer strategy, and the KAUST study could help this quest in two ways. “The first is that by understanding the molecular mechanisms of how FEN1 works, we will understand better how defects in FEN1 cause human diseases and result in genomic instability,” Hamdan said. “The second is that our work defined critical intermediary steps along the path of substrate recognition that are specific to FEN1, which would provide a new direction to target FEN1 specifically.” Rashid, F., Harris, P.D., Zaher, M.S., ... & Hamdan, S. Single-molecule FRET unveils induced-fit mechanism for substrate selectivity in flap endonuclease 1. eLife 6, e21884 (2017).

K AUST DISCOVERY

di sc o ver y.kaust.edu.sa

23


Biological and Environmental Science and Engineering Division

B E S E

SEEKING ADAPTATION FOR CORALS IN TIMES OF STRESS The Red Sea could help inform future practices to safeguard the world’s coral reef ecosystems.

24

AUGUST 2 017

Research at KAUST is providing insights into questions about coral bleaching, how it affects reef ecosystems and how it could be minimized.

ANNA ROIK

The Red Sea, with high levels of salinity and exposure to some of the highest sea temperatures on Earth, provides an ideal base for exploring the potential impacts of global warming on fragile marine ecosystems. With a recent rise in the incidence of coral bleaching occurring on reefs around the world, KAUST researchers are contributing greatly to understanding the phenomenon and how to help corals survive in future. “Coral bleaching is a complex phenomenon that occurs when corals get stressed,” said Associate Professor Michael Berumen, who works in marine biology alongside Professor Carlos Duarte, Associate Professor Christian Voolstra and their teams at the University’s Red Sea Research Center. “Coral has a somewhat surprising stress response, which is to “kick out” certain types of algae that live symbiotically within the coral tissue—although we don’t know exactly why it does this,” Berumen explained. “The

algae give corals their colors, so you can see right through to the white skeleton of the coral animal when bleaching occurs, hence the term.” Coral bleaching has the potential to reverse: algae may be able to return to the corals and help revive and replenish the reef. However, if certain stressors, such as high temperatures and fluctuating nitrogen levels, continue for an extended period, the corals cannot recover and eventually die. Over the past two years, scientists have become increasingly concerned for the future of these fragile yet vital ecosystems following wide-scale bleaching events of increased severity right across the globe.

“In a recent assessment, we estimated that 25-30% of all reefs in the Red Sea were bleached in late 2015,” said Voolstra. “My team study corals as metaorganisms— the coral animal, the algae symbionts and the bacteria that reside together interact and help each other in specific ways. The relationship is carefully balanced and offers significant benefits for the organisms involved.” Voolstra’s team is conducting a genome sequencing study on corals from the northern and southern Red Sea hoping to identify gene variants that make the corals respond differently from one part of an ocean to another. “The Arabian Seas represent the warmest (and coldest) ocean basins where corals live successfully,” said Voolstra. “We aim to pinpoint the specific adaptations of these corals that make them so resilient. We recently showed that some corals associate with a particular algal symbiont, Symbiodinium thermophilum, which is very tolerant to heat and salinity change, thus increasing their resilience. This could one day prove to be a useful tool in helping corals survive extreme conditions.” However, these potential solutions should be approached with caution, say the KAUST team. While certain symbionts can increase resilience, it is just as important to consider all the other stressors that contribute to bleaching and what can be done to limit them. “Maintaining a healthy overall balance on every reef is crucial,” said Duarte. “While we may not be able to prevent bleaching completely,

25-30%

of Red Sea corals were bleached in late 2015

we can help reef recovery by limiting marine pollution and upholding strict fishing laws in specific areas, for example.” One of the best examples of monitoring coral bleaching stems from Australia, where parts of the Great Barrier Reef were closely watched and analyzed by a collaboration between 14 institutions in early 2016. While this level of analysis is not yet possible in the Red Sea, KAUST is wellplaced and well-resourced to enable researchers to conduct careful, methodical investigations on a local level that will provide insights for other sites around the world. To this end, Berumen and his team are conducting surveys of individual reefs in the southern Red Sea, where significant and widespread bleaching occurred in late 2015, resulting in coral mortality rates as high as 50-90% in some localities. Combining their observations of marine life with satellite data regarding changes in water temperatures around reefs can give insights into how temperature fluctuations affect corals and how temperature thresholds for bleaching can change from place to place. “Reconstructing the past ecology of the Red Sea from sedimentary data taken from seabed cores is also invaluable,” said Duarte. “This is another aspect of our work that may help inform future marine management.” “The situation with corals around the world gives us an opportunity to work together and limit further damage,” added Voolstra. “We cannot afford to lose corals because this means we will lose other ecosystems too.”

K AUST DISCOVERY

di sc o ver y.kaust.edu.sa

25


CLOWNFISH ADAPT FOR POPULATION SURVIVAL Identification of candidate pathways in clownfish shows they can control responses to population alterations.

The clownfish (Amphiprion bicinctus) can transition from male to female in the absence of a mature female.

26

AUGUST 2 017

One fish species is able to adjust the gender ratio of its population through changes at the molecular level in response to changing environmental conditions. “Several species of fish— and in particular coral reef fish—are able to swap their sex during their lifespan,” explained Timothy Ravasi, KAUST Professor of Bioengineering from the University ’s Environmental Epigenetics Program. “This is known as sequential hermaphroditism.” Such characteristics can render fish communities more resilient to disruptions that might otherwise prove catastrophic to their reproductive capabilities. For example, clownfish “families” normally comprise one mature male and female plus numerous juveniles. If the female disappears, the remaining male alters hormone levels to transform into a female, restoring the previous gender balance. The precise biology of this is unclear, and Ravasi and his KAUST colleagues set out to identify changes in gene expression within the brain and gonads that drive this process of sequential hermaphroditism. They compared gene activity profiles from fully developed males and females as well as males at multiple stages of the process. After two weeks of being separated from a female, the researchers detected clear changes in gene expression within the brains of males that apparently herald the onset of gender transition, and complementary changes in gonadal gene expression became apparent a few weeks later.

The researchers were subsequently able to map the genetic machinery driving this process. “ We identified a large number of candidate molecular pathways that are potentially able to fine-tune and therefore control the gender ratio in a population of fish,” noted Ravasi. One key candidate is a gene encoding an enzyme called aromatase, which is known to be involved in the production of estrogen. Aromatase was highly expressed in both the brain and the gonads of fish adapting to gender ratio alterations. Ravasi and the research team also found many other genes that are likely to interact with aromatase in managing the degeneration of the testes and the development of the ovaries. With these foundational insights into this complex biological process, Ravasi now hopes to explore how this adaptive process is influenced by environmental factors and specifically climate change. “We are not sure whether the ocean’s warming and acidification can influence the tightly controlled regulation of gender ratio changes,” he said. “We are systematically exposing the fish to end-of-century predicted ocean conditions and trying to understand whether climate change alters these molecular pathways.” Casas, L., Saborido-Rey, F., Ryu, T., Michell, C., Ravasi, T. et al. Sex-change in clownfish: Molecular insights from transcriptome analysis. Scientific Reports 6, 35461 (2016)

K AUST DISCOVERY

di sc o ver y.kaust.edu.sa

27

TILL RÖTHIG

Biological and Environmental Science and Engineering Division

B E S E


Biological and Environmental Science and Engineering Division

TWEAKING THE TRANSCRIPTOME TO TACKLE STRESS Stressed dinoflagellates rewrite their genes during transcription. 28

AUGUST 2 017

S

ingle-celled plankton known as dinoflagellates are shown to cope with stress using an unexpected strategy of editing their RNA rather than changing gene expression levels. The finding by Associate Professor Christian Voolstra

2017 K AUST / ANASTASIA KHRENOVA

Manuel Aranda (left), Christian Voolstra (center) and Yi Jin Liew (right) are studying how different organisms in the Red Sea adapt to stress.

and Assistant Professor Manuel Aranda began when they compared RNA transcripts from two strains of dinoflagellates thought to belong to the same species in the genus Symbiodinium. The transcripts had more differences than expected,

indicating a more distant relationship. Howe ver, the team speculated that the RNA transcripts might instead have been edited, producing different information than that encoded in the cell’s DNA. RNA editing had previously been observed in the mitochondria and plastids of dinoflagellates, but not in genes encoded in the nucleus. Earlier studies by Voolstra and Aranda had shown that gene expression changes very little in dinoflagellates under stressful conditions. The researchers wondered: “What if they do it completely differently? What if they just edit transcripts the way they need instead of changing expression?’” recalled Aranda. To test their hypothesis, the team analyzed transcriptomes from Symbiodinium cultures grown in normal conditions and stressed by cold, heat or darkness. A conservative estimate uncovered 3,300 RNA edits. “This expands the encoding capacity beyond what’s in the genome,” said Aranda, effectively giving the cell a fuzzy genome. “Instead of having just one version of a protein, they can produce multiple different versions by changing the message on a different level.” The team then turned its attention to 229 genes edited in all four growth conditions. The RNA of half of these genes was edited differently in at least one of the stressed cultures, and many of the genes had changes in RNA editing in response to several stress factors. “We’ve shown that short-term stress can be dealt with by RNA editing.

FABIA SIMONA

B E S E

Symbiodinium cells viewed through a light microscope.

“It would be very interesting to check whether coral-symbiont combinations that tolerate high temperatures undergo more or less RNA editing,”

But we don’t yet know how,” said the study’s lead author, Dr. Yi Jin Liew. Understanding the mechanism behind RNA editing and how this machinery is regulated remains an exciting challenge for future research. These findings also raise intriguing questions about the evolutionary and ecological implications of this process. RNA editing may offer dinoflagellates an efficient mechanism for rapid evolutionary experimentation. The ecological implications may be broader still. Many Symbiodinium species are symbiotic with corals, and the coral’s stress tolerance partly depends on the identity of its Symbiodinium partner. “It would be very interesting to check whether coral-symbiont combinations that tolerate high temperatures undergo more or less RNA editing,” said Voolstra. Liew, Y. J., Li, Y., Baumgarten, S., Voolstra, C. & Aranda, M. Condition-specific RNA editing in the coral symbiont Symbiodinium microadriaticum. PLoS Genetics 13, e1006619 (2017).

K AUST DISCOVERY

di sc o ver y.kaust.edu.sa

29


Biological and Environmental Science and Engineering Division

HUBERT PIWONSKI

B E S E

“A friend helped me practice in a pool by diving with different sizes and shapes of simulated fish on popsicle sticks!”

Grey reef sharks at Shaab Rumi reef in the Red Sea, Sudan.

