KAUST Discovery Issue 1

New LED technologies promise to be the next step forward. P. 58

ISSUE ONE - 2015

DISCOVERY.KAUST.EDU.SA

EXPLORING THE BRAIN BY MIMICKING THE BRAINA new collaboration could lead to supercomputers emulating the efficiency of the brain P. 12

LIGHTS UP FOR CHAOTIC STORAGEChaotic optical resonators can trap more light energy than their orderly counterparts P. 63

GETTING MORE FUEL FROM WATERProducing hydrogen from water is improved by creating an orderly catalyst P. 87

Inspiring

SCIENTIFIC DISCOVERY

Our eleven strategically connected Research Centers span across three Academic Divisions, encompassing multiple disciplines and encouraging our faculty, researchers, and students to be entrepreneurial and free-spirited while pursuing research that translates science intodiscoveries and new technologies.

• Advanced Membranes and Porous Materials Center • Catalysis Center• Clean Combustion Research Center• Computational Bioscience Research Center• Center for Desert Agriculture • Extreme Computing Research Center

• Red Sea Research Center • Solar and Photovoltaics Engineering Research Center • Upstream Petroleum Engineering Research Center • Visual Computing Center • Water Desalination and Reuse Center

KAUST Research Centers:

kaust.edu.sa

ur founder, King Abdullah, created KAUST to become a “model for advanced education and scientific research” and

to “promote the economic development and social prosperity of the people of the Kingdom and the world.”

It is this vision that inspires talented peo-ple from around the globe to choose KAUST as their destination for distinctive and collaborative research, where they are free to aim high and to explore the world’s most difficult problems without constraints. As you page through these stories of Discov-ery, I hope that the KAUST values of curios-ity and passion for science and impact will inspire you, as they have for me.

Our research and educational environ-ment is comprised of three Academic Divisions encompassing multiple disci-plines and 11 strategically connected and focused Research Centers to advance science in areas of global significance, including our major research thrusts of food, water, energy, and the environment — the global challenges facing our world.

Our distinctive research and educational focus is supported through exceptional research facilities from our transmission electron microscopes and femtosecond lasers to world-ranked supercomputers and immediate access to the depths of the Red Sea — there is no limit to what our engineers and scientists can achieve.

As a catalyst for innovation and eco-nomic development, KAUST’s network of academic and industry partners offers our global, mobile, and entrepreneurial faculty and students a leading edge in

From Curiosityto Innovation

“Substantial academic and economic contacts make KAUST the ideal environment to nurture innovation and invention, and ultimately, local and global impact.”

OJean-Lou ChameauPresident

today’s increasingly competitive land-scape. Access to corporate partnerships and commercialization tools allows researchers to turn bench science into marketable prototypes without ever leaving the campus. Substantial academic and economic contacts make KAUST the ideal environment to nurture innovation and invention, and ultimately, local and global impact.

The stories highlighted within this publication are a snapshot of the research, discovery, and innovation ongoing at KAUST. Our aspiration to be a destination for scientific and technological education and research continues to energize our people and their ideas. Their passion, dedi-cation, and curiosity propel our journey to serve as a beacon of knowledge within Saudi Arabia and to the world. I invite you to join us in this journey.

Yours in discovery,

Jean-Lou ChameauPresident

1I S S U E O N E

90 69

71

3895

H I G H L I G H T S

91

2061

SOLAR CELLS:A SOLUTION FORBETTER CRYSTALSA fast and cost-efficient fabrication process for high-quality perovskite crystals bridges the gap to silicon.

DNA DIVISION CAN SLOW TO A HALTTermination sites of DNA are shown to stop slow-moving replication forks but not faster ones.

HONEY BEE BEHAVIOR IS IN THE GENESAn integrated set of genetic mechanisms controls whether bees behave as foragers or nurses.

RUN FOR YOUR BRAIN Lactate plays an unexpected role in brain function.

ATOMICALLY FLAT SEMICONDUCTOR DEVICESPerfect interfaces between sheets of two-dimensional semiconductorsenable advanced electronic devices.

NANO THERAPEUTICS HEAT UPSmart, stretchable pads open up a new approach for thermotherapy.

86

7130

A LIGHT LOAD FOR NANO-PORTERSTiny carriers assembled from oppositely charged nanoparticles open to release their cargo under light exposure.

WARMING UP FORTHE DEEP DIVEDevil rays soak up the sun’s heat then make some of the deepest and fastest dives ever recorded in the ocean.34

A MODEL FOR CORAL-ALGAE RELATIONSHIPSAnalysis of sea anemone genome yields unprecedented detail of anemone-algae symbiosis, and may provide a model for coral symbiosis.

PLATE SEPARATION BIRTHS TWO VOLCANIC ISLANDSThe emergence of two volcanic islands in the Red Sea suggests a larger underlying event linked to African Arabian plate separation.

D I S C O V E R I N G N E W M A T E R I A L S

U N D E R S T A N D I N G T H E H U M A N B O D Y

E X P L O R I N G T H E R E D S E A

PH-RESPONSIVE PARTICLES YIELD A TERRIFIC TRAPNanoparticles withpores that expandand shrink couldprove valuable forbiochemical research and drug delivery applications.

HONEY BEE BEHAVIOR

U N D E R S T A N D I N G T H E H U M A N B O D YU N D E R S T A N D I N G T H E H U M A N B O D YU N D E R S T A N D I N G T H E H U M A N B O D Y

2

33

11

8480

8763

ASSESSING SEAWATER SAFETYElevated bacterial populations in waters near beaches and urban areas could pose a problem for desalination plants. 23

72GROWING ON SALTY SOILSKAUST Center for Desert Agriculture leads research to improve crop yields from desert soils.

A ONE WAY TRIPFOR WATERA material for filtration that is easy and cheap to produce could aid water treatment, solvent filtration and membrane-catalysis.

33WATCHING FISH ADAPTTO CLIMATE CHANGEA coral reef fish can acclimate to warm temperatures in just two generations.

GETTING MOREFUEL FROM WATERProducing hydrogen from water is improved by creating an orderly catalyst.

BLUEPRINT GUIDES THE SHAPEOF THINGS TO COMEThe ability to more precisely design an industrial material will support broad applications such as the storage of gas, including CO2.

IMPROVING COMBUSTION FORA CLEANER FUTUREThe Clean Combustion Research Center aims to develop technologies for future fuel formulations, more efficient engines, and new methods for power generation. 84

storage of gas, including CO2.

LIGHTS UP FORCHAOTIC STORAGEChaotic optical resonators can trap more light energy than their orderly counterparts.

A DIFFERENT KIND OF LIGHTThe discovery of the incandescent light bulb has transformed human existence. New LED technologies promise to be the next step forward.

A SOLAR HEATER INSPIRED BY THE LOTUS FLOWERChemical tricks improve the efficiency and durability of photothermal membranes that use sunlight to turn water into steam.

58

U T I L I Z I N G S A LT W A T E R

I M P R O V I N G A LT E R N A T I V E E N E R G I E S

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

87

18ISSUE ONE - 2015

DISCOVERY.KAUST.EDU.SA

3I S S U E O N E

Never miss out on the latest KAUST research

Sign up to receive an e-alert once every two weeks with the latest updates on the exciting research, technologies, and innovations emerging from KAUST.

Visit discovery.kaust.edu.sa to subscribe.

Subscribe to KAUST Discovery

Can Red Sea coral reefs save corals

elsewhere?

Will LED redefine our lives again?

Can chaos trump order when it comes

to data storage?

B I O L O G I C A L A N D E N V I R O N M E N T A L S C I E N C E A N D E N G I N E E R I N G D I V I S I O N

11 12

34Analysis of sea anemone genome may provide a model for coral symbiosis.

A model for coral-algae relationships

23Elevated bacterial populations in waters near beaches and urban areas could pose a problem for desalination plants.

Assessing seawater safety

29Discovery of the mechanism by which a protein confers salt tolerance in plants could boost crop yields in high-saline soils.

Plants coping with salt stress

14Treated wastewater may be suitable for some irrigation uses, but antibiotic-resistant microbes could be a problem.

Resistance requires a rethink of reused water

20Termination sites of DNA are shown to stop slow-moving replication forks but not faster ones.

DNA division can slow to a halt

37Resistance to a popular herbicide provides insight into the control of a key biosynthetic pathway.

Shedding light on the shikimate pathway

26A leader in desalination science, TorOve Leiknes gives a major boost to water treatment research in Saudi Arabia.

KAUST takes on an expert worth his salt

Novel use of sensors and associated high-resolution imaging in agriculture aims to facilitate a more sustainable future.

Sensing for sustainable agriculture40

28A look at life in the depths of the ocean reveals an efficient system of pumping carbon out of the atmosphere.

Ocean’s carbon pump reaches reaches new

36Enzymes crucial to parasite growth offer clues in fight against malaria.

Parasite scan yields new targets

22Wastewater treatments based on bioelectro-chemical systems can generate energy and remove potentially toxic compounds.

Bacterial power to reduce toxicity of water supply

15Mysterious deep dwelling fish are vastly more plentiful than previously thought.

Plenty more fish in the deep sea

30Lactate plays an unexpected role in brain function.

Run for your brain

24Analyses of marine bacteria offer insights into processes of carbon storage and release beneath the sea.

Dynamics of deep-sea carbon deposits

18KAUST Center for Desert Agriculture leads research to improve crop yields from desert soils.

Growing on salty soils

Chemical tricks improve the efficiency and durability of photothermal membranes that use sunlight to turn water into steam.

A solar heater inspired by the lotus flower

A new collaboration could lead to supercomputers emulating the efficiency of the brain.

Exploring the brain by mimicking the brain

Devil rays soak up the sun’s heat then make some of the deepest and fastest dives ever recorded in the ocean.

Warming up for the deep dive38

A coral reef fish can acclimate to warm temperatures in just two generations.

Watching fish adapt to climate change33

Rather than migrating, whale sharks in Tanzania hide surprisingly close to home year-round.

Whale sharks hide in plain sight16

Scientists use traditional biochemistry technique to study interactions that trap cells in circulation.

Helping flowing cells make a connection32

C O N T E N T S

DISCOVER MORE RESEARCH ATdiscovery.kaust.edu.sa

B E S E

5I S S U E O N E

Providing state-of-the-art facilities, training and service to KAUST faculty, students, researchers and industrial partners

The core laboratories are a prominent feature of theKAUST interdisciplinary research ecosystem, with over135 staff, scientists, engineers, technical specialistsand administrative support.

Comprised of eight laboratories organized around one central mission, they provide state-of-the-art facilities, training and service to KAUST faculty, students, researchers and industrial partners.

• Analytical• Biosciences• Coastal and Marine Resources• Imaging and Characterization• Nanofabrication• Supercomputing• Visualization• Workshops

kaust.edu.sa

KAUSTCore Labs

C O M P U T E R , E L E C T R I C A L A N D M A T H E M A T I C A L S C I E N C E A N D E N G I N E E R I N G D I V I S I O N

69Smart, stretchable pads open up a new approach for thermotherapy.

Nano therapeutics heat up

C E EM S

4946The new supercomputer will enable ground-breaking scientific modeling and analysis in Saudi Arabia and worldwide.

Taking computing to the next level

Bendable electronics could help make robust wearable devices that can continuously monitor a person’s health.

Bent, but not broken

63A surprisingly simple algorithm helps computers perceive individual objects inside videos from their movement patterns.

Visual computing hitsa moving target62

Chaotic optical resonators can trap more light energy than their orderly counterparts.

Lights up for chaotic storage

50 52Specialized word search method sheds light on phenotypic similarity of diseases.

Disease researchers have a way with words

A microchip designed to generate and control rogue waves of light on the nano-scale has many potential applications.

Optical chips harness the power of rogue waves

6867Magnetic nanowires with weak magnetic fields and low frequencies can destroy cancer cells without generating heat.

Targeting cancer cells with tiny magnetic wires

An improved peak fitting procedure enables a better determination of protein structures.

Peak performance for proteins

5857Identifying noise in communication signals helps to filter out glitches and improve transmission quality.

Signal noise annoys no more

The discovery of the incandescent light bulb transformed human existence. New LED technologies may be the next step forward.

A different kind of light

54 56A fast computational method optimizes sensor measurement networks for noisy, sparsely observed environments.

Taking the guesswork out of experimental design

Lightweight and low-cost device uses friction inside paper-based coils to transform mechanical motion into electricity.

An origami “slinky” that harvests incidental energy

64 66State-of-the-art facilities and world-class research projects give rise to thriving startup companies based at KAUST.

A breeding ground for successful startups

A novel computing technique recognizes and captures the distinctive surface patterns appearing in videos and images.

Resolving richer textures with computer vision

60 61A tiny device broadens the bandwith to enable absorption with wide-reaching potential for electrical engineering.

Perfect absorption graphene-style

An integrated set of genetic mechanisms controls whether bees behave as foragers or nurses.

Honey bee behavior is in the genes

43 44An algorithm that maximizes the difference between data categories achieves high accuracy in classifying faces.

Finding the face inthe crowd

Metallic nanostructures absorb light better than any other known structures.

The darkestblack

THIS MAGAZINE IS PUBLISHED BY NATURE PUBLISHING GROUPFOR KING ABDULLAH UNIVERSITY OF SCIENCEAND TECHNOLOGY (KAUST)

KING ABDULLAH UNIVERSITY OF SCIENCE AND TECHNOLOGY (KAUST)THUWAL 23955-6900 - KINGDOM OF SAUDI ARABIAWEB: WWW.KAUST.EDU.SANATURE PUBLISHING GROUPTHE MACMILLAN BUILDING - 4 CRINAN STREET - LONDON, N1 9XW, UKEMAIL: [email protected] - WEB: WWW.NATURE.COM

C O N T E N T S

7I S S U E O N E

Collaborate. Innovate

Thrive.

INDUSTRY | INVENTORS | ENTREPRENEURS

Through building a strong culture of entrepreneurship, generating public benefit by commercializing research, and engagingclosely with industry and other partners, KAUST is a hub of innovation and a catalyst for economic development.

innovation.kaust.edu.sa

Collaborate. Innovate

Thrive.

INDUSTRY | INVENTORS | ENTREPRENEURS

Through building a strong culture of entrepreneurship, generating public benefit by commercializing research, and engagingclosely with industry and other partners, KAUST is a hub of innovation and a catalyst for economic development.

innovation.kaust.edu.sa

P H Y S I C A L S C I E N C E A N D E N G I N E E R I N G D I V I S I O N

P ES

Tiny carriers assembled from oppositely charged nanoparticles open to release their cargo under light exposure.

A new, cheap material for filtration could aid water treatment, solvent filtration and membrane-catalysis.

A light load fornano-porters

One-way tripfor water71 72

Nanoscale thin films containing glasslike magnetic states can lead to the development of novel devices.

Glassy spin clusters shatter expectations82

Replacing organic molecules surrounding atomically precise silver nanoparticles allows practical applications.

Ready to use neat and complete nanoparticles83

The fabrication of branched titanium dioxide nanomaterials allows solar cells with an improved performance.

Branching out into solar cells92

Thin film membranes could efficiently separate carbon dioxide and other gases from mixed gas flow streams.

Membranes that can manipulate gases75

KAUST aims to develop technologies for future fuels, more efficient engines and new methods for power generation.

Improving combustionfor a cleaner future80

Researchers reveal a low-impact synthetic strategy for producing highly catalytic supported small nickel nanoparticles.

Softly softly approach for tiny catalyst79

Nanoparticles with pores that expand and shrink could prove valuable for biochemical research and drug delivery applications.

pH-responsive particles yield a terrific trap90

A fast and cost-efficient fabrication process for high-quality perovskite crystals bridges the gap to silicon.

Solar cells: a solutionfor better crystals91

Producing hydrogen from water is improved by creating an orderly catalyst.

Getting more fuel from water87

An underwater landslide triggered by the 2011 earthquake in Japan may have exacerbated the resulting tsunami.

Tsunami: The importance of underwater landslides88

Simulations reveal the final moments of a fuel droplet as it combusts in a spray injection engine.

Spreadingthe flame78

First-time reports of the statistical properties of “whirlpools” show they are frequent and seasonal.

Unlocking the mysteries of red sea eddies76

Performance improvements of indium zinc oxide transistors could lead to enhanced transparent displays.

Water-treated semiconductors up transistor speed74

The ability to more precisely design an industrial material will support broad applications such as the storage of gas.

Blueprint guides the shape of things to come84

Perfect interfaces between sheets of two-dimensional semiconductorsenable advanced electronic devices.

Atomically flat semiconductor devices86

Air layers that wrap around liquid drops can retain their geometries a thousand times longer than theory predicts.

Antibubbles makea splash96

The emergence of two volcanic islands in the suggests a larger event linked to African-Arabian plate separation.

Plate separation births two volcanic islands95

Efficiently extracting the charge required by quantum dot solar cells can be controlledby chemically altering molecules.

On-off switches for quantum devices94

C O N T E N T S

DISCOVER MORE RESEARCH ATdiscovery.kaust.edu.sa

9I S S U E O N E

Supporting researchfrom ideas to impactStarting from the development of project ideas within KAUST and with best-in-class global collaborators, to evaluating and enhancing the impact of the research outcomes and guiding future actions, KAUST’s Office of Sponsored Research supports research at KAUST from ideas to impact.

Global collaborators are invited to attend the January – May 2016 conferencesfunded by the KAUST Office of Sponsored Research.

kaust.edu.sa

January 25-27 Computational and Experimental Interfaces of Big Data and Biotechnology

February 1-3 Catalysis for Artificial Photosynthesis

February 8-10 Dissolution and PrecipitationImplications for Energy Geo-Engineering

February 15-17 Physics and Chemistriesat Hydrophobic Interfaces

February 22-24 From Plant Genomics to Agriculture

February 29 - March 2 Research Conference onImaging & Visualization

March 7-9 Clean Combustion Research Center Workshop of Future Fuels

March 14-16 KAUST/NSF Research Conference on Electronic Materials, Devices and Systems for a Sustainable Future

April 4-6 Physics-Based Descriptions of Flow Architecture in Large Volumes of Reservoir Rock

May 9-11 Scalable Hierarchical Algorithmsfor Extreme Computing

Researchers found inspiration for the new distillation device in the floating lotus flower, which is able to send waxy molecules to repair damage to its hydrophobic leaves.

ROBE

RTO

ORE

CCH

IA /

ALAM

Y ST

OCK

PH

OTO

Chemical tricks improve the efficiency and durability of photothermal membranes that use sunlight to turn water into steam.

A

A solar heater inspired by the lotus flower

point-of-use solar distillation device that can clean up salt-water and wastewater without producing greenhouse gases

has been constructed by a research team from KAUST1.

The key to the new technology is a floating membrane coated with a special light-absorbing polymer that repairs its hydrophobic “skin" when damaged.

For centuries, attempts have been made to use the sun’s heat to distill clean water from polluted sources. Simple solar stills, such as a glass plate placed over a water-filled box, are inexpensive to operate but are also notoriously inefficient. This is because water is a poor light absorber, and any captured heat tends to distribute uni-formly through the still instead of localiz-ing at surfaces where evaporation occurs.

