__MAIN_TEXT__
feature-image

Page 1

TAKE OUR SURVEY P.3 ISSUE 6 / AUGUST 2018

from curiosity to innovation

P OIN T PAT T ER N S T O HEL P PR EDIC T L A ND SL IDE S R A INFA L L S IMUL AT ION S IN S TAT I S T IC A L MODE L S C OUL D A L L O W A C C UR AT E P R E DIC T ION OF D A NG E ROU S L A ND S L IDE S P.8

I N N O VAT I O N T O I M PA C T SCIENCE FOR SOCIETY

D I S C O V E R Y . K A U S T . E D U . S A A U G U S T

Michele De Bastiani Postdoc

2 0 1 8

Learn more KSC.KAUST.EDU.SA

/

In the KAUST Solar Center, material and chemical scientists and engineers collaborate to optimize efficiency, realize conversion and ultimately scale-up solar-energy-derived electricity generation.

P. 3 1

S OL A R ENERGY TA PPED F OR CL E A N WAT ER

A L IGH T T OUCH F OR R E V E A L ING AT OMIC F R A ME W OR K S

A 3D S OL A R -S T E A M G E NE R AT OR DE S IG N S Q UE E Z E S E V E R Y L A S T DROP OF E NE RG Y F ROM S UNL IG H T T O P RODUC E F R E S H WAT E R P.41

M AT E R I A L S T H AT NOR M A L LY BE C OME D A M A G E D IN S IDE E L E C T R ON MIC RO S C OP E S C A N NO W BE IM A G E D W I T H AT OM S C A L E R E S OL U T ION P.56


The Visual Computing Center at KAUST is an interdisciplinary hub for visual computing research. Topics in the Center range from civil engineering to computational mathematics with applications ranging from smart-city planning to the development of new display and sensing technologies. This 360-degree panoramic camera captures multiple views simultaneously and stiches them together to create a 360-degree image or video.

Learn more VCC.KAUST.EDU.SA


EDITOR’S NOTE Dear Reader, KAUST strives to enhance the welfare of society with a special focus on four areas of global significance – food, water, energy and environment. At the start of our 10th year of operation, we take this opportunity to reflect on our progress toward achieving our primary mission of being a catalyst for innovation, economic development and social prosperity in Saudi Arabia and the world. The stories in this issue of KAUST Discovery demonstrate the hard work KAUST researchers have already done in just nine short years to improve lives in Saudi Arabia and beyond. An example of translational science related to the food-water-energy nexus is KAUST’s interdisciplinary research on using renewable energy for water desalination, which is featured in our infographic. Desalination is an energy-intensive process that consumes a significant portion of Saudi Arabia’s energy supply. Because a growing number of countries, like Saudi Arabia, now depend on desalination for both agriculture and drinking water, renewable-powered desalination is a global solution to a global challenge. At KAUST, we have a unique facility with state-of-the-art equipment called the Core Labs. Evidence of the great contributions that the experts who operate these facilities make to KAUST research is the publication of a paper in the journal Science co-authored by Core Lab scientists and Professor of Chemical Science Yu Han along with several members from his lab. The team successfully visualized the delicate structures of previously unobservable molecules in materials at atomic-level resolution, opening up new opportunities to study their structures and understand their functions. Look no further for innovation with potential for societal impact than to

Assistant Professor of Statistics Raphaël Huser’s statistical model for predicting not only where but also how many landslides might occur in a given area depending on climatic circumstances. The model has the potential to allow authorities to take better preventative actions and evacuate people to safer ground, thereby saving lives. Researchers at KAUST are aiming to optimize solar energy with cutting-edge technology and novel ideas. Read about how Associate Professor Peng Wang is achieving near-100-percent energy efficiency using a 3D solar-steam generator that could be used to treat wastewater that can then be used for agriculture.

“A s w e e n t e r i n t o o u r 1 0 t h y e a r, i t i s t i m e t o reflect on our mission to make an impact on the global challenges related t o f o o d , w a t e r, e n e r g y a n d e n v i r o n m e n t .” I hope that you enjoy this issue of KAUST Discovery magazine and that you will share it with your friends and colleagues. On the following page, you will find a QR code, which when scanned with your phone, will direct you to an online survey about the magazine. Your feedback on this survey will help us as we plan future issues. Thank you, Carolyn Unck Managing Editor K AUST DISCOVERY

d isc o ve r y. k a u st. e d u .s a

1


A key goal of the Clean Combustion Research Center is to develop simple, cost-effective processes for supplying clean energy by combustion, partial oxidation or other means relying on chemical energy conversion. This system is a transparent piston in an optical engine that can be used to visualize a flame entering an engine during combustion.

Learn more CCRC.KAUST.EDU.SA


CONTENTS / AUGUST 2018

EDITORIAL COMMITTEE Pierre Magistretti Dean, Biological and Environmental Science and Engineering Division

12

Mootaz Elnozahy Dean, Computer, Electrical and Mathematical Sciences and Engineering Division Magnus Rueping Professor, Chemical Science Physical Science and Engineering Division MANAGING EDITOR Carolyn Unck EDITORIAL TEAM Carmen Denman Alma Hobson ILLUSTRATIONS AND PHOTOGRAPHY Helmy Alsagaff Heno Huang Anastasia Khrenova Xavier Pita KAUST DISCOVERY is published for the King Abdullah University of Science and Technology (KAUST) by the Partnership and Custom Media Unit of Nature Research, part of Springer Nature. King Abdullah University of Science and Technology (KAUST) Thuwal 239556900 – Kingdom of Saudi Arabia Email: discovery@kaust.edu.sa

EARTH, GROUND AND UNDERGROUND 7 BACTERIAL SUPERHEROES MAY SAVE THE DAY FOR CROPS

8 POINT PATTERNS HELP TO PREDICT LANDSLIDES

11 A SEISMIC SHIFT IN OIL EXPLORATION

12 ROCKING THE CRADLE OF HUMANKIND

Genetic analyses of a desert bacterium show it could help to improve crop production in arid lands.

Advanced analysis of seismic data could lead the next wave in oil exploration.

Rainfall simulations in statistical models could allow accurate prediction of dangerous landslides.

10 UNDER PRESSURE— MODELING HUMANINDUCED EARTHQUAKES

A model incorporating the physics of ruptures provides valuable information about human-induced earthquakes.

Geophysical modeling of one of the world’s most important fossil sites reveals the history of the site where early humankind evolved.

CLIMATE AND ADAPTATION Published by Nature Research Custom Media, part of Springer Nature for King Abdullah University of Science and Technology (KAUST).

15 ANCIENT JUMPING GENES MAY GIVE CORALS A NEW LEASE ON LIFE

16 LATER TROPICAL BLOOMS COULD AFFECT MARINE LIFE

19 FINDING NEMO’S GENES: REEF FISH GENOME MAPPED AND SHARED

20 REVEALING HIDDEN RELATIONSHIPS IN DATA

Jumping genes could make an alga, and its coral host, more tolerant to warming sea temperatures.

Tell us what you think! Please complete this online survey

Nemo’s genome has been deciphered and made publicly available, helping researchers further investigate fish ecology and evolution.

Color changes in the northern Red Sea indicate rising sea temperatures could significantly impact tropical marine ecosystems.

18 HIGH SALINITY PROTECTS CORALS FROM HEAT STRESS

Corals living in highly saline waters may be more tolerant to rising water temperatures.

A method to visualize hidden statistical structure helps make sense of environmental data.

K AUST DISCOVERY

d isc o ve r y. k a u st. e d u .s a

3


CONTENTS / AUGUST 2018

ENERGY AND INNOVATION 23 SHAPE-SHIFTERS SOAK UP SUNSHINE

Photosensitive perovskites change shape when exposed to light.

24 ROUND-THECLOCK POWER FROM SMART BOWTIES

Innovative diode design uses ultrafast quantum tunneling to harvest infrared energy from the environment.

26 POWERING THE BOTTOM LINE

A risk-based optimization scheme boosts confidence and profitability for future mixedtechnology power plants.

28 SUSTAINABILITY HINGES ON WATER AND ENERGY USE A plant scientist, a water specialist and a petroleum engineer walk onto a panel, “how do you define sustainability?” one asks.

30 LAYERED OXIDES FOR RECHARGEABLE ZINC BATTERIES

A technique of microwave synthesis of layered oxides enables highcapacity aqueous zinc-ion batteries.

36

The availability of high-resolution data collected by miniaturized satellites heralds a turning point in Earth and environmental sensing from space.

38 MARINE EXPLORATION SENSING WITH LIGHT AND SOUND Unveiling new strategies to improve future wireless underwater sensing networks for marine research and communication.

39 SUPER-ADSORBENT MOF TO CONTROL HUMIDITY A metal-organic framework that can take up twice its weight in water and then release it when humidity falls.

40 GRIME DOES PAY WHEN IT COMES TO WASTEWATER FILTERS

A grimy layer on wastewater filters could slow the spread of antibiotic resistance.

FEATURE 31 FROM INNOVATION TO IMPACT

Establishing sustainable desert agriculture may be the solution for growing twice as much food to feed 9 billion people by the year 2050.

WATER EXPLORATION 36 NEW EYES IN THE SKIES The availability of high-resolution data collected by miniaturized satellites heralds a turning point in Earth and environmental sensing from space.

4

A u g u s t 2 0 18

41 SOLAR ENERGY TAPPED FOR CLEAN WATER

A 3D solar steam generator design squeezes every last drop of energy from sunlight to produce fresh water.

CHEMISTRY AND MATERIALS 43 FLEXING FOR THE NEXT SILICON WAVE

Ultrathin, rigid silicon segments that are wired through interdigitated metal contacts produce ultraflexible high-performance solar cells.

43 CLEANING NANOWIRES TO GET OUT MORE LIGHT A simple chemical surface treatment improves the performance of nanowire ultraviolet light-emitting diodes.

44 TAKING CONTROL AT THE JUNCTION

Fine tuning the composition of nitride alloys can further the development of optical and electronic interface devices.

45 SOMETHING IN THE AIR Synchrotron study reveals oxygen’s influence on the chemistry that surrounds us.

46 SURFACE ENGINEERING GETS THE RED LIGHT

Perovskite particles could improve the performance of solar cells and light-emitting diodes via a simple process to stabilize the nanocrystal surface.

47 THE UNIVERSAL TRUTH ABOUT STICKY SURFACES

Trapping molecules on customdesigned porous surfaces becomes easier with a new model that unifies previous theories of adsorption.

ABOUT THE COVER

Hollow-fiber membrane used to treat wastewater. It performs ultrafiltration, meaning that it removes all bacteria and most viruses. If you would like to update your information, send us an email at discovery@kaust.edu.sa


CONTENTS / AUGUST 2018

High-speed communication systems based on ultraviolet radiation are now in sight.

50 SCIENCE VISUALIZED 49 DNA IMAGING MADE EASY

New method offers efficient and high-throughput way to study the structure of DNA.

50 UNLEASHING ULTRAVIOLET BRINGS VISIBLE IMPROVEMENT

51 LOW PRESSURE REDUCES BUBBLE TROUBLE

52 GIANT AIR POCKETS WIN THE DRAG RACE

54 MAPPING MOVEMENTS OF OCEAN CREATURES GREAT AND SMALL

56 A LIGHT TOUCH FOR REVEALING ATOMIC FRAMEWORKS

57 PUTTING SOME SKIN IN THE TURBULENCE GAME

63 NOT JUST A STEM CELL MARKER

63 ZOOMING IN ON BRAIN FUNCTION

High-speed communication systems based on ultraviolet radiation are now in sight.

53 MIMICKING A SWEET SOLUTION TO MOP UP POLLUTION

A fast and safe method to prepare a 3D porous material that mimics the shape of a honeycomb could have broad applications from catalysis to drug delivery or for filtering air to remove pollutants or viruses.

Big data shows that large marine vertebrates move differently, but consistently, through coastal and ocean waters.

Spray coating and inkjet-based electronics manufacture are among the industrial applications in which liquid droplets are applied to a surface. But minuscule air bubbles that get trapped beneath the droplet can affect the coating’s quality.

Materials that normally become damaged inside electron microscopes can now be imaged with atom-scale resolution.

Creating teardrop-like gas cavities around metal spheres enables practically frictionfree travel through liquids.

Theoretical simulations reveal how subtle changes in friction on an object’s surface can have a large effect on drag.

HEALTH AND GENETICS 59 A DELIVERY PLATFORM FOR GENE-EDITING TECHNOLOGY

Nanomaterial coating enables efficient delivery of CRISPR-Cas9 machinery into the cell.

60 COMPUTER MODELS COMBAT MALARIA

A new malaria metabolic model may uncover better ways to treat a highly deadly disease.

The protein CD34 is predominantly regarded as a marker of bloodforming stem cells but it helps with migration to the bone marrow too.

Faster computations will allow researchers to see the finer details of brain activity in functional brain imaging.

K AUST DISCOVERY

d isc o ve r y. k a u st. e d u .s a

5


From adaptive optics in huge telescopes to likelihood estimation in big data, experts in the Extreme Computing Research Center use linear algebra operations for their core of discovery. They create software for emerging power-efficient, memoryand bandwidth-limited computer architectures to keep KAUST investigators and their worldwide partners at peak computational performance.

Learn more ECRC.KAUST.EDU.SA


EARTH, GROUND AND UNDERGROUND

BACTERIAL SUPERHEROES MAY SAVE THE DAY FOR CROPS

Genetic analyses of a desert bacterium show it could help to improve crop production in arid lands. B E S E The bacterium SA187 has been isolated from the root nodules of an indigenous desert plant that grows in Saudi Arabia. The research team found it has many genes that promote plant growth in stressful environments. Their finding is part of a KAUST project called DARWIN21, which aims to explore the microbial diversity of desert plants and examine their potential

Heribert Hirt (left) and Maged Saad lead the DARWIN21 project, which aims to find bacteria that can help crops become resistant to abiotic stresses that reduce crop productivity.

for use in improving agricultural sustainability in drylands and marginal areas. “We were surprised to find tens of bacteria from completely different taxa that are able to help a variety of plants grow better under abiotic stress conditions,” says plant scientist Heribert Hirt. The UN Food and Agriculture Organization estimates farmers will need to produce 70 percent more food by 2050 to meet the needs of the world’s growing population. At the same time, 70 percent of global annual food production is lost due to challenges from various biotic (pathogens, insects, herbivores) and abiotic (drought, heat, cold) factors, explains Hirt. Crops need to be more stress resistant, but genetic engineering and crop breeding technologies take a long time to develop and they can’t immediately serve the people who need food the most: subsistence farmers who eat what they farm. “So we need fast and low-cost solutions that are affordable and accessible to everyone on the planet,” says Hirt. The DARWIN21 project aims to find bacteria that can help crops become resistant to the most prominent abiotic stresses that are responsible for 60 percent of the

K AUST DISCOVERY

d isc o ve r y. k a u st. e d u .s a

7


EARTH, GROUND AND UNDERGROUND

loss in crop productivity, he says. The researchers treated five-day-old seedlings of a small flowering plant called Arabidopsis thaliana with the bacterium SA187. The plants were then grown in conditions that tested their tolerance to drought, heat and salt stresses. Plants treated with SA187 grew better than those not treated with the bacterium. Analyses also showed that SA187 can adapt to diverse and harsh environments; colonize plants and modulate their hormone production, thus promoting growth; and produce enzymes that protect the plant against pathogenic bacteria, insects and fungi. Significantly, the team compared the genome of SA187 with that of other bacteria and found that it could be a new genus that belongs to the Enterobacteriaceae family of bacteria. Further investigations are required, however, to fully characterize its taxonomic position. The team was able to analyze the bacterium’s genome in detail and to assess the likely functions of many of its genes using KAUST’s computational pipeline, Automatic Annotation of Microbial/Meta Genomes, says bioinformatician Intikhab Alam of the University’s Computational Bioscience Research Center. Identified genes were added to the INtegrated Database of microbial/meta GenOmes (INDIGO) to provide an easy-to-use platform for biologists to further explore these genes. Maged Saad, a research scientist with the team, has developed an application that coats plant seeds with the bacteria before they are sown. This gives the bacteria a competitive advantage to establish on the plant before it is exposed to other bacteria in the soil. Four of Hirt’s students are now establishing a nonprofit company to distribute SA187 to poor subsistence farmers in various parts of the world. “We hope that by increasing the harvest of these farmers, they will be able to buy essential tools, such as tractors, to improve their production and make a sustainable living,” says Hirt. Andres-Barrao, C., Lafi, F.F., Alam, I., de Zelicourt, A., Eida, A.A., Bokhari, A., Alzubaidy, H., Bajic., V.B., Hirt, H. & Saad, M.M. Complete genome sequence analysis of Enterobacter

POINT PATTERNS HELP TO PREDICT LANDSLIDES Rainfall simulations in statistical models could allow accurate prediction of dangerous landslides.

sp. SA187, a plant multi-stress tolerance promoting endophytic bacterium. Frontiers in Microbiology 8, 2023 (2017).