POTENTIAL FOR SAUDI ARABIAN CORAL REEFS TO SHINE

30

AUGUST 2 017

ecosystems,” said Dr. Darren Coker, who worked on the project with KAUST M.S. Alumnus Alexander Kattan and Associate Professor Michael Berumen of the University’s Red Sea Research Center. “This means we can only hypothesize what the natural reef environment would have looked like before human interference through fishing began.” Berumen’s team systematically compared 14 Saudi reefs with 16 offshore reefs in Sudan. The reefs are around 200-300 km apart and share

almost identical environmental conditions in terms of sea temperature, climate and coral species. However, Saudi Arabia has a longestablished history of fishing, while Sudan does not. “There is much more to the story than just the numbers of fish we see,” said Berumen. “ We collected and analyzed data between and within regions to look at fish abundance, biomass and community diversity across all the reefs surveyed.” “ To minimize potential bias, I conducted all the

survey dives myself,” said Kattan, who trained intensively to ensure he could correctly identify fish species and accurately estimate their size underwater. “A friend helped me practice in a pool by diving with different sizes and shapes of simulated fish on popsicle sticks! Because size estimates were converted into biomass, it was vital that I was able to gauge sizes correctly.” The team found that the biomass of top predators in the Sudanese reefs was almost three times that of the Saudi reefs. The top predators

BSIP SA / AL AMY STOCK PHOTO

Careful marine management and stricter fishing laws could enable Saudi Arabia’s coral reefs to thrive. Marine surveys estimating fish population density and diversity are crucial to our understanding of how human activities impact coral reef ecosystems and to our ability to make informed management plans for sustainability. KAUST researchers recently conducted the first baseline surveys of reefs in the southern Red Sea by comparing reefs off the coast of Saudi Arabia with those of Sudan. “A major issue is that there is no established historical record for Red Sea

were far rarer in Saudi Arabian waters, a phenomenon that the researchers attribute to fishing pressures. Furthermore, fish abundance was around 62% higher in Sudan and biomass was 20% higher. There was also slightly greater diversity on the Sudanese reefs.

“This is the strongest evidence yet of the impact of fishing on Saudi Arabia’s reefs,” said Berumen. “While Saudi Arabia appears to have lost many larger fish, these species, including top predators, have not completely disappeared, so there is an opportunity to turn the situation around. Saudi’s reefs could be restored to the condition of the almost pristine Sudanese reefs through careful management and protection, and they could one day thrive as eco-tourism sites.” Kattan, A., Coker, D.J., & Berumen, M. L. Reef fish communities in the central Red Sea show evidence of asymmetrical fishing pressure. Marine Biodiversity advance online publication, 9 March 2017.

AN INFLAMMATORY INFERENCE The surface proteins responsible for navigating immune cells to sites of inflammation are identified.

The protein tags that adorn immune cells and engage with receptors to promote inflammation in the body’s endothelial tissues are not what they were thought to be. A KAUST investigation has identified the true surface proteins expressed by T-cells that mediate this molecular liaison, a finding that could help scientists control inflammation that has gone haywire. “This has significant implications for developing targeted therapies to combat inflammatory diseases such as psoriasis and rheumatoid arthritis,” said Assistant Professor of Bioscience Jasmeen Merzaban, who led the research. The receptor with which the surface proteins on T-cells interact is known as E-selectin. This ‘cell adhesion molecule’ is expressed by tissues that line the inner surface of blood vessels: it acts as a kind of Velcro that clings to T-cells when the endothelium needs to fight off infections from bacteria or viruses. The trouble is that E-selectins can also trigger inflammation when there are no such microbial invaders. These aberrant inflammatory signals can cause autoimmune diseases. However, blocking the hitching of E-selectin to

Single-cell tracking has significant implications for developing targeted therapies to combat inflammatory diseases, such as psoriasis and rheumatoid arthritis.”

T-cells could help reverse that problematic immune reaction. For more than a decade, researchers knew of only two surface proteins expressed by T-cells that could serve as binding partners, or ligands, for E-selection. Yet, mouse studies had shown that reducing expression of these two proteins — PSGL-1 and CD43 — was not sufficient to eliminate the crosstalk between E-selectin and T-cells. That suggested to Merzaban that some other E-selectin ligands might be at play. She and her graduate students, Amal Ali and Ayman Abuelela from KAUST’s Biological and Environmental Science and Engineering Division, used a mass spectrometry approach to identify the full repertoire of E-selectin ligands expressed by T-cells. They detected 10 such proteins, one of which they explored in greater detail owing to its known function as an E-selectin ligand expressed by blood stem cells, the precursors of T-cells. This protein, called CD44, is also expressed on the surface of both ‘helper’ and ‘killer’ T-cells, where it binds E-selectin, the researchers found. Merzaban and her team had discovered a third E-selectin ligand. But, as it turned out, not all these ligands contribute to T-cell tethering. The researchers knocked down the expression of all three ligands, individually and in combination. They discovered that CD44 — not CD43 — worked with PSGL-1 as the E-selectin ligands implicated in inflammation. They confirmed the clinical relevance of these findings by looking at T-cells isolated from patients with psoriasis, a common inflammatory skin condition — which means that “targeting these ligands could be a viable option to treat skin diseases,” says Ali. Ali, A.J., Abuelela, A.F. & Merzaban, J.S. An analysis of trafficking receptors shows that CD44 and P-selectin glycoprotein ligand-1 collectively control the migration of activated human T-cells. Frontiers in Immunology, advance online publication, 3 May 2017.

K AUST DISCOVERY

di sc o ver y.kaust.edu.sa

31


TANE SINCLAIR-TAYLOR

“My interdisciplinary research provides me with the opportunity to collaborate with colleagues from electrical engineering, imaging, machine learning, nanotechnology, genomics, big data and biology. These collaborations are critical to the success of my research and continue to inspire my passion for science.”

The symbiosis between photosynthetic dinoflagellate algae and stony corals underpins the three-dimensional structure of coral reefs that provides a habitat for thousands of different species.

GENE SEQUENCES REVEAL SECRETS OF SYMBIOSIS Genome sequences of dinoflagellate algae indicate how they maintain their symbiotic relationship with corals. Advances in genomic research are helping scientists to reveal how corals and algae cooperate to combat environmental stresses. KAUST researchers have sequenced and compared the genomes of three strains of Symbiodinium, a member of the dinoflagellate algae family, to show their genomes have several features that promote a prosperous symbiotic relationship with corals. Dinoflagellates are among the most prolific organisms on the planet, forming the basis of the oceanic food chain, and their close symbiotic relationships with corals help maintain healthy reefs. However, because dinoflagellates have unusually large genomes, very few species have been sequenced, leaving the exact nature of their symbiosis with corals elusive. “We had access to two Symbiodinium

32

AUGUST 2 017

genomes, S.minutum and S.kawagutii, and we decided to sequence a third, S. microadriaticum,” said Assistant Professor of Marine Science Manuel Aranda at the University’s Red Sea Research Center, who led the project with his Center colleague Associate Professor of Marine Science Christian Voolstra and colleagues from the University’s Computational Bioscience Research Center and Environmental Epigenetics Program. “This allowed us to compare the three genomes for common and disparate features and functions and hopefully to show how the species evolved to become symbionts to specific corals.” The unusual makeup of the three Symbiodinium genomes meant that the team had to adjust their software to read the genomes correctly. Ultimately, their research revealed that

Symbiodinium has evolved a rich array of bicarbonate and ammonium transporters. These proteins are used to harvest two important nutrients involved in coral-dinoflagellate symbiosis: carbon, which is needed for photosynthesis, and nitrogen, which is essential for growth and proliferation. Symbiodinium either evolved these transporters in response to symbiosis or the presence of these transporters allowed Symbiodinium to become a symbiont in the first place, noted Aranda. Aranda, M., Li, Y., Liew, Y.J., Baumgarten, S., Simakov, O., ... & Voolstra, C. R. Genomes of coral dinoflagellate symbionts highlight evolutionary adaptations conducive to a symbiotic lifestyle. Scientific Reports 6, 39734 (2016).

Professor Carlos Duarte Director of the Red Sea Research Center and the Tarek Ahmed Juffali Research Chair in Red Sea Ecology Read more about Carlos and his work at DISCOVERY.KAUST.EDU.SA

Carlos is widely recognized as one of the world’s leading voices on the impacts of climate change on marine ecosystems. He leads an international multidisciplinary research team that looks at how the world’s oceans can help us provide food and fresh water security for current and future generations. Discovering how ocean-based solutions can help solve global challenges in food supply and reducing carbon is a complex problem that requires an international approach across many disciplines.


Computer, Electrical and Mathematical Science and Engineering Division

COLOR-CHANGING COATINGS READY FOR THE BIG TIME Wafer-thin, scratch-proof films can generate a rainbow of colors using random metallic nanostructures. The dazzling colors of peacock feathers arise from the physical interaction of light with biological nanostructures. Researchers have discovered how to exploit this natural trickery known as structural coloration into a large-scale printing

34

AUGUS T 2 017

technology that produces lightweight and ultraresistant coatings in any color desirable. Researchers routinely produce photonic structures to influence the behavior of light for applications, such as fiber-optic communications.

DAVID TIPLING PHOTO LIBRARY / ALAMY

C E M S E

Many groups have used photonic technology to generate new forms of artificial structural colors that take advantage of the entire spectrum of visible light. Moving this technology out of the lab is challenging, however, because photonic nanostructures are often fragile and difficult to produce in practical quantities. Associate Professor Andrea Fratalocchi from the University’s Electrical Engineering Program and colleagues from Harvard University and ETH Zurich used wet chemical techniques to help overcome the difficulties The nanoporous of scalingfeathers of up photonic the plumcolors. Inspired throated cotinga bird inspired the KAUST team’s approach.

by the nanoporous feathers of the plum-throated cotinga bird, the team’s approach began by sputtering a platinum–aluminum based alloy onto a target surface. Then, a process called dealloying dissolves most of the aluminum and causes the remaining metal to reorganize into a bumpy network featuring open nanopores. Next, the researchers deposited an ultrathin layer of protective sapphire onto the metal network to both protect the surface and modify the way in which light interacts with the photonic nanopores. Surprisingly, slight changes of the sapphire thickness from 7 to 53 nanometers yielded remarkable color changes—the initially transparent film underwent stepwise transitions to yellow, orange, red and blue tones. “Controlling these colors

is experimentally very simple and uses coating technologies that are cheap and easily implemented,” said Fratalocchi. “However, understanding how the complex light-matter interactions generate colors took months of work.” The team’s high-level simulations determined that color generation begins when light strikes the metal and generates wave-like entities known as surface plasmons. As the plasmons interact with the randomly distributed pores, they become trapped and modulations in the coating’s refractive index produced epsilon-near-zero regions in the nanopores, where waves propagate extremely slowly. Adding the sapphire film caused additional reflections of the trapped waves, which created a flow of saturated color

through resonance effects. Fratalocchi noted that the way colors are formed in this structure can open the way for “programmable” nanomaterials for many applications. “Imagine a scratch on a car that can be repainted with an extremely thin material without other expensive procedures, or as a lightweight, maintenance-free way to coat airplanes,” he stated. “This technology could be a real revolution.” Galinksi, H., Favraud, G., Dong, H., Gongora, J. S. T., Fratalocchi, A., ... & Capasso, F. Scalable, ultra-resistant structural colors based on network metamaterials. Light: Science & Applications 6, e16233 (2017).

K AUST DISCOVERY

di sc o ver y.kaust.edu.sa

35


SBOL parts for metabolic engineering

Xin Gao (front) and members of his team Ramzan Umarov (left) and Hiro Kuwahara developed an online repository of parts specific to metabolic engineering.