To combat these problems, researchers are developing floating “solar generator" materials that heat up quickly in sunlight and then trap heat at air–water interfaces for steam production.

These devices are usually coated with

water-repellant waxy molecules, such as fluorinated alkyl chains, for better floating. However, damage from ultra-violet rays and oxidative chemicals can degrade the hydrophobic layers, causing the generator to sink.

Inspired by the lotus flower, a plant that restores damage to its hydrophobic leaves through the migration of waxy molecules, Peng Wang and colleagues from the University’s Biological and Environmental Science and Engineering Division developed a self-healing solar generator.

The researchers coated a tightly woven stainless steel mesh with polypyrrole (PPy), a light-absorbing polymer with high photothermal con-version efficiency and bumpy surface microstructures. The team modified the PPy film with fluoroalkylsilane chains, enabling it to act as a reservoir that sup-plies additional hydrophobic chains to

damaged regions through biomimetic self-migration.

The new device nearly tripled the output of freshwater from typical solar stills, thanks to a significant jump in temperature at the air–water interface and a conversion efficiency of close to 60 percent. It also exhibited remarkable damage resistance: after the team used a plasma source to oxidize the mesh and make it sink to the bottom of a beaker, they found a simple one-hour treatment in sunlight was sufficient to restore its self-floating capability.

The team’s first prototype — a trans-parent plastic condensing chamber and solar fan mounted on top of a PPy-coated mesh — floats lightly on the sur-face of seawater and distills a steady stream of water for more than 100 con-secutive hours.

“Careful material selection allowed us to integrate two types of functions into one distillation device,” Wang said. “This has great potential to be employed in point-of-use potable water production.”

1. Zhang, L., Tang, B., Wu, J., Li, R. & Wang, P.

Hydrophobic light-to-heat conversion membranes

with self-healing ability for interfacial solar

heating. Advanced Materials, 17 July 2015 doi:

10.1002/adma.201502362

“A simple one-hour treatment in sunlight was sufficient to restore the mesh’s self-floating capability.”

1 1I S S U E O N E


A new collaboration could lead to supercomputers emulating the efficiency of the brain.

A project to push the limits of supercomputing with high-performance software may also provide fresh insights

into the workings of the brain, say researchers from KAUST.

Although they are often compared to each other, the human brain is differ-ent from a computer. Key differences include the brain’s daily energy require-ments, which are similar to those of a lightbulb, as well as the brain’s ability to build itself. The brain can program itself during development, and then continu-ously reprograms and reconfigures its own architecture in response to every-day experiences.

Brain-inspired or “neuromorphic" computing aims to build machines that emulate the brain to vastly improve their information processing capabilities and make them more energy efficient.

The new project is a collaboration between researchers at the Visualiza-tion Core Lab facility at KAUST — which offers a plethora of state-of-the-art technologies for analyzing and present-ing scientific data — and those at the École Polytechnique Fédérale de Laus-anne (EPFL) in Switzerland. The Swiss researchers are part of the Blue Brain Project, an ongoing international multi-billion Euro effort to reverse engineer the brain down to the molecular level in a supercomputer.

The Saudi-Swiss collaboration aims to develop new supercomputing software that allows the machines to be used as interactive scientific instruments that can simultaneously simulate, visualize and analyze data. Principal investiga-tor, Pierre Magistretti explains that “the exa-scale computers expected to appear

before the end of the decade will gen-erate petabytes of data that would cost millions of dollars just to move.”

“The solution to this is to have fully interactive supercomputing, in which scientists extract data from simulations as they are running, just as they do with other scientific instruments," he says.

Interactive supercomputing will allow researchers to perform in situ visualiza-tions of their data sets, navigate them in real-time and interact with on-going simulations in various ways, a process known as computational steering.

“This technology does not exist today, so supercomputers will require a radi-cally new approach to data and resource sharing,” says Magistretti. “The Blue Brain Project at EPFL has developed a roadmap to reach interactive exa-scale supercomputing.”

The hardware requirements for this include an extremely fast network between the supercomputer running the simulation and the supercomputer that analyses and visualizes the state of the simulation in real time. KAUST, through its considerable supercomputer capacity, is able to provide this capability.

A second aim of the collaborators is to deepen our understanding of what drives the brain to reliably perform

Exploring the brain by mimicking the brain

computations with minimal energy requirements. This will involve gener-ating detailed computer models of the interactions between neurons, the blood vessels in the brain and glial cells, the non-neuronal cells that regulate cer-ebral blood flow and energy uptake by brain cells.

“We aim to analyze these intimate relationships using electron micros-copy data processed to produce 3D fully-immersive virtual reality,” says Magistretti.

The neuron-glia-vascular unit is the basis of activity-dependent energy delivery. The computer model, Magis-retti explains, will help the researchers to understand fundamental brain processes that are responsible for the signals that researchers have detected through func-tional brain imaging techniques such as PET and fMRI.

The ability to properly model the neuron-glia-vascular unit will enable the researchers to reproduce functional brain imaging data in silico, which will help them to understand what goes wrong in certain neuropsychiatric dis-eases.

The majority of this research is being performed at KAUST. “We are recon-structing the electron microscopic images here at KAUST, and we are also developing algorithms that allow us to identify all the cells in each microscope section and transform this information in the virtual reality environment,” says Magistretti.

He explains that EPFL scientists are contributing to some of the modelling algorithms, which will enable the data obtained to be integrated with the inter-national Human Brain Project.

“The ability to properly model the neuron-glia-vascular unit will enable the researchers to reproduce functional brain imaging data in silico.”

KAU

ST V

ISU

ALIZ

ATIO

N C

ORE

LAB

B E S E

1 2

Observation and explorative analysis of the 3D dataset in the Visualization Lab at KAUST.

1 3I S S U E O N E


KAU

ST

Treated wastewater may be suitable for some irrigation uses, but antibiotic-resistant microbes could be cause for concern.

F

Resistance requires a rethink of reused water

resh water is scarce in Saudi Ara-bia, and the majority of this pre-cious resource is used for irrigation to support domestic agriculture.

Some of this water demand could be met by using treated wastewater, and Pei-Ying Hong’s research team at KAUST recently conducted a careful assessment of whether this water is “clean" enough for farm use1.

Hong notes that the total output of Saudi Arabia’s 30 wastewater treat-ment plants could replace as much as 10 percent of the fresh water now being used for irrigation. Unfortunately, this resource is largely unused because of

safety concerns among the general pub-lic. “The majority of treated wastewater is reused for industry, landscaping or for aquifer and river-basin recharge,” she says. “Only a handful of pilot-scale farms in Riyadh utilize treated wastewater to grow agricultural crops.”

Hong and colleagues analyzed the out-put from one plant in Jeddah over the course of a year using a variety of tech-niques to determine the quantity and diversity of the bacterial population in the treated wastewater. On the one hand, the treatment process was generally effective at eliminating known pathogens, including fecal coliform bacteria and Pseudomonas

aeruginosa, which can cause severe infec-tions in individuals with compromised immunity. Based on these widely-used quality criteria, the treated water is suit-able for use on non-food crops.

However, the researchers also saw cause for concern. They detected known antibiotic resistance genes in the bacterial genetic material present in the water samples. If released into the environment, these resistance genes could be taken up by other bacteria to confer protection against commonly-used drugs.

In cultivating nearly 300 bacterial samples from the output water, the researchers observed widespread drug resistance. “Although the overall number of bacteria decreased, the proportion of bacterial isolates resistant to six types of antibiotics increased from 3.8 percent in the input to 6.9 percent in the chlorin-ated output,” says Hong.

Current treated wastewater quality standards do not take this risk into con-sideration, and Hong believes this needs to change and measures broadened. “There is a need to expand the current regula-tions beyond simply defining the density of fecal coliforms,” she says. “There may be a need to monitor for the abundance of antibiotic-resistant opportunistic patho-gens and to assess microbial risk to miti-gate potential risks during reuse.”

Her team now intends to determine the real-world risk from these resistant bacte-ria and whether they survive long enough in the environment to pose a threat.

1. Al-Jassim, N., Ansari, M.I., Harb, M. & Hong, P.-Y.

Removal of bacterial contaminants and antibiotic

resistance genes by conventional wastewater

treatment processes in Saudi Arabia: Is the

treated wastewater safe to reuse for agricultural

irrigation? Water Research 73, 277 –290 (2015).

“There is a need to expand the current regulations beyond simply defining the density of fecal coliforms.”

1 4

B E S E

Mysterious deep-dwelling fish are vastly more plentiful than previously thought and are likely to play a major role in ocean carbon budgets.

A s sailors traverse the world’s oceans, the sonar on their ves-sels reveals a thick layer that changes depth throughout the

day. This “deep scattering layer” puzzled mariners until 1948, when it was shown to be a dense layer of fish whose global biomass is about a billion tons. An inter-national study now suggests that previ-ous estimates of these fish have been significantly short; they may comprise 95 percent of the world’s fish mass and have a dramatic influence on oceanic chemical cycles.

Mesopelagic fish live in the ocean’s dimly lit “twilight” zone at depths between 200 and 1,000 meters. At night, they swim toward the surface to feed on planktonic animals.

During the day, they migrate down-ward where they excrete and respire. Although probably the most abundant vertebrate in the world, these fish have been largely under-researched.

“These fish are difficult to study because they live so deep and we know so little of open ocean ecology,”

explained Xabier Irigoien, director of the Red Sea Research Center at KAUST.

Previous attempts to net the fish for studies had proved futile with the fish easily able to detect and avoid trawl nets. So an international team of scientists collected fish data through echo sound-ers and sonar during daylight hours of a seven month circumnavigation of the globe. They developed a sensitivity analysis of acoustic data which was then corroborated by an existing food web model called ECOTROPH. These showed that the mesopelagic fish mass is at least ten times greater than previous estimates from trawling observations1.

The revised number indicates mesope-lagic fish may play a larger role in energy transfer up the food chain from plank-tonic animals to bigger predators. It defies

Plenty more fish in the deep sea

the picture of the deep ocean as a void if it is able to support efficient food webs.

These findings also challenge our understanding of ocean carbon budgets. After feeding near the surface, mesope-lagic fish swim down into the ocean, effectively transferring surface carbon deeper to the mesopelagic region. They also remove much of the oxygen from the depths through respiration.

“We now better understand the trans-port of CO2 from the surface to deeper waters.” says Irigoien. “We also under-stand how large predatory fish like tuna live in the open ocean where they can feed on those mesopelagic fish.”

Irigoien says future studies aim to learn how ammonium, oxygen and bac-terial activity change in the twilight zone to better understand the role of mesope-lagic fish in biogeochemical cycles of ocean ecosystems.

1. Irigoien, X., Klevjer, T.A., Rostad, A., Martninez,

U., Boyra, G., et al. Large mesopelagic fishes

biomass and trophic efficiency in the open ocean.

Nature Comm. 5, 3271 (2014).

A mesopelagic fish eye and the luminous organ which can emit light indirectly for these deep-dwelling creatures.

RED

SEA

RESE

ARCH

CEN

TER

“We now better understand the transport of CO2 from the surface to deeper waters.”

1 5I S S U E O N E


Whale sharksRather than migrating, whale sharks in Tanzania

hide surprisingly close to home year-round.

T20

15 T

ANE

SIN

CLAI

R-TA

YLO

Rhe whale shark is the largest known fish species, with the biggest specimens spanning more than 14 meters and weighing more than 20 metric tons. Despite their size, these majestic creatures are vulnerable to being caught

in fishing nets, both incidentally and deliberately. A study by KAUST researchers has revealed migratory patterns that could assist in efforts to protect whale shark populations1.

These fish can travel thousands of kilometers to satisfy the demands of their plankton diet, and some data indicate a semi-migratory lifestyle. “Whale sharks that we have studied in the Red Sea clearly leave the study area outside their ‘aggregation season,’” says Michael Berumen from the Red Sea Research Center.

A similar migration pattern has been noted by “citizen scientist” observers in Tanzania, where the animals are a major draw card

B E S E

1 6

for ecotourism. Interested visitors and tour boat operators report observations that, although useful, are not systematic enough to use to accurately map shark behavior.

Working in collaboration with the Marine Megafauna Asso-ciation (MMA), KAUST researchers employed an acoustic telemetry strategy in Tanzania that had been used in Beru-men’s Red Sea-based research. They tagged 30 whale sharks in Tanzania’s Kilindoni Bay with acoustic transmitters, each of which generated a distinct signaling pattern. These were in turn detected by 19 receivers placed at sites where the sharks were known to congregate. “This technology provides a very high-resolution picture about animal movement within a study area,” says Berumen. “We wanted to couple it with MMA-led studies of plankton distribution.”

The data revealed that there is more to whale shark migra-tion than meets the eye. Visual reports of sharks were infre-quent between January and March, suggesting that these fish had departed the area. Acoustic telemetry showed however, that many sharks remained local during this time span, but had simply moved to slightly deeper water further from the

1. Cagua, E.F., Cochran, J.E., Rohner, C.A., Prebble, C.E., Sinclair-Taylor, T.H. et al.

Acoustic telemetry reveals cryptic residency of whale sharks. Biological Letters

11, 20150092 (2015).

Thirty whale sharks in Tanzania’s Kilindoni Bay were tagged with

acoustic transmitters, each of which generated a distinct signaling pattern.

coast, where they were less likely to be seen. The perceived “return” migration of these fish later in the year was actually their movement back to shallow coastal waters. “We found very regular detection of these whale sharks throughout the year,” says Berumen.

He notes that there are more than a dozen other sites world-wide where whale sharks are known to congregate. Demon-stration that other populations also maintain quite a stable residency could inform targeted monitoring and protection strategies close to whale shark areas.

“This technology provides a very high-resolution picture about animal movement within a study area.”

hide in plain sight

1 7I S S U E O N E


S alinity is one of the most chal-lenging issues affecting agri-culture today, and its impact is particularly significant in

desert soils, where high salinity can reduce growth, productivity and repro-duction in sensitive species. Aiming to improve desert agriculture, the Center for Desert Agriculture (CDA) is lead-ing research on salinity tolerance and adaptation from the molecule to the field.

The research, led by Mark Tester, fol-lows a three-step pipeline of discovery, characterization and delivery. The “dis-covery” phase aims to determine the genetic basis of salt-tolerance traits; “characterization” determines how the genes work; and “delivery” will apply this knowledge to crop plants in a bid to

KAUST Center for Desert Agriculture leads research to improve crop yields from desert soils.

Growing on salty soils

improve growth and yield under saline conditions.

The current focus of the discovery phase is on barley and tomato crops with a range of salinity-tolerant rela-tives, which indicates to researchers that both feature genes which could display tolerance, Tester explains. Salinity toler-ance is controlled by multiple genes, and therefore traditional breeding methods have had limited success so far. Instead, the KAUST team is using a range of tools including genetics, genomics, protein engineering, proteomics and chemical genetics in their quest to understand and characterize salinity tolerance.

Their most fruitful approach to date uses a “forward genetics” method to study the control of several traits that contribute to tolerance. Working with

the high-throughput Australian facility “The Plant Accelerator,” the KAUST team quantified naturally-occurring variation to determine a plant’s genetic basis. As Tester explains, “We are letting the plants show us the genes behind differences in salinity tolerance.”

In the delivery phase, the team uses two technologies: marker-assisted selection (MAS) and genetic modifica-tion (GM). In MAS, genes are tracked through a breeding program without the need to measure their effects. This is very efficient where there is high natural variation in a salinity tolerance gene. In collaboration with scientists at Austral-ia’s Commonwealth Scientific Industrial Research Organisation (CSIRO), KAUST researchers were able to elucidate the function of high affinity potassium

LIN

DA P

OLI

K

1 8

B E S E

MAR

K TE

STER

Field trials are key to translating the research into crop breeding: here, a field trial shows naturally-occurring variation in salinity tolerance between wheat varieties.

transporter (HKT) genes, which control transport of sodium from leaves. Intro-duced into durum wheat, a HKT gene provided significant increases in salinity tolerance and has already been repli-cated in at least 20 breeding programs worldwide.

Tester explains that for traits with insufficient natural variation, it may be necessary to use genetic modification to improve tolerance — an option likely to be commercially unpopular because of a lack of consumer confidence in GM technology. “I hope that one day some logical middle ground will be found,” says Tester.

Tester highlights field trials as a cru-cial part of his research, saying the work forms “an important part of the con-tinuum” between fundamental research and true delivery. “Without field meas-urements, it is very difficult to know the relevance of lab-based work,” he says.

Field trials for salinity tolerance are notoriously difficult due to variability. This is where the partnership with the International Center for Biosaline Agri-culture (ICBA), Dubai, comes to the fore, using its experience in field cultivation with saline irrigation to undertake high-quality trials.

The CDA’s research could ultimately lead to the improvement of many crop species, because, as Tester explains, what applies in one plant tends to apply in others. “I would love to make impacts on the production of major cereals such as rice and wheat,” he says.

The KAUST team is also attempting to solve water insecurity, another major impediment to desert agriculture, by “unlocking seawater.” Exploiting salin-ity-tolerant crops in combination with research by the KAUST Water Desalina-tion and Reuse Center studying low-cost desalinization, Tester says, “could create a system where we can use cheap water to irrigate crops with increased salinity tolerance.”

He says this work could “provide a step-change in our ability to grow food in difficult environments and open up the possibility of agriculture on land that has never previously been possible to farm. The impact on global food secu-rity could be great.”

“The KAUST team is also attempting to solve water insecurity, another major impediment to desert agriculture, by ‘unlocking seawater.’”

1 9I S S U E O N E


901Students

135Faculty

424Postdocs

KAUST ata glance

234Research

Scientists

September 2015 data

Termination sites of DNA are shown to stop slow-moving replication forks but not faster ones.

DNA division can slow to a halt

A key mystery of the DNA rep-lication process has been unraveled by researchers from KAUST.

Before a bacterium can divide, it must make a copy of its genetic material, the circular DNA molecules that resem-ble bunched rubber bands, through a process called DNA replication. In this process, the two strands of DNA making up the circular DNA molecule unwind and separate to become templates for generating new strands.

To ensure the process is well regu-lated, the bacterium has set a number of “roadblocks,” or termination sites on the DNA, to ensure the permanent stoppage of replication forks, Y-shaped structures formed between the strands as the DNA molecule splits.

The Nature study, led by KAUST Ph.D. student Mohamed Elshenawy and Asso-ciate Professor Samir Hamdan from the Division of Biological and Environmen-tal Science and Engineering, along with colleagues from the University of Wol-longong in Australia, showed why ter-mination sites were able to permanently stop replication forks in vitro, while in living bacteria, more than 50 percent of the replication forks that moved towards the termination site continued synthesis without stopping1.

A termination site comprises a 23-base pair termination sequence (Ter) bound to the protein terminus

utilization substance (Tus). Tus–Ter is unusual in that it acts like the ratchet-ing knot on a climbing rope by allow-ing progression of replication forks from one direction but not the other. This polarity sets up a “trap” that allows the first arriving fork to enter but not to leave the terminus region until the other fork has arrived.