C E M S E Examining the details of a natural disaster in Italy in 2009 has helped researchers develop a statistical model that could help predict landslides in specific areas under given storm scenarios. Existing landslide susceptibility models use a presence-absence structure to predict whether a landslide is likely within a given area. These binary models, however, are unable to predict vital

8

A u g u s t 2 0 18


EARTH, GROUND AND UNDERGROUND

the landscape before and after the storm. However, they did not have complete data regarding the landslide trigger — the rainfall event — because there was only one weather station in the storm zone.

“M e t h o d o l o g y enables the model to predict not only where, but also h o w m a n y, landslides m a y o c c u r.” “Scientists simply do not have the instrumentation in place to measure every natural disaster in depth,” says LomNatural disasters disrupt important services, such as road access and public transport. bardo. “However, we realized that the data could talk to us information, such as how many landslides might occur on any and help us reconstruct the storm. We knew where the worst, specific slope. repeated landslides had occurred, and logic suggests that these Luigi Lombardo, and his supervisor Raphaël Huser, at KAUST, points were the areas hit by the most rainfall.” with Thomas Opitz at INRA in France, developed a statistical “We included a latent spatial effect in our statistical model to model that exploits the rigorous probabilistic framework of point flexibly capture and reconstruct the evolution of the storm”, says processes. This describes the behavior of random point patterns, Huser. “This latent spatial effect, combined with other variables, such as landslide-triggering locations. such as slope steepness, soil type and vegetation cover, yielded an Their statistical methodology enables the model to predict not unprecedented prediction accuracy.” only where, but also how many, landslides may occur in a given “The benefit of this approach is that we can easily simulate variarea depending on climatic circumstances. ous latent spatial effects, each one with a different pattern, and proThe team used their model to examine data from a 2009 disaster vide a comprehensive set of likely future landslide scenarios as a in Messina, Italy, which followed an intense storm. The model storm evolves,” says Lombardo. “Authorities could then take better generated highly accurate maps of the disaster zone. preventative actions and evacuate people to safer ground. Similar “Following two periods of wet weather, the storm dumped 250 models could be built for other landslide-prone areas in the world.” millimeters of rain on a small area in less than eight hours,” says Lombardo. “The soils on the steep slopes were already saturated, Lombardo, L., Opitz, T. & Huser, R. Point process-based modeling and the deluge resulted in around 5,000 landslides of varying sizes of multiple debris flow landslides using INLA: an application to the across about 100 square kilometers.” 2009 Messina disaster. Stochastic Environmental Research and Risk The team accessed high-resolution satellite images showing Assessment 32, 2179 (2018). K AUST DISCOVERY

d isc o ve r y. k a u st. e d u .s a

9


UNDER PRESSURE— MODELING HUMANINDUCED EARTHQUAKES A model incorporating the physics of ruptures provides valuable information about human-induced earthquakes. P S E Observations of induced earthquakes have inspired researchers to develop a physics-based rupture model to determine the conditions most likely to cause large earthquakes. Potentially hazardous earthquakes can be triggered by human activity, such as extracting oil and gas by fluid-injection or by pumping wastewater into underground reservoirs; however, we have little understanding of the conditions that determine earthquake size and prevent them becoming large and destructive. KAUST postdoc Martin Galis, his supervisor Martin Mai and researchers from Caltech in the United States and Centre National de la Recherché Scientifique in France modeled the physics of earthquake faults. They combined computer modeling, the theory of fracture mechanics,

10

A u g u s t 2 0 18

The researchers modeled various induced earthquake scenarios, such as this one triggered by wastewater injection into a subsurface reservoir layer crossed by a fault. The earthquake rupture grows larger than the zone pressurized by injection.

and observational data to investigate the possible maximum magnitude of induced earthquakes. “We wanted to discover w h i ch f a c tors — su ch a s increased fluid pressure within a reservoir due to injection— play a role in the final size of an earthquake,” says Galis. “To do this, we developed a model to estimate how friction, stress and pressure buildup affect rupturing.”

They were keen to determine the circumstances under which earthquake ruptures would stop naturally or become a dangerous runaway rupture. “A runaway rupture is a self-sustaining rupture that propagates until it stops due to a barrier, such as a low-stress region or a geometrical obstacle,” says Mai. “In contrast, a self-arrested rupture will naturally stop by itself even without

Galis, M., Ampuero, J. P., Mai, P.M., & Cappa, F. Induced seismicity provides insights into why earthquake ruptures stop. Science Advances 3, eaap7528 (2017).

CRONOS / ALAMY STOCK PHOTO 2017 M. GALIS, J.P. AMPUERO, P.M. MAI AND F. CAPPA

Earthquakes cause deaths and injury leaving behind wreckage.

encountering a barrier; these could be considered safer because their size is limited.” Their model shows that as a system is gradually loaded by fluid injection, self-arrested ruptures occur prior to runaway ones. There is a sudden, distinct transition to runaway ruptures that is controlled by the volume of injected fluid, friction levels and the stress on the fault. Interestingly, however, the size of self-arrested ruptures is determined by a product of pore pressure and total pressurized area. Ruptures can also grow beyond the area impacted by fluid pressure. “This means that, while high-pressure injection into a small reservoir may still produce safe self-arrested ruptures, low-pressure injection into a larger reservoir may produce runaway ruptures,” says Galis. “This is consistent with real-world observations; the largest induced earthquakes are linked to low-pressure, large-scale wastewater disposal.” Their results suggest there is no safe universal pressure limit for fluid injection. This has implications for industries using fluid injection because maintaining low pore-pressure alone may not prevent large earthquakes. “Expanding the model to include specific stress patterns, fracture geometry and rock properties may help us to better understand behavior of natural earthquakes,” adds Galis.


EARTH, GROUND AND UNDERGROUND

A SEISMIC SHIFT IN OIL EXPLORATION Advanced analysis of seismic data could lead the next wave in oil exploration. P S E An advanced computational method for processing seismic data developed by KAUST researchers allows the detailed structure of deep oil reservoirs to be imaged at unprecedented resolution, opening new possibilities in the increasingly challenging search for new reserves. Oil exploration is both mysterious and technically challenging. Reserves often occur kilometers underground, with few hints at the surface as to what lies beneath. An important technique used in oil exploration to observe the hidden geological structures that potentially hold trapped oil and gas is the seismic survey. This involves pumping powerful shock waves into the ground and recording the weak sonic vibrations that return to the surface. Seismic surveys are used as a first pass to identify promising structures, which are then drilled to confirm an oil strike. Drilling, however, remains extraordinarily expensive—sometimes tens of millions of dollars per hole—and so the oil

exploration industry relies heavily on relatively inexpensive seismic surveys. The vibrations recorded in a seismic survey hold a surprising amount of information. The outgoing shockwave—generated by a small detonation or heavy vibrating plate—bounces off the boundaries between different rock types and travels at different speeds through the different rock layers. This produces a complex sequence of vibrations at the surface that can reveal basic geological structures. Further analysis of the amplitude and phase of the recorded waveform, known as full waveform inversion, provides another level of structural detail to aid exploration. With much of the Earth’s easily discoverable oil reserves already exploited, and growing costs of Zhen-dong exploration, the search Zhang (left) and for oil is increasingly his supervisor challenging. Tariq Alkhalifah are pioneering The team of Tariq novel approaches A l khalifah and in seismic data processing. do c tora l student

Zhen-dong Zhang have now made a major advancement in seismic data processing that has the potential to redefine the process1,2. “Conventional reservoir characterization methods are mainly based on onedimensional seismic inversion,” says Alkhalifah. “Such methods are stable but rely on assumptions of geological properties and are dependent on the accuracy of the seismic imaging process. Our method, utilizing full waveform inversion, integrates more elaborate additional information to better constrain the results.” Building on full waveform inversion, the team added the capacity to incorporate into the inversion many parameters of the subsurface structure based on geological knowledge and experience or drillhole data. “The key idea is a more complex physics description of the reservoir region with parameterization [additional parameters included] related to fluid content and fracture direction and density,” says Alkhalifah. With the right additional information, the new inversion method is capable of unprecedented structural resolution, resolving critical information like fracture density and orientation—information useful for drilling decisions and horizontal well placements. “Although our method is computationally heavy and puts higher quality requirements on the seismic data, there is a lot of interest in this very hot topic within the oil exploration and production communities,” says Zhang. “With the pace of advancement in computing power, we are well placed to benefit from the expected wave of interest in methods that can provide more accurate descriptions, particularly for fractured reservoirs.” 1. Zhang, Z., Alkhalifah, T. & Naeini, E. Z. Multiparameter elastic full waveform inversion with facies constraints. SEG Technical Program Expanded Abstracts 2017, 15511555 (August 2017). 2. Zhang, Z., Alkhalifah, T., Tsvankin, I. & Oh, J. Estimation of fracture parameters using elastic full-waveform inversion. SEG Technical Program Expanded Abstracts 2017, 3272 - 3276 (2017).

K AUST DISCOVERY

d isc o ve r y. k a u st. e d u .s a

11


Geophysical modeling of one of the world’s most important fossil sites reveals the history of the site where early humankind evolved.

ROCKING THE CRADLE OF HUMANKIND

P S E In the peaceful grasslands of northern Tanzania, a frenzy of research is occurring. The Olduvai area (from the Maasai name “Oldupai” for a native succulent plant) came to fame through the findings of Kenyan archaeologists and paleoanthropologists Louis and Mary Leakey. Their research, beginning in the 1950s, uncovered numerous fossil hominins (the tribe of great apes, including modern humans) and stone tools dating back as far as two million years and earned the area the nickname “cradle of humankind.” Olduvai has since become a hub for those exploring the origins, and future, of humanity. Paleoanthropologists, however, no longer have sole claim here. A full picture of human evolution cannot be gleaned from fossils alone, but relies on understanding their environmental context. To this end, a team of KAUST’s geophysicists are conducting crucial surveys of the site’s geology. Using state-of-the-art techniques developed for oil exploration, Gerard Schuster, Sherif Hanafy and doctoral student Kai Lu, with scientists from Indiana University,

12

A u g u s t 2 0 18

USA, and Liverpool University, UK, are mapping the shape and structure of the Olduvai Basin’s bedrock. This is no mean feat because the basin is 6 kilometers wide and almost half a kilometer deep. It comprises a complex mixture of sedimentary and volcanic rocks, traversed by multiple geological faults. Lying at the heart of the East African Rift Zone, where the tectonic plates making up the Earth’s crust are moving apart, Schuster explains that the basin, “evolved and deepened over time as the ancient lake above it expanded, contracted and shifted laterally in space, partly caused by a sequence of eruptions of neighboring volcanoes.” Rewriting history Two complementary experimental approaches are used: boring wells to extract physical cores of sediment laid down over millions of years and the KAUST team’s seismic imaging studies. Together, they are rewriting the geological history of Olduvai. The seismic experiments are based on a remarkably simple premise: a heavy weight is repeatedly slammed onto the ground, creating vibrations that travel

Local Maasai staff lay out the geophones, a crucial piece of equipment in seismic imaging of the Olduvai Basin.


EARTH, GROUND AND UNDERGROUND

The seismic field crew working in Olduvai Gorge, including Sherif Hanafy (blue shirt, fourth from right) and Kai Lu (red shirt, second from right).

were able to penetrate. This indicates that the bedrock lining the basin may be around 4 million years old and that environments suitable for hominins may be equally ancient: “much older,” says Hanafy, “than previously extrapolated from exposed rocky outcrops.” The base layers of the basin were probably derived from nearby volcanoes, which may have influenced the environment, including water availability, in the distant past. This in turn would have impacted upon early hominids, who needed “water, a favorable climate, trees for protection and open plains for foraging, all of which were provided at Olduvai,” explains Hanafy.

“T h e b e d r o c k l i n i n g t h e

2017 SHERIF HANAFY

basin may be around through it until they are reflected or refracted (bent) as they move from one material to another (in the same way that light reflects off a mirror or bends as it enters water). A series of receivers (known as geophones) are placed just below the ground to monitor these reflected and refracted waves. By recording the time taken for the waves to reach each of the geophones, the team can calculate the speed at which they traveled. In a similar way to ultrasound scanning, these measurements are built into a picture of the subsurface geology, including the basin’s shape and size and the location of buried faultlines. Complex and logistically challenging, the method is intriguing to local people, many of whom are employed on the project. As Hanafy explains, “they are used to working with paleoanthropologists and geologists, but this is the first time they have worked with geophysicists.” The project has inspired some youngsters to develop a potentially life-changing interest in science—with one even traveling to KAUST to study. The results of this research suggest that the Olduvai Basin, once considered shallow, is more than 400 meters deep, almost twice as deep as the boreholes

4 million years old and that environments suitable for hominins may be e q u a l l y a n c i e n t .” A new documentary In Lasting Marks, a celebrated documentary about this work, the University of Liverpool’s Ian Stanistreet argues that seismic imaging helps us understand the entire makeup of Olduvai: geological, climatic and otherwise. The changing climate has proven a challenge to mankind throughout our history: if we can better appreciate this history, we may be moved to alter our trajectory. As the director of Lasting Marks, Sarah Schuster-Johnson, eloquently explains, “the dedicated and passionate Olduvai researchers carefully interpret marks from an undeciphered history, a history that paved the way for our existence and our future on this planet.” K AUST DISCOVERY

d isc o ve r y. k a u st. e d u .s a

13


The Red Sea Research Center aims to establish the role of oceanographic and climate gradients in structuring the Red Sea ecosystem and its vulnerability to change. Members of the Center perform studies to elucidate the structure and function of corals in the Red Sea using species like these polyps of Stylophora pistillata.

Learn more RSRC.KAUST.EDU.SA


2017 JIT ERN CHEN

C L IM ATE A ND A DA P TATION

Symbiodinium microadraticum is a unicellular alga that provides its coral host with photosynthetic products in return for nutrients and shelter.

ANCIENT JUMPING GENES MAY GIVE CORALS A NEW LEASE ON LIFE Jumping genes could make an alga, and its coral host, more tolerant to warming sea temperatures.

B E S E A particular gene is shown by researchers to help the heat tolerance of an alga that lives symbiotically with coral, which could potentially help Red Sea corals adapt to some warming. Symbiodinium is a unicellular alga that provides its coral host with photosynthetic

products in return for nutrients and shelter. However, high sea temperatures can cause the breakdown of this symbiotic relationship and lead to the widespread expulsion of Symbiodinium from host tissues, an event known as coral bleaching. If bleached corals do not recover, they starve to death, leaving only their white, calciumcarbonate exoskeleton. Now, researchers from KAUST have identified special genes, called retrotransposons, which could help the algae adapt more rapidly to heat stress. First authors postdoc Jit Ern Chen and Ph.D. student Guoxin Cui and team, conducted analyses to determine which genes were turned on or off when Symbiodinium was exposed to heat stress. Surprisingly, most genes commonly associated with heat stress were turned off, while a small number of retrotransposons were turned on.

K AUST DISCOVERY

d isc o ve r y. k a u st. e d u .s a

15


C L IM ATE A ND A DA P TATION

Retrotransposons are small genetic sequences that have the ability to replicate and position themselves in new locations in their host’s genome. “The ability of retrotransposons to copy themselves and integrate these new copies into the host genome makes them genetic parasites,” says geneticist and principal investigator Manuel Aranda. “Every integration event is basically a new mutation in the host genome. Very often these new copies disable or disrupt host genes. However, sometimes they can also change how certain genes behave. They are often bad, like most mutations, but some can produce advantageous effects.”

“P r o d u c i n g m o r e mutations increases the chance of generating a b e n e f i c i a l o n e.” Aranda and his team suggest that the activation and replication of Symbiodinium’s retrotransposons in response to heat stress could lead to a faster evolutionary response, “since producing more mutations increases the chance of generating a beneficial one that allows the symbionts to cope better with this specific stress,” Aranda explains. The team next plans to investigate coral genomes to find out if they too have retrotransposons that are activated in response to heat stress. “If they do, it would mean they might be able to genetically adapt faster than we thought,” says Aranda. They also plan to investigate the possibility of “hijacking” the molecular machinery of retrotransposons to engineer more resilient genomes in both Symbiodinium and their coral hosts. Chen, J. E., Cui, G., Wang, X., Liew, Y. J. & Aranda, M. Recent expansion of heatactivated retrotransposons in the coral symbiont Symbiodinium microadriaticum. The ISME Journal 12, 639-643 (2018).

16

A u g u s t 2 0 18

LATER TROPICAL BLOOMS COULD AFFECT MARINE LIFE Color changes in the northern Red Sea indicate rising sea temperatures could significantly impact tropical marine ecosystems. P S E Monitoring phytoplankton abundance could help to identify areas in the oceans that are susceptible to the impacts of climate change, suggest researchers.