SHARING EXPERT EXPERIMENTAL KNOWLEDGE TO EXPEDITE DESIGN A repository of metabolic information provides a quick reference tool for designing useful synthetic biological systems. A reference tool specific to metabolic engineering that optimizes processes to make cells produce useful substances gives researchers a common language and will facilitate novel designs. When building synthetic biological systems, the number of available biological components and interactions is mind boggling. To make them accessible, a global community of researchers developed the Synthetic Biology Open Language (SBOL), an online standard that allows experimental and computational biologists to quickly exchange and reuse designs.

36

AUGUST 2 017

Now, Dr. Hiroyuki Kuwahara and Associate Professor Xin Gao of the KAUST Computational Bioscience Research Center (CBRC) collaborated with co-workers in China and the US to take this a step further by developing an SBOL repository of parts specific to metabolic engineering. “So far, support for SBOL has been lacking in metabolic engineering,” said Kuwahara. “But, since many applications of synthetic biology focus on biosynthesis of high-value natural products, such as biofuels, cosmetics, perfumes and drugs, we thought that a repository of

would be useful.” Kuwahara, Gao and co-workers drew on several existing databases to compile the new, easily searchable repository of metabolic parts, which they named SBOLme, because it is entirely compliant with SBOL. SBOLme contains several thousand chemical compounds, enzyme classes, metabolic proteins and metabolic reactions from almost 4000 different organisms, and all the parts are annotated with information about their common interactions and thermodynamics. This will make it possible for researchers to design new ways of carrying out useful reactions, as Kuwahara explained: “Suppose you want to design a pathway to produce 1,3-propanediol, a commodity chemical mainly used to make polyester fiber from glycerol that is readily available and inexpensive. This would involve introducing two enzymatic reactions into a microbe that could perform the job. SBOLme has all the metabolic parts you need to specify this pathway within the microbe, and it allows you to exchange and discuss the design with colleagues.” “Finally, when you publish your paper, you would include your design in the SBOL format so that readers can find it.” Kuwahara and Gao say that the talented computer scientists at KAUST and the CBRC’s cluster computing facilities played a vital role in the success of their project. They hope to continue developing computational methods that help facilitate the design of metabolic engineering. Ultimately, they plan on making the industrial-scale use of microbes for producing useful chemicals accessible. The potential applications of metabolic engineering include the production of new drugs and the storage of information on strands of DNA. Kuwahara, H., Cui, X., Umarov, R., Grünberg, R., Myers, C.J. & Gao, X. SBOLme: a repository of SBOL parts for metabolic engineering. ACS Synthetic Biology 6, 732-736 (2017).

RIGHT PAGE: ROBERT HARDING / AL AMY STOCK PHOTO, LEFT PAGE: 2017 K AUST / ANASTASIA KHRENOVA

C E M S E

A SAFE SWEEP O F W E AT H E R D ATA A statistical technique for automatically cleaning erroneous data from weatherballoon observations will improve the accuracy of weather forecasting.


“It’s really intriguing to think of molecules not as static elements but rather as responsive entities you can engineer at the nano level.”

C E M S E

“ A radiosonde is a small, expendable instrument package that is suspended below a two-meter-wide balloon filled with hydrogen or helium.” of the wind vector that is skewed with a long tail of rare extreme values,” said Sun. “This makes it possible to flag observations that are very likely to be errors as potential outliers without removing extreme values.” In addition to its application to new daily data, this error-detection scheme can also be used on the huge volumes of radiosonde observations held in archives around the world. “We are developing an outlier-detection method that is fast and automatic. We will be able to use this method to quickly process the millions of records in the archive,” said Sun. “We are also considering the possible effect of climatic change when developing the new method.” Sun, Y., Hering, A.S. & Browning, J.M. Robust bivariate error detection in skewed data with application to historical radiosonde winds. Environmetrics 28, e2431 (2017)

Associate Professor Niveen Khashab 2017 L’Oréal-UNESCO For Women in Science Laureate

Upper Atmosphere

FONDATION L’OREAL

WEATHER BALLOONS CARRYING DISPOSABLE RADIOSONDES ARE RELEASED TWICE A DAY AT 700 LOCATIONS AROUND THE WORLD TO MAKE OBSERVATIONS OF THE UPPER ATMOSPHERE.

Earth’s upper atmosphere, making them vital for satellite data, weather forecasting and climatology research. “There are far too many errors in the data to correct by hand, so we need an automatic method for identifying such random errors,” explained Sun. There are automatic methods for removing systematic errors from the data, such as changes in location or measurement units. However, there has been no way to remove genuinely erroneous data, including data-entry mistakes, transmission errors or imprecise tracking of the balloon, without also deleting extreme but real measurements—which are some of the most important data for forecasting. Looking specifically at wind data, Sun and her co-workers developed a statistical approach that achieves robust differentiation between extreme values and random errors. “Our approach considers a more realistic distribution

SCIEPRO / GETT Y IMAGES

T

wice a day, weather balloons are released into the atmosphere from 700 locations around the world to observe conditions in the upper atmosphere. Since the 1920s, there have been tens of millions of these radiosonde launches, producing an enormous archive of data that is critical to weather forecasting and climate modeling. In such a large data set, inevitable errors can significantly affect modeling outcomes. Ying Sun, KAUST Assistant Professor of Applied Mathematics and Computational Science, collaborated with researchers from the Colorado School of Mines and Baylor University to develop a method to remove these errors using a robust statistical analysis of the data. “A radiosonde is a small, expendable instr ument package that is suspended below a two-meter-wide balloon filled with hydrogen or helium,” explained Sun. “Sensors on the radiosonde measure height, pressure, temperature and dew point; they also calculate wind speed and direction by tracking the position of the radiosonde in flight. Radiosonde observations are the only direct measurements of the

Learn more about Niveen and her work at KAUST.EDU.SA

Niveen designs smart nanomaterials that can be programmed to respond in a particular way to different stimuli, such as light and electrical current. In addition to environmental and industrial applications, these nanomaterials are used for biomedical applications, such as cell-specific drug delivery, to minimize harm to healthy cells. Her team has also demonstrated that such assemblies can be used as extremely sensitive sensors and imaging agents to improve early detection of disease.


Computer, Electrical and Mathematical Science and Engineering Division

C E M S E developed a system called ScaleMine that offers a tenfold acceleration compared with existing methods. “FSM involves a vast number of graph operations, each of which is computationally expensive, so the only practical way to support FSM in large graphs is by massively parallel computation,” he said. In parallel computing, the graph search is divided into multiple tasks and each is run simultaneously on its own processor. If the tasks are too large, the entire search is held up by waiting for the slowest task to complete; if the tasks are too small, the extra communication needed to coordinate the parallelization becomes a significant additional computational load. Kalnis’ team overcame this limitation by performing the search in two steps: a first approximation step to determine the search space and the optimal division of tasks and a second computational step in which large tasks are split dynamically into the optimal number of subtasks. This resulted in search speeds up to ten times faster than previously possible. “Hopefully this performance improvement will enable deeper and more accurate analysis of large graph data and the extraction of new knowledge,” Kalnis said.

A new data mining strategy that offers unprecedented pattern search speed could lead to new insights from massive data.

DIVIDE AND CONQUER PATTERN SEARCHING

40

AUGUST 2 017

relationships among objects,” e x p l a i n e d Pro f e s s o r o f Computer Science Panagiotis Kalnis, leader of the research team from the KAUST Extreme Computing Research Center. “Graphs are widely used in many modern applications, including social networks, biological networks like protein-to-protein interactions, and in communication networks like the internet.” In these applications, one

K AUST DISCOVERY

of the most important operations is the process of finding recurring graphs that reveal how objects tend to connect to each other. The process, which is called frequent subgraph mining (FSM), is an essential building block of many knowledge extraction techniques in social studies, bioinformatics and image processing as well as in security and fraud detection. However, graphs may

contain hundreds of millions of objects and billions of relationships, which means that extracting recurring patterns places huge demands on time and computing resources. “In essence, if we can provide a better algorithm, all the applications that depend on FSM will be able to perform deeper analysis on larger data in less time,” Kalnis noted. Kalnis and his colleagues

ALISTAIR SCOT T / AL AMY

Searching for recurring patterns in network systems has become a fundamental part of research and discovery in fields as diverse as biology and social media. KAUST researchers have developed a pattern or graph-mining framework that promises to significantly speed up searches on massive network data sets. “A graph is a data structure that models complex

MOPIC / AL AMY

A new data-mining strategy that offers unprecedented pattern search speed could glean new insights from massive datasets.

Abdelhamid, E., Abdelaziz, I., Kalnis, P., Khayyat, Z. & Jamour, F. ScaleMine: Scalable parallel frequent subgraph mining in a single large graph. International Conference for High Performance Computing, Networking, Storage and Analysis SC16 (2016).

IMPROVING CONNECTIONS FOR SPATIAL ANALYSIS A statistical model that accounts for common dependencies in spatial data yields more realistic results. A statistical model for spatial data, such as temperatures at different locations, that more accurately represents the geographical relatedness among measured variables has been developed by KAUST researchers. Robust and realistic statistical models are critical to almost all fields of scientific research and engineering. Choosing the wrong statistical model for a given data set can lead to a potentially catastrophic misinterpretation of results. “Spatial statistics involves modeling variables measured at different spatial locations,” said Marc Genton, Professor of Applied Mathematics and Computational Science at KAUST. “Many existing models, called copulas, cannot properly capture the spatial dependence among variables, such as when the dependence between variables becomes weaker with increasing distance—as is the case with temperature.” Genton, with his colleagues Dr. Pavel Krupskii and Professor Raphaël Huser, designed The researchers demonstrated the usefulness of their factor copula model by applying it to the analysis of daily mean temperatures across Switzerland.

a copula that can handle different types of dependencies among variables. Their model also offers simpler interpretation of the data compared with other models: this interpretation, put simply, says there exists an unobserved common factor that affects all the variables simultaneously. “For example, temperature data in a small geographical region may be subject to common weather conditions, which can be thought of as a common factor,” explained Genton. “To represent such situations, we have used a standard Gaussian model and added a common random factor that affects all the variables simultaneously, which is a plausible assumption in many spatial applications.” A Gaussian model is one of the most fundamental and versatile of statistical models. It is used to describe a random distribution of values about an average value similar to the classic bell curve in which most measured values occur near the average with two tails on either side. These tails represent the increasing rarity of significantly higher or lower values from the average. The Gaussian model is particularly powerful in Genton’s factor-based copula because it allows for natural integration of a common-factor dependence among variables. The researchers demonstrated the usefulness of their factor copula model by applying it to the analysis of daily mean temperatures across Switzerland. Their model performed well compared with other statistical approaches and gave a more robust representation of the underlying dependence between geographical locations. Looking forward, Genton explained, “Our copula can be used to model any variable measured repeatedly in time at different spatial locations, such as daily or hourly temperature or wind data at different weather stations, or to model pollution levels measured using weather balloons or satellites.” Krupskii, P., Huser, R., & Genton, M.G. Factor copula models for replicated spatial data. Journal of the American Statistical Association (2016).

di sc o ver y.kaust.edu.sa

41


Ali Charara wants to use graphic cards in computers to process complex mathematical problems.