Hamdan and his team suspected that the energy from movement (or kinet-ics) might be acting on these termina-tion sites. They used single-molecule imaging to record molecular mov-ies that zoomed in with high tempo-ral and spatial resolution on the fate of Escherichia coli replication forks as they approached a termination site from either direction.

Their results showed that efficiency of fork arrest is weakened by kinetic competition between the rate of strand separation by the helicase motor at the fork and the rate of rearrangement of Tus–Ter interactions that maintain Tus’s strong grip on the DNA. This means

that faster moving forks beat Tus–Ter rearrangement and displace Tus, while slower ones are effectively blocked.

This resolves a long-standing mystery that has clouded our understanding of DNA replication, and also has impor-tant implications for all domains of life.

“These findings are striking for the field of enzymology,” Hamdan stated. He noted that the demonstration that the rates of individual enzymes fluc-tuate during catalysis and that rates can differ among presumably identical enzyme molecules are both novel con-tributions of single-molecule imaging to biology.

“This study demonstrated for the first time that these intrinsic properties of enzyme molecules actually impact biol-ogy,” explained Hamdan.

The communication between molec-ular motors and double-stranded DNA binding proteins is a common feature in DNA replication, repair, recombination and transcription, and also in instances where conflict occurs between these processes. The evolution of different responses to the average rate of differ-ent molecular motors could regulate the communication among these processes, Hamdan said.

1. Elshenawy, M. M. Jergic, S., Xu, Z-Q., Sobhy, M.A.,

Takahashi, M. et al. Replisome speed determines the

efficiency of the Tus-Ter replication termination

barrier. Nature 525(7569): 394-398 (2015).

KAU

ST“This study demonstrated for the first time that these intrinsic properties of enzyme molecules actually impact biology.”

B E S E

2 0

Single-molecule imaging reveals that DNA replication termination in E. coli is mediated by kinetic competition between speed of strand separation by the replisomal helicase

and rearrangement of Tus–Ter interactions during separation of the first six base pairs of Ter. Multiple termination sites are required to insure fork stoppage.

Wastewater treatments based on bioelectrochemical systems can generate energy while removing potentially toxic compounds.

B

Bacterial power to reduce toxicity of water supply

made analysis tricky,” explained Werner. The team found that levels of TOrC

removal for eight of the compounds were similar in both BESs to conven-tional treatment systems. The removal of caffeine and the antibiotic trimetho-prim was slightly better in MECs. They also discovered the TOrCs were pre-vented from passing into the treated water either through biotransforma-tion or sorption, the binding of the compound to the bacterial biofilm or electrode.

The findings could encourage more widespread use of BESs in wastewater treatment in the future. “Further work is needed, but our results are promis-ing and highlight an additional ben-efit of BES technology as a potential alternative to current practices,” Wer-ner said.

ioelectrochemical systems (BESs) are as effective as con-ventional wastewater treatment systems at removing hazardous

chemicals like pharmaceuticals, show researchers from KAUST.

In arid countries like Saudi Arabia, where water reuse and reclamation is necessary, it is essential to find cost-effective, energy-efficient methods to remove trace organic compounds (TOrCs) from water. Current wastewater treatment techniques require expensive and energy-intensive membrane filter-ing or ozonation to remove TOrCs.

A key advantage of BESs is their abil-ity to concurrently treat water and con-vert chemical energy from wastewater into usable electricity or biogas.

Craig Werner, Pascal Saikaly, Gary Amy and colleagues from the Water Desalina-tion and Reuse Center tested two types of BESs — microbial fuel cells (MFCs) and microbial electrolysis cells (MECs) — to determine their ability to remove ten dif-ferent TOrCs from wastewater1.

Bioelectrochemical systems utilize the characteristics of bacteria known as exoelectrogens, which are capable of harvesting energy from the oxidation of organic matter in wastewater. The energy is generated in the form of electricity in MFCs and hydrogen gas in MECs.

“Wastewater treatment plants using MFCs could feasibly help power them-selves, so there is considerable interest in using the technology in rural parts of developing countries where access to the main electricity grid is limited,” said Werner. “But before such systems such can be implemented, we need to know if BESs can also reduce levels of TOrCs in treated water.”

The team evaluated a complex cock-tail of compounds comparable to those found in wastewater and natural waters, including five pharmaceuticals, two antibiotics, a flame retardant, a pesticide and an insecticide.

“All of these compounds were present at low concentrations and have different physical and chemical properties, which

1. Werner, C. M., Hoppe-Jones, C., Saikaly, P.E.,

Logan, B.E. & Amy, G.L. Attenuation of trace

organic compounds (TOrCs) in bioelectrochemical

systems. Water Research 73, 56-67 (2015).

Pascal Saikaly and Ph.D. student Zhongwei Wang in the Water Desalination and Reuse Center.

KAU

ST

2 2

B E S E

Elevated bacterial populations in waters near beaches and urban areas could pose a problem for desalination plants.

T he seas that flank Saudi Ara-bia offer a valuable source of household water, but coastal waters also accumulate pol-

lution and waste, making it critical to assess the quality of the seawater being processed at desalination plants. Pei-Ying Hong and Burton Jones, researchers from the Biological and Environmental Science and Engineer-ing Division, have conducted a “census” of bacteria at different sites off the Red Sea’s coast to determine the conditions in those waters and assist future moni-toring efforts1.

Saudi Arabia’s 30 desalination plants supply half of the nation’s fresh water for domestic use, and major cities like Riyadh and Makkah are depend com-pletely on such facilities. “Desalinated water can account for approximately 90 percent of these cities’ domestic water needs,” says Hong. However, these cities also produce considerable wastewater, which ends up being returned to the sea after processing at treatment plants.

Hong and Jones set out to measure how human contamination impacts desalination. They collected water samples from eight sites near sewage

treatment plants, city shorelines and recreational beaches.

The researchers used both traditional culture techniques and more modern molecular assays to detect bacterial species typically associated with human waste, as well as a variety of pathogens linked to opportunistic infections.

Remarkably, the waters near the sew-age plant outflow generally contained acceptable levels of both classes of bac-teria.

“This suggests that the treatment plants in Jeddah were achieving good removal efficiencies for conventional contami-nants in wastewater,” says Hong.

In contrast, several beach samples had elevated levels of fecal enterococcal species, and both the beach and urban samples contained a greater variety of both pathogenic and non-pathogenic microbes.

Hong notes that although most of

Study co-author Moustapha Harb collects water from the rosette sampler used to assess coastal water quality.

Saudi Arabia’s desalination plants usu-ally draw in water from fairly far off-shore, some of the plants in the Jeddah area could be at risk.

“Depending on the sea currents and flow direction, these facilities may be impacted by contaminated near-shore waters and would require more robust treatment strategies,” she says. Her group intends to follow up by determin-ing the extent to which the presence of these bacteria actually impedes the pro-duction of clean drinking water.

Importantly, several of the molecular tests employed in this study revealed microbial markers that could potentially be used to assess general water quality. To assemble a more detailed picture of the “health” of the Red Sea, Hong will collaborate with the Red Sea Research Center to apply these and other moni-toring techniques to track how micro-bial communities shift throughout the year.

KAU

ST

1. Ansari, M.I., Harb, M., Jones, B. & Hong, P.-Y.

Molecular-based approaches to characterize

coastal microbial community and their potential

relation to the trophic state of Red Sea. Scientific Reports 5, 9001 (2015).

Assessing seawater safety

“Hong and Jones set out to measure how human contamination impacts desalination.”

2 3I S S U E O N E

Analyses of marine bacteria offer insights into processes of carbon storage and release beneath the sea.

Dynamics ofdeep-sea carbon deposits spikes interest

B E S E

2 4

colleagues at KAUST suggests that these molecules only remain because they are too diluted for bacteria to use them efficiently1.

The seas contain more than 70 per-cent of the planet’s DOC — primarily the degraded remnants of plant and ani-mal life. Duarte explains that this pool remains very stable over time, which belies the notion that a large proportion

of dissolved organic carbon cannot be degraded by marine bacteria.

An alternative model suggests that DOC pools contains digestible com-pounds that are simply too dilute to pro-vide useful nutrition, although this has proven challenging to confirm. “We pre-viously lacked the capacity to concen-trate DOC and characterize its molecular composition,” explains Arrieta.

He and his colleagues addressed this question by analyzing samples from 14 sites across the Atlantic and Pacific. They consistently observed that experi-mentally increasing the concentration of DOC within a given sample stimulated the growth of deep-sea bacteria within that sample. Indeed, the organisms behaved exactly as would be predicted for microbes given access to increasing amounts of nutrients. “All the experi-ments we performed suggest a universal relationship between DOC concentration and bacterial growth rate throughout the world’s oceans,” says Duarte.

To follow up, Duarte and colleagues profiled the organic molecules in their deep-sea samples. Instead of observing a relatively narrow range of indigestible compounds, they identified considerable diversity, including thousands of organic compounds. They hypothesize that many of the molecules in oceanic DOC reser-voirs are not resistant to digestion, but are comprised of “leftovers” that remain after bacteria have feasted on more use-ful molecules. These remnants are still edible, but may be too dilute to justify the metabolic effort required to process them.

The data therefore suggest that the ocean’s repositories of DOC are unexpect-edly dynamic and not merely a continu-ous siphon for excess global carbon. In future studies, Duarte and Arrieta intend to confirm that the “dilution hypoth-esis” is responsible for maintaining DOC equilibrium. “We plan to test the appli-cability of this model to the entire ocean, and to go deeper into the composition of the thousands of molecules forming the ocean’s DOC pool,” says Duarte.

cientists have long specu-lated that “dissolved organic carbon” (DOC) molecules accumulate within Earth’s

oceans because marine bacteria can-not metabolize them. If this theory is correct, it could suggest a potential solution for safely storing extracted atmospheric carbon. However, research from Carlos Duarte, Jesus Arrieta and

S1. Arrieta, J.M., Mayol, E., Hansman, R.L.,

Herndl, G.J., Dittmar, T. & Duarte, C.M. Dilution

limits dissolved organic carbon utilization in the

deep ocean. Science 348, 331–333 (2015).

The Rosette sampling system was used to collect deep-

sea water samples.

KAU

ST


2 5I S S U E O N E

A leader in desalination science, TorOve Leiknes gives a major boost to water treatment research in Saudi Arabia.

S audi Arabia’s hot and arid cli-mate presents many challenges for the safe and efficient man-agement of water resources.

With no surface freshwater available, the Kingdom relies on groundwater aquifers and desalinated seawater for drinking and other needs, and on some

recycling of wastewater for agricul-ture. Current solutions are expensive and energy intensive, so researchers at KAUST are trying to revolutionize the treatment and re-use of salt water.

The University recently appointed one of the world’s leading experts in water treatment technologies, TorOve Leiknes,

as the head of its Water Desalination and Reuse Center. Having worked in the field for more than 20 years, Leiknes has extensive experience in developing low-cost, highly efficient water treatment systems across the world from Africa to the United States. His speciality is membrane technology, which includes

KAUST takes on an expert worth his salt

TorOve Leiknes (right) and his Ph.D. student Luca Fortunato (left)

in their laboratory at KAUST.

KAU

ST

2 6

B E S E

adapted filtering systems for seawater desalination and advanced wastewater treatment.

“Membrane technology is a core aspect of advanced water treatment,” says Leiknes. “Using chemical, physical and biological processes, together with membranes, makes desalination and wastewater reuse achievable. Our goal is to develop integrated hybrid systems that can produce high-quality water as efficiently and cheaply as possible.”

A major obstacle to efficiency is “biofouling”— the accumulation of bio-films and biological substances on the membranes used to filter the water. The build-up constricts water flow through the membrane by increasing hydraulic resistance, and can significantly reduce production.

“No matter how good your mem-brane is, fouling will always build up — it is a natural biological process which has been going on for millions of years,” says Leiknes. “There are two current schools of thought on tackling this. One aims to eradicate biofilms completely, which is an almost impos-sible challenge. The other school, which I am more inclined to follow, is to work with the biology and learn to manipu-late it: to create systems which work efficiently in spite of the build-up of biofilms.”

Conventional techniques to investi-gate biofouling involve taking samples by physically breaking up membrane modules and analyzing biofilm

build-up. However, this can disrupt the natural processes behind biofouling, such as water flow through the biofilm. Leiknes and his team therefore hope to develop in-situ, non-invasive monitor-ing of biofouling and biofilm formation, to retain this essential data.

“The properties and characteristics of the biofilm evolve continuously; it is a very dynamic process,” explains Leiknes. “The kind of biological processes at work and the changes taking place at any given moment are key to learning how we can work with it and ultimately manipulate it in our favor.”

The team are currently developing a low energy, gravity-driven biofilm-based membrane reactor for wastewater treatment. Under this process, a par-ticular type of biofilm adapted by the researchers so that it has low hydraulic

resistance is allowed to accumulate on the membrane. The adapted bio-film does not interfere with the water filtration as much as natural biofilms can, and so the system can maintain a constant level of clean water produc-tion, albeit at a lower rate of flow than conventional methods. This reduces the need to “fight” biofouling and therefore the need for constant maintenance. The new system could be used in any facil-ity where water is re-used.

In collaboration with the Visual Computing Center, the team is also working on ways of capturing images of biofouling processes in situ and has designed and built a new working bio-reactor module for this task. “A camera mounted on a mechanical arm controls exactly where detailed images are taken around the membrane module,” explains Leiknes. “Using coherent optical tomog-raphy we can collect a huge amount of data to create 3D images of the biofilm — a similar imaging technique used to analyse brain scans. Combined with time series monitoring, we have a 4D system to analyze the dynamic evolution of bio-film development.”

Leiknes has big plans on a microscopic scale. He aims to examine the micro-scopic stages of biofilm growth, a process which is incredibly difficult to see and predict. “Ultimately we would like to be able to build biofilm sensors which would allow engineers to detect and monitor initial biofouling of membranes and take steps to alleviate it.”

The computer imaging technology at KAUST allows TorOve Leiknes and his team to monitor the build up of biofilms on membrane meshes in great detail. Here, the areas in bright red indicate where the highest levels of biofilm have accumulated.

TORO

VE L

EIKN

ES

“Using coherent optical tomography, we can collect a huge amount of data to create 3D images of the biofilm. Combined with time series monitoring, we have a 4D system to analyze the dynamic evolution of biofilm development.”

2 7I S S U E O N E


A look at life in the depths of the ocean reveals an efficient system of pumping carbon out of the atmosphere.

T

Ocean’s carbon pump reaches new depths

he transfer process of carbon dioxide from the atmosphere to the deep sea is more efficient than previously thought, shows

a study of phytoplankton from the open ocean led by researchers from KAUST.

The ocean acts as a “carbon sink,” meaning that carbon dioxide from the atmosphere is absorbed by phytoplank-ton that, when attached to other parti-cles, sink to depths of more than 1,000 meters. Recycling of carbon from these depths back into the atmosphere takes centuries.

This “biological carbon pump” has been studied extensively near coastlines where phytoplankton are abundant. Susana Agusti from the Red Sea Research Center and a team of collaborators from Spain set out to discover whether the same pro-cess occurs in the deep (bathypelagic) waters of the major oceanic basins where plankton are less abundant.

“Sampling of the deep ocean is diffi-cult and time-consuming, and as a con-sequence, the bathypelagic waters are still poorly explored,” explains Agusti. “The information we have about large, remote oceanic areas is limited.” The researchers joined the Malaspina 2010

Circumnavigation Expedition, an inter-disciplinary research project led by the Spanish National Research Council that examines the impact of global change on the oceans. The researchers sampled the bathypelagic waters of the Atlantic, Indian and Pacific Oceans at depths of 2,000 to 4,000 meters.

To sample the waters efficiently, the team developed a new oceanographic device called the Bottle-Net, which allowed them to select the depth inter-vals at which samples were collected. Each deployment and recovery of the sampling system took four hours, with the team then analyzing the collected samples at sea.

They found that healthy phytoplank-ton, which mostly included diatoms, were present at the sampled depths. As phy-toplankton require sunlight to produce energy and cannot survive for long at such depths, their presence shows that the biological carbon pump works effi-ciently throughout the oceans, regardless of the abundance of phytoplankton at the surface.

“We tested the resistance of phyto-plankton to the conditions of bathy-pelagic waters and found that half the population dies every three to 24 days,” explains Agusti. “Diatoms that sink simply by gravity would require 1,000 to 5,000 days to reach a depth of 4,000 meters, leaving no chance that any would still be alive.”

“Our results demonstrate that the mechanism that removes anthropogenic carbon dioxide into the deep ocean is fast and therefore more efficient than previ-ously believed,” concludes Augsti.

A colony of oceanic diatoms similar to those found at a depth of 4,000 meters during the Malaspina 2010 Circumnavigation Expedition.

1. Agusti, S., Gonzalez-Gordillo, J. I., Vaque,

D., Estrada, M., Cerezo, M. I. et al. Ubiquitous

healthy diatoms in the deep sea confirm deep

carbon injection by the biological pump. Nature

Communications 6, 7608 (2015).

KAU

ST

“We tested the resistance of phytoplankton to the conditions of bathypelagic waters and found that half the population dies every three to 24 days.”

B E S E

2 8

Discovery of the molecular mechanism by which a protein confers salt tolerance in plants could boost crop yields in high-saline soils.

T he role of protein LSm5 in reg-ulating accurate and specific splicing across the genome, par-ticularly of genes involved in

salt stress tolerance, has been revealed by a team of researchers from KAUST.

To express any gene in the cell, the encoding DNA is first transcribed to pre-messenger RNA (pre-mRNA). Prior to this, any intermittent non-coding parts must be removed before mature mRNA can be exported and translated. This removal process, known as pre-mRNA splicing, can occur at several sites, which explains why a single gene is able to encode several different proteins.

Splicing is carried out by the spliceo-some, a complex molecular machine which is made up of many different proteins and RNA particles. One of those proteins was known to be LSm5 although researchers were unsure of its exact function in splicing. Also unclear was the regulatory mechanism by which a specific spliced product is produced accurately.

Led by Liming Xiong, a team from the Biological and Environmental Science and Engineering Division carried out genetic screens on Arabidopsis plants — a commonly used model— to find an lsm5 mutant in which the lsm gene function is turned off. They also generated transgenic plants overexpressing the normal LSm5 gene. Next they sequenced the full set of mRNA produced by the plant, known as the transcriptomes, and compared the

results of the lsm5 mutant plant with the wildtype and the overexpressor.

The team found that the lsm5 mutant had a higher frequency of alternative and inaccurate splicing compared to the wildtype. Conversely, overexpression of LSm5 resulted in precisely the opposite, suggesting that LSm5 plays a role in regulating specificity and accuracy. On closer inspection, they found salt-stress related genes were particularly affected.

The team could also show the growth of LSm5 overexpression plants was less

inhibited by salt stress, phenotypically corroborating what was expected from the transcriptomic results.

This new knowledge, explains Xiong, not only helps clarify a fundamen-tal molecular mechanism necessary in higher life forms, but also provides the key for engineering salt-tolerant plants.