C L IM ATE A ND A DA P TATION

Winter seasonal blooms of phytoplankton growth in the northern Red Sea are starting later, lasting for shorter periods, and ending earlier as sea surface temperatures rise. Phytoplankton, microscopic marine plants, are at the bottom of the food chain for many organisms, including humans, so a warming climate is likely to have a significant cascading impact on marine ecosystems and beyond. “Phytoplankton form the base of oceanic food webs and support the growth of many marine organisms, including zooplankton, invertebrates, fish and large mammals, such as whales,” says John Gittings, an oceanography Ph.D. candidate at KAUST. “Phytoplankton are also important

KAUST researchers Ibrahim Hoteit (left) and John Gittings examined ocean color changes collected over nearly two decades in the northern Red Sea.

sequesters of carbon dioxide and help regulate Earth’s temperature. Through photosynthesis, they are also responsible for about 50 percent of the oxygen we breathe.” Researchers examined ocean color changes over an 18-year period (1998 to 2015) in the northern Red Sea. The data comes from European Space Agency satellite sensors that detect phytoplankton absorption of light for the process of photosynthesis. The team charted this data over time and compared it to temperature changes at the sea’s surface and within its deeper layers using computer simulations they had developed for the Red Sea. They found that when the winters were warmer there was a rise in sea surface temperatures, leading to a decrease in heat exchange between the sea and the atmosphere. This, in turn, reduced mixing of deeper nutrient-loaded water with the more superficial layers of water where the phytoplankton live. Changes in nutrient availability for phytoplankton means that their winter seasonal growth spurts are later and shorter. The northern area of the Red Sea is unique and differs from the more southern parts: its phytoplankton dynamics, and thus ecosystem, are more similar to other tropical ocean masses. This means it can serve as a model ecosystem for other tropical marine ecosystems, explains Gittings. The study foreshadows changes regarding when and how much phytoplankton is available in the tropics for marine larvae feeding, explains earth modeling expert Ibrahim Hoteit. “Combining our results with similar studies that looked at the effects of less phytoplankton and altered bloom timing on higher levels of the food chain may give clues to how the ecosystem responds and how humans may be affected,” he says. Studies have shown that a shift in bloom timing in the tropics by just a few weeks can decrease the survival rates of small zooplankton and fish. Also, phytoplankton abundance is linked to the survival of fish larvae on tropical coral reefs. “Commercially important species may be affected, ultimately impacting human populations that depend on coastal fisheries as an important source of protein,” Hoteit adds. The team plans to further investigate the mechanisms contributing to the formation and maintenance of phytoplankton blooms, and how these might change within different climate change scenarios. Gittings, J. A., Raitsos, D. E., Krokos, G. & Hoteit, I. Impacts of warming on phytoplankton abundance and phenology in a typical tropical marine ecosystem. Scientific Reports 8, 2240 (2018).

K AUST DISCOVERY

d isc o ve r y. k a u st. e d u .s a

17


HIGH SALINITY PROTECTS CORALS FROM HEAT STRESS Corals living in highly saline waters may be more tolerant to rising water temperatures.

B E S E Scientists have long suspected that corals living in very salty water can also tolerate higher water temperatures, but the link has never been verified. Now, KAUST researchers have shown that salinity directly influences the ability of the sea anemone Aiptasia, a model for coral, to cope in warmer water and may have identified the compound that helps this process. “We, like others, had observed that corals from highly saline waters like the Red Sea can tolerate high water temperatures, but no one had systematically analyzed this,” says Ph.D. student Hagen Gegner, who worked on the project with his supervisor Christian Voolstra and colleagues. “We conducted heat stress experiments to determine the effects of different salinity levels on two Aiptasia strains and their associated symbionts, strains of the dinoflagellate algae Symbiodinium.” The sea anemone Aiptasia is closely related to reef-building corals, and it is regularly used as a model organism for corals because it is easier, cheaper and quicker to grow than corals themselves. The researchers chose two Aiptasia strains, H2 and CC7, each of which hosts a

18

A u g u s t 2 0 18

Systematic experiments on a species of sea anemone indicates that increased salinity promotes thermotolerance in the presence of specific symbionts. The findings hold implications for the impact of climate change on coral reefs.

different Symbiodinium strain. When corals and anemones are under heat stress, they respond by expelling their symbionts in a process called bleaching, which can kill corals if stresses persist. The team reared Aiptasia anemones at a constant temperature of 25 degrees Celsius before transferring them into low-, medium- and high-salinity tanks. Each tank was then heated to 34 degrees Celsius and maintained at the higher temperature. They measured Symbiodinium levels at the beginning of the experiment and again once bleaching had occurred. “For one of the anemones y mbi ont c ombi nat i ons , the severity of bleaching was significantly reduced as

salinity increased,” says Gegner. “Although both combinations lost Symbiodinium at all salinity levels, more were retained by Aiptasia H2. This also coincided with limited damage to the animal’s photosynthetic efficiency.” A previous study led by Voolstra showed that a compound found in corals called floridoside is increased, or upregulated, under high-salinity conditions. Floridoside is an antioxidant that also regulates osmotic pressure within the animal. This means it may counter the stress-induced overproduction of toxic reactive oxygen species within cells and help prevent severe bleaching. “We know thermotolerance is increased at high salinity for certain host-symbiont

2018 HAGEN M. GEGNER

C L IM ATE A ND A DA P TATION


C L IM ATE A ND A DA P TATION

“T h e r m o t o l erance is increased at high salinity for certain host-symbiont relat i o n s h i p s .”

Gegner, H.M., Ziegler, M., Rädecker, N., Buitrago-López, C., Aranda, M., & Voolstra, C.R. High salinity conveys thermotolerance in the coral model Aiptasia. Biology Open 6, 1943-1948 (2017).

Orange clownfish, Amphiprion percula, live among sea anemones, providing them with oxygen and nutrients while gaining shelter from predators.

FINDING NEMO’S GENES:

REEF FISH GENOME MAPPED AND SHARED

Nemo’s genome has been deciphered and made publicly available, helping researchers further investigate fish ecology and evolution. B E S E The genome of the orange clownfish, immortalized in the film Finding Nemo, has been deciphered, giving researchers the most detailed information so far on reef fish genomics. “The nemo genome is composed of 24 chromosomes. We were able to sequence about 97 percent of the underlying genome sequence and then place about 98 percent of that sequence into the 24 chromosomes of the species,” says computational biologist, Robert Lehmann. “By any measure, that is a remarkable effort and represents a very complete genome assembly.” KAUST researchers have made their data available to the scientific community on http://nemogenome.org ahead of the journal publication of their results. The orange clownfish, Amphiprion percula, is a mainstay of marine biology research: it is used as a model species to answer questions related to social organization, sex change, habitat selection,

predator-prey interactions and the effects of climate change and ocean acidification on fish. Availability of this genome assembly as a community resource will help researchers more deeply understand ecology and evolution of reef fish. The team used state-of-the-art technology to sequence the orange clownfish genome. “We began by using single-molecule real-time (SMRT) sequencing, a technology that has only recently become affordable to most research groups,” says co-author Damien Lightfoot, a molecular biologist on the team. Traditionally, genome sequencing is performed by reading many short stretches of a genome followed by deciphering and re-assembling these small pieces. The smaller the pieces, however, the more difficult it becomes to put them back together in the right order. SMRT sequencing differs from standard methods by producing relatively long reads of the DNA. Using bioinformatics programs and the resources of KAUST’s Supercomputing

K AUST DISCOVERY

d isc o ve r y. k a u st. e d u .s a

19

2017 TANE SINCLAIR-TAYLOR

relationships and that floridoside is abundantly present at high salinity,” says Gegner. “Now we need to determine if floridoside is the molecule that confers thermotolerance w it hin sp e cific host-symbiont relationships. We also need to conduct experiments in actual corals to understand how this might affect both individual corals and reef ecosystems.”


C L IM ATE A ND A DA P TATION

Core Lab and expertise from the third-generation sequencing team in the Bioscience Core Lab, Lehmann and the team rebuilt the DNA pieces into even longer ones—averaging 639 thousand nucleotides in length. Because the orange clownfish genome comprises approximately 939 million nucleotides, the team used another method to determine the likelihood that different pieces of the genome belonged next to each other. “By doing this, we were able to put the pieces together to assemble nearly complete chromosomes,” says Lehmann.

“M o s t d e t a i l e d information so far on reef fish g e n o m i c s .” The team assessed the completeness of their genome assembly by comparing it to the high-quality genome assemblies of 26 other fish species. The completeness of the orange clownfish genome was only surpassed by that of the Nile tilapia. Interestingly, the three most complete fish genome assemblies currently available are those achieved by SMRT sequencing. The team is currently sequencing the genomes of other reef fish species and planning to compare them to answer questions about how genome structure and evolution relate to differences in fish traits, such as their responses to climate change. Lehmann, R., Lightfoot, D.J., Schunter, C. Michell, C.T., Ohyanagi, H., Mineta, K., Foret, S., Berumen, M., Miller, D.J., Aranda, M., GojoBori, T., Munday, P.L. & Ravasi, T. Finding Nemo’s Genes: A chromosome-scale reference assembly of the genome of the orange clownfish Amphiprion percula. biorxiv preprint published 8 March 2018.

REVEALING HIDDEN RELATIONSHIPS IN DATA A method to visualize hidden statistical structure helps make sense of environmental data. C E M S E Prediction of climate and weather relies on statistical models that can capture variability at one location over time as well as the relationship

20

A u g u s t 2 0 18

with other geographical locations. Sometimes future conditions at one location can be predicted from the current conditions at another location, while in other cases there may be no such correlation. The


C L IM ATE A ND A DA P TATION

Huang Huang (left) and Ying Sun have developed a method for visualizing the spatio-temporal covariance properties of a dataset, which will help make sense of environmental data.

assumption of whether two sites are covariant in one way or another can have profound implications for the accuracy of the statistical model, and so the choice of space-time covariance is crucial. Ying Sun and her student Huang Huang from KAUST have now developed a method for visualizing the spatio-temporal covariance properties of a dataset, greatly simplifying

an important modeling step that previously demanded painstaking exploratory data analysis. “We propose an easy and convenient way to visualize the properties of the covariance structure in the data, which will help practitioners choose appropriate statistical models for covariances,” says Sun. “In particular, this method is useful for data that are observed sparse in space and dense

in time, which is often the case for observations from weather stations, for example.” Sun and Huang considered two key types of covariance—symmetry and separability. Symmetry implies that the spatial-temporal processes are reversible in time, while separability indicates that the correlation in time does not interact with that in space. “Assuming a fully symmetric or a separable covariance leads to a much simpler model and thus fast computations,” says Sun. “However, this model assumption may be violated in many real applications, leading to less accurate estimation and prediction.” Huang and Sun used a functional data analysis approach to construct test functions from the covariances in time series data between location pairs. These test functions effectively summarize the properties of separability or symmetry and can be displayed as boxplots that show the degree of nonseparability or asymmetry. “We applied this approach to meteorological observations and simulated weather data from some commonly used climate models,” says Huang. “In the reported examples for a study area in the North Atlantic Ocean, this method showed that wind speed and surface temperature have different covariance structures in different seasons.” The visualization can be computed relatively quickly for a handful of monitoring stations, and the researchers note that the computational efficiency can be improved for larger numbers of stations by dividing the problem into subregions. Nevertheless, the method provides a valuable tool that will greatly assist practitioners. Huang, H. & Sun, Y. Visualization and assessment of spatio-temporal covariance properties. Spatial Statistics (2017).

K AUST DISCOVERY

d isc o ve r y. k a u st. e d u .s a

21


The main objective of the chemical scientists in the KAUST Catalysis Center is to make a global impact by developing the catalytic processes of the future, including sustainable, carbon-free energy sources and optimized use of fossil fuel resources, minerals and water. An Avantium high-throughput reactor is used to develop new catalysts for converting CO2.

Learn more KCC.KAUST.EDU.SA

Irina Yarulina Postdoc


ENERGY A ND INNOVATION

SHAPE-SHIFTERS SOAK UP SUNSHINE Photosensitive perovskites change shape when exposed to light. C E M S E A crystalline material that changes shape in response to light could form the heart of novel light-activated devices. Perovskite cr yst als have received a lot of attention for their efficiency at converting sunlight into electricity, but new work by scientists at KAUST shows their potential uses extend far beyond the lightharvesting layer of solar panels. Photostriction is the property of certain materials to undergo a change in internal strain, and therefore shape, with exposure to light. Organic photostrictive materials offer the greatest shape change so far reported in response to light—a parameter known as their photostrictive coefficient—but their response is slow and unstable under ambient conditions. The perovskite material changes size when exposed to light.

Electrical engineer Jr-Hau He and his colleagues have looked for photostriction in a new family of materials, the perovskites. “Perovskites are one of the hottest optical materials,” says He. His work now shows there’s more to their interesting optical properties than solar energy harvesting. The researchers tested a perovskite called MAPbBr3 and revealed it had strong and robust photostriction behavior. To extensively test the material’s photostriction capabilities, the team developed a new method. They used Raman spectroscopy, which probes the molecular vibrations within the structure. When bathed in light, photostriction alters the internal strain in the material, which then shifts the internal pattern of vibrations. By measuring the shift in the Raman signal when the material was placed under mechanical pressure, the team could calibrate the technique

“T h e r o b u s t and stable photostriction of perovskites m a ke s t h e m useful for a ra n g e o f possible d ev i c e s .”

and so use it to quantify the effect of photostriction. “We demonstrated that in situ Raman spectroscopy with confocal microscopy is a powerful characterization tool for conveniently measuring intrinsic photoinduced lattice deformation,” says Tzu-Chiao Wei, a member of the team. “The same approach could be applied to measure photostriction in other materials,” he adds. The perovskite material proved to have a significant photostriction coefficient of 1.25 percent. The researchers also showed that the perovskite’s photostriction was partly due to the photovoltaic effect—the phenomenon at the heart of most solar cell operation. The spontaneous generation of positive and negative charges when the perovskite is bathed in light polarizes the material, which induces a movement in the ions the material is made from. The robust and stable photostriction of perovskites makes them useful for a range of possible devices, says Wei. “We will use this material to fabricate next-generation optoelectronic devices, including wireless remote switchable devices and other light-controlled applications,” he says. Wei, T.-C., Wang, H.- P., Li, T.-Y. & He, J.-H. Photostriction of CH3NH3PbBr3 perovskite crystals. Advanced Materials 29, 1701789 (2018).

K AUST DISCOVERY

d isc o ve r y. k a u st. e d u .s a

23


ROUNDTHE-CLOCK POWER FROM SMART BOWTIES

Innovative diode design uses ultrafast quantum tunneling to harvest infrared energy from the environment.

24

A u g u s t 2 0 18

C E M S E Most sunlight striking the Earth is absorbed by its surfaces, oceans and atmosphere. As a result of this warming, infrared radiation is emitted constantly all around us—estimated to be millions of gigawatts per second. A KAUST team has now developed a device that can tap into this energy, as well as waste heat from industrial processes, by transforming quadrillionthof-a-second wave signals into useful electricity.

Unlike solar panels that are limited by daylight hours and weather conditions, infrared heat can be harvested 24 hours a day. One way to achieve this is to treat waste or infrared heat as high-frequency electromagnetic waves. Using appropriately designed antennas, collected waves are sent to a rectifier, typically a semiconductor diode, that converts alternating signals to direct current charge for batteries or power devices. Putting these ‘rectenna’ designs into practice has been


ENERGY A ND INNOVATION

was the nanoscale overlap of the two antenna arms, which required very precise alignment,” says postdoctoral researcher Gaurav Jayaswal. “Nonetheless, by combining clever tricks with the advanced tools at the University’s nanofabrication facility we accomplished this step.”

“T h e r e i s n o commercial diode in t h e wo r l d that can o p e ra t e a t such high f r e q u e n c y.”

difficult. Because infrared emissions have very small wavelengths, they need micro- or nanoscale antennas that are not easy to fabricate or test. Additionally, infrared waves oscillate thousands of times faster than a typical semiconductor can move electrons through its junction. “There is no commercial diode in the world that can operate at such high frequency,” says Atif Shamim, project leader. “That’s why we turned to quantum tunneling.” Tunneling devices, such

The researchers discuss the nanoscale overlap of the two antenna arms (from left to right: Azat Meredov, Gaurav Jayaswal, and Prof. Atif Shamim).

as metal-insulator-metal (MIM) diodes, rectify infrared waves into current by moving electrons through a small barrier. Since this barrier is only a nanometer thin, MIM diodes can handle highfrequency signals on the order of femtoseconds. To generate the intense fields needed for tunneling, the team turned to a unique ‘bowtie-shaped’ nanoantenna that sandwiches the thin insulator film between two slightly overlapped metallic arms. “The most challenging part

By choosing metals with different work functions, the new MIM diode could catch the infrared waves with zero applied voltage, a passive feature that switches the device on only when needed. Experiments with infrared exposure revealed the bowtie successfully harvested energy solely from the radiation, and not from thermal effects, as evidenced by a polarizationdependent output voltage. “This is just the beginning—a proof of concept,” says Shamim. “We could have millions of such devices connected to boost overall electricity generation.” Jayaswal, G., Belkadi, A., Meredov, A., Pelz, B., Moddel, G. & Shamim, A. Optical rectification through an Al2O3 based MIM passive rectenna at 28.3 THz. Materials Today Energy 7, 1–9 (2018).