TAKING GRAPHICS CARDS BEYOND GAMING A highly efficient mathematical solver designed to run on graphics processors gives scientists and engineers a powerful new tool for a common computational problem. The graphics cards found in powerful gaming computers are now capable of solving computationally intensive mathematical problems common in science and engineering applications, thanks to a new solver developed by researchers from the KAUST Extreme Computing Research Center. “One of the most common problems in scientific and engineering computing is solving systems of multiple simultaneous equations involving thousands to millions of variables,” said David Keyes, Professor of Applied Mathematics and Computational Science, who also led the research team. “This type of problem

42

AUGUS T 2 017

comes up in statistics, optimization, electrostatics, chemistry, mechanics of solid bodies on Earth and gravitational interactions among celestial bodies in space.” In typical applications, solving such problems is often the main computational cost. Thus, acceleration of the solver has the potential to considerably impact both the execution time and the energy consumption required to solve the problem. “Graphics processing units (GPUs) are very energy efficient compared with standard high-performance processors because they eliminate a lot of the hardware required for standard processors to

execute general-purpose code,” explained Keyes. “However, GPUs are new enough that their supporting software remains immature. With the expertise of Ali Charara, a Ph.D. student in the Center who spent several months as an intern at NVIDIA in California, we have been able to identify many things that we can either innovate or improve upon, such as redesigning a common solver.” The key to making a more efficient solver is maximizing the trade-off between the number of processors and the memory available to temporarily store the computational data. Memory remains expensive, so finding a way to execute more computation using less memory is critical to solving the problem of computational cost. “Charara designed a solver scheme that operates directly on data ‘in place’ without making an extra copy,” explained Dr. Hatem Ltaief, a Senior Research Scientist from the project’s team. “This means a system twice as large can be stored in the same amount of memory.” Usually, operations on simultaneous equations are carried out by progressing sequentially over columns in the data of the matrix of values derived from the equations. Charr converted the columns into a series of tasks on small, computationally efficient, rectangular and triangular blocks recursively carved out of the matrix. This redesigned triangular matrix-matrix multiplication implementation achieves up to eightfold acceleration compared to the speed of existing implementations. “Now, every user of an NVIDIA GPU has a faster solver for a common task in scientific and engineering computing at their disposal,” said Keyes. The solver is due to be integrated into the next scientific software library for NVIDIA GPUs. Charara A., Ltaief H. & Keyes D. Redesigning triangular dense matrix computations on GPUs. European Conference on Parallel Processing. Springer International Publishing (2016).

RIGHT PAGE: OUSSAMA KHATIB, LEFT PAGE: 2017 K AUS T / ANASTASIA KHRENOVA

C E M S E

DEEP THINKING BRINGS UNDERWATER ROBOT TO LIFE An international, multidisciplinary collaboration that led to the world’s first underwater robotic avatar.

I

t began with KAUST marine scientist Christian Voolstra’s frustration with his “clunky” equipment. His colleague, electrical engineer Khaled Salama, knew how to build things and had some contacts at Stanford University’s robotics laboratory that could help. They, in turn, knew the people at the California-based Meka Robotics who made robot arms. Scientists talking to scientists led to a visionary international collaboration that produced the world’s first underwater robotic avatar. Ocean One is not your run-of-themill robot. It acts as the extension of a human operator who uses a haptic-visual interface to feel and see what the robot encounters. Similar in size to a human diver, Ocean One has the mobility and dexterity

required to maneuver and gently grasp objects. Theoretically, it can function at unlimited depths because its sensitive electronics are immersed in oil to protect them from the pressure of the deep sea. It’s also semi-autonomous—able to navigate and control its buoyancy. Most robots have every movement programmed, explained Associate Professor Voolstra from the University’s Red Sea Research Center. “However, this thing is intelligent. It knows how to swim; you just need to tell it where to swim.” This frees Ocean One’s operator to focus on the specific tasks that the robot is being sent to do. The interface consists of two joysticklike devices with a grasp-and-pinch controller, a 3D display that provides visual input from the robot’s cameras and a graphical user command center

that displays the data coming from the robot’s many sensors. It was no small feat to design an underwater robot that can do more than human divers or remotely operated vehicles. Professors Voolstra and Salama wanted it to be smart, dexterous and able to travel deep beneath the ocean’s surface while still in contact with its operator on the surface. This multidisciplinary international team began by creating a virtual interactive environment, similar to a computer game, in which they could test basic functions they wanted their future robot to have. Using joysticks, they were able to test what it feels like when the virtual robot holds something or how it might move things from place to place. “We didn’t want to end up with

K AUST DISCOVERY

di sc o ver y.kaust.edu.sa

43


Computer, Electrical and Mathematical Science and Engineering Division

Similar in size to a human diver, Ocean One acts as the extension of a human operator.

something that worked in freshwater but not saltwater, so we needed to simulate every single thing,” explained Salama. “The virtual environment we created gave us so much information that it helped us with the design,” continued Salama. “You’re not just building the hardware; you’re building the whole environment that goes with it.” Collaboration was key as the two teams learned about each other’s needs. Salama admits that he knew little about marine science. “I can design something that moves, but I had no clue about what is needed in the ocean,” he said. Voolstra, however, concedes he was awed by the robotics experts. “You go into the lab with people who have built robots since they were fifteen. Then you explain the properties of water and discover they have no idea about it and you realize it’s levelling off,” he chuckled. “Coming together is awesome.” Salama’s team learned a lot about sensors by visiting Stanford’s robotics laboratory run by computer scientist, Oussama Khatib. In turn, Voolstra invited some of the Stanford students to go snorkeling in the Red Sea. “Sometimes you just really need to swim in the ocean to get the scale of what you are working on,” he explained. The students saw some of the Red Sea’s spectacular corals and even a pod of dolphins. You’re

44

AUGUST 2 017

“The potential for applications is limitless. Imagine a fleet of robotic avatars working on a petroleum installation where you don’t want to send people to do a task.”

Khatib, O., Yeh, X., Brantner, G., ... Voolstra, C., Salama, K. et al. Ocean One: A robotic avatar for oceanic discovery. IEEE Robotics & Automation Magazine 23, 20-29 (2016).

2017 KAUST / ANASTASIA KHRENOVA

not actually solving a research question when you do this, Voolstra explained, but it’s really useful in ensuring that these worlds merge. “The students were also ten times more motivated after the visit,” he said. Ocean One was initially tested at Stanford’s Avery Aquatic Center. Then it was taken to France where it successfully embarked on a mission, as a proof of concept, to retrieve an artifact from the 17th century naval vessel, La Lune. Voolstra hopes to use a robot like Ocean One to study the Red Sea’s coral reefs at depths below those accessible by human divers where about 75% of reef biomass exists. “The majority of ecological processes actually happen at depths where we rarely do research,” he said. “Plus, these twilight reefs might serve as important refuges because shallow-water corals are exposed to the full force of ocean warming and climate-change effects. “But potential for applications is limitless,” said Salama. Other robotic avatars could be used to search for and retrieve hazardous materials from inhospitable settings or perform disaster prevention and recovery operations. “Imagine a fleet of robotic avatars working on a petroleum installation where you don’t want to send people to do a task,” he continued. “It’s putting a human body in an environment where you cannot go, with a robot as a mediator, and where you don’t have to think about every single step the robot takes but rather focus on the task at hand,” explained Voolstra. “I really think this is a revolution.” A revolution, he and Salama insist would not have been realized without support from KAUST. Salama recalls the University’s support of the project by saying “We believe in this type of technology. We are willing to assemble the team if you guys are willing to think about big things.”

OUSSAMA KHATIB

C E M S E

KAUST researchers Doha Hamza (right) and Jeff Shamma have developed a way for paired strangers to buddy up to make better use of bandwidth.

BLIND MATCHMAKING FOR MORE EFFICIENT WIRELESS NETWORKS Autonomously pairing network users could expand the capability of the next generation of wireless networks.

A network management scheme developed by KAUST allows users from different network providers to pair up to make better use of the available wireless spectrum although the two users know little about each other. Wireless networks are groaning under the strain of an ever-increasing number of mobile devices and data-hungry applications, such as video streaming. This means network engineers are searching for alternative methods to utilize the available wireless bandwidth. Although wireless technology is improving all the time, a major source of inefficiency persists in the way that telecommunication companies divide

up the wireless spectrum—the range of radio frequencies available for wireless communications. Dr. Doha Hamza and Jeff Shamma, Professor of Electrical Engineering, have developed a way for strangers to pair up to make better use of the available bandwidth. “Cognitive radio technology, as we call it, is a promising approach to solve the wireless spectrum scarcity problem,” explained Hamza. “This technology allows secondary unlicensed users to access the primary licensed users’ frequency bands. To make this possible, the primary and secondary users need to be robustly paired in a way that ensures

mutual benefit while maintaining quality-of-service constraints.” Hamza and Shamma turned to a subfield of game theory called matching theory to deal with the cognitive radiopairing problem. Matching theory is a mathematical framework for forming pairs from two groups that is already used routinely for several applications, such as organ-exchange programs, college admissions and communications networks. “Primary users and secondary users need to be matched so that the partnership is mutually beneficial and binding,” said Shamma. “Different partnerships can provide different benefits, and primary and secondary users can have preferences over possible partnerships; however, unlike conventional applications for matching theory, there is no central authority to regulate the market, meaning that primary and secondary users have limited information about the preferences of other actors.” To address the lack of centralization, the researchers developed a “blind” matching algorithm involving a relatively simple learning process. The agents meet one-on-one and make proposals based on their current aspirations. The proposals may be accepted or rejected, resulting in the forming and breaking of partnerships. Likewise, agent aspirations regarding the potential benefit of finding a partner may also rise and fall. The algorithm is broadly applicable to general-matching settings, but is particularly useful for implementing in cognitive-radio networks. Shamma explained that “despite the blind encounters and limited information, we showed that this simple dynamic converges to a stable-matching state in which no pair of agents has an incentive to break their current matches in favor of others.” Hamza, D. & Shamma, J. BLMA: A blind matching algorithm with application to cognitive radio networks. IEEE Journal on Selected Areas in Communications. 35, 302-316 (2017).

K AUST DISCOVERY

di sc o ver y.kaust.edu.sa

45


Computer, Electrical and Mathematical Science and Engineering Division

C E M S E

Devendra Singh (left) and Muhammad Hussain work toward deformable thermoelectric materials.

STRETCHING TOWARD ENERGY EFFICIENCY

46

AUGUST 2 017

up this heat and turn it back into useful electricity that they could use to maximize electrical output. The key to the useful behavior of thermoelectric materials, such as bismuth telluride and antimony telluride, is that when one side of the material is hot and the other side is cold, they spontaneously generate an

electrical voltage. The greater the temperature gradient, the more power they generate. But to date, thermoelectric generators (TEGs) have almost invariably been made from solid blocks of thermoelectric materials. “ We envisioned that a stretchable TEG would achieve more output power as it can easily maintain a longer

distance between the hot end and the cold end,” said Muhammad Hussain, Associate Professor of Electrical Engineering at KAUST, who led the research. The cold end of the stretchable TEG can be pulled further away from the heat source, maximizing the temperature gradient. Hussain’s team made the flexible TEGs by coating

©2017 IEEE. REPRODUCED WITH PERMISSION FROM REF 1.