“High soil salinity in the arid and semiarid regions severely limits the pro-ductivity of many agricultural plants. Increased plant tolerance to salt stress is an important means to increase crop yields in these regions and could also make irrigation with brackish water pos-sible,” explains Xiong. “This is particu-larly important for countries like Saudi Arabia, where a lack of fresh water has limited its agricultural production.”

1. Cui, P., Zhang, S., Ding, F., Ali, S., & Xiong, L.

Dynamic regulation of genome-wide pre-mRNA

splicing and stress tolerance by the Sm-like

protein LSm5 in Arabidopsis. Genome Biology,

15 (1), R1 (2014).

Arabidopsis plants engineered to overexpress LSm5 protein were less inhibited by high salinity in the soil compared to mutant variants that had the gene encoding LSm5 knocked out.

RF C

ORB

IS V

ALU

E / A

LAM

Y ST

OCK

PH

OTO

“Increased plant tolerance to salt stress is an important means to increase crop yields in these regions and could also make irrigation with brackish water possible.”

Plants coping with salt stress

2 9I S S U E O N E

Lactate plays an unexpected role in brain function.

ARun for your brain

small molecule released into the bloodstream after strenu-ous exercise can enhance brain function through its signaling

role that promotes changes in neural connections, according to a new study by researchers at KAUST1.

Lactate is produced after brief periods of intense physical exertion, when oxy-gen-deprived muscle cells burn glucose anaerobically for energy. As a result, measurements of blood lactate concen-tration are widely used in clinical studies of exercise and in athlete performance testing. In the brain, lactate is mostly

Lactate released during exercise can improve the function of neurons in the brain, which may explain the beneficial effect of physical exercise on the brain.

PETE

R CR

OW

THER

/ AL

AMY

STO

CK P

HO

TO

3 0

B E S E

formed from glucose by non-neuronal cells called astrocytes, but its role in the organ is still poorly understood.

The new study reveals an unexpected role for lactate as a modulator of neu-ronal function and may also help to explain the beneficial effects of physi-cal exercise on the brain.

Pierre Magistretti from the Biologi-cal and Environmental Science and

Engineering Division and his col-leagues isolated neurons from

mouse neocortex and grew the cells in Petri dishes. They

then added lactate to

the cultures and found that it induced expression of c-FOS, an “immediate-early” gene that is switched on as soon as neurons become active. It also induced expression of Arc and Zif268, which are early genes that turn on a neuronal plasticity program.

Expression levels of these genes and the concentration of their corresponding proteins increased 3 – 5.5-fold, peaking one hour after lactate was added to the cells. Lactate also induced expression of the BDNF gene, which encodes a growth factor involved in later stages of neu-ronal plasticity. This gene reached its maximum levels about four hours after lactate treatment.

Experiments revealed that lactate exerts these effects by activating the NMDA receptor, which plays a key role in long-term potentiation (LTP), a form of synaptic plasticity underlying learn-ing and memory.

In 2011, Magistretti and collaborators demonstrated that formation of long-term memories depends upon lactate released from astrocytes2, and this new study extends this knowledge by identifying the underlying molecular mechanism.

“We are now carrying out a transcrip-tome analysis of all genes induced by lactate,” says Magistretti. “We have found more than 50 — it’s a Pandora’s box we have opened!”

Numerous other studies performed in both animals and humans over the past decade show that physical exercise can enhance brain functions such as memory, but how this happens is still unclear. These new findings provide a direct link between physical exercise and brain function. In the future, Magistretti and his colleagues plan to further expand on this link.

1. Yang, J., Ruchti, E., Petit, J.–M., Jourdain, P.,

Grenningloh, G. et al. Lactate promotes plasticity

gene expression by potentiating NMDA signaling

in neurons. Proceedings of the National Academy of Sciences 111, 12228 (2014).

2. Suzuki, A., Stern, S.A., Bozdagi, O., Walker, G.W.,

Huntley, R.W. et al. Astrocyte-neuron lactate

transport is required for long-term memory

formation. Cell 144, 810-23 (2011).

“We have found more than 50 genes induced by lactate — it’s a Pandora’s box we have opened!”

3 1I S S U E O N E


A modern twist on a traditional biochemistry technique lets scientists study interactions that trap cells in circulation.

H ealthy blood stem cells and invasive tumor cells use similar mechanisms to exit the circula-tory system and penetrate other

tissues. An experimental strategy devel-oped by Assistant Professor of Bioscience Jasmeen Merzaban and colleagues at KAUST allows for quantitative study of the earliest stages of this process1.

“Cell migration is a multi-step process in which a number of adhesion molecules find their partners and mediate interac-tion of cells in the flow to the endothe-lial cells lining blood vessels,” explained Merzaban.

Her team focused on an endothelial protein known as E-selectin, but it has been difficult to characterize how this adhesion molecule captures circulat-ing cells.

One method to study protein-protein interactions is immunoprecipitation, in which researchers use antibodies to purify a specific protein and capture other phys-ically-associated binding partners in the process. However, immunoprecipitation is ineffective at detecting weak or fleet-ing interactions and offers limited insight into the rates at which molecules bind and separate.

Dina AbuSamra, a Ph.D. student in Merzaban’s group, tried to counter these

Helping flowing cells make a connection

Schematic of an assay for measuring the interaction between E-selectin proteins (green) and their binding partners (white) that have been captured by antibodies (white) immobilized on a surface plasmon resonance chip.

deficiencies by developing an immu-noprecipitation assay based on surface plasmon resonance (SPR), a technique that can measure molecular interactions in real-time.

The researchers first prepared SPR sen-sors with antibodies that efficiently cap-ture known binding partners of E-selectin and exposed them to flowing solutions of extracts from cells that express this pro-tein followed by purified E-selectin. They were then able to accurately measure the speed and durability with which E-selec-tin binds to two of its target proteins.

Their results departed notably from prior predictions, which suggested that E-selectin binds and releases its targets quickly. However, these studies were conducted under relatively artificial conditions and focused on individual or “monomeric” molecules of E-selectin, a protein that often pairs off to form “dimers”.

“Our results suggested that these ligands bound monomeric E-selectin

1. AbuSamra, D.B., Al-Kilani, A., Hamdan, S.M.,

Sakashita, K., & Gadhoum, S.Z. et al. Quantitative

characterization of E-selectin interaction with

native CD44 and PSGL-1 using a real-time

immunoprecipitation-based binding assay. Journal of Biological Chemistry jbc-M114, (2015).

transiently with fast on- and off-rates, but bound dimeric E-selectin with remarkably slow on- and off-rates,” said Merzaban. This suggests that rapid but weak interac-tions with individual E-selectins initially capture circulating target cells and slow them enough to form more durable con-nections with dimers.

Their data also revealed how carbo-hydrate molecules on CD44 contribute to E-selectin binding. Merzaban’s team is now working to further dissect the molecular-scale details of this interaction mechanism to be able to manipulate it for clinical purposes.

“Our aim would be to direct the delivery of cells, such as therapeutic stem cells, to sites where they are needed,” she said.

KAU

ST

3 2

B E S E

A coral reef fish can acclimate to warm temperatures in just two generations.

F ish may be better able to cope with warming seas than previously assumed if the surprising results of experiments on one coral reef

species apply more generally.Timothy Ravasi and Michael Berumen

from the Biological and Environmental Science and Engineering Division won-dered how the common reef fish Acan-thochromis polyacanthus would cope with the rises in water temperature that may result from climate change1.

Collaborating with researchers from the ARC Centre of Excellence for Coral Reef Studies at James Cook University in Australia, they compared the offspring of fish in two situations: “developmen-tal” and “trans-generational”. The former were reared in water that was either 1.5 or 3°C warmer than the usual optimum temperature straight after hatching. The trans-generational group, however, con-sisted of fish whose parents had also been exposed to the higher temperatures from the time they had hatched.

Sufficient oxygen to meet energy demands, especially when active, is a chal-lenge for fish in warmer waters. Specifi-cally, higher temperatures reduce the fish’s “aerobic scope”, the difference between its resting and maximum metabolic rates.

Unsurprisingly, the aerobic scope of the “developmental” group fish, whose parents had not lived in warm waters, was significantly reduced. Surprisingly the trans-generational fish whose parents had lived in warmer water had a normal aerobic scope — they had acclimated to the temperature rise.

The team went on to look at the molec-ular mechanisms behind the acclimation.

1. Veilleux, H. D., Ryu, T., Donelson, J. M., van

Herwerden, L., Seridi, L. et al. Molecular processes

of transgenerational acclimation to a warming

ocean. Nature Climate Change (2015)

KAU

ST

Watching fishadapt to climate change

Watching fish

“The significance of this study is that we show the molecular changes that occur in these fish which enable them to adapt really fast — in just two generations,” says Ravasi.

The experiment is an example of non-genetic inheritance, a theory first pro-posed by Lamarck. One route for this is through epigenetic effects, Ravasi explains.

The KAUST team sequenced the tran-scriptomes (RNA) from cells in the fish’s livers to find which genes were being up- or down-regulated as a result of trans-generational exposure. Ravasi says they found 53 up-regulated or down-regulated genes which affect pathways required by this particular fish to restore its aerobic scope. “Nearly two thirds of most highly up-regulated genes in the trans-generational group are concerned with lipid, protein and carbohydrate metabolism,” he adds.

Other up-regulated genes are involved in the immune and stress response, he explains, but surprisingly, heat-shock proteins were not affected. “This sug-gests that there are different mechanisms of long-term acclimation and short-term heat stress,” he notes.

The spiny damselfish Acanthochromis polyacanthus acclimates rapidly to warmer seas.

“The experiment is an example of non-genetic inheritance. One route for this is through epigenetic effects.”

3 3I S S U E O N E

Analysis of sea anemone genome yields unprecedented detail of anemone-algae symbiosis, and may provide a model for coral symbiosis.

A model for coral-algae relationships

B E S E

3 4

T he sea anemone Aiptasia may be a viable model for investi-gating the mechanisms behind symbiotic relationships of algae

with corals. New findings by research-ers from KAUST with international col-leagues revealed a new class of proteins that provides important clues about how algae live with their undersea hosts1.

The first complete genome of the sea anemone Aiptasia — which, like corals, has a symbiotic relationship with pho-tosynthetic algae — has been assembled and analyzed to better understand the molecular and cellular processes that drive the synergistic partnership.

Symbiosis occurs when two separate organisms work closely together to sur-

vive. Coral polyps depend on sym-biosis with a specific alga living within their tissues to maintain a healthy coral colony. The under-

lying mechanisms of this symbiotic rela-tionship are little-known, partly due to the immense difficulties of carrying out experiments on live coral reefs.

“The symbiosis between coral and algae is the backbone of coral reef eco-systems,” explained Christian Voolstra, Associate Professor of Marine Science in the Red Sea Research Center, who was part of the international research team. “With corals threatened by environmen-tal change and anthropogenic impact, there is a need for a model organism that can help us understand corals’ responses to stress.”

Aiptasia can be easily studied under laboratory conditions. Similar to many other corals, Aiptasia hosts algae and these manufacture 90 percent of its energy. In return, the anemone provides

the algae with a share of its nutrients and a sheltered environment.

When Voolstra’s team studied the genome for Aiptasia to learn about symbiosis, they were astonished by the wealth of information revealed by their analyses, including their discovery of a new class of proteins called cnidarian ficolin-like proteins, or CniFLs.

“CniFLs appear to be prime candidates for mediating recognition between the algae and the animal host,” Voolstra explained. “If we understand how these proteins work, we can identify algae that confer specific characteristics — in the symbiont-host relationship — for exam-ple, the ability to better tolerate heat. This knowledge could enable us to help corals switch to more resistant symbionts in impacted environments.”

The researchers were also surprised by the number of genes in Aiptasia that appear to be inherited from its algal (and also bac-terial) symbionts. They are conducting fur-ther research into these genes at the same time as they study the CniFL proteins.

“Our analysis illustrates just how finely-tuned is this metaorganism — the Aiptasia animal host, its symbiotic algae and its associated bacteria — and how it has evolved,” Voolstra said. “Creating a symbiosis model system will allow quan-tum leaps forward in our understanding of reef-building corals, providing criti-cal guidance for practical applications in coral reef conservation.”

Analysis of the complete genome for the sea anemone Aiptasia helps in the understanding of cnidarian-algae symbiosis. Findings include a new class of proteins and groups of inherited genes coming from the algae, and suggest that Aiptasia can be a viable model for studying coral-algae symbiosis.

KAU

ST

1. Baumgarten, S., Simakov, O., Esherick, L.Y., Liew,

Y.J., Lehnert, E. et al. The genome of Aiptasia, a sea

anemone model for coral biology. Proceedings of the National Academy of Sciences published ahead of print

August 31, 2015 (doi:10.1073/pnas.1513318112)

3 5I S S U E O N E


GetsocialwithKAUSTFollow us onsocial media:

KAUSTofficial @kaust_newskausteduKAUSTkaustofficial

Parasite scan yields new targets

early half the world’s popula-tion is at risk from malaria, a disease that kills more than 600,000 people globally each

year. Research into an “on/off switch” within the genes of the parasite that causes malaria has revealed enzymes that control how cells develop and differ-entiate. Identifying these enzymes could pinpoint targets for future treatments of the deadly disease.

Malaria is caused by infection from mosquito-borne parasitic protozoans of the Plasmodium type. This single-celled microorganism progresses through sev-eral distinct life cycle stages, with each stage affected by a suite of enzymes that modify phosphate tags on other proteins to switch them “on” or “off”.

During the development stages of Plas-modium, a lot of research has scrutinized the role of enzymes that chemically add the phosphate groups. However, there has been little research into the role of enzymes that remove the phosphate tags known as protein phosphatases.

Using a range of molecular and bio-chemical techniques, Rita Tewari and col-leagues at the University of Nottingham, in collaboration with researchers from KAUST, Oxford and London, studied the genes coding each phosphatase enzyme in

N Plasmodium berghei, the mouse-infective relative of the human malaria parasite Plasmodium falciparum1.

The research team focused on how the phosphatases affect the parasite’s life cycle in infected mice.

“Our comprehensive analysis revealed the unique and essential roles of indi-vidual protein phosphatases in malaria parasite development,” says Stefan Arold of the Biological and Environ-mental Science and Engineering Divi-sion at KAUST.

The study revealed around 30 such genes in each species. Importantly, most of the mouse parasite’s phosphatases were nearly equivalent to the human par-asite’s versions of these same enzymes.

What’s more, the team discovered that 16 of the 30 genes encoding protein

phosphatases in P. berghei were essen-tial for parasite growth in the mouse. An additional six phosphatase genes were needed for the parasite to complete its life cycle in the mosquito.

To characterize the operation of the genes that encode protein phosphatases, the team analyzed several physical and functional features. These included the expression pattern of phosphatase genes, the gene interaction profile and the three-dimensional structural fea-tures of the phosphatase enzymes in P. berghei parasites.

The team observed distinct expression patterns for each phosphatase at various life stages of the parasite, including key roles in its sexual and asexual development.

“Our results strongly encourage tar-geting protein phosphatases to combat malaria and provide a specific list of protein phosphatases as prime tar-gets,” says Arnab Pain, one of the lead authors and associate professor of bio-science at KAUST.

Enzymes crucial to parasite growth offer clues in fight against malaria.

A Plasmodium ookinete, the developmental stage that invades the mosquito midgut, with two different

phosphatases shown in green, the surface of the parasite marked in red and the nucleus stained in blue.

GU

TTER

Y, D

.S. E

T AL

./CEL

L H

OST

& M

ICRO

BE

1. Guttery, D.S., Poulin, B., Ramaprasad, A., Wall,

R.J., Ferguson, D.J. et al. Genome-wide functional

analysis of Plasmodium protein phosphatases

reveals key regulators of parasite development

and differentiation. Cell Host & Microbe 16,

128–140 (2014).

“Our results strongly encourage targeting protein phosphatases to combat malaria, and provide a specific list of protein phosphatases as prime targets.”

3 6

B E S E

Resistance to a popular herbicide provides insight into the control of a key biosynthetic pathway.

R esearchers have now linked light sensitivity to a certain metabolic pathway as a means to understand herbcide resis-

tivity. One metabolic route of plants, known as the shikimate pathway, is a fundamental production line for sec-ondary metabolites and essential amino acids and is disrupted by the herbicide glyphosate. Widespread glyphosate use has promoted the evolution of resistant weeds mostly through causing muta-tions in the herbicide’s target enzyme EPSPS.

Now, scientists from KAUST and Pur-due University in the U.S., have discov-ered a new mechanism of resistance based on light-receptive phytochromes, which reveals a light-dependent system of control over the shikimate pathway. This can explain temporal variations in glyphosate effectiveness and may con-tribute to enhanced production of useful plant metabolites.

Altanbadralt Sharkhuu and Chris

Gehring from the Biological and Envi-ronmental Science and Engineering Division introduced mutations in the model plant Arabidopsis by insert-ing small pieces of bacterial DNA into its genome. One mutant, gre1, showed glyphosate resistance. Further inves-tigation showed that this resistance depends on light quality and intensity, and genetic analyses indicated that gre1 is deficient in phytochrome B (phyB).

PhyB is present in active and inac-tive forms dependent on the ratio of red to far-red light. In gre1 this response is impaired, causing over-production of the components of the shikimate pathway, including EPSPS, and therefore resist-ance to glyphosate. Evidence for this is that over-production of phyB causes glyphosate-hypersensitivity.

Gehring explains that “the key dis-covery is that phyB regulates the shi-kimate pathway, which is central to the biosynthesis of highly valuable

secondary metabolites and aromatic amino acids.”

Two enzymes of the pathway contain molecular motifs associated with phy-tochrome interactions. Significantly, two further enzymes contain elements associated with circadian regulation. The KAUST team therefore looked for — and confirmed — circadian variation in the pathway by quantifying gene expression throughout the day. They found that the shikimate pathway is regulated not just by phyB, but by an integrated system including the innate circadian clock.

The team proposed that while the clock maintains general control of the path-way, phyB can override this in response to changing environmental conditions.

The effectiveness of glyphosate is known to be affected by the time at which it is sprayed. Variation in the shi-kimate pathway under the control of the circadian clock, phyB and chang-ing light quality now explains why and offers methods for best glyphosate use to reduce environmental impact.

“This opens the possibility to use light quality regimes to boost the production of specific metabolites,” adds Gehring. The team is currently testing this in green algae, which also use the shikimate pathway.

1. Altanbadralt, S., Narasimhan, M.L., Merzaban,

J.S., Bressan, R.A., Weller, S., et al. A red and far-

red light receptor mutation confers resistance to

the herbicide glyphosate. The Plant Journal 78,

916-926 (2014).

“The key discovery is that phyB regulates the shikimate pathway, which is central to the biosynthesis of highly valuable secondary metabolites and aromatic amino acids.”

Herbicide resistance: shedding light on the shikimate pathway

KAU

ST

3 7I S S U E O N E

Devil rays soak up the sun’s heat and then make some of the deepest and fastest dives ever recorded in the ocean.