K AUST DISCOVERY

d isc o ve r y. k a u st. e d u .s a

25


ENERGY A ND INNOVATION

POWERING THE BOTTOM LINE A risk-based optimization scheme boosts confidence and profitability for future mixed-technology power plants. C E M S E | P S E A scheme to balance risks may help realize the benefits of being able to combine complementary power technologies, such as thermal generation, wind power and energy storage. Such benefits include lower capital costs and more responsive and reliable energy delivery while leveraging renewable energy technologies Optimizing the operation of a mixed-technology power plant is vital to make such power generation profitable and reliable. However, this is far more complex than for single-technology units due to the simultaneous fluctuations in generation caused by inconsistent wind, for example, as well as fluctuations in energy storage levels and market electricity prices. While optimization schemes have been proposed for such virtual power plants (VPPs), the existing approaches take a rigidly risk-neutral approach to dealing with uncertainty in future conditions. Now, by integrating risk parameters into an efficient optimization program for VPP operation, Ricardo Lima and colleagues Omar Knio and Ibrahim Hoteit from KAUST have developed a platform that allows the system to be tweaked for better reliability and profitability. “Renewable energy resources are inherently uncertain,” explains Lima. “The operation and interaction of these resources with the electricity market brings uncertainty about how to best maximize profit.” Furthermore, “this methodology enables us to capitalize on wind ensembles from weather forecast models, accounting for the uncertainties inherent in future projections,” says Hoteit The problem considered by Knio’s team is the optimization of operations and electricity market participation for a VPP comprising a thermal unit, such as a conventional gas-fired power plant, a wind farm and

26

A u g u s t 2 0 18

a pumped storage hydro unit for energy storage. The goal of the calculation is to predict the optimal energy output of the thermal unit and input/output from the hydro unit, with conThermal unit dispatch sideration for fluctuating wind Pump-storage hydro unit conditions and electricity price dispatch in the market, which will optimize profit over the next few hours. “The key issue for optimization is always the balance Self-scheduling between level of detail of the Forward contracting model and the capacity for obtaining optimal solutions from it,” says Lima. “In this work, we propose efficient approaches to solve large probThe challenge is the optimization of operations lems and push the limits of the and electricity market problem sizes we can solve participation for a VPP in reasonable computational comprising a thermal unit, such as a conventional gastimes.” fired power plant, a wind farm This is a large-scale calculaand a pumped storage hydro unit for energy storage. tion problem with many variables even before the inclusion of risk, which presents significant challenges for finding the most accurate solution. To be able to consider the additional complexity of risk, the team had to develop an efficient calculation scheme, which they achieved by calculating the two parts in parallel. The result is a framework that can accommodate both conservative risk-avoidance and aggressive risk-seeking approaches


ENERGY A ND INNOVATION

First-Stage First-Stage Decisions Decisions Self-scheduling Self-scheduling Forward contracting Forward contracting

Second-Stage Second-Stage Decisions Decisions

Thermal unit Thermal dispatch unit dispatch Pump-storage Pump-storage hydro unithydro dispatch unit dispatch Sell and buy Sellelectricity and buy electricity in the poolin the pool

1 Week

1 Day

1 Week

1 Day

1 Hour Resolution 1 Hour Resolution

Sellelectricity and buy electricity Sell and buy in the poolin the pool

Forward contracting Forward contracting

“ The key issue for optimization is always the balance between level of detail of the model and the capacity for obtaining o p t i m a l s o l u t i o n s f r o m i t .”

of risk-averse decisions that hedge against low profits due to the uncertainty in future wind-power generation and electricity prices,” says Lima. Lima, R. M., Conejo, A.J., Langodan, S.,

Hoteit, I. & Knio, O.M. Risk-averse formulations and methods for a virtual power plant. Computers and Operations Research 96, 350-373 (2018).

K AUST DISCOVERY

d isc o ve r y. k a u st. e d u .s a

27


At the KAUST Sci-Café “The Science of Sustainability,” three scientists from different disciplinary backgrounds discuss how sustainability links their research through an energy-water-food nexus. From left to right, John Tannaci (panel moderator) Mark Tester, TorOve Leiknes and Tadeusz Patzek.

SUSTAINABILITY HINGES ON WATER AND ENERGY USE A plant scientist, a water specialist and a petroleum engineer walk onto a panel, “how do you define sustainability?” one asks. The term sustainability is hard to define and even harder to put into practice. Three KAUST scientists from different disciplinary backgrounds discuss how sustainability links their research through an energy-water-food nexus. Tad Patzek has had a career as a petroleum and chemical engineer and also as a physicist. As someone who works with finite resources he has thought hard about sustainability. For him it is about quality and durability. He says, “a

28

A u g u s t 2 0 18

cyclic process can be sustainable if it is maintained without loss of quality ‘forever,’ and if the environment into which this process dumps its wastes also maintains its integrity forever.” Fossil-fuel extraction is clearly not a cycle and therefore cannot be sustainable, he explains. “My profession is completely unsustainable by any definition. The field is completely linear: you start an oil field, you produce oil and then it ends.” Therefore we need to use fossil fuels

sparingly and for high-value uses that really demand them; we need to seek out alternatives to fossil fuels for our everyday needs. Mark Tester describes himself as “just a plant guy” who uses his knowledge of plants to develop more sustainable crops. “I define sustainability as action at a global and biological level to help people to do what they do in perpetuity without degrading the planet and its resources,” he says. Tester is driven to connect research with daily life, and he does this through improving understanding of how plants work and adapt. “I want to know why some plants tolerate salinity,” says Tester. “Coastal areas have different sets of plants to inland areas: so what genes are in coastal plants that are missing on the genes growing inland?” Tester is particularly interested in learning how plants adapted to living inland differ from

those on the coast and how this could help to grow crops in desert soils. “What trade-offs are plants making to live in a salty environment?” he asks. “We can use that knowledge to help plants to maintain their growth when their conditions are suboptimal, such as low in nitrogen or phosphorus, or especially with scarce or brackish water.” TorOve Leiknes is an environmental engineer with a focus on water sustainability and his definition includes notions of social and economic development within a framework of environmental protection. But we need to consider what is happening in society, he says, and to appreciate the complex system that includes both society and nature. “The Millennium Development Goals (established following the Millennium Summit of the United Nations in 2000) begin with the elimination of poverty because this relates back to


ENERGY A ND INNOVATION

economic and social growth and protecting the environment,” explains Leiknes. While these three specialists have different emphases in their definition of sustainability, they all agree that the dominant paradigms of societal valuation of natural resources must change. Patzek challenges the current narrative of prioritizing growth over the environment. Our priorities are all wrong, he claims, “we need to consider the environment first and then everything else.” “Environmental services, like drinking water, are not there forever and cannot be abused forever,” says Patzek. “Much of our water comes from desalination, but we don’t see the cost of producing that water. We waste that water every day, and that is wasting power.” It’s imp or tant, agrees Leiknes, to consider both the amount of energy required to provide water and the amount of water required to produce energy. “But it is also important to factor food into this relationship, especially because 75 percent of the world’s growing population are predicted to live in urban and peri-urban areas by 2050. It is vital to consider a nexus that includes energy, water and food.” “In these urban environments you need water, energy and food; but, then you also have very expensive water discharged as waste,” continues Leiknes. “So we have a resource that isn’t currently viewed as a resource that can be used. Agriculture puts the biggest demand on freshwater sources, so my interest is in the overlap of water and food, and to ask if we can reclaim water in an urban environment for urban agriculture.” Tester agrees that water

warrants a strong focus in terms of sustainability. “We are sleep walking to a disaster in terms of both ground water and surface water,” he says. “I want to develop a new system of agriculture where we stop basing irrigation on fresh water—which must be saved for more high-value uses—and instead use brackish water that isn’t currently suitable for agriculture.” So if we can use this without depleting soil quality and water quality, then we can make water resources more sustainable.

“They all agree t h at t he d o minant paradigm s of so c i etal

Sci-Café is an interactive discussion between KAUST scientists, community members and a Facebook live audience in a casual setting. Audience members are encouraged to ask questions and explore how interdisciplinary scientific research solves the real-world challenges of today.

valuat i on of nat ural reso urces must change.” So when a plant scientist, water specialist and petroleum engineer walk onto a panel, it’s really no joke. We need to actively consider how we value oil, water and food and make changes locally and globally. This article is based on a SciCafé event held at KAUST on 21 February 2018: The Science of Sustainability bit.ly/sustainabilityscicafe

K AUST DISCOVERY

di s co v e r y. kau s t. e d u . sa

29

Join in the conversation on how KAUST faculty are designing tomorrow through their research @kaustofficial/facebook live


Vanadium-containing layered oxides synthesized using a simple and fast microwave process can be used as cathodes in aqueous zinc-ion batteries. Their unique structure is shown to store large amounts of zinc ions, resulting in higher battery capacity. Zinc-ion batteries are safer, more environmentally friendly and cheaper than lithium-ion batteries.

LAYERED OXIDES FOR RECHARGEABLE ZINC BATTERIES

A technique of microwave synthesis of layered oxides enables high-capacity aqueous zinc-ion batteries. P S E Layered oxides can form the basis of high-performance materials for battery electrodes. A KAUST team has developed a cheap and simple technique that creates this crucial element for rechargeable zincion cells. Lithium-ion batteries power most of our everyday electronic devices, such as cell phones and laptop computers. But there is a growing need to store energy on much larger scales, such as retaining the electricity generated by solar cells for

30

A u g u s t 2 0 18

use at night. Scaling lithium-ion battery technology up to such an industrial-level application is expensive and presents serious safety issues, including toxicity and the flammability of the electrolytes. The team, led by Husam Alshareef, is instead developing zinc-ion batteries that use a water-based electrolyte, which has the advantages of being air stable, safe, environmentally friendly and cheap. “Aqueous batteries based on zinc ions can offer a safer, cost-effective solution to lithium-ion batteries for grid storage,” says Alshareef. “Furthermore, they use more

environmentally friendly materials than lead-acid batteries.” Lithium-ion and zinc-ion batteries work by electrically storing ions in an electrode. During charging, ions flow through an electrolyte from one electrode to another, where they are captured by a process known as intercalation. This means that electrode materials are key to optimizing a battery’s performance. One family of materials that has shown much promise in recent zinc-ion battery research is vanadium-based compounds. These materials have a layered and very open atomic-crystal structure with plenty of spaces for trapping and storing zinc ions. The team has now developed microwave approaches to rapidly synthesize cathode materials for zinc-ion batteries. To demonstrate their process, the team synthesized pyrovanadate (Zn 3V 2O 7(OH) 2· 2H 2O) and vanadium oxide bronze (Ca0.25V2O5·nH2O) cathodes. The precursors are dissolved in deionized water, and exposed to microwave radiation to induce a reaction and form the desired crystal phases in minutes. This zinc-ion battery, they show, can achieve an energy density of as much as 260 watt-hours per kilogram, which is much higher than previously reported aqueous zinc-ion batteries and commercial lead-acid batteries, with improved stability. The team believes that their microwave technique could also be useful for creating other vanadium-based compounds, explains Chuan Xia, Ph.D. student and lead author of the study. “We made compounds in which zinc is replaced with other cations that created larger metaloxide polyhedra that are able to intercalate an even larger number of zinc ions,” says Xia. 1. Xia, C., Guo, J., Lei, Y., Liang, H., Zhao, C. & Alshareef, H. N. Rechargeable aqueous zinc-ion battery based on porous framework zinc pyrovanadate intercalation cathode. Advanced Materials 29, 1705580 (2017). 2. Xia, C., Guo, J., Li, P., Zhang, X. & Alshareef,H.N., Highly stable aqueous zincion storage using layered calcium vanadium oxide bronze cathode. Angewandte Chemie International Edition 57, 3943 –3948 (2018).

© 2018 WILEY-VCH VERLAG GMBH & CO. KGAA, WEINHEIM, REPRODUCED FROM REF. 2

ENERGY A ND INNOVATION


FE AT URE

FROM

I N NOVATION I M PAC T TO

PHOTO BY LUKAS SYNEK.

Establishing sustainable desert agriculture may be the solution for growing twice as much food to feed 9 billion people by the year 2050.

Center-pivot irrigation of an alfalfa crop, in the Tabuk region, Saudi Arabia.


FE AT URE

SCIENCE FOR SOCIETY INNOVATION AND TRANSLATIONAL RESEARCH

KAUST places great emphasis on translating university know-how into real-world impact, say Kevin Cullen, vice president of Innovation and Economic Development, and John Tannaci, associate vice president for research How do you define innovation and translational research? Kevin: Innovation is about doing new things, or about doing old things in new ways. In the KAUST context, it is about getting our research and know-how translated into the Saudi economy and community for the benefit of broader society. John: Translation means building expertise toward a research goal, and then getting the right entrepreneurial ecosystem in place to harvest that. Translation doesn’t always mean commercial applications; research can translate to government policy, or to a wide variety of other outcomes. Where does innovation and translation sit within the KAUST mission? John: Innovation and translation were built into the founding of the University. KAUST was envisioned to be a catalyst for transforming lives, which manifests itself in a number of ways. Our 10 Research Centers are where a lot of this goal-oriented research happens. Kevin: No other university I have come across has the mission of innovation, translation and economic development as explicitly stated and supported as we have here. We spend a lot of time working with faculty and students to ensure they know how to take their ideas forward and to develop partnerships. Students take this understanding with them into the workplace. How do you support innovation and translation at KAUST? Kevin: We are very much about a relationship model, which means partnering for impact. Large companies like Saudi Aramco, through to small- to medium-sized enterprises (SMEs) and start-ups, can use technology to create jobs and prosperity in a way a university never can. We can identify and facilitate these partnerships between researchers and companies.

32

A u g u s t 2 0 18

John Tannaci, associate vice president for research. Dr. John Tannaci has over 15 years of experience as a researcher, faculty member and administrator. At KAUST, he works with all faculty members to support their research goals, including innovation and translation.

John: On the research side, we make strategic decisions to focus on certain goals to build the critical mass needed to harvest the translational elements. One example is the sensors initiative. We’ve built expertise around self-powered sensors for several applications, including flexible skin-like sensors to monitor marine animals. Another example is laserbased lighting, which can potentially save 80 percent of lighting energy. Both of these projects involve collaborations with other universities. By setting up collaborations in targeted areas, we can truly stimulate translation. Have notions of innovation changed during your career? Kevin: One notion that has certainly changed is the role of the university in the innovation system. When I came into this line of work, the university was seen as a source of inventions—patents, licenses and spinout companies. But a recent UK study showed that IP makes up only 2 percent of the total knowledge flow from the university sector. The majority of knowledge flow happens between people, through startup companies, collaborative research, consultancy and training. KAUST sees collaboration with industry, and outreach and engagement with SMEs, as a much more impactful way of getting university knowledge translated into use.


KSA’s Vision 2030 outlines a plan to advance Saudi Arabia through three key themes: a vibrant society, a thriving economy, and an ambitious nation. How is KAUST delivering in these themes? Kevin: We are working on projects in all of those areas. One area we contribute to specifically is the target to grow SME contribution to GDP from 20 to 35 percent by 2030. Since KAUST was founded, we have trained 5990 entrepreneurs—students, staff and external entrepreneurs. If we can double or triple that number, then we approach numbers that will have an impact in the economy. We think we have a model to engage with the SME community at scale, and that includes the creation of our own SMEs through our very ambitious startup program. What examples of research translation has KAUST produced so far? John: We know that it takes time to build critical mass. The fact that in less than 10 years, KAUST already has examples of translation is amazing to me and it is only going to accelerate moving forward. Consultancy and guiding government policy are forms of translation where KAUST is already having an impact. One area where we see great potential for research translation is in modeling the waves, wind, currents and environmental data of the Red Sea. One of these models can be used to inform developers how

Kevin Cullen, vice president of Innovation and Economic Development. Dr. Kevin Cullen has over 20 years of experience in academic innovation and business development. Throughout his career, he has helped elevate universitybased innovation enterprises that have led to the launch of more than 250 startup companies and numerous products and services.

high above sea level new infrastructure should be built. We also have impressive aquaculture expertise. One large project supports the Vision 2030 target to boost Red Sea aquaculture productivity tenfold. This project started in the Core Labs, but got so big we had to transition it to a start-up company. And then in desalination, we have a technology called MEDAD, which uses waste heat or solar, to lower the energy it takes to produce fresh water. It started as a pilot at KAUST, and now they are looking at building a 2,000-cubic-meter per-day facility up the coast in Yanbu. What is the key to successful innovation and translation at KAUST and what will be the ultimate measure of success? John: For us to be successful in this capacity, we need a balance of goal-oriented and curiosity-driven research, partnerships, and incredible shared facilities like the Core Labs to really push translation. KAUST is one of the few places with all those elements firmly entrenched. Kevin: At this point we are still in push mode— success comes when you get into pull mode, where the innovation demand in the economy is actively driving the dynamo. When I’ve got a queue of entrepreneurs at my door wanting to take technology from the university, then I’ll know we’ve succeeded. K AUST DISCOVERY

d isc o ve r y. k a u st. e d u .s a

33


WATER E X PLOR ATION

NEW EYES IN THE SKIES The availability of highresolution data collected by miniaturized satellites heralds a turning point in Earth and environmental sensing from space.