A

dding elasticity to the impressive properties of materials known as thermoelectrics could help us conserve more power. From laptop chips and automobile exhaust pipes to industrial machinery, for most devices, a lot of the energy they consume is lost as heat. Flexible thermoelectric materials can mop

2017 K AUST / ANASTASIA KHRENOVA

Deformable thermoelectric materials add a new twist to the design of energyscavenging devices.

bismuth telluride or antimony telluride onto a helically shaped flexible paper or polymer substrate. Hussain explained that this helical architecture is what allowed the TEG to flex and stretch in any direction while maintaining its mechanical integrity. A simple spiral shape, made from a paper substrate (which has lower thermal conductivity than the polymer), was the best design, generating more than twice the power when stretched than when laid flat. Hussain has a couple of initial applications in mind for his stretchy TEGs. “For wearable gadgets, they can be very useful,” he said. “Another immediate area we are looking into is thermoelectric power from ships and automobiles. Their top surface is under the sun and their bottom surface is always in the water or in the shade.” “Stretchable TEGs could be used in almost any application where there is waste heat to be recaptured, Hussain added. Traditionally, to enhance the power production from a TEG, the thought process has singularly focused on improving the thermoelectric properties of various thermoelectric materials. We have clearly shown that the architecture of the TEG is equally important to enhancing the power production independent of the thermoelectric material used.” Rojas, J. P., Singh, D., Conchouso, D., Arevalo, A., Foulds, I. G. & Hussain, M. M. Stretchable helical architecture inorganic-organic hetero thermoelectric generator. Nano Energy 30, 691–699 (2016).

THE CREST OF WAVEFORMS FOR NEXT-GEN RADAR A new method for shaping the waveform generated by multiantenna radar systems is inexpensive and practical. By adapting the interaction between several independent radar transmissions in real time, KAUST researchers have shown that it is possible to vastly improve target identification and range using multiple input, multiple output (MIMO) radar systems. Radar is used extensively in civilian and military aviation to identify and monitor aircraft movements and potential meteorological dangers as well as being a critical component of flight control and surveillance systems. Radar works by transmitting a radio signal from an output antenna and monitoring a receiving antenna for any detected reflections—akin to shining a spotlight into darkness to see what might be out there. Radar systems are now very sophisticated, and with advanced signal processing, it is now possible to discriminate between different types of objects from considerable distance. MIMO radar promises better performance by being able to more adaptively shape the output waveform to concentrate the power of the transmitted signal in a specific direction and by An example of beam pattern shaping using KAUST’s MIMO waveform computation scheme.

transmitting multiple types of signal adapted to better match a broader range of targets. “MIMO radar uses several transmitting and receiving antennas at the same time, where the user can choose a different transmitted signal for each antenna,” explained lead researcher and graduate student Taha Bouchoucha. “Our work was on the transmitter side, developing a simple way of constructing the transmitted waveforms to steer the signal to a specific region in space.” There has been extensive research into MIMO radar systems, but the stumbling block has been the computational complexity of designing each individual waveform to produce the desired combined “beam pattern” after the waveforms have interacted in space. Under the supervision of Professor Mohamed-Slim Alouini and Associate Professor Tareq Al-Naffouri, Bouchoucha focused on finding ways to simplify and accelerate these calculations. “We took advantage of a mathematical framework called the two-dimensional Fourier transform combined with fast and efficient algorithms to generate the Fourier transform parameters,” said Bouchoucha. “Waveform generation using our approach is inexpensive and practical, and it gives complete flexibility and freedom to focus the transmitted signal in a specific region in space.” The computation scheme has already been filed with the United States Patent and Trademark Office as a significant breakthrough in MIMO technology. “Being part of this project as a Master’s student was a great experience,” said Bouchoucha, who is now a doctoral researcher at the University of California Davis. “It was an exceptional research environment with inspiring mentors and peers who helped me develop.” Bouchoucha, T., Ahmed, S., Al-Naffouri, T., & Alouini, M.-S. DFT-based closedform covariance matrix and direct waveforms design for MIMO radar to achieve desired beampatterns. IEEE Transactions on Signal Processing 65, 2104–2113 (2017).

K AUST DISCOVERY

di sc o ver y.kaust.edu.sa

47


Imane Boudellioua and Robert Hoehndorf developed a tool that may help find the genetic cause of some “mystery” illnesses.

ALGORITHM SCOURS DATASETS TO DIAGNOSE MEDICAL MYSTERIES

A new tool uses genetic and clinical information to find the root cause of unexplained illnesses.

An algorithm developed by KAUST scientists has the potential to help patients with mysterious ailments find genetic causes for their undiagnosed diseases. It works by first identifying presumed harmful variants in a patient’s genome. The algorithm then cross-references the various mutations against large databases linking genes and symptoms and determines the likelihood of any given gene variant being implicated in the patient’s disease. Other tools available to scour the genome for harmful mutations tend to rely solely on DNA sequence data. Meanwhile, the team’s new PhenomeNET Variant Predictor (PVP) system includes clinical information from a

48

AUGUST 2 017

patient’s medical record as well. It also incorporates reams of phenotype data from systematic evaluations of mice and zebrafish that match DNA changes to disease features.

“We desperately need more high-quality phenotype data from model organisms.” “Ours uses more information than other tools, and we look for potential causative variants, not just a deleterious variant,” explained Assistant Professor

Boudellioua, I., Mahamad Razali, R.B., Kulmanov, M., Hashish, Y., Bajic, V.B., ... & Hoehndorf, R. Semantic prioritization of novel causative genomic variants. PLoS Computational Biology 13, e1005500 (2017).

2017 K AUST / ANASTASIA KHRENOVA

Robert Hoehndorf, who led the study, along with his Ph.D. student Imane Boudellioua. In their new paper, the researchers used a retrospective dataset from the UK and the Supercomputing Laboratory at KAUST to show that PVP accurately identified the causative gene variants responsible for congenital hypothyroidism. Mutations in a number of different genes are known to cause the disease, leading to an underproduction by the thyroid gland in the neck of iodine-containing hormone needed for normal growth and development. As reported, PVP pinpointed the gene variants responsible for congenital hypothyroidism in individual patients, both in sequence datasets that spanned the entire genome and in those that included only the protein-coding portion. Hoehndorf envisions the tool becoming a part of the clinical geneticist’s diagnosis routine. For a patient with a suspected genetic disease, doctors could sequence that person’s genome, give a full clinical workup and then run the algorithm. “PVP should be able to identify the variant or variants causing the patient’s phenotypes (symptoms) directly in most cases,” he said. Still, there’s room for improvement. Hoehndorf explained that PVP can find pathogenic DNA variants in genes that have already been implicated in disease, either in people or in lab organisms; however, around two-thirds of the protein-coding genes in mice still await full characterization. While more genes have been characterized in zebrafish, the evolutionary distance between fish and humans (and differences in experimental protocols) makes this kind of crossspecies comparison more challenging. “We desperately need more highquality phenotype data from model organisms, in particular the mouse, to improve our system,” Hoehndorf said.

“I never imagined I would start a business based on my Ph.D. thesis. Completing my master’s and doctoral education at KAUST ignited my passion as an innovator and my commitment to finding real-life opportunities for impact.” Co-founders Edward Canepa and Ahmad Dehwah install a Sadeem monitoring system.

Ahmad Dehwah Cofounder of KAUST startup Sadeem, ranked #13 in 2016 Forbes Middle East 50 Most Promising Startups Discover more about the KAUST startup process at INNOVATION.KAUST.EDU.SA

Ahmad is part of the founding team behind Sadeem, a wireless sensor network that is the world’s first solar-powered urban flood and traffic real-time monitoring system. As students, they established the company through the help of the KAUST startup support programs. Now as entrepreneurs, they are located at the KAUST Research and Technology Park and continue to improve their smart city technologies and grow as a business in part through the support, mentorship and global networks of KAUST.


Physical Science and Engineering Division

P S E

HIGH-SENSITIVITY CAMERAS REVEAL THE ATOMIC STRUCTURE OF METAL-ORGANIC FRAMEWORKS

Atomic-resolution TEM imaging a metal-organic framework was achieved for the first time using a direct-detection electron-counting camera.

50

AUGUST 2 017

2016 K AUS T / IVAN GROMICHO

Highly sensitive electron cameras allow researchers to see the atomic structure of metal-organic frameworks. A method for fine-scale imaging of a from Gatan, a company specializing in class of materials that is useful for gas electron microscopy, Lawrence Berkestorage and separation is needed. How- ley National Laboratory and others in ever, typical visualization methods emit China. Their collaboration resulted in an electron dose that can cause damage an adaptation of high-resolution transto the structure of some materials. mission electron microscopy (HRTEM) One of these materials are metal- using state-of-the-art direct-detection organic frameworks (MOFs) , three- electron-counting cameras. dimensional structures made up of metal The downfall of using HRTEM to ions connected by organic ligands. MOFs image MOFs is that the high-energy are useful for gas storage and separation electrons that pass through the sambecause they can be designed to have ple cause damage to the structure. By precise pore sizes of molecular dimen- modifying HRTEM using high-sensions and large void spaces (porosity) sitivity detectors, the team acquired images with an electron dose low within their frameworks. “To thoroughly understand the performance of metal-organic frameworks in various applications, we need to know their structures at the atomic level because their macroscopic behavior is determined by their microscopic structure,” explained Yu Han, KAUST Associate Professor of Chemical Science. By visualizing these structures, researchers can uncover important clues about how these materials self-assemble to create their trademark pores. Several members of the University’s Advanced Membranes and Porous Materials Center joined forces with the University’s Imaging Symmetry-imposed and lattice-averaged HRTEM image and Characterization Core of the metal–organic framework ZIF-8 (black and white) with a structural model overlaid to show the position of Lab and with colleagues the zinc ions and organic ligands (in color).

enough not to damage the structure of MOFs. Ultimately, the group produced high-resolution images of their atomic structures. As a study case, the team applied their method to ZIF-8, a MOF comprising zinc ions connected by organic 2-methylimidazole linkers. They were able to image its structure with a resolution of 0.21 nanometers (one nanometer is one billionth of a meter), a resolution high enough to image the individual columns of zinc atoms and organic linkers. This helped the researchers to reveal the surface and interfacial structures of ZIF-8 crystals. “The results unraveled that porosity generated at the interfaces of ZIF-8 crystals is different from the intrinsic porosity of ZIF-8, which influences how gas molecules transport in ZIF-8 crystals,” explained Han. This work sets the foundation for the use of nondestructive atomic-level HRTEM imaging of other materials, including polymers and two-dimensional materials. Zhu, Y., Ciston, J., Zheng, B., ... & Han, Y. Unravelling surface and interfacial structures of a metal– organic framework by transmission electron microscopy. Nature Materials 16, 532–536 (2017).