Warming upevil rays have long been thought of as ocean surface dwellers, enjoying the warmer waters near the surface where

they are often seen. However, after track-ing a group for months, scientists show these large, winged fish are some of the best divers of the ocean and have special adaptations for such deep, fast dives.

Researchers from KAUST with inter-national colleagues from the U.S. and Portugal used specially modified darts to attach tags to 15 Chilean devil rays (Mobula tarapacana) to record their movement for up to nine months1. About then the tags would come off and float to the surface, transmitting their data in

small fragmented bursts to a satellite.“We know little about this species and

so our job was to piece together this information and reconstruct the animals’ behaviors,” explains Michael Berumen, from the Red Sea Research Center. “It’s like putting together a puzzle.”

Devil rays were shown to make regular journeys to nearly 2,000 meters below the surface — depths that would normally crush a submarine, and with tempera-tures lower than 4 degrees Celsius. They did these dives daily at blazing speeds of 22 km/h, which is similar to the fastest fish or marine mammal.

The researchers were surprised by the data they were collecting. “I was

TAN

E SI

NCL

AIR-

TAYL

ORD

B E S E

3 8

for the deep diveanalyzing the data as it came in and was shocked to see how deep they were diving,” said Camrin Braun, a former KAUST M.S. student. “When I calculated their diving speed, I thought I’d made a mistake. It was pretty exciting when we crunched the numbers a second time and confirmed how fast the rays can dive.”

Travelling to depths at rapid speeds requires some adaptation. Scientists have

long been puzzled by the presence of a network of blood vessels around the devil ray’s brain called rete mirabile, which usually keeps the brains of animals warm. This organ did not make sense for a crea-ture that usually basks under the sun.

Berumen suggests that this adapted organ directs heat towards the brain

that has been generated by the rays’ muscles dur-ing their rapid dives. This heat keeps the brain warm and the rays’ eyesight sharp — making them keen hunters at these

depths which may be rich with fish or squid. In between dives, the devil rays

1. Thorrold S.R., Afonso, P., Fontes, J., Braun, C.D.,

Santos, R.S., Skomal, G.B., Berumen, M.L. Extreme diving

behaviour in devil rays links surface waters and the

deep ocean. Nature Communication 5, 4274 (2014).

“This adapted organ directs heat towards the brain that has been generated by the rays’ muscles during their rapid dives.”

would bask in the sun, warming up for the next dive.

With so much basic science unknown — and these rays are increasingly hunted for use in alternative medicine in Asia — this research adds a vital piece of the biological puzzle. “It is a difficult pros-pect to protect animals when we are still relatively ignorant of their behavior and ecology,” says Berumen, adding that he is hopeful these new findings will help international conservation efforts.

3 9I S S U E O N E


Novel use of sensors and associated high-resolution imaging in agriculture aims to facilitate a more sustainable future.

E ffective management of agricul-tural land and crops to produce plentiful, good quality food is paramount across the globe.

Scientists at KAUST are at the forefront of research using the latest sensing technologies to investigate crop yields, plant health and irrigation management with the aim of improving agriculture systems.

Matthew McCabe from the Water Desalination and Reuse Center and Mark Tester from the Center for Desert Agricul-ture, use a variety of sensors and mod-eling systems to analyze multiple facets of crops and plant growth. The scope of their work ranges from large-scale imag-ing of entire farms to producing intricate details pertaining to the health of indi-vidual leaves.

A crucial component of healthy plant growth is, of course, water. Much of McCabe’s research focus is on the hydro-logical cycle, examining fluxes such as evaporation and rainfall along with water stores — such as soil moisture and groundwater — and how they change over space and time.

“My team and I develop 30-year global maps of evaporation and soil moisture for climate studies, as well as smaller scale projects, such as examining crop-water use at the indi-vidual farm level,” explains McCabe. “Recently we began exploring how to use unmanned autonomous vehicles

Sensing for sustainableagriculture

(UAVs) to determine key characteristics of agricultural systems.”

Sensors carried by UAVs could pro-vide the high-resolution, real-time data needed to explore such factors as daily water use, crop health and condition and potential yields.

The technology underpinning UAVs, together with the sensing equipment they carry, has rapidly advanced in recent years, but the development of sci-entifically robust algorithms and mod-eling frameworks needed to analyze this wealth of data has not kept up — which is where McCabe and co-workers come in.

“We now have miniaturized sensors that can retrieve information across different portions of the electromag-netic spectrum, from standard digital cameras to systems spanning visible to near-infrared and thermal infrared wavelengths,” explains McCabe. “We are developing new metrics of crop con-dition from these advanced sensors to be incorporated into models estimating water use, heat-stress in plants, fertilizer needs and even to map pest and disease infestations.”

While McCabe aims high with UAVs monitoring plant health and water use in entire crops, Tester and his team are using sensors to gauge how individual plants respond to different environmen-tal stimuli.

Using The Plant Accelerator facility in Australia, Tester and his team can image

and monitor 2000 plants simultaneously as they grow, gathering vast amounts of detail on each plant and their responses to imposed changes in temperature, water use and salinity, for example. Near-infrared cameras allow the visu-alization of water content in plant tis-sues, while infrared cameras pick up the effects of temperature changes. Transfer-ring some of these imaging technologies to both controlled environment rooms and in the field at KAUST will be the next stage for this research.

“We now also use laser-sensing

KAU

ST

4 0

B E S E

equipment, allowing us to build 3D images of the entire structure of indi-vidual plants,” says Tester. “By generat-ing a point cloud using the lasers, we then mesh the points together using algorithms developed by the Visual Computing Center. If we combine the 3D structural images with 2D camera data, we can unfurl the life story of every sin-gle leaf on every plant, giving us unprec-edented views of how plants behave.”

Tester’s current research explores how certain plants can tolerate salinity better than others. Three examples are barley,

tomatoes and quinoa. “The key is to work out how they do it— what genes allow them to survive and indeed thrive on

salt water?” notes Tester. “If we could grow staple crops such as rice and wheat modified to survive on sea-water irriga-tion, this would open doors to address-ing future food and indeed fresh water shortages.”

With the rapid advances in sensors for use in agriculture on the ground, in the air and even via space-based satellites, the future looks bright for crop management and improvement from the micro level to wide scale agriculture. KAUST research-ers will undoubtedly continue to be at the forefront of such research.

“We now have miniaturized sensors that can retrieve information across different portions of the electromagnetic spectrum.”

Dr. Matthew McCabe and his team are using UAVs to examine whole agricultural

fields and study growth patterns.

4 1I S S U E O N E


#destinationKAUSTA destination for scientific and technological education and researchkaust.edu.sa

An algorithm that maximizes the difference between data categories achieves high accuracy in classifying faces.

I

Finding the face in the crowd

magine being asked to pick out a particular face among a sea of peo-ple. Researchers from KAUST have come up with a method to accu-

rately sift complex biological data.Xin Gao and his team have developed

an algorithm that achieves high accuracy in difficult classification problems1.

Biological data are often presented with dizzying complexity. They can be made up of many samples, with thou-sands of features per sample, and need to be converted into a simpler form for analysis.

Popular statistical methods for com-plexity reduction, such as principal com-ponent analysis, assign both positive and negative values to the simplified data. Thus, explains Gao, they cannot fit to the non-negative nature of some practi-cally useful data, such as image and gene expression data.

Instead Gao and postdoctoral fellow Jingyan Wang from the Computer, Elec-trical and Mathematical Science and Engineering Division improved upon a method that does not assign negative

numbers, the so-called non negative matrix factorization (NMF). A complex dataset is expressed as a matrix — each row is a feature and each column a sample — and is then broken down into simpler matrices with fewer features for representation of the data. NMF is first “trained” on known data and then used to represent test data.

Gao and Wang utilized the fact that each sample in a training set can be assigned to a particular class. They then increased the distance between any two pairs belonging to different classes to develop Max-Min NMF. “Instead of deal-ing with all the inter-class pairs equally, we pick the closest inter-class pair and maximize the distance so that all other

inter-class pairs will also be separated simultaneously,” says Gao.

They applied Max-Min NMF to face classification using images of 11 peo-ple bearing different facial expressions. Each image was treated as a sample with 1024 features. First, they trained Max-Min NMF to derive a low dimensional matrix that represented the faces and then showed that they could assign any grey scale image to the correct person. “A practical example,” says Gao, “is the face recognition system of U.S. Customs and Border Protection.”

In future work through a collabora-tion with researchers from the Univer-sité Claude Bernard Lyon in France, Gao wants to take face recognition to an even more challenging level by extending it to distinguish images of twins’ faces. Not only will they be able to pick a stranger from a crowd, but they will be able to tell him from his twin brother.

1. Wang, J.-Y. & Gao, X. Max-min distance

nonnegative matrix factorization. Neural

Networks 61, 75-84 (2015).

Dr. Xin Gao and Dr. Jingyan Wang developed an algorithm that, trained to simplify a matrix of faces, can assign a new image to the right person.

“Not only will they be able to pick a stranger from a crowd, they will be able to tell him from his twin brother.”

KAU

ST

4 3I S S U E O N E


Metallic nanostructures absorb light better than any other known structures.

M The darkest black

The bodies of Cyphochilus beetles are covered with very thin scales of chitin filaments that make them whiter than paper or any other artificial material produced so far.

JOH

N H

ORS

TMAN

/ITCH

YDO

GIM

AGES

ON

FLI

CKR

etallic nanostructures that are perfect light absorbers in the visible and infrared spectrum have been fabri-

cated by researchers from KAUST. The structures, whose design replicates the colorful wings of beetles, are the darkest light absorbers known1.

C E EM S

4 4

100 nm

The shimmering colors seen on the wings of some beetles arise from a physical structure on the micro and nanoscale that has evolved to scat-ter light for a colorful appearance. The beetle species Cyphochilus in particular has wing structures that make them the whitest known insect.

The researchers used the Cyphochilus wings to develop a perfect light absorber based on the inversion principle. A struc-ture that inverses the properties of white beetles will be black and absorb light. This structural variation of the beetle structure consists of a gold nanorod to which a gold nanosphere is attached. The nanorods behave like tiny antennas that pick up light at all colors from the environment.

As the light passes through the rod, it gets trapped in the nanosphere, where it bounces back and forth until the light is completely absorbed. The absorp-tion capacity of the structures is about 26 percent higher than that of carbon nanotubes, the strongest light absorber identified.

The high light absorption has applica-tions for energy harvesting, explained Andrea Fratalocchi of the Computer,

Electrical and Mathematical Science and Engineering Division, who led the collaborative research team along with Yu Han of the Physical Science and Engi-neering Division.

“We are already employing these structures in the context of water desali-nation and they showed world record efficiency performances,” he said. They can also be used as catalyzers for chemi-cal reactions or for the production of biofuel from sunlight.

The structure can also emit light under specific conditions. If excited at one particular color — such as green — that

1. Huang, J., Liu, C., Zhu, Y., Masala, S., Alarousu,

E., Han, Y. & Fratalocchi, A. Harnessing structural

darkness in the visible and infrared wavelengths

for a new source of light. Nature Nanotechnology

doi:10.1038/nnano.2015.228 (2015).

green light condenses and the structures emit red light in a very narrow region of the energy spectrum. This region cor-responds to the minimum energy wave-length where light can spread out across the material.

The main advantage of the structures is their extremely high light absorp-tion. Fratalocchi pointed to the possi-bility of their structures being used for hydrogen production, as hydrogen is a versatile and efficient energy storage material.

“One of the greatest current energy challenges is that it cannot be stored in large quantities which means we need to produce vast quantities of energy even if we do not consume it all,” explained Fratalocchi. “Hydrogen can be a game-changing technology with a system that is totally clean, abun-dant and renewable, and that can be used on demand and stored in large amounts.”

The wings of Cyphochilus, the whitest known insect, provide the conceptual framework to develop the blackest material in the world.

KAU

ST

“Hydrogen can be a game-changing technology with a system that is totally clean, abundant and renewable, and that can be used on demand and stored in large amounts.”

4 5I S S U E O N E


Taking computing to the next level

4 6

C E EM S

The new supercomputer will enable ground-breaking scientific modeling and analysis in Saudi Arabia and worldwide.

W hen scientists first pow-ered up Shaheen in 2009, KAUST joined the ranks of the supercom-

puting elite. Shaheen, then the fourteenth most powerful computer in the world, quickly became indispensable. “About 20 percent of the faculty here use com-

puting as the main way of driving dis-covery,” says David Keyes, director of the Extreme Computing Research Center at KAUST.

The University is now ramp-ing up the capacity for discovery with the new Shaheen-Cray XC40, a next-generation supercomputer which went online in May. The facility was acquired and will be managed by the Supercomputing Core Lab at KAUST.

Keyes says the upgrade was not due to concern about the ranking of computing power. “It’s not a mat-ter of vanity, as everybody gets a

higher-powered system,” he explains. “It’s actually a matter of being able to justify your operational expenses.” Alongside climbing costs for data gener-ation, KAUST was confronted by loom-ing hardware and software obsolescence, as IBM has discontinued development of the BlueGene supercomputer family to which Shaheen belongs.

KAUST put out a tender for manufac-turers interested in building Shaheen’s successor, and the call was answered by Cray, a U.S. company. The Seattle-based firm assembled a system with nearly 200,000 processors and the capacity to perform 5 quadrillion floating-point operations per second — a mathemati-cal “gold standard” metric of processor performance. This represents an approxi-mately 30-fold boost over the first Shaheen, and Keyes notes that the new supercomputer is also six times more power efficient than its predecessor.

Cray also produced proprietary hard-ware features, such as “DataWarp”— an additional layer of memory that improves application performance — and a custom-ized internal network configuration

KAU

ST

4 7I S S U E O N E


that enables the computer’s many pro-cessors to communicate efficiently.

Vladimir Bajic’s team at the Computa-tional Bioscience Research Center will be among the first to make use of the new facility. They plan to assemble, annotate and extract knowledge from vast col-lections of biological data — for exam-ple, modeling the interactions between networks of genes and proteins within a cell. “Shaheen-Cray XC 40 has a much better and more flexible architecture that allows us to use it efficiently for many problems we simply could not run on the old Shaheen,” says Bajic.

Geoscientist Georgiy Stenchikov is excited about the potential to accelerate his climate modeling investigations. “Our group was one of the most active users of Shaheen,” he says. “The new Shaheen will allow us to improve our spatial reso-lution by an order of magnitude, moving environmental research at KAUST to a new horizon.”

The new facility also offers added power for new faculty members such as seismologist Daniel Peter, who will use computational approaches to build sophisticated maps of our planet’s inte-rior to predict earthquakes and locate natural resources, among other quests. “We describe it as a Human Genome Pro-ject for the Earth,” says Keyes.

Much of the research processed by the supercomputer will directly benefit Saudi Arabia. For example, Jean-Luc Brédas at the Solar and Photovoltaics Engineering Research Center is com-putationally modeling materials for next-generation solar cells to sustain-ably power the Kingdom. His efforts are being complemented by those of Sten-chikov’s group, which is generating data to address critical environmental issues — including identification of optimal locations for future solar farms. “We’re focused on in-depth analysis of extreme events like flash floods, dust storms and the combined effects of industrial activities and dust on air quality and climate over the Arabian peninsula,” says Stenchikov.

Many external groups will also ben-efit from Shaheen-Cray XC 40, includ-ing corporate partners like the Saudi

Basic Industries Corporation (SABIC), as well as academic collaborators overseas. KAUST is looking to develop a com-mercial data center for business clients which could help defray the costs of run-ning the supercomputer.

Keyes believes that the new Shaheen, which is Arabic for “falcon”, will also become a powerful shared asset for research universities throughout the region. “We would like to get King Fahd University and King Saud University and other institutions on board and provide the opportunity to grow their faculty and graduate research in the direction of high-performance computing,” he says. The supercomputer’s capacity will inevi-tably become inadequate over time, but KAUST has ensured the system’s lifespan will be maximized.

As part of the deal, Cray has agreed to support a potential four-fold future upgrade in processing power. This could keep Shaheen-Cray XC 40 near the top of its class for up to seven years — giving supercomputer experts at KAUST ample time to contemplate the possibilities for an even bigger and faster Shaheen. “We are aiming to be in the space of not just using supercomputers, but using our experience at the leading edge to be thinking about next-generation sys-tems,” says Keyes.

“The new Shaheen, which is Arabic for ‘falcon’, will also become a powerful shared asset for research universities throughout the region.”

The new Shaheen-Cray XC40 is about 30 times faster than the first Shaheen supercomputer.

KAU

ST

4 8

C E EM S

Bendable electronics could help make robust wearable devices that can continuously monitor a person’s health.

E

Bent, but not broken

ffective wearable technology to monitor health indicators is a step closer after KAUST researchers developed flexible

electronic circuits that continue to work even when bent and folded like a thin piece of paper.

While there has been rapid progress made in flexible electronics, the chal-lenge remains to find suitable materials that retain excellent electrical perfor-mance even when bent or strained. Most electronic devices are currently based on silicon, which has excellent electrical properties and is abundant and cheap. However, silicon’s usefulness is limited because it is unyielding and brittle.

Muhammad Mustafa Hussain from the Division of Computer, Electrical and Mathematical Science and Engineer-ing and colleagues have now designed a flexible electronic circuit which keeps functioning even when bent sharply many times. Their approach was to first create the electronic components on a conventional silicon substrate and then show how these can be transposed onto a more malleable substrate1.

Hussein explains that bendable cir-cuits have many potential uses — such as devices that could be attached directly to the skin to continuously monitor a patient’s pulse, blood pressure or blood glucose level, negating the need for needles or finger pricks. A device’s reli-ability, however, is compromised by repeated flexing of the circuit. “The fin-ger joint and the shoulder have different bending radii and, in the case of the jaw, a flexible device bends many times as we talk and eat,” says Hussain.

Building on past success with metal oxide semiconductors, Hussein’s team set out to measure how acute and repeti-tive bending affects the performance of these flexible circuits. They fabricated their capacitors on a rigid silicon sub-strate then placed the sample in a gas that etches away the silicon, leaving only a thin fabric that is both flexible and semi-transparent. The researchers then put these circuits under a series of mechanical stresses to investigate how they affect their electrical properties.

First, they measured an essen-tial capacitor property known as the

breakdown voltage — the maximum volt-age that can be applied across the device before it stops functioning properly. Surprisingly, they found that increasing the strain produced better performance. For example, when the capacitors were bent 180 degrees, their device proved to be three times less prone to breakdown when bent at the small radius of curva-ture of 5 millimeters compared to a wider 50 millimeters curvature.

They then tested the decline in the device’s performance with repeated flex-ing. When the device was bent 50 times the function was reduced — the break-down voltage fell to about 12 percent of its initial value — and after 100 bends it failed completely. The researchers attrib-uted this to the fracture of the fabric, however, and now plan to try adding polymeric support to the final device to increase its endurance.

Bendable electronic circuits have potential applications in healthcare technologies that can be attached directly to the skin.

1. Ghoneim, M. T., Kutbee, A., Ghodsi Nasseri, F.,

Bersuker, G. & Hussain, M. M. Mechanical anomaly

impact on metal-oxide-semiconductor capacitors

on flexible silicon fabric. Applied Physics Letters 104, 234104 (2014).