2017 PLANET

B E S E The advent of small, specialized satellites called CubeSats are transforming our ability to monitor the Earth’s surface and the impact of human activity on the planet. Scientists at KAUST are pioneering research techniques based on CubeSat data and are excited about the potential of these satellites, particularly for the fields of hydrology and precision agriculture. Traditional satellite data used for research, collected predominantly by government space agencies, presents certain limitations. Generally, either the data provides high spatial resolutions occasionally— detailed images taken every two weeks—or the data provides low spatial resolution frequently. In the latter scenario, significant details can be missed. CubeSats are changing this paradigm, collecting meter-scale spatial detail over Earth’s terrestrial surfaces every day. “I certainly didn’t expect these constraints to be lifted any time soon,” says hydrologist and remotesensing specialist, Matthew McCabe. “Normally, satellite design takes years—researching and developing sensors, negotiating with a government space agency and funding bodies—before possibly seeing your mission chosen for launch. Then, there’s the chance that something could go wrong upon launch or deployment or that you simply don’t get the data you need.” Recent advances in CubeSat technology could change this. These shoebox-sized satellites are comparatively cheap to make and launch: they are built from off-the-shelf components and sensors and sent into orbit either as companion payload or on small, reusable rockets. Once launched, CubeSats orbit the Earth at heights of 350 to 500 kilometers for a period

36

A u g u s t 2 0 18

of a few weeks to more than a year, relaying data to Earth (before ultimately burning upon re-entry into the atmosphere). The great advantage of their small size and cost means that “constellations” of CubeSats can be launched, setting up a conveyor belt of satellites capturing multiple high-resolution images at high temporal repeat rates. “This kind of high-resolution repeatability from space has never been available before,” says McCabe. “It has the potential to transform fields, such as disaster management and response by monitoring and directing relief efforts, or to track environmental change by identifying illegal deforestation in the Amazon, for example. If we can observe and identify problems before, or as they arise, we can take action to address them.” McCabe’s team recently launched a project in line with the Saudi Arabian government’s Vision 2030 that uses data from CubeSats and other satellites to help monitor water and food security issues. With agriculture using vast quantities of the Kingdom’s limited freshwater supplies, the team will use these satellite data to monitor crop health and irrigation rates to build up a clear picture of the country’s water use. This work will help guide future policies in water security. A CubeSat is a shoe box-sized satellite built from off-theshelf components and sensors, making them comparatively cheap to build and launch.


WATER E X PLOR ATION

The small size and relatively low cost of CubeSats mean they can be used to offer high-resolution images that can be used for more efficient agriculture.

Similarly, the status of global food security could be analyzed using data from CubeSats. As McCabe’s team recently demonstrated, it is now possible to retrieve high-quality imagery of individual fields daily, down to a resolution of three meters. From these, machine learning techniques can assess the health and condition of individual crops using measurements, such as leaf-area index and transpiration rates. This will enable more accurate predictions of potential yields and can verify when and where problems start, allowing farmers to take appropriate action. “CubeSat technology also allows us to interrogate data to find out which crops are being grown where,”

“T h e t e a m w i l l u s e data to monitor crop health and irrigation rates to build up a clear p i c t u r e o f t h e c o u n t r y ’s w a t e r u s e .”

adds McCabe. “In African countries, for example, there are few records showing what each farmer grows on their small piece of land. This information could pass into globally relevant databases to help tackle food security issues by tracking supply.” CubeSats are largely being built and launched by commercial companies at present, although space agencies, such as NASA and ESA, are also funding some CubeSat and nano-sat initiatives. “I’ve developed a strong collaboration with a CubeSat company called Planet,” says McCabe (www.planet. com). “Data from their CubeSat missions are available to scientists in all different fields for analysis—it’s an incredible resource. Although most CubeSats don’t carry expensive, research-grade components, meaning calibration can be a problem, we’re working on a range of innovative machine learning and modeling techniques that provide research quality data for Earth observation.” McCabe sees the potential of CubeSats in providing new insights across environmental sciences but also in providing a platform for the demonstration of novel sensors and technologies in space. By harnessing these emerging systems, strategies that address some of the major global challenges in food, water and environment could soon be implemented. McCabe, M.F., Aragon, B., Houborg, R. & Mascaro, J. CubeSats in hydrology: Ultrahigh-resolution insights into vegetation dynamics and terrestrial evaporation. Water Resources Research 53, 10017–10024 (2017).

K AUST DISCOVERY

d isc o ve r y. k a u st. e d u .s a

37


WATER E X PLOR ATION

From left to right: Prof. Slim Alouini, Abdulkadir Celik, Nasir Saeed and Assoc. Prof. Tareq Al-Naffouri.

MARINE EXPLORATION SENSING WITH LIGHT AND SOUND Unveiling new strategies to improve future wireless underwater sensing networks for marine research and communication.

C E M S E Oceanic sensor networks that collect and transmit high-quality, real-time data could transform our understanding of marine ecology, improve pollution and disaster

38

A u g u s t 2 0 18

management, and inform the multiple industries that draw on ocean resources. A KAUST research team is designing and optimizing underwater wireless sensor networks that could vastly improve existing ocean sensing equipment.

“Currently, underwater sensors use acoustic waves to communicate data,” explains Nasir Saeed, who is working on a new hybrid opticalacoustic sensor design with colleagues Abdulkadir Celik, Mohamed Slim Alouini and Tareq Al-Naffouri. “However, while acoustic communication works over long distances, it can only transmit limited amounts of data with long delays. Recent research has also shown that noise created by humans in the oceans adversely affects marine life. We need to develop alternative, energy-efficient sensors that limit noise pollution while generating high-quality data.” One option is to use optical

communication technology instead, but light waves will only travel short distances underwater before they are absorbed. Optical sensors also rely heavily on pointing and tracking mechanisms to ensure they are correctly orientated to send and receive signals. The team therefore propose a hybrid sensor capable of transmitting both acoustic and optical signals simultaneously. In this way, a data-collection buoy on the water surface can communicate with every sensor in a network spread out beneath it. However, marine research requires accurate measurements taken from precise locations, so scientists need to know where every sensor


WATER E X PLOR ATION

is at any given time. The team used mathematical modeling to develop a proof-of-concept localization technique. “Using our technique, the sensors transmit their received signal strength information (RSSI) to the surface buoy,” says Saeed. “For a large communication distance, the sensors use acoustic signals, but if the sensor is within close range of another sensor, it will send an optical signal instead.”

“S c i e n t i s t s need to know where every sensor is at any g i v e n t i m e .” Multiple RSSI measurements for each sensor are collected by the surface buoy. The buoy then weights these measurements to give preference to the most accurate readings before calculating where each sensor is positioned. Alouini’s and Al-Naffouri’s teams propose that their sensors will require a new energy source rather than relying on short-term battery power. They envisage an energy-harvesting system that powers fuel cells using microscopic algae or piezoelectric (mechanical stress) energy.

SUPER-ADSORBENT MOF TO CONTROL HUMIDITY

A metal-organic framework that can take up twice its weight in water and then release it when humidity falls. P S E Humidity control is a vital aspect of air conditioning, but high energy requirements make conventional methods expensive and environmentally damaging. Researchers have developed a metal-organic framework (MOF) that, within its range of applications, could control humidity in an eco-friendly and cost-effective way. MOFs encompass metal centers or clusters held in a porous framework by organic linker groups. The key to designing a MOF with specific properties is the ability to control the size and chemical structure of the pores by varying the metal and organic parts within each framework. Dalal Alezi completed her Ph.D. in Mohamed Eddaoudi’s research group at KAUST where a wide range of MOFs are being developed for gas separation, purification and chemical catalysis. This work was part of her doctoral research, and she has since moved on to an assistant professor role at King Abdulaziz University. “Our super-adsorbent material has unique properties,” explains Alezi. Two breakthrough achievements with the new water-adsorbing MOF (Cr-soc-MOF-1) are its

stability in water, unlike many highly porous MOFs, and its high-capacity internal pores that can adsorb twice the weight of the MOF as water. Another vital feature is the easy reversibility of the water uptake. The water adsorbed when humidity levels are high can readily be released when the humidity falls. This yields an ideal material for controlling humidity in restricted spaces. “Regulating escalating humidity levels, especially indoors and in confined environments, such as aircraft cabins and air-conditioned buildings, is a critical challenge,” says Youssef Belmabkhout, a senior research scientist in Eddaoudi’s group. He adds: “The conventional systems consume large amounts of energy, require intricate design and excessive cost.” This new material is just one product of Eddaoudi’s long-term commitment to exploring the capabilities of MOFs. “To the best of our knowledge, our new wateradsorbing MOF outperforms all existing MOFs in terms of capacity, reversibility and cyclic performance,” says Eddaoudi. The easy reversibility of this MOF will be crucial for its commercial applications. The team have already maintained the exceptional water uptake and release through more

Saeed, N., Celik, A., Al-Naffouri, T.Y. & Alouini, M-S. Energy harvesting hybrid acousticoptical underwater wireless sensor networks localization. Sensors 18, PiiE51 (2018).

Three co-authors of the study (L-R): Himanshu Aggarwall, Norah Alsadun and Prashant Bhatt.

K AUST DISCOVERY

d isc o ve r y. k a u st. e d u .s a

39


WATER E X PLOR ATION

GRIME DOES PAY WHEN IT COMES TO WASTEWATER FILTERS A grimy layer on wastewater filters could slow the spread of antibiotic resistance. B E S E Super-adsorbent crystals of Cr-soc-MOF-1.

Dalal Alezi

than 100 adsorption-desorption cycles. Eddaoudi also emphasizes that wateradsorbing MOFs are ready to provide effective solutions to challenges other than regulating humidity, such as tackling water scarcity and environmental sustainability, in energy-efficient ways. Possibilities include harvesting drinkable water from air for use in water desalination and purification.

“O u t p e r f o r m s all exisiting MOFs in terms o f c a p a c i t y, reversibility and cyclic p e r f o r m a n c e .” The researchers are now working to scale up their water-adsorbing materials in order to demonstrate commercial potential and move into real-world applications. Abtab, S.M.T., Alezi, D., Bhatt, P.M., Shkurenko, A., Belmabkhout, Y., Aggarwal, H., Weseliński,L.J., Alsadun, N., Samin, U., Hedhili, M.N. & Eddaoudi., M. Reticular chemistry in action: A hydrolytically stable MOF capturing twice its weight in adsorbed water. Chem 4, 94-105 (2018).

40

A u g u s t 2 0 18

Accumulating grime on sewage treatment membranes has long been considered a problem, yet it may help remove antibiotic-resistant bacteria and antibiotic resistance genes from wastewater that is treated in anaerobic membrane bioreactors. Because wastewater is laced with antibiotics used in hospitals, homes and agriculture, treatment plants are potential hotspots for bacteria to develop resistance and transfer resistance genes between species. Peiying Hong of KAUST’s Water Desalination and Reuse Center, together with her Ph.D. student Hong Cheng, wanted to know how the biofouling, or buildup of grime, of membranes that filter pollutants from sewage affects their ability to filter antibiotic-resistant bacteria and bacterial antibiotic resistance genes. “The conventional wisdom is that biofouling is a problem and, as engineers, we would like to eradicate the biofoulant layer because it hinders the flow of water,” explains Cheng.

“But, our study showed that biofouling can help remove contaminants from wastewater by functioning as a layer that adsorbs them.” Hong and Cheng used a labsized bioreactor fed with synthetic wastewater containing three types of antibiotic-resistant bacteria and three types of antibiotic resistance genes. The experimental reactor treats wastewater using nonoxygen-consuming, or anaerobic, microorganisms that consume and degrade its solid materials and pollutants. Anaerobic membrane bioreactors have potential as sustainable alternatives to the aerobic membrane bioreactors. The aerobic ones use oxygen-consuming microorganisms to degrade pollutants, requiring lots of energy to aerate the system. The treated wastewater was filtered through three increasingly Peiying Hong (left) and Ph.D. student Hong Cheng study the biofouling of membranes that filter pollutants from sewage and antibiotic-resistant bacteria and bacterial antibiotic resistance genes.


WATER E X PLOR ATION

fouled membranes. These results were compared with similarly treated wastewater filtered through a new, clean membrane. Hong and Cheng found the removal of antibiotic resistance genes from the treated wastewater improved as the biofoulant layer on the membranes thickened. But removal of the antibioticresistant bacteria did not follow the same pattern. The new, unfouled membrane removed up to 99.999 percent of the bacteria from the wastewater. As the biofoulant layer started accumulating, this efficiency dropped to 99 percent, but then rose again to 99.999 percent when the anaerobic membrane became critically fouled, a phase where the biofoulant layer no longer thickens. “This suggests that long-term operation of anaerobic membrane bioreactors may be beneficial,” says Cheng. “These results mean that membranes made with surface coatings that mimic biofoulant layers could help remove undesirable contaminants from wastewater,” says Hong, “including those that spread antibiotic resistance.” The team plans to scale up their bioreactor to treat wastewater generated locally by the KAUST community. They are also collaborating with Ikram Blilou from the Plant Sciences program to test the use of the reactor’s treated wastewater for irrigating agricultural crops. “We hope this multidisciplinary study involving expertise from applied microbiology, engineering, and plant sciences will provide a comprehensive outlook on how to best use treated water,” says Hong.

SOLAR ENERGY TAPPED FOR CLEAN WATER A 3D solar steam generator design squeezes every last drop of energy from sunlight to produce fresh water. B E S E Purifying water to make it clean enough to drink takes a lot of energy. A KAUST team has found a way to efficiently produce clean fresh water using the energy in sunlight. The 3D solar steam generator, which works with nearperfect energy efficiency, could be used as an environmentally friendly way to turn seawater into drinking water, as well as to clean wastewater. Key to the solar steam generator is a ‘photothermal’ material that soaks up sunlight and converts the captured energy into heat. When placed on a wet surface, water drawn into the hot photothermal material turns to steam, which can be captured as pure water. Making photothermal materials that capture the entire spectrum of energy in sunlight has been Peng Wang’s recent research focus. Dark-colored materials called mixed metal oxides have proven to be robust and effective photothermal substances. Until now, Wang and his team made solar steam generators using flat photothermal sheets. “Our previous work pushed the energy efficiency of planar photothermal materials close to their theoretical limit,” says Wang. Going 3D

was the logical next step, he says. Wang’s 2D materials were losing energy via two main mechanisms: reflection of the incoming sunlight, and thermal radiation shed from the hot material into the surroundings. Wang overcame these losses by making 3D cup-shaped photothermal structures. The wall of the cup recaptured virtually all of the energy that was being lost through these two routes. In fact, rather than losing energy to the surrounding environment, the cup was able to harvest extra energy from it. Using infrared imaging to measure the cup’s temperature, the team showed that although the bottom of the cup gets hot in sunlight, rapid water evaporation from the wall of the cup carries heat away, so the cup’s wall is cooler than their surroundings. The wall therefore draws in heat from the ambient air around them – an additional energy source on top of the solar energy. “This lead to our record high water evaporation rate,” says Wang. The team’s first solar steam generator, reported in 2015, had a solar-to-waterevaporation energy efficiency of 56 percent. “In this work we achieved near 100 percent efficiency,” he says. The team’s next step will be to test the device with real water samples, and its ability to deal with salt and biological fouling, before they work on process scale up. Shi, Y., Li, R., Jin, Y., Zhuo, S., Shi, L. Chang, J., Hong, S., Ng, K-C & Wang, P. A 3D photothermal structure towards improved energy efficiency in solar steam generation. Joule 6, 1171-1186 (2018).

Cheng, H. & Hong, P. Removal

2018 RENYUAN LI

of antibiotic-resistant bacteria and antibiotic resistance genes affected by varying degrees of fouling on anaerobic microfiltration membranes. Environmental Science & Technology 51, 21 12200–12209 (2017).

Solar-steam generation treats wastewater and has a great potential to provide fit-for-purpose water for agriculture.

K AUST DISCOVERY

d isc o ve r y. k a u st. e d u .s a

41


The goals of the Water Desalination and Reuse Center are relevant to challenges faced by Saudi Arabia and the world. Researchers are tasked with developing and optimizing processes that can provide potable water in drought-stricken areas. This Osmo Inspector is used to test different types of membranes to determine their suitability for use in bioreactors for wastewater reclamation.