K AUST DISCOVERY

di sc o ver y.kaust.edu.sa

51


Physical Science and Engineering Division

P S E and so have a significant influence on the engine’s design,” noted Farooq. “Like all fuels, light naphtha contains hundreds of compounds, so to perform detailed engine optimization, we need a simpler model of the fuel that is called a surrogate fuel.” The researchers compared auto-ignition properties of light naphtha with two surrogates—a simple primary reference fuel surrogate and a more complex surrogate—over a range of temperatures, pressures and fuel/air ratios. Operating at high temperatures, they first used a shock tube to study the autoignition behavior of the surrogates over different pressures. However, at lower temperatures reactions take longer, so a rapid compression machine was used

GOLD STANDARDS FOR NANOPARTICLES

Researchers from the KAUST Clean Combustion Research Center collaborated with the Fuel Technology Team from Saudi Aramco to work on the new technique.

THE RACE FOR MORE EFFICIENT ENGINES

52

AUGUST 2 017

A shock tube used to model the auto-ignition properties of light naphtha.

engines have their advantages, we need a new type of engine that utilizes the strengths—while avoiding the drawbacks—of current engine technologies.” Compression-ignition and sparkignition engines, commonly referred to as diesel and gasoline engines, have fuel efficiencies of only 35 to 40%. A new engine design called a gasoline compression-ignition (GCI) engine, however, promises efficiencies of up to 55% as well as releasing fewer harmful soot and nitrogen oxides compared to current engines. However, realizing these benefits requires a fuel with auto-ignition properties somewhere between gasoline and diesel. “The auto-ignition properties determine the performance of the engine

2016 K AUST

could open the potential for more advanced engines to run on fuels that release fewer GHG emissions. “Optimizing fuel performance and engine designs must go hand-in-hand if we want to reduce emissions and improve engine efficiencies,” Farooq said. “Although gasoline and diesel

© 2017 NATURE PUBLISHING GROUP. REPRODUCED WITH PERMISSION FROM REF 1.

Understanding how small organic ions stabilize gold nanoparticles may allow for better control.

New technique lays the foundation for greener transport fuels and next generation engines. The search for better engine performance powered by less polluting fuels will benefit from a new modeling technique developed at KAUST. Reducing the greenhouse gases (GHG) released from the production and burning of fuels like diesel and gasoline —significant contributors to climate change—is a huge challenge facing the transportation industry. Aamir Farooq, Associate Professor of Mechanical Engineering, and colleagues from the KAUST Clean Combustion Research Center (CCRC) worked with the Fuel Technology Team from Saudi Aramco and used an innovative technique for testing the properties of light naphtha, a fully blended low-octane highly paraffinic fuel. Farooq explained that this technique

“Although gasoline and diesel engines have their advantages, we need a new type of engine that utilizes the strengths— while avoiding the drawbacks— of current engine technologies.”

Expanding the potential of gold nanoparticles for a range of uses requires methods to stabilize the clusters and control their size. A new study reveals how simple organic citrate ions, derived from readily available citric acid, can interact with gold atoms to yield the stable nanoparticles needed for further research. Such clusters of gold atoms are proving increasingly useful as catalysts, drug delivery systems, anti-cancer agents and components of solar cells, among other applications. “The potential applications of gold nanoparticles could have a huge impact on society, and understanding stabilizers like citrate might be crucial to progress,” said

1 nm

Gold nanoparticles imaged at atomic resolution.

Jean-Marie Basset, Director of the Catalysis Center and Distinguished Professor of Chemical Science. With this work, Hind Abdullah Al-Johani, a recent graduate of KAUST and now Associate Professor of Chemistry at Tabuk University, became the first Saudi woman to be published as a first author in Nature Chemistry. Along with coworkers in UK, Switzerland and France,

to extend the observation time for the reactions. They found the complex surrogate almost perfectly matched the light naphtha, and in particular at lower temperatures, providing a full picture of its auto-ignition characteristics. “Our work has produced the first auto-ignition model for light naphtha, and it is being used by Saudi Aramco’s Research Center in Detroit to optimize GCI engine designs,” Farooq said. Javed, T., Nasir, E.F., Ahmed, A., Badra, J., Diebbi, K., ... & Farooq A. Ignition delay measurements of light naphtha: A fully blended low octane fuel. Proceedings of the Combustion Institute 36, 315–322 (2017).

the researchers have shown different ways that citrate ions can bind to gold atoms at the surface of nanoparticles. They also discovered how to influence the binding mode by controlling the ratio of the nanoparticle/citrate ions, so tweaking the structures and properties of the nanoparticles. “The experimental and theoretical characterization of these systems is challenging due to the flexible nature of the interaction between citrate and gold,” said Basset. Collaboration between KAUST teams was essential to meet the challenges of creating stabilized nanoparticles and analyzing and imaging them at high resolution. One reason for gold’s usefulness in medical applications is its chemically stable nature. Other researchers have shown that this allows gold to carry drugs through the body without causing chemical side effects. Controlling the structure

of gold nanoparticles could also fine tune their interaction with light to exploit a phenomenon known as surface plasmon resonance. This may allow the energy of light to be harnessed to kill cancer cells. Attaching antibodies can guide the nanoparticles to the specific cells that need treatment. The type of interaction with light depends on nanoparticle structure and could also yield applications in solar cells and microelectronics. The researchers consider that the insights from this work at KAUST may also be applicable to some other metals and plan to explore this as the next phase of the research. “We want to take on that wider challenge,” said Basset. Al-Johani, H., Abou-Hamad, E., Jedidi, A., Widdiefield, C. M., ... & Basset, J.-M. The structure and binding mode of citrate in the stabilization of gold nanoparticles. Nature Chemistry (2017).

K AUST DISCOVERY

di sc o ver y.kaust.edu.sa

53


Physical Science and Engineering Division

P S E

Polarized optical microscopy of drop cast thin film featuring a “coffee ring.” The thin film was sequentially crystallized by solvent vapor annealing where crystallization is initiated from the thick rim of the “coffee ring,” propagating toward the thinner center.

A

chance observation of crystals forming a mark that resembled the stain of a coffee cup left on a table has led to the growth of customized polycrystals with implications for faster and more versatile semiconductors. Thin-film semiconductors are the foundation of a vast array of electronic and optoelectronic devices. They are generally fabricated by crystallization processes that yield polycrystals with

54

AUGUS T 2 017

a chaotic mix of individual crystals of different orientations and sizes. Significant advances in controlling crystallization have been made by a team led by Associate Professor Aram Amassian of Material Science and Engineering at KAUST. The group included individuals from the KAUST Solar Center and others from the University’s Physical Science and Engineering Division in collaboration with Cornell University. Amassian

said, “There is no longer a need to settle for random and incoherent crystallization.” The team’s recent discovery began when Dr. Liyang Yu of the KAUST team noticed that a droplet of liquid semiconductor material dried to form an outer coffee-ring shape that was much thicker than the material at the center. When he induced the material to crystallize, the outer ring crystallized first. “This hinted that local thickness matters for

initiating crystallization,” said Amassian, which went against the prevailing understanding of how polycrystal films form. This anomaly led the researchers to delve deeper. They found that the thickness of the crystallizing film could be used to manipulate the crystallization of many materials. Most crucially, tinkering with the thickness also allowed fine control over the position and orientation of the crystals in different

ARAM AMASSIAN

Varying the thickness of crystallizing materials facilitates control over the patterns and properties of crystals.

© 2016 AMERICAN PHYSICAL SOCIETY. REPRODUCED WITH PERMISSION FROM REF 1.

COFFEE-RING EFFECT LEADS TO CRYSTALLIZATION CONTROL IN SEMICONDUCTORS

regions of a semiconductor. “We discovered how to achieve excellent semiconductor properties everywhere in a polycrystal film,” said Amassian. He explained that seeding different patterns of crystallization at different locations also allowed the researchers to create bespoke arrays that can now be used in electronic circuits. This is a huge improvement to the conventional practice of making do with materials whose good properties are not sustained throughout the entire polycrystal nor whose functions at different regions can be controlled. “We can now make customized polycrystals on demand,” Amassian said. Amassian hopes that this development will lead to high-quality, tailored polycrystal semiconductors to promote advances in optoelectronics, photovoltaics and printed electronic components. The method has the potential to bring more efficient consumer electronic devices, some with flexible and lightweight parts, new solar power generating systems and advances in medical electronics. And all thanks to the chan ce observation of an odd pattern in a semiconductor droplet. The team will now explore ways to move their work beyond the laboratory through industry partnerships and research collaborations. Yu, L., Niazi, M. R., Ngongang Ndjawa, G. O., Li, R., Kirmani, A. R., ... & Amassain, A. Programmable and coherent crystallization of semiconductors. Science Advances 3, e1602462 (2017)

LEVITATION TRICK GIVES DRAG THE SLIP Plunging hot spheres into viscous liquids reveals a way to reduce fluid resistance without complex engineering procedures. The erratic scooting of water droplets around sizzling frying pans occurs when layers of trapped vapor cause the drops to briefly float. A team from KAUST has shown that this process, known as the Leidenfrost effect, can be used to significantly cut the drag forces faced by objects traveling through liquids. A baseball’s special stitches and the dimples on golf balls are not just cosmetic. At sufficient speeds, these rough textures cause a thin boundary layer of air flowing over the sphere to behave turbulently and reduce the friction to a level below that of smooth surfaces. This so-called drag crisis lets these balls achieve longer and more stable trajectories. Recently, Sigurdur Thoroddsen, Professor of Mechanical Engineering, and Dr. Ivan Vakarelski investigated techniques to trigger drag without invoking the crisis phenomenon. They achieved this by reversing usual Leidenfrost procedures and immersing hot spheres into liquids. With sufficient evaporation, a vapor layer formed that acted as lubricant to reduce liquid-solid Free-fall experiments and simulations show that spheres enveloped by special vapor layers (rightmost frames) travel with significantly less wake through liquids.

friction. This approach enabled hot spheres to move twice as fast as cooler orbs during free-fall experiments. However, both the drag crisis and Leidenfrost-induced levitation take place under a narrow range of a parameter, known as the Reynolds number, which relates fluid viscosity and density to the size and speed of a traveling sphere. In their latest work, Vakarelski, Thoroddsen and collaborators in Australia used liquids with unique stabilizing properties to dramatically expand the conditions under which Leidenfrost vapor layers diminish drag forces. The researchers dropped the scalding spheres into tall vertical tanks containing perfluorocarbons, liquids often used as refrigerants that evaporate more easily than water. High-speed video cameras captured the free-fall trajectories of spheres in perfluorocarbons with widely different viscosities to explore a range of drag conditions. Surprisingly, the vapor layer reduced friction by much more than was expected, and did so successfully for Reynolds numbers spanning three orders of magnitude. Modeling of this process revealed that the Leidenfrost effect induced the liquid flowing around the sphere to slip and take on different velocities. Thoroddsen explained that, “As we slowly introduce more slip, this progressively reduces the drag. The partial slip is determined by the relative viscosity of the liquid and the gas molecules in the vapor layer.” The team anticipates that vapor layers naturally sustained on superhydrophobic surfaces, or induced via bubble injection, may stimulate development of unexpected frictioncutting techniques. “These experiments just give an upper bound for drag reduction—once engineers see the possibilities, the potential payoff could be large,” added Thoroddsen. Vakarelski, I. U., Berry, J. D., Chan, D. Y. C. & Thoroddsen, S. T. Leidenfrost vapor layers reduce drag without the crisis in high viscosity liquids. Physical Review Letters 117, 114503 (2016).