KAU

ST

4 9I S S U E O N E


W

Specialized word search method sheds light on phenotypic

similarity of diseases.

Disease researchers have a way with words

ords and phrases associ-ated with symptoms of common diseases are used to identify complex con-

cepts in medical texts and to point to significant patterns that help identify the genes and pathways that underlie clus-ters of diseases.

Researchers from KAUST worked with scientists in the U.K. to develop a specialized word search of scientific literature called semantic text-mining1. The work identifies shared traits in rare, common and infectious diseases for the first time at scale. It also provides,

notes Robert Hoehndorf of the Com-puter, Electrical and Mathematical Science and Engineering Division at KAUST, “a tantalizing overview of the phenotypic structure of the human ‘dis-easome.’”

Researchers routinely catalog data of signs and symptoms relating to geneti-cally based diseases through electronic resources, such as the Online Mendelian Inheritance in Man (OMIM) and Orphanet databases. However, extending similar methods to common and infectious dis-eases has proved challenging due to the lack of an infrastructure providing the

huge number of phenotypes associated with them.

“To take on this task, we needed very large computational capacity,” explains Hoehndorf. “Using ‘ontologies’— formal representations of the concepts and rela-tions within a domain — we designed a method that identifies concepts referring to phenotypes of common and rare dis-eases within millions of published papers and abstracts and used these concepts to establish the phenotypic similarity between a large number of common and rare diseases.”

The team’s method of grouping diseases

5 0

C E EM S

allows for new approaches to identify the genes and pathways that underlie clusters of phenotypically similar diseases.

“If we know something about dis-ease A, but not about disease B, finding phenotypic similarity between the two diseases suggests they may result from a mutation or disturbance of genes or processes with a common pathway, and points to new investigations into disease B,” explains Hoehndorf.

The researchers’ work is freely avail-able at http://aber-owl.net/aber-owl/diseasephenotypes/ (and in a visualiza-tion environment at http://aber-owl.net/

others that are better characterized, or those having well-established genetic underpinnings.

“Our resource can also help to prior-itize candidate genes in genome-wide and phenome-wide association studies — currently a major challenge —as well as aid the development and repurposing of drugs,” Hoehndorf explains.

aber-owl/diseasephenotypes/network/). Access to this work will allow other scientists to formulate new hypoth-eses about poorly understood diseases through their phenotypic similarity to

1. Hoehndorf, R., Schofield, P. N.& Gkoutos,

G. V. Analysis of the human diseasome

using phenotype similarity between

common, genetic, and infectious diseases.

Scientific Reports 5, 10888 (2015).

KAU

ST

A map of the human diseasome in which nodes represent diseases and colors are based on general types of diseases. Proximity between the signs and symptoms of the diseases is used as an attraction force between the nodes so that diseases that appear close together in the map generally have similar signs and symptoms.

“Access to this workwill allow other scientists to formulate new hypotheses about poorly understood diseases.”

5 1I S S U E O N E


A n unexpected observation of rogue waves of light could ultimately lead to better pre-diction systems for weather

events and natural disasters by improv-ing researchers’ understanding of the mechanisms that underpin chaotic wave events1.

Natural catastrophic events are inher-ently unpredictable, stemming from high-energy, chaotic systems that are dif-ficult to understand or emulate. Andrea Fratalocchi and his team from KAUST, in collaboration with researchers at univer-sities in the U.K. and the Netherlands, are inspired by such random and complex phenomena for new technologies.

“We were collaborating to build new optical chaotic resonators for enhanced energy storage,” says Fratalocchi from the Division of Computer, Electrical and Mathematical Science and Engineer-ing. “While performing theory on these structures, we saw huge photonic waves appear in our simulations. We had no idea where these fascinating structures came from, and we decided to investigate further.”

The researchers built an optical chip of just 40 micrometers in size, designing its shape to maximize the potential for

A microchip designed to generate and control rogue waves of light on the nano-scale has many potential applications.

Optical chips harness the power of rogue waves

KAU

ST

1. Liu, C., van der Wel, R.E.C., Rotenberg, N., Kuipers,

L., Krauss, T.F. et al. Triggering extreme events at

the nanoscale in photonic seas. Nature Physics, 11358-363.

creating rogue waves of light. Frataloc-chi came up with the idea for the quarter-stadium shape of the chip following his mathematical studies in a field described as “chaotic billiards”.

“If you launch a classical particle inside such a system, it follows a totally random trajectory,” explains Frataloc-chi. “When we directed photons into our quarter-stadium shaped chip via the micro-scale optical channel, we saw numerous waves formed that evolve completely randomly to generate a ‘pho-tonic sea.’”

Within this sea, the researchers could control the formation of rogue waves by limiting the number of waves flowing

through the chip at any one time. The exact shape of the chip improved the researchers’ control over the waves — rather like accurately designing the coastline of a small lake.

Their insights could translate to other domains and prove invaluable to scien-tists hoping to understand and predict natural disasters such as tsunamis. Rogue waves are also known to create distur-bances in data communication networks, which Fratalocchi hopes could be allevi-ated. “We have shown that rogue waves manifest themselves in a window where the losses of a system are perfectly bal-anced — not too high, not too low. We could add an absorber into communica-tion networks to increase the losses to a point where the rogue waves simply disappear,” he says.

Many other applications are possible. For instance, using the chips to develop an ultrafast and highly secure crypto-graphic system could offer further poten-tial for communication networks, notes Fratalocchi.

“When we directed photons into our quarter-stadium shaped chip… we observed the formation of numerous waves that evolve completely randomly, generating a ‘photonic sea.’”

C E EM S

5 2

A nano-scale optical chip developed by KAUST researchers could have widespread applications in natural

hazard prediction and telecommunication networks.

5 3I S S U E O N E


A fast computational method optimizes sensor measurement networks for noisy, sparsely observed environments.

A shock-tube combustion method was used to demonstrate the effectiveness of the optimization method.

TTaking the guesswork out of experimental design

KAU

SThe capture of information about environments and processes is ubiquitous in modern society, from recording weather patterns

to measuring traffic density and indus-trial process parameters. These measure-ments, when collated, provide data for predictive modelling and process opti-mization.

Determining exactly how many sen-sors to use and their optimal location, however, has significant implications for the reliability and value of the infor-mation obtained and for the cost of the measurement system itself.

Quan Long, Marco Scavino and Raul Tempone from KAUST, in collaboration

5 4

C E EM S

“As physical systems become increasingly complex, the optimization of experimental design becomes more computationally intensive.”

with Suojin Wang from Texas A&M University in the U.S., have developed a computational method that can quickly derive an optimized “experimental design” for complex, noisy systems with little available data1.

“Experimental design is an important topic in engineering and science,” says Tempone. “It allows us to optimize the locations of sensors to achieve the best estimates and minimize uncertainties, especially for real, noisy measurements.”

Using an established approach known as Bayesian optimization, which com-bines data and contextual information in a mathematically rigorous frame-work, Tempone and his colleagues pooled their expertise in computational methods, statistics and numerical anal-ysis of partial differential equations. From this they developed a scheme that could compute an optimized design

even for poorly understood or “low-rank” systems.

“As physical systems become increas-ingly complex, the optimization of experimental design becomes more com-putationally intensive,” says Tempone. “Our fast method can be used in situations where a large number of parameters need to be estimated while data are sparse.”

Numerical modelling schemes are commonly used to optimize measure-ment networks by brute-force calcula-tion using real data. The reliability of numerical optimization, however, is only as good as the data used in the compu-tation and — even with today’s super-computers — the computations can take a very long time. Analytical methods, on the other hand, use computationally effi-cient equations to describe a system in approximate terms. Analytical schemes also generally require good data, but this

obstacle was overcome through the use of some sophisticated mathematics.

The significance of this work is that we pushed the boundary of an analytical method, called the Laplace approximation, from the conventional Gaussian scenario to low-rank distributions,” says Tempone.

The team demonstrated the effec-tiveness of their optimization method by applying it to a range of engineer-ing applications, including impedance tomography, shock-tube combustion and seismic inversion. “This new method can be applied in almost any field, from medi-cal imaging to reservoir monitoring and sensor technologies,” Tempone notes.

1. Long, Q., Scavino, M., Tempone, R. & Wang, S. A

Laplace method for under-determined Bayesian

optimal experimental designs. Computer Methods in Applied Mechanics and Engineering 285,

849–876 (2015).

5 5I S S U E O N E


Lightweight and low-cost device uses friction inside paper-based coils to transform mechanical motion into electricity.

U

An origami “slinky” that harvests incidental energy

sing the ancient Japanese technique of origami to fold paper sheets and Teflon films into three-dimensional spring

structures, researchers from KAUST have developed an electrical “nanogenerator” that can power tiny sensors and software networks using mechanical energy har-vested from the environment1.

Mechanical energy harvesters are devices that can capture trace amounts of energy from normal occurrences — vibrations from passing trains or the footsteps of pedestrians, for instance — and convert them into usable electricity. One of the most effective ways to do this is via a phenomenon known as tribo-electricity. This effect, familiar to any-one zapped by built-up static electricity, occurs when two materials of different polarities make contact intermittently. The repeated rubbing causes electrons to jump from one surface to another, creat-ing an electric potential proportional to external force.

Researchers have exploited this behavior to produce triboelectric

nanogenerators (TENGs) that slide or tap together for small-scale energy produc-tion. Moving electrons between adjacent surfaces in TENGs, however, is generally performed with “triggers” that move in one direction only — a limitation that prevents capture of the full range of potential energy.

Jr-Hau He from the Division of Com-puter, Electrical and Mathematical Sci-ence and Engineering at KAUST, along with international collaborators set out to solve this puzzle using shape-shifting, paper-based origami structures. First, the team folded regular printer paper into four “L”-shaped pieces and then interconnected them into a spring-like subunit. After gluing aluminum foil and Teflon sheets to the paper substrate, they linked the subunits together into an inte-grated device resembling a Slinky toy.

When an external force compresses the Slinky-TENG, the Teflon film con-tacts the paper and steals electrons from

its surface. Releasing the force expands the slinky and separates the two surfaces, causing the accumulated electrons to flow through the aluminum foil to a ground circuit. Repeating the compression gen-erates another potential difference that draws electrons from the ground to the aluminum foil — a periodic cycle that har-vests energy through multiple stretching, lifting and twisting motions.

The researchers’ device produced micro-Watts of power per square meter — enough to power four commercial LED bulbs — and operated for more than 10,000 cycles without deterioration. The Slinky-TENG also acts as a self-powered pressure sensor that differentiates the weight of different coins by the voltages they produced.

“Using paper, one of the most inex-pensive and widely-accessible materi-als, to generate electricity can make the triboelectric nanogenerator useful and even disposable,” says He. “Origami techniques can extend the applications of nanogenerators remarkably.”

A paper-based slinky structure can be easily stretched and recombined to turn mechanical motions into electric output signals.

REPR

OD

UCE

D W

ITH

PER

MIS

SIO

N F

ROM

REF

1 2

015

AMER

ICAN

CH

EMIC

AL S

OCI

ETY

1. Yang, P.-K., Lin, Z.-H., Pradel, K. C., Lin, L.,

Li, X. et al. Paper-based origami triboelectric

nanogenerators and self-powered pressure

sensors. ACS Nano 9, 901–907 (2015).

“Origami techniques can extend the applications of nanogenerators remarkably.”

5 6

C E EM S

Identifying noise in communication signals helps to filter out glitches and improve transmission quality.

A n algorithm that estimates extraneous noise in radio-frequency communication signals can help to eliminate

annoying interruptions in WiFi or digi-tal television transmissions.

The background hiss of a poor-qual-ity radio broadcast is often caused by random fluctuations in the receiver’s electronic circuits. In contrast, impulse noise is a relatively rare form of inter-ference that can be caused by nearby electrical devices being switched on.

Impulse noise, according to Tareq Al-Naffouri of KAUST, brings such high power that it obliterates the signal. Turning on a light may cause clicks in a radio signal, for example, or momen-tarily cause a television screen to blank. “Impulse noise is also among the most severe limiting factors in ADSL (Asym-metric Digital Subscriber Line) commu-nications,” Al-Naffouri adds.

Al-Naffouri and his colleagues from the Division of Computer, Electrical and Mathematical Science and Engi-neering addressed this problem using a widely-used technology in wireless communication systems called orthog-onal frequency division multiplexing (OFDM). This carves up a band of radio frequencies into many narrower bands, each of which carries a separate data stream.

To ensure that these subcarriers do not interfere with each other, each is separated by very narrow “guard bands” which are a tight range of fre-quencies that carry no data. “It’s like a group of people talking in a hall — they have to spread out so that conversations don’t get mixed up,” says Al-Naffouri.

The team’s algorithm looks at these guard bands — which are supposed to be silent— for any sign of impulse noise. Then it uses these measurements to estimate the size and sources of the impulse noise. Finally, it subtracts that noise from the received signal, produc-ing a noise-free signal.

The detailed calculations involved in this process are complex and require a lot of computing power to implement quickly enough to mitigate impulse noise. So the researchers streamlined the process to reduce the overall com-plexity of the algorithm while main-taining effective noise filtering.

“The systems performs very well, and with simple processing one can increase the transmission rate by 30 percent compared to current standards,” says Al-Naffouri.

His team’s simulations suggest that the same approach might also be useful in improving the quality of underwater communication systems. “We hope to conduct real experiments at KAUST and move to prototype our ideas,” notes Al-Naffouri.

1. Al-Naffouri, T. Y., Quadeer, A. A. & Caire, G.

Impulse noise estimation and removal for OF1DM

systems IEEE Transactions on Communications 62,

976-989 (2014).

Tareq al-Naffouri works to improve communication.

Signal noise annoys no more

“It’s like a group of people talking in a hall — they have to spread out so that conversations don’t get mixed up.”

KAU

ST

5 7I S S U E O N E

The discovery of the incandescent light bulb has transformed human existence. New LED technologies promise to be the next step forward.

TA different kind of light

he International Year of Light in 2015 marks 1,000 years since the production of Ibn Al-Haytham’s pioneering work on optics, Kitab al-Manazir. Since then, light has

grown ever more intrinsic in our lives, from fiber optic cables that are the con-duit of modern communication to the blinking LEDs that inform and entertain us. Now research from the Computer, Electrical and Mathematical Science and Engineering Division at KAUST is contributing to the next generation of lighting technology which promises to continue transforming our world.

For most of human history, light was produced from heat — candles, lanterns or open fires. The invention of the electric

KAUST research is going beyond LEDs to develop solid-state lighting

solutions based on lasers.

KAU

ST

5 8

C E EM S

light bulb has been an effective tool for more than a century, but the technology is energy intensive. While the advent of light-emitting diodes (LED) has changed the picture, KAUST research is going beyond this stage to develop solid-state lighting solutions based on lasers.

LEDs are solid-state devices that pro-duce light by using electricity to recombine electrons with holes, which are positively charged particles, in a semiconductor. This releases a certain amount of energy as light, the color of which depends on the material of the semiconductor. For instance, gallium nitride-based LEDs can reach higher efficiencies than older tech-nologies by producing visible light directly instead of through heat or fluorescence.

“Lights using semiconductor lasers can reach very high efficiencies,” says Boon Ooi, the head of the laboratory. “The typi-cal efficiency of LEDs is 40-50 percent. With lasers, we can hit 70 percent or beyond.” A laser-based light would need only 4W of power for the same luminos-ity as a standard 60W incandescent bulb. The equivalent fluorescent light draws 14W — even a LED consumes more than twice the energy of a laser-based light.

This low power requirement makes a laser-based light an especially attractive option where electricity is scarce or unre-liable, since they can readily be powered by solar-charged batteries. Even in coun-tries where energy is cheap, such as Saudi Arabia, their efficiency offers significant benefits. Lighting currently accounts for 30 percent of the energy consumption in the Kingdom, and energy demand is expected to double in the next 10 years. Most of the lights in Saudi Arabia are incandescent or halogen lamps and replacing these with solid-state lights, whether based on LEDs or lasers, would significantly reduce consumption and help offset the anticipated increase in energy demand.

Ooi left a professorship in the United States to join KAUST several years ago. “In the U.S., you just become another successful professor, but the vision for KAUST is different,” he explains. Ooi says the abundant resources and supportive research environment at KAUST give him an opportunity to make a bigger impact.

He has been able to expand his research group and explore new avenues and, in 2013, his lab was awarded a five-year, multi-million dollar grant by King Abdulaziz City for Science and Technol-ogy (KACST) to form a Technology Inno-vation Center focused on laser-based solid-state lighting. Ooi’s lab is working with Shuji Nakamura at the University of California, Santa Barbara, a co-recipient of the 2014 Nobel Prize in Physics for his role in the invention of the blue LED and laser, in an effort to develop red, green and blue semiconductor lasers bright enough for lighting. They produced a high brightness red laser last year and are currently patenting orange and yel-low lasers.

However, Ooi says a true green

semiconductor laser remains beyond their reach due to the difficulty in finding an appropriate semiconduc-tor material — the same challenge that Nakamura faced with the blue LED and laser. Ooi’s group is currently exploring different angles, such as using nanow-ires or new materials to produce the elusive color.

Ooi’s goal is to integrate red, green and blue lasers on to a smart chip in the next few years. By varying each laser’s contri-bution, the chip will produce any color. Lights based on this technology will be more efficient than LEDs and have better color. There are also interesting trans-formative applications of this technology. Ooi’s team is piloting using red and blue laser-based lights to grow plants indoors on shelving units. The lights produce very little heat, minimizing the need for cooling and the water lost to evapora-tion. If successful, this approach could be applied to dramatically increase the agricultural potential of arid countries like Gulf states.

Another promising application is a high-speed undersea communication system being developed with KAUST colleague Mohamed-Slim Alouini. Sea-water absorbs very little blue light, and a narrow spectrum laser can transmit data much faster than existing optical or ultrasound techniques. So far, the team has successfully transmitted data through ten meters of water at over 1Gb/s, at least 100 times faster than current technologies. For comparison, ultrasound reaches 50kb/s while opti-cal transmission ranges between 1 and 10Mb/s.

As the International Year of Light dawns, the photonics lab at KAUST is poised to offer the benefits of a new kind of light. To promote their research, the team is planning to host “Lightfest-2015” in Jeddah to educate the public about the benefits of newer technologies. Addition-ally, light was a main theme of the 2015 Winter Enrichment Program at KAUST, with movies, workshops and experiments to help explain the ubiquitous phenom-enons. With the expected efficiency of laser-based lighting and the wide range of its applications, the future is looking bright.

“As the International Year of Light dawns, the photonics lab at KAUST is poised to offer the benefits of a new kind of light.”

5 9I S S U E O N E


Metamaterial Technology

Metascreen Technology

THz/Infrared Light

Metaferrite

Graphene

Metal

A tiny device broadens the bandwith to enable absorption with wide-reaching potential for electrical engineering.