Learn more WDRC.KAUST.EDU.SA

Imene El Tall

Research Technician


C HEMIS TRY A ND M ATERI A L S

FLEXING FOR THE NEXT SILICON WAVE Ultrathin, rigid silicon segments that are wired through interdigitated metal contacts produce ultraflexible highperformance solar cells. C E M S E A strategy that uses a screen-printed aluminium circuit to make silicon solar cells extremely flexible could enable them to become portable power sources. Developed by KAUST, such power sources could help to satisfy the growing demand for wearable and implantable devices, foldable displays and vehicle-integrated solar panels. Crystalline silicon is naturally abundant and highly scalable and has reliable and consistent photovoltaic properties that are appealing for the development of industrial solar cells. However, its rigidity and weight have hindered its application for flexible electronics. Attempts at enhancing material flexibility by generating thin films, while maintaining device performance, have fallen short: the resulting solar cells have shown a drop in performance for films thinner than 250 micrometers. “At this thickness, one cannot achieve flexible silicon solar cells,” says team leader, Muhammad Hussain. Now, Hussain’s team has created a corrugated array comprising thin, Rigid (left) and flexible crystalline silicon-based solar cells.

rigid silicon segments using so-called interdigitated back contact solar cells. The segments are interconnected by screen-printed aluminum contacts. These contacts are positioned at the rear to optimize light absorption at the front of the solar cell and facilitate any modifications of the active silicon material. The array can bend and adopt various configurations, such as zigzags and bifacial structures, without cracking or losing its power conversion efficiency. Starting from large-area crystalline silicon solar cells, the researchers etched a small portion of the cells into 140-micrometer-thick strips, while keeping the thickness of the remaining portion above 240 micrometers. “This allowed us to lower the bending radius of the cell to 140 micrometers while retaining the efficiency of the bulk (18%), record achievements for both silicon solar cell efficiency and bendability,” says lead author Rabab Bahabry, a graduating doctoral student from Saudi Arabia who received her bachelor’s degree in physics from King Abdulaziz University. The researchers demonstrated that a series of five corrugated solar cells lit up multicolored light-emitting diodes. They also wrapped the cells around a glass mug to power a miniature humidity detection system placed on a plant leaf. When exposed to light from a desk lamp and humid conditions, the system turned on an LED and sent a notification to a smartphone. The team is currently investigating ways to exploit these corrugated solar cells, which, according to Hussain, can be deployed in the most complex topologies. “Our approach is suitable for the Internet of Things and can meet a wide application spectrum,” he says. Bahabry, R.R., Kutbee, A.T., Khan, S., Sepulveda, A.C., Wicaksono, I., ... & Hussain,M.M. Corrugation architecture enabled ultra-flexible wafer-scale high-efficiency monocrystalline silicon solar cell. Advanced Energy Materials 12, 1702221 (2018).

Treating aluminum-gallium-nitride nanowires with a diluted potassiumhydroxide solution can enhance the ultraviolet light output power as compared to an untreated device.

CLEANING NANOWIRES TO GET OUT MORE LIGHT

A simple chemical surface treatment improves the performance of nanowire ultraviolet light-emitting diodes. C E M S E A technique for reducing the loss of light at the surface of semiconductor nanostructures has been demonstrated by scientists at KAUST. Some materials can efficiently convert the electrons in an electrical current into light. These so-called semiconductors are used to create light-emitting diodes or LEDs: small, light, energyefficient, long-lasting devices that are increasingly prevalent in both lighting and display applications. The color, or wavelength, of the emitted light can be determined by choosing the appropriate material. Gallium arsenide, for example, emits predominantly infrared light. For shorter wavelengths that move into the blue or ultraviolet region of the spectrum, scientists have turned to gallium nitride. Then, to tune down the emission wavelength, aluminum can be added, which alters the spacing between the atoms and increases the energy bandgap. However, numerous factors prevent

d isc ove r y. k a u st. e d u .s a

43


C H E M I S T R Y A N D M AT E R I A L S

all the radiation created in the semiconductor escaping the device to act as an efficient light source. Firstly, most semiconducting materials have a high refractive index, which makes semiconductor–air interfaces highly reflected—at some angles all light bounces backwards in a process known as total internal reflectivity. A second limitation is that imperfections at the surface act as traps that reabsorb the light before it can escape. Postdoc Haiding Sun and his KAUST colleagues, including his supervisor, Assistant Prof. Xiaohang Li, Prof. Boon Ooi and Assistant Prof. Iman Roqan, have developed LEDs that are made up of a tight array of dislocation-free nanometer-scale aluminum-galliumnitride nanowires on a titanium-coated silicon substrate. More light can be efficiently extracted due to the presence of the air gaps between nanowires via scattering. The trade-off however is that arrays of nanowires have a larger surface area than a planar structure. “Because of the large surface-to-volume ratio of nanowires, their optical and electrical properties are highly sensitive to their surroundings,” says Sun. “Surface states and defects will lead to low-efficiency light-emitting devices.” Sun and the team show that treating the nanowires in a diluted potassiumhydroxide solution can suppress the surface reabsorption by removing dangling chemical bonds and preventing oxidization. Their results showed that a 30 second treatment led to a 49.7 percent enhancement in the ultraviolet light output power as compared with an untreated device. “We aim to improve our device’s performance in several ways,” says Sun. “For example, we will optimize the nanowire growth conditions, we will use quantum-well structures in the active region and we will use different metal substrates to improve the lightextraction efficiency. Sun, H., Shakfa, M.K., Muhammed, M.M., Janjua, B., Li, K.-H., Lin, R., Ng, T.K., Roqan, I.S., Ooi, B.S. & Li, X. Surface-passivated AlGaN nanowires for enhanced luminescence of ultraviolet light emitting diodes. ACS Photonics 5, 964-970 (2017)

44

A u g u s t 2 0 18

The KAUST team, including Kaikai Liu (left) and Xiaohang Li, show that varying boron content enables tuning of the electric polarization at the interface between boron aluminum nitride and boron gallium nitride alloys.

TAKING CONTROL AT THE JUNCTION Fine tuning the composition of nitride alloys can further the development of optical and electronic interface devices. C E M S E Controlling the electronic properties at the interface between materials could help in the quest for improvements in computer memory. KAUST researchers show that varying the atomic composition of boron-nitridebased alloys enables tuning of an important electronic property known as polarization. When an electric field is applied to a single atom, it shifts the center of mass of the cloud of negatively charged electrons away from the positively charged nucleus it surrounds. In a crystalline solid, these so-called electric dipoles of all atoms combine to create electric polarization.

Some materials exhibit a spontaneous polarization, even without an external electric field. Such materials have potential uses in computer memory, however, this application requires a material system in which the polarization is controllable. Visiting Student Research Program (VSRP) student Kaikai Liu, his supervisor Xiaohang Li and coworkers investigated one approach to polarization engineering at the interface between boron-nitridebased alloys. Spontaneous polarization is strongly dependent on the structure and composition of the atomic crystal. Some materials, known as piezoelectrics, can change polarization when physically deformed.


2017 ZHANGDONG WANG

C HEMIS TRY A ND M ATERI A L S

The team used software called the Vienna ab initio Simulation Package to investigate the electronic properties of the ternary alloys boron aluminum nitride and boron gallium nitride. They looked at how they change as boron replaces aluminum and gallium atoms, respectively. “We calculated the spontaneous polarization and piezoelectric constants of boron nitride alloys within a newly proposed theoretical framework and the impact of the polarization at junctions of these two materials,” says Liu. The team showed that the spontaneous polarization changes very nonlinearly with increasing boron content; this contradicts previous studies that assume a linear relationship. The reason for this nonlinearity is attributed to the volume deformation of the alloy’s unusual atomic structure, known as wurtzite. The nonlinear change of the piezoelectric polarization is less pronounced, but evident. This arises because of the large difference in atomic spacing between boron nitride and both aluminum nitride and gallium nitride. Furthermore, boron aluminum nitride or boron gallium nitride can become nonpiezoelectric when the boron content is more than 87 percent and 74 percent, respectively. This work shows that a large range of spontaneous and piezoelectric polarization constants could be made available simply by changing the boron content. This could be useful for developing optical and electronic junction devices formed at the interface between conventional nitride semiconductors and either boron aluminum nitride or boron gallium nitride. “Our next step will be to experimentally test the proposed junctions, which our theory predicts could have much better device performance than current approaches,” says Liu.

SOMETHING IN THE AIR Synchrotron study reveals oxygen’s influence on the chemistry that surrounds us. P S E Chemical reactions that produce pollutants in the atmosphere, and the chemistry of fuel combustion inside a vehicle engine, have some striking similarities. For each set of reactions, oxygen’s role is key. Studying oxygen’s part in combustion and atmospheric chemistry could help scientists improve both engines and reduce air pollution, KAUST researchers have shown. Volatile organic compounds (VOCs) are gaseous molecules that are emitted into the air from the tail pipes and smoke stacks of vehicles, factories and power plants, as well as from living plants. VOCs undergo a sequence of auto-oxidation reactions with oxygen from the surrounding air to form highly oxygenated molecules that contribute to air pollution and produce aerosols that are known to affect the climate. Auto-oxidation also occurs during the ignition and combustion of fuels. But revealing the identity of the molecules from these reactions has been difficult, say Zhandong Wang and Mani Sarathy from the Clean Combustion Research Center, who co-led the work. “The highly oxygenated intermediates produced from auto-oxidation are very reactive

and decompose quickly,” Wang says. So Wang, Sarathy and their team developed an advanced experimental setup to sample these elusive molecules before they decompose. “We used a sophisticated technique—a jet-stirred reactor coupled with synchrotron radiation photoionization and molecular-beam mass spectrometry—at the Advanced Light Source in Berkeley,” says Wang. The team also used a high-resolution atmospheric-pressure chemicalionization mass spectrometer at the Analytical Core Laboratory at KAUST to analyze combustion autooxidation products. Current theoretical models of combustion chemistry assume that one, or possibly two, oxygen molecules can attach to a fuel molecule during auto-oxidation. Wang and Sarathy’s results show that at least three sequential oxygenaddition reactions, and possibly more, can take place. “Our most significant finding is that auto-oxidation processes leading to auto-ignition are much more complex than previously thought,” says Wang. A representative fuel molecule showing oxygen molecules (right, red) and 2-methylheptane (right, grey and white) meeting in a jet-stirred reactor. The highly oxygenated molecules that result (left) are detected by advanced mass spectrometry.

Liu, K., Sun, H., AlQatari, F., Guo, W., Liu, X., Li, J., Torres Castanedo, C. G. & Li, X. Wurtzite BAlN and BGaN alloys for heterointerface polarization engineering. Applied Physics Letters 111, 222106 (2017).

K AUST DISCOVERY

d isc o ve r y. k a u st. e d u .s a

45


C HEMIS TRY A ND M ATERI A L S

“We have shown that many large hydrocarbon and oxygenated fuels exhibit extensive auto-oxidation, and when these pathways are included in models, they significantly alter simulation results.”

“M o r e accurately simulate fuel combustion and to potentially improve the performance of real e n g i n e s .” Updating these models will allow the team to more accurately simulate fuel combustion and to potentially improve the performance of real engines. But the findings are broader reaching. “We are working with the atmospheric scientists from University of Helsinki to further explore analogous auto-oxidation processes in atmosphere and combustion. Our goal is to use our combustion experience to develop models for atmospheric aerosol formation via VOC auto-oxidation. This could significantly improve simulations to predict air pollution and global temperature.” Wang, Z., Popolan-Vaida, D.M., Chen, B., Moshammer, K., Mohamed, S.Y., Wand, H., Sioud, S., Raji, M.A, ...& Sarathy, S.M. Unraveling the structure and chemical mechanisms of highly oxygenated intermediates in oxidation of organic compounds. Proceedings of the National Academy of Sciences 114, 13102–13107 (2017).

46

A u g u s t 2 0 18

SURFACE ENGINEERING GETS THE RED LIGHT

Perovskite particles could improve the performance of solar cells and light-emitting diodes via a simple process to stabilize the nanocrystal surface. P S E A method for chemically stabilizing optical nanocrystals, without degrading their electrical properties, has been developed by scientists at KAUST. Halide perovskites are in an exciting class of materials for optoelectronics and photovoltaics. These materials efficiently absorb visible light, possess long charge-carrier diffusion lengths and are easy and cheap to produce. The performance of optical devices can also be improved by incorporating nanometer-scale particles, which have far superior lightemitting and -absorbing properties than the bulk material from which they are derived. So it is unsurprising that scientists are keen to combine these two approaches. The challenge is that tiny perovskite particles aren’t always chemically stable, and their atomic crystal structure is difficult to control. Att a c h i ng m ol e c u l e s , referred to as ligands, can stabilize a nanocrystal. But this so-called passivation can form an electrically insulating shell

around the particle that inhibits their effectiveness in electronic devices. Now, Osman Bakr’s group, and co-workers from KAUST and ShanghaiTech University, has created halide perovskite nanocrystals made from cesium-lead-iodide passivated by 2,2´-iminodibenzoic acid (IDA) ligands. They show that this provides the necessary chemical stability while remaining useful for optoelectronics. And the passivation was simple: just adding IDA powder into the nanocrystal solution and using a centrifuge to remove any excess. Th e t e a m c h o s e I DA because it is a bidentate ligand, meaning that it bonds to the nanocrystal at two sites. “The conventional ligands used in these applications, such as oleic acid, are dynamic on the surface of the perovskite nanocrystals and easily come loose,” says Jun Pan, the first author on the paper. “That’s why we apply a double carboxylic group to strongly bind on the surface, which also

Stabilizing optical nanocrystals without degrading their electrical properties could underpin improvements in the performance of solar cells (L-R): Osman Bakr, Jun Yin, Jun Pan and Lutfan Sinatra.


C HEMIS TRY A ND M ATERI A L S

stabilizes the perovskite crystal phase at room temperature.” Pan and his team compared the optical properties of both the passivated and unpassivated samples and observed that the treatment improved the photoluminescent quantum yield—a measure of how many photons are emitted for every photon absorbed—from 80 percent to over 95 percent. And while the intensity of light emitted from the unpassivated nanocrystals had dropped significantly five days later, the IDA-treated samples were still emitting light at 90 percent of their initial level 15 days later. Passivating the surface of perovskite nanocrystals with IDA molecules improves their stability and their optical and electrical properties, making them useful for optoelectronic devices. The team demonstrated that their stabilized halide perovskite nanocrystals were suitable for optoelectronic applications by using them to build lightemitting diodes. The red-light generating devices again outperformed the unpassivated control device in terms of maximum luminance and luminous power efficiency. “The next step is to realize more stable perovskite structures and to create an LED with performance above 10 percent based on perovskite nanocrystals,” says Pan. Pan, J., Shang, Y., Yin, J., De Bastiani, M., Peng, W., Dursun, I., Sinatra, L., El-Zohry, A. M., Hedhili, M. N., Emwas, A.-H., Mohammed, O. F., Ning, Z. & Bakr, O. M. Bidentate ligand-passivated CsPbI3 perovskite nanocrystals for stable near-unity photoluminescence quantum yield and efficient red light-emitting diodes. Journal of the American Chemical Society 140, 562−565 (2018).

Complex Adsorbent Porous Structure Mesopore 2-50nm Micropore <2nm

Gas Molecules

Macropore >50nm

Multi-peak Energy Distribution

Adsorbent

Adsorbate

Adsorption Site

1

Energetically Heterogeneous Patch

Energetically Heterogeneous Surface

Single-peak Energy Distribution

THE UNIVERSAL TRUTH ABOUT STICKY SURFACES

Trapping molecules on customdesigned porous surfaces becomes easier with a new model that unifies previous theories of adsorption. B E S E Many purification tools, from simple charcoal filters to complex desalination plants, rely on solids with millions of tiny pores to capture and remove contaminants without chemically binding to them. Now, a KAUST team has identified the key factors that connect adsorption on different kinds of porous surfaces, solving century-old problems of predicting uptake on unknown substances. In the early 1900s, the concept of adsorption isotherms emerged to describe how adsorbents behave in the presence of steadily increasing amounts of molecules. These graphs have distinct shapes that depend on atom-scale surface properties— for example, whether particles stick in single layers or multilayers—and quickly became essential for designing and understanding purification setups. The majority of absorbents, chemists found, could be sorted into one of six isotherms after a few experimental measurements. However, modern adsorbents with

heterogeneous pore structures, such as metal-organic frameworks (MOFs), are proving more difficult to model. While these materials benefit from high-throughput testing of numerous samples, the need for individual isotherm measurements slows discovery considerably—a situation experienced by Professor Kim Choon Ng at KAUST’s Water Desalination and Reuse Center. “We were working to improve treatment of seawater, and using isotherms was very tedious,” says Ng. “Everyone had to do their own trial and error work for particular applications, and there was no real theory to help people design absorbents.” With researchers Muhammad Burhan and Muhammad Shahzad, Ng aimed to find out how the different isotherms could be combined into a single universal model. They proposed subdividing surfaces with nanometer-scale pore variations into tiny patches that adsorb guest molecules under similar thermodynamic and kinetic conditions. By introducing a probability factor to define the energy distribution of each patch, the team created a mathematical function capable of spotting significant characteristics of adsorbent surfaces. Comparisons between predictions generated by the universal model and literature isotherms revealed the power of the new approach. Not only did the theoretical data match the measured experiments for all six isotherm categories, but multiple peaks appeared in the energy distribution plots when heterogeneous conditions are detected—parameters that may prove critical for development of innovative materials with fine-tuned sorption capabilities. “Each adsorbent-adsorbate pair has its own distinct energy distribution function, which allows us to capture all the information in the isotherms,” explains Ng. “Materials scientists should be able to use techniques, such as acidification, to expand pore sizes in metal-organic frameworks and shift their energy distribution to increase uptake.”