K AUST DISCOVERY

di sc o ver y.kaust.edu.sa

55


A flexible logic sensor made from carbon nanotubes and graphene oxide films can sense humid objects without touching them.

AUGMENTED REALITY AT YOUR FINGERTIPS A flexible, carbon-based device that responds to humidity in two ways can sense 3D objects without touching them. The intuitive touch screens integral to smartphones caused a sensation when first released, and they remain popular for many consumer electronics. But these input devices are moving into three dimensions with a sensor that tracks the position and speed of human fingers in free space. Thin films made from carbon nanotubes or graphene oxides have electrical properties that are highly sensitive to humidity. Both substances absorb water molecules and transform them into charged hydronium ions (H 3O +) that modify thin

56

AUGUST 2 017

film conductivity in reversible, repeatable ways. They do this at faster speeds than traditional humidity sensors. The direction of conductivity change, however, depends on the nanomaterial—graphene oxide tends toward higher conductivity with H 3 O + additions, while nanotubes become more resistive. Dr. Yanlong Tai and Professor Gilles Lubineau realized that a combination of these tiny nanomaterials could be used to power a recognition system based on gestures rather than touch. “These 3D non-contact sensors,” explained Tai, “require

generation of three different signals during a one-time measurement.” The duo envisioned that an appropriate mix of nanotubes and graphene oxides would give triple response patterns—positivenegative-negative, for example, to the natural humidity surrounding a fingertip. However, to achieve sufficient signal resolution to process a finger’s 3D position, they needed clearer insight into the contradictory response of nanotubes and graphene oxide to humidity. According to Lubineau, absorbed H3O+ ions induce mechanical stress inside the

Tai, Y. & Lubineau, G. Humanfinger electronics based on opposing humidityresistance responses in carbon nanofilms. Small 13, 1603486 (2017).

2016 KAUST / IVAN GROMICHO

nanomaterials that alters the material’s bulk conductivity and the junction conductivity between individual nanoparticles. “Both films rely on the same two mechanisms, but the balance between them is totally different,” said Lubineau. “A key challenge was to be able to correctly separate the physics of each effect in the different microstructures.” By experimenting with sensors containing different microstructure layouts, the team deduced that a net model, where conductivity follows a grid-like system of intercrossed pathways, could explain the humidity-induced resistance of nanotube films. Graphene oxide, on the other hand, was best represented by an overlapping scale design that introduced favorable capacitive effects in the presence of H3O+. The researchers used this knowledge to fabricate a flexible, transparent device that measures the distance, speed and direction of a fingertip placed above it. This prototype also worked with vapor from human breath, and it is poised to make gesture sensing a part of digital input interfaces. “It’s usually hard to make non contact sensors operate with different moisture levels,” said Lubineau. “Our findings here may promote their use in augmented reality setups.”

“The things I appreciate most at KAUST are the professional camaraderie and the ability for a work-life balance. I’m surrounded with brilliant colleagues and am also afforded the luxury of time so I don’t have to choose between my professional career and my personal life. Here, I can enjoy both to their fullest.”

Associate Professor Mani Sarathy 2015 Highly Cited Researcher, Clarivate Analytics. Ranked among the top 1% most frequently cited in engineering Learn more about living and working at KAUST.EDU.SA

Mani’s research explores the environmental impact of conventional and alternative fuels and their combustion systems. He utilizes fundamental chemical kinetic models and experiments to predict fuel combustion and pollutant formation in energy systems. When he is not in the lab exploring combustion chemistry, he likes to discover new heights in the Saudi Arabian desert.


Physical Science and Engineering Division

P S E

AN INTERNATIONAL LANGUAGE FOR SOLAR ENERGY FIELDS Standardized reporting of energy conversion efficiency could help to develop photocatalysts to produce renewable fuels.

2016 K AUS T

R

esearchers at KAUST have reviewed the various definitions and terminologies used to measure and report on the energy conversion efficiencies in different solar energy fields. They offer recommendations to make it easier to assess the relative merits of innovations in this challenging arena. Making greater use of sunlight’s abundant energy as an alternative and sustainable power source is a key priority for researchers worldwide. The drive towards more efficient and more extensive use of solar energy is also a prominent goal of the University to promote in-Kingdom research and development. The KAUST Catalysis Center works on ways to develop catalysts that can harness solar energy to power the chemistry that creates alternative fuels—for example, by splitting water into hydrogen and oxygen gases. “Saudi Arabia is privileged

58

AUGUST 2 017

to possess both existing and future energy resources,” said Kazuhiro Takanabe, Associate Professor of Chemical Science and a member of the Center, referring to the Kingdom’s oil reserves and abundant solar energy. “At our Center, we are working on building the bridge from current energy production methods to those of the future.” Takanabe and his Ph.D. student Muhammad Qureshi focused their review on the use of powder photocatalysts to accelerate light-driven reactions in liquids. This process of heterogeneous photocatalysis is one of the most significant procedures used to harness light for fuel production and environmental remediation. “We hope to draw attention to the problem of different measuring and reporting systems and suggest procedures that will allow easier comparison among the results from different laboratories,” said Takanabe.

Ph.D. student Muhammad Qureshi (left) and Associate Professor Takanabe in front of a photocatalytic reactor conducting a water-splitting experiment.

This is a vital issue because the most effective and economically viable solar energy solutions can only be identified if the efficiency of different methods can be accurately compared. Takanabe also pointed out that some research papers contain inaccuracies and are inconsistent, partly because of the different systems of measurement and reporting. The KAUST team proposed a unified system to report the key variables linked to the efficiency of different photocatalytic materials, and they give an example based on their own work. Quantifying the key variables is focused on three measurements, which are the photon flux through each photoreactor, the photocatalytic rate at which maximized incident photons are absorbed and the accurate measurement of reactant consumption and product generation. The researchers hope that their review and proposals will assist research teams around the world in their quest to develop an increasingly solar-powered future. Qureshi, M. & Takanabe, K. Insights on measuring and reporting heterogeneous photocatalysis: efficiency definitions and setup examples. Chemistry of Materials 29, 158–167 (2017).

K AUST DISCOVERY

di sc o ver y.kaust.edu.sa

59


Physical Science and Engineering Division

P S E

The defining property of a semiconductor is its so-called bandgap: the barrier that prevents electrons within a specific energy range from flowing through a material. KAUST Professor Lance Li and his team collaborated with colleagues from Taiwan and used a simple model to determine the band alignment in an exciting new class of semiconductors called two-dimensional transition-metal dichalcogenides (TMDs). The simple concept of bandgap enables a single semiconducting material, such as silicon, to perform the operations required by electronic devices. When two or more semiconductors are combined, the device affords a broader range of functionality and boasts improved performance and efficiency. To understand how such heterostructures behave, it is crucial to know how the bandgaps of the two materials align. Although graphene and TMDs are atomically thin, the lack of a bandgap in graphene limits its application to electronics while the presence of a bandgap in TMDs allows them to be stacked into heterostructures. It is, however, difficult to experimentally determine band alignment between these layers. Li has

Chiu, M.-H., Tseng, W.-H., Tang, H.-L., ... & Li, L-J. Band alignment of 2D transition metal dichalcogenide heterojunctions. Advanced Functional Materials 27, 1603756 (2017).

VACUUM WSe2 S Se

60

Mo W

AUGUST 2 017

CBO

CBM MoS2

Coordinationdriven selfassembly leads to the formation of micrometerscale toroids.

THE POWER OF

2016 KAUST / XAVIER PITA

A simple model is shown to accurately predict the electronic properties of a combination of 2D semiconductors.

now proven that the concept known as the Anderson model, a simple, computationally inexpensive way of determining band alignment, is applicable to this system. The Anderson model assumes that when two semiconductors are placed together, they share a common zero in their energyband structure known as the vacuum level. Bandgap alignment can then be determined directly from calculated values of bandgaps and offsets. Until now, it was unclear whether this assumption would hold true in atomic-layer TMDs. Li and his team addressed this by measuring the energy of the bandgap in three TMDs, molybdenum disulfide, tungsten disulfide and tungsten diselenide, using a method called ultraviolet photoelectron spectroscopy. They then applied the Anderson model to predict the band alignment. They compared these calculated values with direct experimental measurements from X-ray photoelectron spectroscopy of two heterostructures. Agreement between the values obtained by the two methods indicated that the Anderson model holds true. The team suggests that this is because of unique van der Waals surfaces, which ensure an absence of dangling atomic bonds that would otherwise prevent the vacuum levels in the two materials from aligning. “Our next step is to build heterojunctions based on the knowledge gained from the theory,” said Li. “We will research several heterostructures for various applications, such as solar cells and light-emitting diodes.”

ATTRACTION Hybrid organicinorganic materials can self-assemble into tiny doughnutlike structures. Engineered nanometer- and micrometer-scale structures have a vast array of uses in electronics, sensors and biomedical applications. Because these are difficult to fabricate, KAUST researchers

2016 KAUST / MING-HUI CHIU

ANDERSON’S MODEL HOLDS FOR 2D MATERIALS

are trying a bottom-up philosophy, which harnesses the natural forces between atoms and molecules such that microstructures form themselves. This approach, a departure from the usual top-down approach, involves the etching away of material to leave the desired sculpted structure behind; however, because this approach can be tricky, expensive and time consuming, KAUST researchers became motivated to find a new approach. Associate Professor of Chemical Science Niveen

Khashab and her team and colleagues from the Imaging and Characterization Core Lab and the Max-PlanckInstitute of Colloids and Interfaces in Germany demonstrated this bottom-up approach in the self assembly of microscale toroids (doughnut-shaped forms), made of both inorganic and organic materials. A number of forces can bring atoms and molecules together. These include surface tension, electrostatic attraction and repulsion and a weak fundamental force known as van der Waals

interactions. The toroids created by Khashab’s team were formed via metal coordination. A metallic sodium chloride atom, an amphiphilic (both hydrophilic and lipophilic) molecule called saponin and a polymer known as chitosan were combined and formed weak chemical bonds. This is a result of what is known as coordination-driven self assembly,” explained Khashab. “The metal ions interact with different chemical motifs, leading to the formation of novel frameworks and morphologies.”

Within just a few minutes, coordination bonding between the iron atoms and the oxygen and the hydrogen in the molecules initially drives the self assembly of star-like nanostructures. Repulsive electrostatic and hydrophobic interactions then lead to the formation of toroids. The toroids were approximately 3.9 to 4.8 micrometers in diameter and held their shape even a month after fabrication. Disassembly of the microstructures required five hours of mechanically stirring the solution. There are numerous naturally occurring biological structures that take a toroid shape; for example, proteins and DNA of some types of viruses and bacteria selfassemble in this way. Many of these are known to play an important role in the formation of pores in biomembranes. This research could help to build a better understanding of how these complex biostructures are created and provide a way of mimicking them at the molecular level. “Next, we hope to prepare a new generation of these hybrid structures with a temperature-responsive gap size,” said Khashab. “These toroid structures could be used as pockets for active catalysis and separation.” Al-Rehili, S., Fhayli, K., Hammami, M. A. Moosa, B., ... & Khashab, N. M. Anisotropic self-assembly of organic-inorganic hybrid microtoroids. Journal of the American Chemical Society (2016).