A

Perfect absorption graphene-style

nanosca le near-per fec t absorber, or “metascreen”, which operates at terahertz and infrared frequencies,

has been developed by researchers at KAUST1. Using geometrically patterned graphene coupled with a metal-backed “dielectric” substrate, the new absorber will have broad application in electrical engineering, from communication net-works to solar cell technology.

Graphene, a two-dimensional structure comprising carbon atoms arranged in a hexagonal lattice, has remarkable electronic properties such as high conductivity and stability. When combined with noble-metal nanostructures, graphene’s so-called “plasmon mode” triggers the creation of coherent, tunable electron oscillations. These enable researchers to control — theoretically, at least — the absorption of light at different frequencies.

“The quest for the ‘perfect’ absorber has been ongoing for some time,” says Mohamed Farhat, a member of the team led by Hakan Bagci of the Computer, Electrical, and Mathematical Sciences and Engineering Division, who worked on the project in collaboration with

Pai-Yen Chen at Wayne State Univer-sity, U.S.

“The challenge is to find a material that can absorb significant electromag-netic energy, ideally 100 percent, which is present at different frequencies — for example, in the light shining on solar cells,” explains Farhat. “Such absorbers would vastly improve the efficiency and sensitivity of these devices.”

The main problem with existing absorber designs is that they only operate on lim-ited bandwidths, so not all the energy from multiple frequencies is absorbed.

Bagci and his team spent considerable time designing an absorber whose opera-tive bandwidth would be maximized — aiming to utilize terahertz and infrared ranges.

Their absorber comprises a one-atom thick graphene sheet on a metal-backed dielectric substrate. The magnetic reso-nance of the substrate effectively widens

the frequency range over which the gra-phene’s plasmon mode is sustained. The plasmon mode allows for the cancella-tion of magnetic fields reflected by the metallic background, widening the band of absorption.

The team used mathematical models to calculate the material properties of graphene and its response to different electromagnetic interactions. “We used extensive numerical simulations to ver-ify our design, which can be optimized for given sets of geometry and substrate materials depending on the intended applications,” explains Farhat. ”The new absorber is simpler than previous designs and easier to fabricate.”

Near-perfect absorbers have numerous potential applications, from sensors and spatial light modulators, to energy har-vesting, infrared camouflage and cloak-ing mechanisms. Farhat is confident the new design will make a major impact and hopes to work with experts in different fields to further expand the project.

1. Chen, P-Y. Farhat, M. & Bagci, H. Graphene

metascreen for designing compact infrared

absorbers with enhanced bandwidth.

Nanotechnology 26, 164002 (2015).

“The new absorber is simpler than previous designs and easier to fabricate.”

KAU

ST

6 0

C E EM S

An integrated set of genetic mechanisms controls whether bees behave as foragers or nurses.

A

Honey bee behavior is in the genes

pis mellifera, the European honey bee, has become a key model organism for decipher-ing the interplay between

genes, behavior and the environment. A study led by KAUST researchers shows that genes play a large part in control-ling the roles played by bees during their life cycle.

With its complex social structure and well-understood genome, the honey bee is an ideal species for genetic research. As a worker bee matures, it is observed to graduate from hive-bound “nurses” — tending larvae and maintaining the hon-eycomb — to outdoor guards or foragers. These behaviors correlate with different patterns of gene activity, but little was known about how the genes are controlled.

Vladimir Bajic, director of the Com-putational Bioscience Research Center, leads an international team studying how genes instruct bee behavior. Bajic’s team cataloged genes known as differentially expressed genes (DEGs) that differed in activity between nurses and foragers. More than 1,000 genes varied between the two bee roles, of which about 500 were more active in each group. In nurse bees, most DEGs were involved in nutri-tion, whereas in foragers, the DEGs had functions including growth, development

and nervous system operation. This may indicate the wider range of complex mental tasks performed by foragers.

The researchers used a new technique called CAGEscan to analyze the genes. This technique sequences the region at the start of each gene, including its control sequences, which are called promoters.

They next identified 26 genes (also differentially expressed) encoding regu-latory proteins known as transcription factors, which interact with promoters to switch the DEGs on or off. By matching short sequences called motifs in the DEG promoters to which corresponding tran-scription factors bind, they could deter-mine which transcription factors control which genes.

As Bajic noted, “these motifs play a crucial role in understanding gene expression regulation, as they con-nect the regulated genes with the

transcription factors that control them.”The results suggest that a strikingly

small number of transcription factors con-trol the vast majority of behavior-specific genes in bees. In foragers, almost half the DEGs were mainly controlled by just five transcription factors representing a crucial set of switches managing bee behavior.

The team also found that many honey bee gene sequences contain multiple alternative start sites, some unique to either foraging or nursing bees. This is the first time such a mechanism has been linked to changes in behavior.

In honey bees, the genetic mechanisms uncovered by Bajic’s team are responsible for the perfect balance within the hive, where every bee has a specific role in maintaining a strong and healthy colony.

Bajic believes the team’s insights into the links between genetics and behavior have implications that “cannot be spe-cific to honey bees… many behavioral characteristics of higher organisms could be controlled by gene expression pat-terns,” he said.

1. Khamis, A.M., Hamilton, A.R., Medvedeva,

Y.A., Alam, T., Alam, I. et al. Insights into the

transcriptional architecture of behavioral

plasticity in the honey bee Apis mellifera. Scientific Reports 5, 11136 (2015).

“In honey bees, the genetic mechanisms uncovered by Bajic’s team are responsible for the perfect balance within the hive.”

KAU

ST

6 1I S S U E O N E


A surprisingly simple algorithm helps computers perceive individual objects inside videos from their movement patterns.

C

Visual computing hits a moving target

omputer programs that automat-ically spot objects and bounda-ries in videos are fundamental to today’s film industry as well as

future robotic technology. Taking a cue from nature, researchers from KAUST have developed a way to use the distinc-tive motion patterns of an object to iden-tify and track its shape1.

Most object-detecting algorithms ana-lyze signals such as color and texture to define an object from its background. When the image information becomes too complicated, however, the elemen-tary statistics used for segmentation begin to break down and cause detec-tion errors. Current programs have to be “trained” with large data simulations run

from different viewpoints and illumina-tion conditions to locate objects with sufficient certainty.

Ganesh Sundaramoorthi and Yanchao Yang from the Computer, Electrical and Mathematical Science and Engineering Division opted to tackle this problem

Ganesh Sundaramoorthi leads his team in visualization techniques.

with a dynamic model based on object movement. Just as humans can better recognize a moving animal than a static, camouflaged one, the researchers theo-rized that comparing how certain shapes move, deform or depart from view as the video plays could effectively seg-ment objects from their backgrounds. This would be possible even in complex conditions.

Computing shapes from movement pattern data, however, can sometimes be ambiguous. Sundaramoorthi uses the example of how the rotating stripes on a traditional barbershop pole appear to move simultaneously up and down. Adding to this uncertainty is that a number of different factors and noise patterns encompass object motion in videos, making them hard to isolate with algorithms.

The KAUST team designed an algo-rithm that calculates how shapes in an image deform to match the next frame, and checks for occlusions — the appear-ance or disappearance of objects from view. They found that these two factors were key to recovering movement.

Solving such equations can, however, involve heavy computational resources. So the researchers designed a geometry-based framework that codes how the shapes deform into a compact math-ematical metric. “Surprisingly, this leads to a simple and efficient computational algorithm that eliminates the need for sensitive tuning parameters,” says Sund-aramoorthi.

Trials on videos revealed that the new algorithm results in a template that warps around objects and finds their shapes far more effectively than con-temporary programs. “Even though the motions uncovered by our algorithm may not coincide exactly with reality, they are sufficient to segment objects accurately,” notes Sundaramoorthi. “This takes us one step closer to automating processes in robotic control and high quality three-dimensional videos.”

“This leads to a simple and efficient computational algorithm that eliminates the need for sensitive tuning parameters.”

1. Yang, Y. & Sundaramoorthi, G. Shape

tracking with occlusions via coarse-to-

fine region-based Sobolev descent. IEEE Transactions on Pattern Analysis and Machine Intelligence 37, 1053–1066 (2015).

KAU

ST

C E EM S

6 2

efficiently store certain wavelengths of light but not others. For this reason, con-ventional optical resonators have strug-gled with limited applications for the storage of light energy from broadband sources such as sunlight.

The team performed a numerical simu-lation to show theoretically that a reso-nator with chaotic deformities can store up to six times as much energy as its conventional counterpart.

In testing this experimentally, the team used a series of stadium-shaped planar photonic crystals with changes in their macroscopic geometry to produce vary-ing degrees of chaos. The researchers showed that a fully chaotic optical reso-nator can trap twice as much energy as a non-chaotic optical resonator.

This was a good result but the research-ers noted there was room for improve-ment.

Chaotic optical resonators can trap more light energy than their orderly counterparts.

C

Lights up for chaotic storage

haos tends to be something best avoided, but now KAUST and an international team show that when it comes to increas-

ing energy storage in optical resonators, chaos trumps order1.

Andrea Fratalocchi of the Computer, Electrical and Mathematical Science and Engineering Division explains that a sys-tem is described as chaotic if it is highly sensitive to its inceptive conditions. In such systems, a tiny tweak in initial con-ditions can lead to seismic differences in the final outcome.

“Chaos is often seen as detrimental, and we typically spend a lot of effort try-ing to minimize it in man-made devices,” says Fratalocchi. “However, if properly understood, chaos can underpin novel energy and imaging applications.”

Fratalocci’s team applied chaos theory to optical resonators — a major compo-nent of lasers — which are highly opti-mized devices that use an arrangement of mirrors for trapping light energy. However, this light energy is limited to narrow frequency bands: for example the widely used “L3” photonic crystal, a two-dimensional optical resonator, can

A representation of the light energy spatial distribution in a chaotic resonator.

They also studied the lifetime of pho-tons of various light modes in chaotic optical resonators to find their values were approximately the same. They sug-gest convergence of photonic lifetimes has improved the transfer of energy, which may explain the optical resona-tor’s improved storage capacity.

Although the researchers carefully con-trolled the shape of the planar photonic crystals, they were unsure if they had accurately estimated the energy stored inside these crystals. To check this, they used a three-dimensional arrangement of polystyrene spheres, each modified to exhibit chaotic deformities. Their results showed that a fully chaotic sphere can absorb 10 percent more energy from a halogen lamp, a broadband light source.

These results have potential for a novel series of application across physics and technology, say the researchers, which range from sensing to lasers, energy harvesting and cavity quantum electro-dynamics.

1. Liu, C., Di Falco, A., Molinari, D., Khan, Y., Ooi, B.

S. et al. Enhanced energy storage in chaotic optical

resonators. Nature Photonics 7, 473–478 (2013).

KAU

ST

“If properly understood, chaos can underpin novel energy and imaging applications.”

6 3I S S U E O N E


State-of-the-art facilities and world-class research projects give rise to thriving startup companies based at KAUST.

T echnological advances and exciting research at KAUST in recent years have led to the for-mation of several startup com-

panies through the Visual Computing Center directed by Wolfgang Heidrich. From interactive platforms for present-ing Islamic history and culture to auton-omous drones generating 3D maps of entire city districts, researchers are at the forefront of new technology-based business.

A fine example of a startup based at KAUST is FalconViz, which is led by

A breeding ground for successful startups

KAU

ST

6 4

C E EM S

Neil Smith, Mohamed Shalaby and Ph.D. candidate Luca Passone and their team. The researchers have developed a new way of aerial surveying and mapping using high-resolution cameras attached to remote-controlled “quadcopters”, or unmanned aerial vehicles (UAVs). They successfully produced detailed maps of the ancient Saudi Arabian neighborhood of Al-Balad within Jeddah. Al-Balad was awarded World Heritage Site status by UNESCO in 2014.

Many of Al-Balad’s ancient build-ings are in a poor state and are often

unsafe for surveyors to access on foot. Traditional surveying methods are slow and painstaking and there were con-cerns that, without intervention using new technology, significant informa-tion would be lost as the frail structures deteriorated.

The UAVs designed and built by Fal-conViz operate fifty meters above the ground, and are controlled by a pilot whose goggles allow him to sit in a “virtual cockpit”. When it came to cre-ating images of Al-Balad, however, the team experienced some unexpected difficulties. “Al-Balad is a huge, highly congested old city,” describes Smith. “We tried flying one mission manually and found it was very easy to lose our bearings because all the buildings look very similar from the air. In order to systematically cover the entire 250,000 square-meter area, we spent a lot of time creating detailed autonomous mission plans so that our UAV could fly over the area without the pilot.”

Each UAV is fitted with a high-reso-lution camera and can quickly capture data of buildings and neighborhoods in great detail. Specialist imaging software then transforms the image data into detailed three-dimensional maps, plans and models. “We use ‘Structure-from-Motion,’ a method of extracting a 3D structure from many overlapping digi-tal images,” says Smith. “The algorithms use a change in camera position for each image to find the distance between them, triangulating the 3D positions of pixels in overlapping images. The more motion and movement around an area, the more complete the 3D model becomes.”

The cameras can also take continual

video footage of the areas surveyed. The level of detail provided by FalconViz allows surveyors, historians and city planners to have views of cities they have never had before, and the technol-ogy has further far-reaching potential applications. “We hope our mapping and survey system will allow first responders to be more effective in dis-aster situations by providing real-time maps of the disaster area, for example,” explains Smith.

In a similar pursuit of preservation of history and culture, another startup company at KAUST led by Jens Sch-neider provides computer applications for disseminating information about the religiously significant city of Makkah and general information about Islamic culture to a wide audience. Through interdisciplinary research projects based at KAUST, the team developed platforms for mobile phones, comput-ers, interactive information boards in museums and even wearable comput-ing technology such as augmented real-ity glasses. These applications provide virtual tours, interactive maps and a host of information about the culture and history of Islamic cities. The team is now collaborating with organiza-tions from government ministries to small businesses to provide customized hardware and software for smart cities of the future.

A third system also developed by Schneider and colleagues is also improving cities by monitoring crowds in real-time. Called HACHID, the sys-tem comprises easily-installed hard-ware and software that can be used to track and count people in high-density crowds gathering in mosques, airports or in other public places. The research-ers behind HACHID hope that it will prove invaluable in planning safe, large-scale events.

The creation and nurturing of these startups was made possible through the continued and substantial support of the Innovation and Economic Development office at KAUST. These innovative com-panies will provide much-needed sup-port for developing smarter cities and preserving sites of historical significance for future generations.

The team at FlaconViz use unmanned aerial vehicles to produce detailed 3D maps and images of entire districts.

“We hope our mapping and survey system will allow first responders to be more effective in disaster situations by providing real-time maps of the disaster area, for example.”

6 5I S S U E O N E


A novel computing technique recognizes and captures the distinctive surface patterns appearing in videos and images.

S tudies suggest that the human visual system relies on indica-tors of texture to differenti-ate between objects. A team

from KAUST has developed a method to enhance the way computers decipher tex-ture through an innovative digital image processing program1.

As bandwidth is increasingly taken up by video traffic, the software could prove critical to computer vision recognition systems and may yield faster internet video streaming.

To replicate natural texture solving processes, scientists are developing ways to analyze textons, groups of pixels that describe the repeating units of a texture. But recognizing random and irregular textons in textures — such as the bark of a tree, for instance — is challenging. Cur-rent techniques aggregate statistics within neighborhoods surrounding a pixel and can help “firm up” the texton description. However, this approach fails at texture boundaries when unrelated data is aggre-gated, leading to image analysis errors.

Ganesh Sundaramoorthi and colleagues in the U.S. cracked the texture code by overhauling the strategy.

“The problem is how to construct an invariant descriptor that depends on texture when the texture itself is unknown, says Sundaramoorthi. “To make a robust system, we had to elimi-nate the concept of choosing neighbor-hoods altogether.”

To replace the concept, the researchers formulated an estimation problem where both the descriptors and the texture boundaries are solved together by con-tinuously checking each other’s values.

They programmed novel “shape-tai-lored” descriptors that use Poisson-like partial differential equations (PDEs) to analyze data such as light radiance and color channels in an image. An optimiza-tion algorithm then refines initially large neighborhoods into ever smaller pixel groups until surface patterns are accu-rately traced out.

The team found their method automati-cally detected textures in a wide range of

Resolving richer textureswith computer vision

1. Khan, N., Algarni, M., Yezzi, A. & Sundaramoorthi, G.

Shape-tailored local descriptors and their application

to segmentation and tracking. IEEE Conference on Computer Vision and Pattern Recognition (2015).

examples under challenging video and image conditions.

“The PDEs provide some invariance like traditional descriptors, but their key dif-ference is that they are naturally defined within regions of arbitrary shape,” Sunda-ramoorthi explains.

One application that may be improved by the research is video compression. Some estimates predict that 80-90 percent of all Internet activity in the year 2019 will be video traffic, a situation that calls for more efficient bandwidth use.

Sundaramoorthi notes that decipher-ing textures is redundant and far more demanding of bits than the information they convey.

“None of the best video compression schemes take this into account, but our texture segmentation scheme may bring us closer to this,” he says.

Automatic analysis of complex textures within digital images may lead to improved machine learning and video compression applications.

DEJA

N K

RSM

ANO

VIC

/ ALA

MY

STO

CK P

HO

TO

C E EM S

6 6

Magnetic nanowires with weak magnetic fields and low frequencies can destroy cancer cells without generating heat.

I

Targeting cancer cells with tiny magnetic wires

ncubating cancer cells with nickel nanowires before exposing them to a weak magnetic field can kill them, report researchers from

KAUST1.The multidisciplinary team led by

Jürgen Kosel from the Computer, Elec-trical and Mathematical Science and Engineering Division and Tim Ravasi from the Division of Biological and Environmental Science and Engi-neering exposed colon cancer cells to various alternating magnetic fields. In early tests, only a small percentage of the cells were destroyed. This indicated

that the fields on their own were fairly harmless.

Colon cancer cells were then incu-bated with two different concentrations of nickel nanowires. The cells internal-ized most wires in less than an hour. The internalization of the lower con-centration of nanowires did not lead to significant cell death. However, promis-ingly, the internalization of the higher concentration resulted in the death of 11 percent of the cancer cells.

Next the researchers exposed the nanowire-containing cells to an alter-nating magnetic field and noticed a

more significant result: the number of cells killed reached 38 percent when the cells incubated with the higher nanowire concentration were exposed to a 1 kHz alternating magnetic field.

The researchers suggest that applying the magnetic field triggered vibrations in the nanowires and generated changes in cell functions and structures that eventually led to cell death. Changing the duration of exposure to the mag-netic field from 10 to 30 minutes made no relevant difference.

“There have only been a few attempts to study magnetic nanowires for the treatment of cancer cells,” says Kosel. “We are the first ones to use nanowires with only a few tens of nanometers in diameter.”

This method shows promise for future potential medical applications. It allows remote control of nanowires localized in cancer cells to trigger a specific response. Also, since only weak mag-netic fields are required to obtain sig-nificant results, “they are not harmful to people and can be generated by sim-ple, cheap and compact tools,” explains Maria Contreras, Ph.D. student and first author of the study.

Kosel stresses that many factors still need to be taken into account before this new method can be employed. The team plans to continue improving the efficiency of the method and testing it on various cancer cells.