Differences in pore sizes on absorbent surfaces can be better understood with a model that spots tiny regions where gases attach at similar energies

Ng, K. C., Burhan, M., Shahzad, M. W. & Ismail, A. B. A universal isotherm model to capture adsorption uptake and energy distribution of porous heterogeneous surface. Scientific Reports 7, 10634 (2017).

K AUST DISCOVERY

d isc o ve r y. k a u st. e d u .s a

47


The work accomplished by experts in the Computational Bioscience Research Center is focused on human health and medicine and microbial engineering informatics. Nematostella vectensis is a model organism for researchers in the Center to examine the evolutionary origin of the brain.

Learn more CBRC.KAUST.EDU.SA


SCIENCE VISUALIZED

DNA IMAGING MADE EASY

New method offers efficient and highthroughput way to study the structure of DNA.

1,450

Total number of alumni

2018 MONICA MARINI

P S E It may be the most famous structure in biology, but it wasn’t until a few years ago that biophysicist Enzo Di Fabrizio and his colleagues took the first direct images of the DNA double helix with an electron microscope. Now, Di Fabrizio and his lab group at KAUST have improved upon their groundbreaking technique, tweaking the protocol to make it simpler and faster. “It’s an efficient and highthroughput alternative to more conventional techniques,” says Monica Marini, postdoctoral fellow in Di Fabrizio’s lab and the first author of the new study. For the past six decades the only way to get 3D renderings of the building blocks of life was using a technique called X-ray crystallography: however these pictures were only abstractions, not true photographs, based on interpretations of diffracted X-rays. It wasn’t until 2012 — when Di Fabrizio, back in his native Italy, produced the first direct image of DNA — that researchers got a faithful picture of the double helix. Di Fabrizio moved to KAUST in 2013 and since then his group has been steadily improving and building upon the original imaging protocol, which involved transmission electron microscopy (TEM), a technique in which electrons are beamed onto photographic film. Their method involves spreading minute droplets of fluid containing DNA on to silicon wafers etched with tiny cylindrical pillars and holes. As the droplets dry out, the DNA stretches itself out

90%

Employment rate

Alumni working in-Kingdom

45%

*June 1, 2018

0.27 nm

0

0.5

1.0nm

From top to bottom: SEM image of DNA bundles homogeneously suspended over a superhydrophobic device. In the related HRTEM image the fringes have a spacing of 2.7 Å, in good agreement with the diffraction pattern: both cases show the distance between two bases in the DNA double helix.

across the microscopic bed of pillars, creating spools of interconnected thread. In the past, Di Fabrizio’s team then applied TEM to capture images of the DNA strands directly. But now, they’ve

K AUST DISCOVERY

di s co v e r y. kau s t. ed u . sa

49

Join us

kaust.edu.sa


SCIENCE VISUALIZED

also performed a more straightforward diffraction analysis of the TEM beams — thus “creating an experiment that’s quite similar, in terms of physical principles, to that done by the scientists who first discovered the DNA structure,” says Andrea Falqui, who has collaborated with Di Fabrizio in previous works.

“The d i f f ra c t i o n patte r n of high - e nerg y e l e c t rons s hows t he d i st a n ce b e t we e n t wo b a s e s i n t he D N A d o u ble he l i x .” As Di Fabrizio and Marini show, this diffraction-based approach produced pictures that measured the distance between rungs of the DNA ladder just as accurately as direct TEM imaging. Now, the researchers plan to use this technique to image more complex arrangements Marini, M., Allione, M., Lopatin, S., Moretti, M., Giugnia, A., Torre, B. & Di Fabrizio, E. Suspended DNA structural characterization by TEM diffraction. Microelectronic Engineering 187–188, 39–42 (2018).

50

A u g u s t 2 0 18

UNLEASHING ULTRAVIOLET BRINGS VISIBLE IMPROVEMENT High-speed communication systems based on ultraviolet radiation are now in sight. C E M S E Military and civil authorities could benefit from secure optical communication systems that use light to carry messages between moving vehicles. Researchers have now demonstrated rapid data transfer using ultraviolet-B (UV-B) light, which provides many advantages over visible light. Optical communications systems using visible lasers and light emitting diodes (LEDs) suffer from interference due to the high levels of visible light in sunlight. What’s more, the transmitter and receiver must be aligned very precisely, which is very difficult for vehicles on the move. “Accurate beam alignment for point-to-point (or line-ofsight) optical communication is challenging—slight movements of just a few millimeters might break the communication link,” says Ph.D. student Xiaobin Sun who worked on the project with professors Boon Ooi and Slim Alouini, alongside other coworkers at KAUST and the Chinese Academy of Sciences in Beijing. “This problem motivates us to

look for a nonlineof-sight communication system.” This is where U V- B b e c om e s useful. UV-B from the sun is mostly absorbed by ozone in the upper atmosphere, so it doesn’t interfere with communications. Also, UV-B gets scattered in different directions by aerosols and common molecules, meaning the signal spreads out from the source to cover a wide area and accurate alignment of the beam is not required. Sun, Ooi, Alouini and coworkers are developing high-performance UV-LED sources and highly sensitive detectors that receive UV signals quickly and accurately. In their latest work, they used

UV-light scattering is used for diffuse line-ofsight optical communications.


SCIENCE VISUALIZED

LOW PRESSURE REDUCES BUBBLE TROUBLE

Spray coating and inkjet-based electronics manufacture are among the industrial applications in which liquid droplets are applied to a surface. But minuscule air bubbles that get trapped beneath the droplet can affect the coating’s quality. P S E Sigurdur Thoroddsen and his team from KAUST set up an experiment to test whether bubble formation would be suppressed at lower air pressures. The team created a vacuum chamber equipped with a high-speed camera to observe droplet bubble formation. “Reducing the air pressure had many advantages, including decreasing the bubble size and suppressing splashing,” says Kenneth Langley, Thoroddsen’s Ph.D. student. But there’s a sweet spot, he adds. “We discovered that if you reduce the pressure too much, you will entrain more gas bubbles than at higher pressures.” At these low pressures, the team observed the usual central disk of air is trapped, but the droplet then unexpectedly trapped a second, outer ring of air, which quickly collapsed into individual bubbles. Li, E., Langley, K.R., Tian, Y.S., Hicks, P.D. & Thoroddsen, S.T. Double contact during drop impact on a solid under reduced air pressure. Physical Review Letters 119, 214502 (2017).

Pressure Gauge

Syringe Pump Drop Collector

Motor

Vacuum Pump rro r

their concept in a low-power system, the team plan to increase the optical power and sensitivity until they achieve long-distance nonline-of-sight UV communications with high data transmission rates. “These interdisciplinary collaborative efforts between the photonics and communication theory groups at KAUST are paving the way toward the next frontier for optical wireless communication systems,” says Alouini.

Mi

an LED to send pulsed UV-B signals to a sensor comprising two antireflective lenses that collect and focus the UV-B light into a photodetector. The team observed strong power transmission even when the angle between source and detector was increased up to 12 degrees, demonstrating that direct line-of-sight was not required. Moreover, the system transmitted data at a record-breaking rate of 71 megabits per second (Mbps). “Other groups have used different types of UV sources for transmitting relatively slow nonline-of-sight signals for communications,” says Ooi. “We are the first to achieve multiple tens of Mbps transmission using UV-B LEDs.” Now that they have proven

Pulsed Laser High speed Camera

Glass M

irr or

Long-distance Microscope

Sun, X., Zhang, Z., Chaaban, A.,

air

Ng, T.K., Shen, C. Yan, J., Sun, H., Li, X., Wang, J, Li, J., Alouini, M-S & Ooi, B. 71-Mbit/s ultraviolet-B first contact

LED communication link based on 8-QAM-OFDM modulation. Optics Express 25, 2326723274 (2017).

K AUST DISCOVERY

di s co v e r y. kau s t. e d u . sa

air disk

51

wet

air

From left to right: high-speed camera images captured 0.1, 1.3 and 18 microseconds after first contact of the liquid droplet on the glass platform.


SCIENCE VISUALIZED

GIANT AIR POCKETS WIN THE DRAG RACE Creating teardrop-like gas cavities around metal spheres enables practically friction-free travel through liquids.

times the volume of the metal. The giant air pockets sped down the 2-meter-deep liquid chamber and reached a constant velocity—matching predictions of near-zero drag conditions. By racing their giant air cavities against identically sized plastic projectiles, the team demonstrated that gases decreased drag coefficients by an order of magnitude compared to solids. Analyses also showed the cavity’s fall velocity can be calculated exactly from the initial sphere density and the volume of trapped air. “We showed the sphere-in-cavity can be explained by very simple equations—this could make its way into textbooks,” says Vakarelski. Vakarelski, I. U., Klaesboer, E., Jetly, A., Mansoor, M. M., Aguirre-Pablo, A. A., Chan, D. Y. C. &

P S E

Thoroddsen, S. T. Self-determined shapes and

A method that spontaneously generates torpedoshaped air pockets around objects could help oil tankers and other heavy vessels to save energy through reducing friction and drag in water. Previous research has shown that metal spheres heated to 400 degrees Celsius will free-fall twice as fast in liquids as room temperature orbs. The secret lies in a thin bubble of evaporated gas that materializes around the hot balls and stops liquid molecules from sticking and creating friction. But, even after the researchers Ivan Vakarelski and Siggi Thoroddsen stabilized this gas layer with superhydrophobic coatings on the spheres, the drag forces remained too large. So they looked to create thicker gas layers that would reduce drag even further. The researchers noticed hot spheres fell faster when they were dropped into the liquid instead of being released inside it. Highspeed video cameras revealed that at impact, the spheres were enveloped by an air pocket that pinched off into a teardrop-like shape, five to 15

Science Advances 3, e1701558 (2017).

52

A u g u s t 2 0 18

“H o t s p h e r e s f e l l faster when they we r e d r o p p e d i n t o t h e liquid instead of being r e l e a s e d i n t o i t .”

REPRODUCED FROM REFERENCE 1 UNDER A CREATIVE COMMONS LICENSE © 2017 AAAS

Comparisons between 3D-printed plastic torpedoes and teardrop-shaped air cavities that form around metal spheres reveal that gas bubbles can practically eliminate hydrodynamic drag forces.

velocities of giant near-zero drag gas cavities.


MIMICKING A SWEET SOLUTION TO MOP UP POLLUTION A fast and safe method to prepare a 3D

The repeating regular hierarchical structures are shown by scanning electron microscopy (SEM) images that illustrate how the honeycomb structure has formed at the surface of the material (top) and within the material (bottom).

porous material that mimics the shape of a honeycomb could have broad applications from catalysis to drug delivery or for filtering air to remove pollutants or viruses. The lattice of a honeycomb or the symmetry of a diatom are among complex living structures whose patterns and shapes have long inspired scientists. One recent application is to develop artificial hierarchical porous materials that are stable, yet have a large surface area and the ability to selectively extract materials. The complexity and pattern repeatability across scales from individual compartments to the entire structure, have made it difficult to build them at the nanoscale. A team from KAUST, led by Suzana Nunes, has proposed a simple method that, in just five minutes, can produce a flexible film with a complex hierarchical structure that has repeating patterns of interconnected, regularly shaped pores. With experts in the Imaging and Characterization Core Lab, the researchers used the block copolymer called polystyrene–b–poly (tertbutyl acrylate) (PS–b–PtBA) to demonstrate this method. They tested various concentrations of PS–b–PtBA with different solvent mixtures with the resulting solution cast on a glass plate and evaporated for different time periods to promote the nucleation and growth of cavities with highly porous interconnecting walls. The resulting film was then immersed in water to rinse off the solvent and halt the phase separation. “By using this method we create an important platform to design artificial porous materials which replicate a highly ordered porous and complex systems mimicking nature,” explains lead author, Stefan Chisca. “These have potential use for separations and biological scaffolds.” Chisca, S., Musteata, V-E., Sougrat, R., Behzad, R.R., Nunes S. Artificial 3D hierarchical and isotropic porous polymeric materials. Science Advances 4, eaat0713 (2018).

A cross section of SEM images show that the spherical compartments are interconnected through nanochannels of 15 nm in diameter.

A TEM tomograph shows a 3D surface rendering of a thin section of the film.

A 3D reconstruction of SEM images at the macroscale by serial block face shows the spherical compartments that are a tiny 5μm in diameter.

K AUST DISCOVERY

d isc o ve r y. k a u st. e d u .s a

53


SCIENCE VISUALIZED

MAPPING MOVEMENTS OF OCEAN CREATURES GREAT AND SMALL Big data shows that large marine vertebrates move differently, but consistently, through coastal and ocean waters.

54

A u g u s t 2 0 18

A whale and a turtle differ in size, shape and lifestyle but their patterns of movement are surprisingly similar, reveals the largest collection of movement data for a diverse group of large marine vertebrates. A team of 58 researchers from nine countries and 45 research institutions has collated a satellite telemetry dataset for a diverse set of large marine megafauna: it includes more than 2.8 million locations from more than 2,600 tracked individual animals. And for some species it includes data from as long ago as 1985. Knowing how megafauna move through coastal and oceanic environments will help marine managers to better understand the impacts of human activities on these animals and identify habitats for conservation, explains Carlos Duarte,

2017 HUBERT PIWONSKI

B E S E


SCIENCE VISUALIZED

The largest ever collected data set of marine megafauna movements shows that big marine animals move differently, but consistently, through coastal and ocean waters.

a KAUST co-author of the study, and cofounder of the international collaborative effort, the Marine Megafauna Movement Analytical Program. The tracked animals included 50 types of marine megafauna that are evolutionarily separated by millions of years and use different modes of locomotion—they fly, swim, walk or paddle. The team monitored speed and movement of species of turtles, sharks, dolphins, sea lions, whales and sea birds, such as penguins, gulls and shearwaters.

“O n t h e c o a s t , t h e y m o v e m o r e e r r a t i c a l l y, which is consistent with a search b e h a v i o u r.” Such an enormous and diverse data set enables scientists to draw conclusions not possible from movement data of a single species. “The major advancement of the results reported come from the possibility to compare not only multiple species of marine animals with different modes of locomotion, but also from exploring variability between individuals within species,” explains Duarte. “This confirmed that the remarkably conserved movement patterns, and their flexibility with habitat,

apply both when comparing vastly different species, such as turtles and whales, and when comparing individuals using different habitats within a species” The study found that movement patterns are largely determined by the species, but also influenced by the habitat they move through. “In the open ocean, animals tend to move in straighter lines, reflecting the movement to a specific location. While on the coast, they move more erratically, which is consistent with a search behavior, reflecting that the animal is searching for food and remaining vigilant against predators,” says Duarte. Michael Berumen, another KAUST coauthor of the study, further explains how this information potentially informs conservation: “While animals moving in the open ocean showed surprising consistency in their movement patterns, animals in coastal habitats have much more plasticity and thus perhaps have greater resilience to human alterations of coastal ecosystems.” Sequiera, A.M.M., Rodriguez, J.P., Eguiluz, V.M., Harcourt, R., Hindell, M. et al. Convergence of marine megafauna movements patterns in coastal open oceans. Proceedings of the National Academy of Sciences of the USA 115, 3072-3077 (2018).

K AUST DISCOVERY

d isc o ve r y. k a u st. e d u .s a

55


SCIENCE VISUALIZED

Materials that normally become damaged inside electron microscopes can now be imaged with atom-scale resolution.

A LIGHT TOUCH FOR REVEALING ATOMIC FRAMEWORKS P S E To understand how atomic structure impacts biological function and chemical behavior, researchers often turn to high-resolution transmission electron microscopy (HRTEM). Many compounds, however, are too sensitive for these microscopes as powerful electron beams can knock out atoms or cause adverse heating. A team from KAUST has now developed a set of tools that can minimize beam damage in HRTEM using low doses of electrons.

56

A u g u s t 2 0 18

Metal–organic frameworks (MOFs), with their sponge-like structure, are typical materials too delicate for HRTEM imaging. These compounds, with some of the highest surface areas ever recorded and customizable nanoscale pores, have enormous potential in gas storage and catalysis. But most MOFs breakdown during initial imaging stages when the microscope tries to align its beam with the crystal’s repeating zone axis. Daliang Zhang, Kun Li and colleagues from KAUST’s Imaging and Characterization

Core Lab collaborated with Yu Han’s group to find gentler ways of characterizing MOFs. Previously, the team had shown that special electron detection cameras can capture atom-scale-sized images using a low dose of a few electrons per pixel. However, this approach required sampling large numbers of randomly oriented MOFs to spot crystalline zones. To make alignment simpler, the KAUST researchers developed a one-step procedure based on a parameter called the Laue circle that appears when electron beams encounter periodic structures. “Once we see a Laue circle, we know the crystal’s current orientation and the deviation angle from the desired position,” explains Zhang. “We can then align the crystal using a computer-controlled tilting process.”

Another problem is that beam-sensitive materials often move during electron microscopy imaging. To reduce this type of blurring, the team first took a series of short-exposure frames. Then, through a mathematical Fourier transform technique, they converted the image data of each pixel into a series of sine waves. Filtering out waves with weak amplitudes enabled the researchers to spot true periodic features and correct for image drift. The researchers demonstrated the potential of their new HRTEM methods by resolving detailed features of aromatic rings and metalexposed surfaces of a zirconium-based MOF, as well as subtle structural changes induced by heating. The resulting crystal-clear images may impact fields beyond MOFs as well.