K AUST DISCOVERY

di sc o ver y.kaust.edu.sa

61


Physical Science and Engineering Division

P S E aromatic components present attractive interactions with hydrogen atoms in CH4. “Adsorbents have been a long-standing territory of inorganic materials,” said Lai. His team’s findings demonstrate that, besides their greater stability and ability to overcome fouling, organic polymers outperform conventional inorganic

adsorbents. “Therefore, it is time to consider organic and hybrid materials for next-generation adsorbents,” he added “Our adsorbent can be directly used in a well-established gas separation technology called pressure swing adsorption,” said Lai. The researchers are now investigating

ways to increase the adsorption capacity of their material. Wang, X., Liu, Y., Ma, X., Das, S. K., Ostwal, M., ... & Lai, Z. Soluble polymers with intrinsic porosity for flue gas purification and natural gas upgrading. Advanced Materials 29, 1605826 (2017).

RECONSTRUCTING THE RED SEA’S CLIMATE PATTERNS An advanced numerical model is helping researchers better understand the variability of the Red Sea’s climate patterns.

Associate Professor Zhiping Lai (left) and Professor Ingo Pinnau stand in front of their colleagues while holding a model of a porous material which they designed to have strong CO2 affinity.

SETTING REGENERABLE POLYMER TRAPS

62

AUGUST 2 017

requires a lot of energy and capital, which has restricted its large-scale use. Adsorbents consisting of porous materials with regular structures, such as zeolites, metal-organic frameworks and mesoporous silicas, have emerged as attractive alternatives to amine scrubbing because of their large surface area and good selectivity. However, their pores are readily damaged and blocked from the build-up of heavy hydrocarbons in flue gas and natural gas, which depletes their adsorption capacity. When fouled or broken, these low-stability structures are difficult to restore. KAUST Associate Professor Zhiping Lai and colleagues from the University’s Advanced Membranes and Porous Materials Center have created a recyclable polymer-based adsorbent

that is stable under normal operational conditions. “If deteriorated or fouled, this structure can be easily disassembled to release the fouling agents and later regenerated through a simple solutioncasting process,” said Lai. The researchers produced their adsorbent by modifying an intrinsically porous polymer using a DNA-like functional group called DAT. Showing stronger CO2 affinity, the adsorbent also displayed greater affinity with CH4 than N2 compared to its precursor. According to Lai, the DAT group plays multiple roles here. It forms a hydrogenbonded network of polymer chains that obstructs large pores and hinders the transport of N2-sized molecules. Its numerous Lewis base-like nitrogen atoms enhance the CO2 affinity while its

© 2016 JOHN WILEY AND SONS, REPRODUCED WITH PERMISSION FROM REF 1

Adsorbents that effectively isolate CO2 from other gases, such as nitrogen (N2) and methane (CH4), have been developed by KAUST using polymers with built-in porosity. Such polymer-based materials would help to control CO2 levels released into the atmosphere and existing in natural gas. Unlike their typical analogues, these polymers generate micropores because their rigid, ladder-type chain structure prevents dense packing. Industrial facilities, such as oil refineries and natural gas processing plants, typically depend on amine scrubbing for CO2 removal. In this process, CO2-rich acid gas passes through an aqueous solution of highly reactive amines that transform and retain the pollutant in solution. However, this corrosive gas treatment

2017 KAUST / ANASTASIA KHRENOVA

Stable and recyclable materials synthesized using intrinsically porous polymers selectively retain CO2 from exhaust emissions and natural gas.

Red Sea climate data covering the period between 2000 and 2014 has been reconstructed highly accurately at smaller time and space intervals than ever before by KAUST researchers, who used an advanced numerical weather modeling system that incorporates all weather data from the region. The system, called the Advanced Research version of Weather Research and Forecasting (WRF-ARW), was developed by the United States National Centers for Environmental Prediction to reconstruct and forecast weather data based on current conditions. Ibrahim Hoteit, Associate Professor of Earth Science and Engineering at KAUST, and his colleagues took advantage of the advanced computational facilities at the University to customize the system and generate high-resolution regional climatic data covering relatively small timescales and geographic areas over the Red Sea. To do this, they combined low-resolution global reconstructed climatic data covering

relatively large geographic areas and timescales with available satellite and in situ observations over the region. “The study generated and validated much-needed high resolution atmospheric and wave datasets for the Red Sea and adjoining region,” noted Hoteit. “These highresolution datasets more accurately describe the regional climatic features of this region than available global products.” The model revealed that the maximum temperatures in the summer months are in north Sudan and the central Arabian Peninsula. In the winter, the maximum temperatures are found in the Tokar region, a 110-kilometer-wide valley located approximately in the

30N

B

A

middle of the African side of the Red Sea. The model also clearly shows the evolution and duration of the Red Sea Convergence Zone and the conditions that favor its intensification. In the winter, tropical and extra tropical wind systems converge in this zone in the middle of the Red Sea, leading to localized cloudy skies and drizzle in an otherwise largely cloudand rain-free area, explained KAUST Research Scientist Hari Dasari, the lead author of the study. The research highlights the utility of the WRF-ARW for producing high resolution data in the Red Sea region that can further help in understanding Red Sea circulation, its C

D

27N 24N 21N 18N 15N 12N 9N

33E 36E 39E 42E 45E

33E 36E 39E 42E 45E

SUMMER

33E 36E 39E 42E 45E

33E 36E 39E 42E 45E

WINTER

m/s 10 9 8 7 6 5 4 3 2.5 2 1.5 1 0.5

10

The researchers’ analysis covered a rectangular-shaped area around the Red Sea.

ocean surface processes and marine biodiversity, the researchers say. The team is currently working on minimizing uncertainties in the model’s predictions and improving the quality of the generated data sets. They are also developing new higher-resolution datasets covering longer time periods for the entire Middle East region. In addition, the researchers are using the model to study some extreme events that recently affected Saudi Arabia, such as the Jeddah floods of November 2009 and January 2011 and the Makkah storm of September 2015, with the aim of assessing their predictability. They also plan to build a seasonal prediction system of the atmospheric circulation over the Saudi Arabian peninsula. Viswanadhapalli, Y., Dasari, H. P., Langodan, S., Challa, V. S. & Hoteit, I. Climatic features of the Red Sea from a regional assimilative model. International Journal of Climatology 37, 2563– 2581 (2017).

K AUST DISCOVERY

di sc o ver y.kaust.edu.sa

63


charge. However, this agility is compromised when researchers try to shrink skyrmions to the smallest size possible— the smaller they get the more likely they are to get pinned because of the relative increase in defect site dimensions. To improve these devices, Manchon and international collaborators tried to understand the fundamental momentum transfer between charge currents and magnetic whirlpools. Using intense X-rays generated at Berkeley University’s Advanced Light Source, the team captured timeresolved images of whirlpool patterns called magnetic vortices as they gyrated along a nanometer-wide half-ring track. By pinpointing the position of the vortex core from the imaging sequence, they obtained accurate data about a parameter, known as the nonadiabatic spin-transfer torque, which is crucial for electrical manipulations. Surprisingly, the measured non-adiabatic torque was far greater than values predicted by existing models. To account for this discrepancy, a theoretical analysis by Manchon showed the extra twisting was provided by another force—the emergent Hall effect, which occurs when electrons travel through a magnetic whirlpool. “In a nutshell, electrons experience a force that pushes them sideways, but it doesn’t come from the local magnetization itself; instead it arises from the topology of the magnetic texture,” explained Manchon. “This effect produces an extra spin-polarized current that exerts a torque on the whirlpool.” The researchers found that the additional non-adiabatic torque intensifies when the size of the whirlpool is reduced—a driving force that may offer a way to overcome defect pinning at the nanoscale. “This might be an interesting compromise to seek, especially in the context of skyrmion-based data storage,” added Manchon. The torque needed to manipulate nanoscale magnetic whirlpools, represented here as red and blue regions with opposite signs, have now been revealed with high-powered synchrotron light. The arrow shows the direction of motion.

INFORMATION STORAGE WITH A NANOSCALE TWIST Discovery of a novel rotational force inside magnetic vortices makes it easier to design ultrahigh capacity disk drives. Swirling objects known as magnetic vortices and skyrmions can be miniaturized without sacrificing mobility, a KAUST-led international research team has found. These findings are relevant for future “race-track” memory technologies that feature massive densities of moveable magnetic bits. In nanometer-thin magnetic films, such as iron-nickel alloys, the region separating two magnetic domains or defects can adopt tiny whirlpool-like patterns. Some of these patterns, called skyrmions, resist unraveling even when packed tightly together, and they can also be directed with small electric currents. These features have made the skyrmions attractive targets for research into high-capacity memory devices. One concept zips skyrmions around a loop then past a stationary read/ write head to eliminate the need for mechanical components used in today’s hard drives. Aurelien Manchon, an Associate Professor of Material Science and Engineering at the University, notes that one of the main reasons for the appeal of skyrmions is their ability to avoid defects or uneven patches in thin films that would normally trap or “pin” a magnetic

64

AUGUST 2 017

“This effect produces an extra spinpolarized current that exerts a torque on the whirlpool.”

Bisig, A., Akosa, C. A., Moon, J.-H.,... & Manchon, A. Enhanced non-adiabaticity in vortex cores due to the emergent Hall effect. Physical Review Letters 117, 277203 (2016).

AMR RAHMA / PARTNERSHIPS & CUSTOM MEDIA NATURE RESEARCH

P S E

“I’m in an environment where I have the support and associated freedom that’s needed to focus on big ideas. This scientific independence has helped my research gain momentum and fosters fresh perspectives in my fundamental research.”

Associate Professor Ying Wu 2017 Phononics Young Investigator Read more about KAUST publications at DISCOVERY.KAUST.EDU.SA

Ying works on the development of innovative models and computational tools to describe wave propagation in complex systems. Her contributions to effective medium theories and her published work on phononic crystals and metamaterials continue to gain global attention. Overall, faculty who join KAUST experience a significant increase in scientific journal publications and, according to the 2018 QS World University Rankings, KAUST is #1 in the world on the Citations per Faculty indicator.


“I’ve always been a curious and passionate person and at KAUST I am surrounded by like-minded engineers and scientists. From furthering my research to organizing the first TEDxKAUST university event and participating in the annual Winter Enrichment Program, I get to continuously explore and embrace new possibilities.”

Mireille Hantouche Ph.D. student, Mechanical Engineering Learn more about what it’s like to be a KAUST student at WWW.KAUST.EDU.SA

Beyond her research on uncertainty quantification in chemical kinetic models, Mireille takes advantage of many programs and activities at KAUST that foster expansive thinking. Studying at KAUST in a diverse and global community provides a holistic graduate experience that extends beyond the classroom and into distinctive academic, cultural and recreational experiences.

KAUST Discovery - Issue 4  

From curiosity to innovation

Read more
Read more
Similar to
Popular now
Just for you