SCIENCE VISUALIZED

New algorithms based on geometric tricks and mathematical transformations enable high-resolution electron microscopes to quickly align and image materials, such as metal– organic frameworks, that are sensitive to beam damage.

PUTTING SOME SKIN IN THE TURBULENCE GAME

Theoretical simulations reveal how subtle changes in friction on an object’s surface can have a large effect on drag. P S E

A TEM grid is picked out from a storage box.

“ The exp er tis e of t he KAUST Core Labs was crucial for changing our HRTEM experiments from a trialand-error process to one that is nearly routine,” says Han. “Now, we can study a number of delicate structures that are conventionally considered inexplorable, which is really exciting,” adds Zhang.

C2018 WAN CHENG

Zhang, D., Zhu, Y., Liu, L., Ying, X., Hsiung, C.-E., Sougrant, R., Li, K. & Han, Y. Atomicresolution transmission electron microscopy of electron beam– sensitive crystalline materials. Science 359, 675-679 (2018).

An algorithm that improves simulations of turbulent flows by enabling the accurate calculation of a parameter called skin friction has been developed by researchers from KAUST and the California Institute of Technology. The application of this algorithm may help aerospace and shipping industries to develop more fuel-efficient transportation. Computing turbulent flow over bluff bodies, such as spheres or cylinders, has many practical engineering applications. However, the large number of parameters involved to accurately solve turbulence simulations means that researchers have to take shortcuts—typically only large, whirlpool-like eddies are computed exactly, while smaller scales of motion can only be modeled to approximation. Large-eddy simulations are confounded by phenomena known as the drag crisis. Conventional explanations of these sudden changes of drag are due to turbulent transition, which changes the flow pattern on body surface. However, these explanations are ambiguous and do not provide a complete understanding. Physicist Ravi Samtaney explains that one of the problems with predicting drag crisis effects is capturing the subtle changes in boundary layers and friction within very complex fluid dynamics. Experimentally it is very difficult to capture near-surface flow especially when the surface is non-smooth or moving surface,” explains KAUST researcher, Wan Cheng. “Computing skin friction from numerical simulation is revealing and exciting”. The team suggested that skin friction might help to explain the physical mechanism of the drag crisis. They investigated a model where fluid flows over a smooth-walled cylinder1 and a cylinder with grooves2. By incorporating methods for the accurate calculation of the skinfriction equation into their code, the team’s research reveals small-scale separation/

reattachment cells that play a significant role. For grooved cylinders, they find the turbulence transition is not the key feature causing the drag crisis.

“S k i n f r i c t i o n might help to explain the physical mechanism of t h e d r a g c r i s i s .” “Large-eddy simulations are the future of computational fluid dynamics in industrial and aerodynamics applications, and skin friction can be an important measure in optimizing this design” notes Samtaney. 1. Cheng, W., Pullin, D. I., Samtaney, R., Zhang, W., & Gao, W., R. Large-eddy simulation of flow over a cylinder with ReD from 3:9×103 to 8.5×105: a skin-friction perspective. Journal of Fluid Mechanics 820, 121–158 (2017). 2. Cheng, W., Pullin, D. I., Samtaney, R., Large-eddy simulation of flow over a grooved cylinder up to transcritical Reynolds numbers. Journal of Fluid Mechanics 835, 327-362 (2018).

K AUST DISCOVERY

d isc o ve r y. k a u st. e d u .s a

57


Researchers in the Ali I. Al-Naimi Petroleum Engineering Research Center take a 21st century approach to energy research. They focus on the flow of fluids, gases and materials through reservoirs. This piece of carbonate rock is from the outcrops of the Jubalia formation found near Riyadh, Saudi Arabia. At depth, these are equivalent to carbonate reservoirs.

Learn more ANPERC.KAUST.EDU.SA

Clara Modenesi Ph.D. student


H E A LT H A N D G E N E T I C S

A DELIVERY PLATFORM FOR GENE-EDITING TECHNOLOGY Nanomaterial coating enables efficient delivery of CRISPR-Cas9 machinery into the cell. P S E | B E S E A new delivery system for introducing gene-editing technology into cells could help safely and efficiently correct disease-causing mutations in patients. The system, developed by KAUST scientists, is the first to use sponge-like ensembles of metal ions and organic molecules to coat the molecular components of the precision DNA-editing technology known as CRISPR/Cas9, allowing efficient release of the genome-editing machinery inside the cell. “This method presents an easy and economically

The zeolitic imidazolate framework forms a cage-like scaffold over the CRISPR/Cas9 machinery.

feasible route to improve on the delivery problems that accompany RNA-based therapeutic approaches,” says Niveen Khashab, the associate professor of chemical sciences who led the study. “This may permit such formulations to be eventually used for treating genetic diseases effectively in the future.” Khashab, who has a background in chemical science, was supported by Assistant Professors of bioscience Jasmeen Merzaban and Mo Li. CRISPR/Cas9 has a double delivery problem: For the gene-editing technology to work like a molecular Swiss Army knife, both a large protein (the Cas9 cutting enzyme) and a highly charged RNA component (the guide RNA used for DNA targeting) must each get from the outside of the cell into the cytoplasm and finally into the nucleus, all without getting trapped in the tiny intracellular bubbles that are known as endosomes.


H E A LT H A N D G E N E T I C S

To solve this problem, Khashab and her lab turned to a nano-sized type of porous material known as a zeolitic imidazolate framework, which forms a cagelike structure into which other molecules can be placed. The researchers encapsulated the Cas9 protein and guide RNA in this material and then introduced the resulting nanoparticles into hamster cells. The encapsulated CRISPR-Cas9 constructs were not toxic to the cells. And because particles in the coating material become positively charged when absorbed into endosomes, they caused these membrane-bound bubbles to burst, freeing the CRISPRCas9 machinery to travel to the nucleus, home to the cell’s genome. There the gene-editing technology could get to work.

“T h e s e c a g e - l i k e stuctures are biocompatible and can be triggered o n d e m a n d .” Using a guide RNA designed to target a gene that caused the cells to glow green under fluorescent light, Khashab and her team showed that they could reduce the expression of this gene by 37 percent over four days with their technology. “These cage-like structures are biocompatible and can be triggered on demand, making them smart options to overcome delivery problems of genetic materials and proteins,” says the study’s first author Shahad Alsaiari, a Ph.D. student in Khashab’s lab. The researchers plan to test their system in human cells and in mice, and eventually, they hope in clinical trials. Alsaiari, S.K., Patil, S., Alyami, M., Alamoudi, K.O., Aleisa, F.A., Merzaban, J., Li M. & Khashab, N.M. Endosomal escape and delivery of CRISPR/Cas9 genome editing machinery enabled by nanoscale zeolitic imidazolate

COMPUTER MODELS COMBAT MALARIA A new malaria metabolic model may uncover better ways to treat a highly deadly disease.

framework. Journal of the American Chemical Society 140, 143–146 (2018). IMAGE CREDIT: REPRINTED (ADAPTED) WITH PERMISSION FROM ALSAIARI, S.K., PATIL, S., ALYAMI, M., ALAMOUDI, K.O., ALEISA, F.A., MERZABAN, J., LI M. & KHASHAB, N.M. ENDOSOMAL ESCAPE AND DELIVERY OF CRISPR/CAS9 GENOME EDITING MACHINERY ENABLED BY NANOSCALE ZEOLITIC IMIDAZOLATE FRAMEWORK. JOURNAL OF THE AMERICAN CHEMICAL SOCIETY 140, 143–146 (2018). © 2018 AMERICAN CHEMICAL SOCIETY

60

A u g u s t 2 0 18

B E S E

|

C E M S E

As one of the world’s deadliest pathogens, Plasmodium spreads relentlessly from host to host. But a computer model created by KAUST scientists may reveal and help exploit the parasite’s unknown

weaknesses to uncover new options for treating malaria. The Plasmodium parasite needs both a mosquito and vertebrate host to reproduce and complete its life cycle. Through what would otherwise be harmless insect bites, Plasmodium rapidly multiplies and spreads from


H E A LT H A N D G E N E T I C S

mosquitoes to human hosts, where it causes malaria and kills nearly half a million people worldwide each year. As Plasmodium infects red blood cells, transmits between hosts and reproduces, the single-celled parasite takes different forms. A key limitation of current malaria drugs is that they only treat the form of Plasmodium that actively causes malaria symptoms. Yet, treatments that target the pathogen’s transmitting form may nip the disease in the bud. Searching for potential malaria drug targets, Ph.D. student Alyaa Abdel-Haleem

KAUST researchers predict potential drug targets in the malaria parasite’s metabolism that may reveal new treatment options for malaria. The research team includes (L-R): Xin Gao, Takashi Gojobori, Katsuhiko Mineta and Alyaa M. Abdel-Haleem.

and her colleagues investigated the Plasmodium genetic blueprint. They focused on the genes involved in metabolism— the chemical reactions that allow the parasite to grow, reproduce and respond to its environment. “Our aim in this study was to provide a model that catalogues metabolic differences between species and life-cycle stages to explore novel treatment strategies and targets,” explains Abdel-Haleem. First, the scientists created computer models that combined the genetic blueprint of Plasmodium with information

on how metabolic genes turned on and off in five different species and at five different stages of its life cycle. They then deleted genes in their models and ran simulations to test which genes were integral to the parasite’s survival. The scientists have already come across several potential targets. For one, the simulations revealed that in its symptomcausing form, the B vitamin pantothenate is an essential vitamin the Plasmodium falciparum species require for replication, while the same factor is not crucial for the growth of the malaria species that infect rodents. “A potential strategy is for vaccination to block this important pathway for the parasite’s growth and to limit its survival and propagation,” Abdel-Haleem says. Abdel-Haleem and her supervisors, Takashi Gojobori and Xin Gao, with computational support from Katsuhiko Mineta hope their Plasmodium simulation model will help uncover even more drug treatment leads. They highlight that the models can be used to translate findings across experimental models and human-infecting species. Meanwhile, the team will continue to add more genetic information about Plasmodium as it becomes available. “The most crucial step is to keep the model updated for future use,” says Abdel-Haleem. Abdel-Haleem, A. M., Hefzi, H., Mineta, K., Gao, X., Gojobori, T. et al. Functional interrogation of Plasmodium genus metabolism identifies species- and stage-specific differences in nutrient essentiality and drug targeting. PLoS Computational Biology 14, e1005895 (2018).

K AUST DISCOVERY

d isc o ve r y. k a u st. e d u .s a

61


GET SOCIAL WITH KAUST

follow us on social media

(screen shot of kaust other social media page)

KAUSTofficial @kaust_news kaustedu kaustofficial KAUST

discovery.kaust.edu.sa


H E A LT H A N D G E N E T I C S

2017 JASMEEN MERZABAN

ZOOMING IN ON BRAIN FUNCTION Scrambled Control

CD34-Knockdown

Cells without CD34 (above) lack the tentacle-like extensions (red arrows below) that help cells bind to adhesion molecules in the bone marrow.

NOT JUST A STEM CELL MARKER

C E M S E

The protein CD34 is predominantly regarded as a marker of bloodforming stem cells but it helps with migration to the bone marrow too. B E S E A protein used to identify blood-forming cells is much more than a mere surface marker. New research shows that this protein, known as CD34, also plays a key role in binding adhesion molecules in the bone marrow. The discovery that this binding aids in the proper engraftment of blood-forming stem and progenitor cells following their transplantation is a result that opens the door to “improving the migration of these cells for therapeutic endeavors,” says Jasmeen Merzaban, the KAUST biochemist who led the team. Stem cell transplants are used to treat patients with a variety of life-threatening blood disorders. These stem cells, when derived from an adult (as opposed to from cord blood), are isolated by giving the donor a drug that causes stem cells in the bone marrow to mobilize and enter the bloodstream. The blood is then run through a device that extracts all the cells expressing CD34. These CD34-positive cells can give rise to all the various types of blood components—but they’re not the only ones with this ability. Some cells that don’t express this surface marker can do the same; however, CD34-negative cells in circulation aren’t as good at finding their way to the bone marrow. Thus, doctors have tended to focus on CD34 selection as an easy and effective means of enriching for highpotential blood stem and progenitor cells despite the longstanding mystery of the normal biological function of CD34. Merzaban and her colleagues revealed

one of the functions of this protein by first testing different populations of blood-forming cells for their ability to bind adhesion molecules. They showed that only those cells expressing CD34 could do so, and an unbiased protein screen revealed that CD34 itself was responsible for this binding. Knocking down the protein confirmed CD34’s essential role in cell migration. According to the study’s first author, Dina AbuSamra, a former doctoral student in Merzaban’s lab now at Harvard Medical School, the results have therapeutic implications beyond simply understanding transplantation. As she points out, the CD34 protein that’s found on the surface of leukemic stem cells is different from the one on healthy blood-forming stem cells. There is potential to exploit this difference “to identify leukemic stem cells and, in theory, target them using various approaches,” AbuSamra says. Merzaban also suggests that CD34negative blood-forming stem cells—a population currently overlooked in transplantation medicine—could be manipulated in ways that boost their binding abilities. Adding these cells to the CD34positive population might collectively augment overall efficiencies of the procedure, leading to long-term success following transplants. AbuSamra, D.B., Aleisa, F.A., Al-Amoodi, A.S., Ahmed, H.M., Chin. C.J., Abuelela, A.F., Bergam, P., Sougrat, R. & Merzaban, J.S. Not just a marker: CD34 on human hematopoietic stem/progenitor cells dominates vascular selectin binding along with CD44. Blood Advances 1, 2799-2816 (2017).

Faster computations will allow researchers to see the finer details of brain activity in functional brain imaging.

A computationally efficient data-processing scheme will make it possible to see correlations in brain activity between different parts of the brain at unprecedented resolution. The statisticsbased computation scheme, developed by researchers, also tackles one of the most critical problems of medical and biological imaging—how to process imaging data fast enough to realize the full exploratory power of the latest high-resolution imaging techniques. The development of functional magnetic resonance imaging (fMRI) in the early 1990s was one of those true Eureka moments for brain research. Using existing noninvasive MRI technology, fMRI maps the distribution of blood oxygen in the brain, which is closely correlated with brain activity. With fMRI, it is possible to take snapshots of brain activity in response to specific stimuli, such as speech, responding to memory questions or visual scenes. While fMRI is capable of taking high-resolution images consisting of hundreds of thousands of points or voxels, it is an enormous computational task to map the correlations between simultaneous brain function across different areas of the brain. Even with the range of computing power available today, such computations are not feasible by direct

K AUST DISCOVERY

d isc o ve r y. k a u st. e d u .s a

63


methods and so require a more computationally efficient approach. Marc Genton and Hernando Ombao from KAUST, in collaboration with Stefano Castruccio from the University of Notre Dame in the United States, have addressed this problem. They developed a statistics-based computational scheme that matches activity in different parts of the brain at different spatial scales, from whole-of-brain to smaller regional structures and down to the tiniest brain volume. “Using a statistical approach, our multiresolution approach essentially breaks up the spatial component of the fMRI data

into different scales—from global to local,” says Ombao. Developed as part of a collaboration with the stroke rehabilitation center at the University of California Irvine, the computation scheme calculates the statistical shape of increasingly large populations of activity readings in a way that lends itself readily to distributed computing, making it highly efficient. Not only does this solve the computational issue, it improves the interpretability of results, ensuring that the connectivity between activities can be characterized both within each brain region and

The multiscale statistical scheme efficiently captures correlated activity between different parts of the brain.

across different brain regions. “It is important to take into account how spatially separated neuronal units communicate with each other in modeling fMRI data in order to avoid misleading results, such as false activations, or an inability to detect activity.” says Ombao. “Correct identification

of activated and inactivated units will help us to improve our understanding of human brain function in both healthy and diseased populations.” ​ Castruccio, S., Ombao, H. & Genton, M.G. A scalable multiresolution spatio-temporal model for brain activation in fMRI. Biometrics early online article 22 January 2018

1,019 students registered from 73 countries * Fall 2017

Apply today: kaust.edu.sa

64

A u g u s t 2 0 18

REPRODUCED WITH PERMISSION FROM REFERENCE 1.© 2018 THE INTERNATIONAL BIOMETRIC SOCIETY

H E A LT H A N D G E N E T I C S


The Advanced Materials and Porous Membranes Center brings chemical scientists together with chemical and electrical engineers to work on problems related to petrochemicals, natural gas processing and air separation. Membranes like the tiny cylindrical ones shown here are the future of sustainable industrial separations.

Learn more AMPM.KAUST.EDU.SA


In the KAUST Solar Center, material and chemical scientists and engineers collaborate to optimize efficiency, realize conversion and ultimately scale-up solar-energy-derived electricity generation. Learn more KSC.KAUST.EDU.SA

Michele De Bastiani Postdoc

Profile for KAUST

KAUST Discovery - Issue 6  

KAUST Discovery - Issue 6  

Recommendations could not be loaded

Recommendations could not be loaded

Recommendations could not be loaded

Recommendations could not be loaded