Applying the magnetic field triggered vibrations in the nanowires and generated changes in cell functions and structures that eventually led to cell death.

1. Contreras, M. F., Sougrat, R. Zaher, A., Ravasi, T.,

Kosel., J. Non-chemotoxic induction of cancer cell

death using magnetic nanowires. International

Journal of Nanomedicine 10, 2141-2153 (2015).

KAU

ST

“The researchers suggest that applying the magnetic field triggered vibrations in the nanowires and generated changes in cell functions and structures that eventually led to cell death.”

6 7I S S U E O N E


An improved peak fitting procedure enables a better determination of protein structures.

A

Peak performance for proteins

method to more accurately determine the structure of pro-teins using nuclear magnetic resonance (NMR) spectros-

copy has been developed by researchers at KAUST1.

Proteins play a key role in cell func-tion, and vital to a protein’s performance is its molecular structure, which usually assumes a complex three-dimensional shape.

A common method of identifying pro-tein structures uses x-ray scattering tech-niques, but this approach requires proteins to be available in crystalline form. NMR offers a better approach because it can resolve molecular structures in cells, therefore being uniquely suited to also measure the dynamics of proteins.

NMR measures an atom’s energetic states with high sensitivity and enables researchers to study the bonds between atoms in a molecule and even the local atomic geometry around the atoms.

A protein can consist of many thousands

of atoms that contribute to NMR signals, and so the measured spectra are extremely complex. Interpreting the protein structure from these is difficult and requires sophis-ticated computer models.

An obstacle to analyzing NMR spec-tra is that some of the signals are very small and detecting them against a noisy background is difficult. Some existing computer algorithms can manage such peak detection. In these the NMR signal is divided into small sections, known as “windows”. Then the algorithm deter-mines the background for each window and extracts the NMR peaks.

The trick is to find the right tradeoff, explains research leader Xin Gao from the Computer, Electrical and Mathemati-cal Science and Engineering Division at KAUST.

“On one hand, you need to remove the noise from the spectrum as much as possible,” says Gao. “On the other hand, there is the risk of accidentally removing real signals.”

The filtering algorithm developed by the researchers is an extension of prior schemes and makes it easier to find the right balance. It features a better detection of the edges of peaks in the spectra which other techniques tend to smooth over, thus making signals more difficult to isolate. The new algorithm is also independent of the window size used, which represents a considerable practical advance.

The new detection leads to a better real-time study of protein dynamics, com-ments Gao. “We already have an in-house automated system that can determine small and medium size protein structures without human intervention. In future, we hope that by combining the proposed noise removal filter, and our in-house tools, we will be able to push the limit to larger proteins,” says Gao.

1. Cannistraci, C.V., Abbas, A. & Gao, X. Median

Modified Wiener Filter for nonlinear adaptive spatial

denoising of protein NMR multidimensional spectra.

Scientific Reports 5, 8017 (2015).

KAU

ST

An automatically calculated structure for the protein TM1112 derived from NMR spectra.

6 8

C E EM S

KAU

ST

Smart, stretchable pads open up a new approach for thermotherapy.

W

Nano therapeutics heat up

earable technology offers better control and flexibility of thermother-apeutic approaches, and

now a stretchable electronic patch that can be wirelessly controlled has been developed by a research team from KAUST1.

Managing pain is an intrinsic part of many therapeutic processes and an important aspect of healthcare. Heat is commonly used to mitigate the effects of pain. “A digital interactive, stretchable and reusable thermal patch can deliver controlled heat to specific parts of the human body,” explains

Muhammad Hussain from the Com-puter, Electrical and Mathematical Sci-ence and Engineering Division.

Currently available heat-generating patches rely on chemical reactions. A better route to create therapeutic patches, however, is to use electrical heating — which can be applied control-lably and repeatedly — and so can bet-ter manage how the heat is applied to the skin. However, the problem for such patches is that the heating elements — currently electrical conductors such as copper — are too rigid to conform to the movements of skin.

Straight electrical wires can break

easily when stretched, so the KAUST researchers have designed electrical cir-cuits whose curved, spring-like shapes are far more flexible. “Copper thin films cannot be stretched in their natural state, but due to the lateral spring struc-tures we designed, we achieved record stretchability of about 800 percent from a metal,” comments Hussain.

The stretchable copper circuits can be fabricated on a flexible plastic substrate. These patches are lightweight and can be easily attached to the skin. Depend-ing on the voltage applied, tempera-tures in the patch can reach up to 80 degrees. The electrical circuits also allow further functionality. For example, the researchers added an antenna to provide wireless control via a smartphone over the patch temperature.

As well as being attached to the skin, these patches have applications inside the human body, notes Hus-sain. “The same device with further optimization can be used as implant-able thermotherapy for cancerous cell destruction,” he says. Other stretchable electronic devices have already been demonstrated for internal applications, and exposing cancer cells to heat is a known therapeutic approach.

Skin patches have come a long way from their first, basic uses. Thanks to the development of stretchable elec-tronics, complex therapeutic as well as diagnostic uses may soon be feasible, concludes Hussain. “We are working with world renowned pharmaceutical companies on the commercialization of the patch,” he adds.

1. Hussain, A.M., Lizardo, E.B., Torres Sevilla, G.A.,

Nassar, J.M. & Hussain, M.M. Ultrastretchable and

flexible copper interconnect-based smart patch

for adaptive thermotherapy. Advanced Healthcare Materials 4, 665–673 (2015).

“The same device with further optimization can be used as implantable thermotherapy for cancerous cell destruction.”

Muhammad Mustafa Hussain and Aftab Hussain test out flexible, stretchable circuits that can be processed into therapeutic wearable patches.

6 9I S S U E O N E


Located on the shores of the Red Sea, KAUST is both a premier university and a city. The services and amenities of KAUST offer an exceptional quality of life, from schools to recreation to personal enrichment. We are a community where more than 100 nationalities learn, live, and thrive together.

Explore what it’s like to work, live andplay at KAUST at kaust.edu.sa

#destinationKAUST

Tiny carriers assembled from oppositely charged nanoparticles open to release their cargo under light exposure.

U

A light load fornano-porters

ltra-small hollow carriers that can be activated to deliver rela-tively large bioactive “freight” could play a central role in bio-

logical applications, such as encapsulat-ing enzymes to be used for replacement therapy, bacteria for immunization or even biocatalysis, show researchers from KAUST1.

Until now these tiny carriers, called colloidosomes, have been comprised of self-assembled nano-sized building blocks — such as silica nanoparticles and polymer-based rod-shaped microparti-cles — at the oil-in-water or water-in-oil interfaces of emulsion droplets. As well as being unstable and highly porous,

typically their shells have micron-sized diameters that limit their biologi-cal applicability. While multilayering prevents the passive leakage of cargo molecules through pores, covalent cross-linking effectively stabilizes the shell but traps large cargos.

Niveen Khashab from the KAUST Advanced Membranes and Porous Mate-rials Center has developed the first light-responsive nano-sized colloidosomes using silica nanoparticles bearing opposite charges. She explains that these unique structures originate from a self-assembly process driven by simple electrostatic forces. Held together through these non-covalent inter-nanoparticle interactions,

the colloidosomes readily disassembled under ultra-violet light irradiation.

To create the new carriers, Khashab’s team designed a positively charged organic linker that turned neutral when exposed to light and incorporated it in silica nanoparticles at two different con-centrations to generate the oppositely charged building blocks. Nanoparticles containing a low linker composition pre-sented a negative charge, whereas those displaying high linker content were posi-tively charged in water. When mixed in water and added to an organic solvent, these nanoparticles produced stable col-lodoisomes in oil-in-water emulsions.

Khashab explains that a charge rever-sal occurs depending on the nanoparticle organic content at the point the linkers were neutralized by light. In positively charged nanoparticles with higher organic composition, this neutralization exposed the negatively charged siloxy groups, switching the overall nanopar-ticle charge from positive to negative. Negatively charged nanoparticles exhib-ited an increase in negative charge upon irradiation, resulting in repulsive forces between negatively charged nanoparti-cles within the colloidosomes, triggering their disassembly.

The colloidosomes also effectively encapsulated dye molecules in their cavity in oil-in-water emulsions and released most of them under light-induced disassembly.

The researchers now plan to enable the newly developed carriers to transport and release water-repelling compounds, high-molecular-weight molecules and nanoparticles. “These carriers hold large cargo molecules, including proteins, making them applicable to vaccination and enzyme replacement therapy,” says Khashab. For instance, these capsules could deliver the necessary enzyme to its site of action in patients suffering from genetic enzyme deficiencies, eliminating the need for constant enzyme injections.

1. Li, S., Moosa, B. A., Croissant, J. G. and Khashab,

N. M. Electrostatic assembly/disassembly of

nanoscaled colloidosomes for light-triggered

cargo release. Angewandte Chemie International Edition Advance online publication: 27 April

2015. 23, 6908 - 6912 (2015).

Niveen Khashab and Basem Moosa work in the lab.

KAU

ST

7 1I S S U E O N E


A material for filtration that is easy and cheap to produce could aid water treatment, solvent filtration and membrane-catalysis.

One-way trip for water

KAU

ST

The process of complexation-induced phase separation produces membranes

with a dense surface layer (gold-colored) on a more porous region (blue).

P ES

7 2

A cheap and cost-effective tech-nique for making water- and solvent-filtering polymers has been developed by a team of

researchers at KAUST1.Membranes are thin films permeable

by some particles but act as a barrier to others and are used for removing salt or contaminants such as dirt, bacteria or even viruses from water. A common method for constructing such structures is to combine the thin but dense mem-brane or skin with a thicker porous mate-rial that provides mechanical support.

The processes used to construct these composite membranes are complicated or require expensive materials, which prevents production on a commercial scale.

Klaus-Viktor Peinemann and his Ph.D. student Luis Francisco Villalobos from the KAUST Physical Science and Engineering Division have come up with a simple and scalable process for building multi functional membranes. Their composite membrane needs only one casting step and one polymer solu-tion to prepare and is then treated with two successive baths, as Peinemann

explains. “This process is simple and we can easily prepare defect-free coat-ings with thicknesses that are difficult to obtain with conventional coating procedures,” he says.

The KAUST team named their tech-nique “complexation-induced phase separation”. It works by connecting long chains of polymer molecules — referred to as cross-linking — with metal ions. Peinemann and his colleagues made a solution comprised of a polymer and an organic solvent, deposited it on a substrate and dipped it in a bath con-taining the metal ions dissolved in the same solvent.

This was followed by immersion in a second metal-free non-solvent bath. They could show that complexation-induced phase separation produces

1. Villalobos, L. F., Karunakaran, M. & Peinemann,

K.-V. Complexation-induced phase separation:

Preparation of composite membranes with a

nanometer-thin dense skin loaded with metal ions.

Nano Letters 54, 3166–3171 (2015).

a dense surface layer of cross-linked polymer–metal complexes separated by a well-defined interface from a more porous region beneath it.

The advantages of the new phase sepa-ration process are that it is fast and easy to control, which enabled the research-ers to tailor the precise structure of their asymmetric membrane. For example, they were able to vary the thickness of the skin between fifteen nanometers and six micrometers. They could also alter the morphology of the membrane surface and the porosity of the support structure by altering the type of metal ion used, which included silver, palladium, cobalt, nickel and copper.

“So far we have demonstrated the complexation-induced phase separa-tion process with two polymers,” says Peinemann. “Next we hope to identify a number of other polymers suitable for this new formation process.”

Klaus-Viktor Peinemann and Francisco Villalobos looking at polymer solutions.

“We hope to identify a number of other polymers suitable for this new formation process.”

KAU

ST

7 3I S S U E O N E


Performance improvements of indium zinc oxide transistors could lead to enhanced transparent displays for screens and phones.

A

Water-treated semiconductors up transistor speed

transistor four times faster than those currently used in high-res displays for smart-phones or tablets has been

developed by KAUST researchers using a simple de-ionized water treatment1.

Transparent electronics is an emerging area of research with significant poten-tial in applications such as displays and smart windows. Transistors for display applications are used to switch display pixels on and off and so they need to be fast to enable better display resolution.

Current transistors are often made from silicon however this is limited by its lack of electron speed and transparency. Oxide semiconductors, the proposed replace-ments, are see-through and have greater

electron mobility, enabling them to be used in displays with natural light. This eliminates the need for back light which consumes most of the display power, explains Husam Alshareef from the Divi-sion of Physical Science and Engineering. A popular class of materials is based on zinc oxide — which is both transparent and a good conductor of electrons — but better performance will depend on faster zinc oxide transistors.

Improvement of these transistors requires streamlining the fabrication process. One key challenge with elec-tronic materials includes impurities such as missing oxygen atoms in the crystal structure and surface remnants from the fabrication process, typically a layer of

zinc. Processes used to treat these in the silicon industry are not suitable for transparent oxide semiconductors.

The researchers from KAUST have now demonstrated that transistors made from indium-only doped zinc oxide (IZO) have a dramatic increase in performance if they undergo a simple treatment with de-ionized water prior to the final semi-conductor crystallization anneal.

Treatment with de-ionized water reduces the number of missing oxygen atoms in the crystal and also leaches out some of the remaining zinc from the surface. After the treatment, the KAUST team annealed the device leaving the IZO layer itself with less zinc. IZO with lower zinc and oxygen vacancy content has higher charge carrier mobility, further improving charge transport.

In first tests, the process improves the speed of electrical charges passing through the transistor by up to a factor of six. Their speed is four times higher than that of devices used in current smart-phone or tablet generations. “Being a transparent oxide semiconductor, IZO can also be used in other devices where transparency is needed, such as smart windows, concealed sensors and power efficient circuits,” says Alshareef.

Pradipta Nayak, lead author of the study, adds: “We used chemical synthe-sis methods at low temperature, which means that these devices are compatible with flexible plastic substrates,” thereby increasing the potential applications of this technology.

1. Nayak, P.K., Caraveo-Frescas, J.A., Wang, Z.,

Hedhili, M.N. & Alshareef, H.N. Six-fold mobility

improvement of indium-zinc oxide thin-film

transistors using a simple water treatment.

Advanced Electronic Materials 1, 1500014 (2015).

“IZO can also be used in other devices where transparency is needed, such as smart windows, concealed sensors and power efficient circuits.”

The new transistors developed by Husam Alshareef can be used to boost the speed of transparent electronics.

KAU

ST

7 4

P ES

Thin film membranes could efficiently separate carbon dioxide and other gases from mixed gas flow streams.

T

Membranes that can manipulate gases

he options for selectively cap-turing carbon dioxide have been widened by KAUST research-ers who have created a versatile

adsorbent material in the form of thin-film membranes1.

As well as the potential to control the level of atmospheric carbon dioxide in our warming world, says Mohamed Eddaoudi from KAUST, “this technology may also lead to applications in other types of gas separation”.

Eddaoudi and colleagues from the KAUST Advanced Membranes and Porous Materials Research Center have recently developed several innovations in the field of metal-organic frameworks (MOFs). These hybrid materials contain metal ions or metal clusters joined by organic chemical moieties known as linkers. Adjusting the structure of the linkers and the metallic centers allows the intrinsic properties of MOFs to be fine-tuned, which means they can be adapted to many useful chemical

functions, including highly selective gas adsorption and catalysis.

Some of the most versatile MOFs intro-duced by Eddaoudi have structures simi-lar to zeolite minerals, and are therefore known as ZMOFs. Until now, efforts to fabricate thin-film ZMOF-membranes have been hampered by pinhole defects. These tiny flaws disturb the selectively, which means some specific molecules are retained by the membrane while others pass through.

A key success achieved by the KAUST researchers is to create ZMOF-mem-branes without these defects. Eddaoudi says his team performed various gas per-meation studies to confirm their films are

free of any pinhole defects. The nega-tively charged “anionic” framework of the membrane allows substitution of the positively charged extra-framework ions (“cations”) in the large cavities to further fine-tune the interactions with molecules flowing through the cavities.

The ZMOF-membranes are grown on a porous aluminum oxide substrate and have been tested with carbon dioxide mixed with other industrial gases, includ-ing hydrogen, nitrogen and methane. The new membranes demonstrated highly selective permeability towards carbon dioxide, which could allow it to be selec-tively extracted from a mixed gas stream.

“The main advantages of membrane technology over conventional separation methods are lower energy costs, reduced footprint size and modular design,” says Eddaoudi.

The researchers can now explore the full range of options and develop the technology toward scaling up and even-tual commercialization. Other possibili-ties applications include selective gas sensing systems. A patent on the discov-ery has been filed and several compa-nies have expressed interest in exploring commercial opportunities.

1. Al-Maythalony, B. A., Shekhah, O., Swaidan, R.,

Belmabkhout, Y., Pinnau, I. & Eddaoudi, M. Quest

for anionic MOF membranes: continuous sod-ZMOF

membrane with CO2 adsorption-driven selectivity. Journal of the American Chemical Society 137, 1754-1757 (2015).

“The new membranes demonstrated highly selective permeability towards carbon dioxide.”

KAU

ST

7 5I S S U E O N E

T he Red Sea is a narrow basin with warm and highly saline water that supports a rich and diverse marine ecosystem. It is

of immense ecological and commercial importance, yet little is known of a cru-cial oceanographic aspect— the proper-ties of its eddies.

Eddies are clockwise or counter-clockwise circular movements of water that play a significant role in transport-ing heat, nutrients and organic material in the ocean. Now a KAUST and U.S. research team shows that these marine “whirlpools” are more frequent than had been supposed and that they follow a distinct seasonal pattern.

“In the Red Sea, eddies profoundly affect the social and economic lives of people living in the surrounding coun-tries,” explains Ibrahim Hoteit from the Division of Physical Science and Engi-neering. “Knowledge of how regularly these eddies occur and how they behave would help, for instance, improve local ocean forecasts, as well as help the coast-guard undertake search-and-rescues; responses to oil spills or concentrate dis-charges; or marine planners to formulate conservation plans.”

To gather information on eddy prop-erties, the KAUST researchers and

First-time reports of the statistical properties of “whirlpools” show they are frequent and seasonal.

Unlocking the mysteries of Red Sea eddies

Eddies in the narrow Red Sea are more frequent than previously expected. Ibrahim Hoteit uses

a 3D visualization to explore the physical oceanography of the Red Sea.

TUN

DE G

ASPA

R/KA

UST

7 6

P ES

colleagues at Scripps Institution of Oceanography in San Diego, U.S., con-sidered satellite data collected since 1992 along with numerical model simulations of the Red Sea circulation1.

The team analyzed the number, size and frequency of eddies observed. Over the 20-year data period, the team was surprised to find 4,998 eddies — a higher number than they expected — given the long narrow shape of the Red Sea. Eddies are usually observed in the open ocean where strong winds and currents form. The data revealed most eddies occurred in the central basin and the average eddy life span was six weeks.

The team also identified a significant seasonal cycle of eddy intensity. Peak-ing in February — perhaps due to the cooling effects of the winter wind jets blowing to the north — the intensity and spin tended to gradually decrease until August. After a sharp drop, eddy fre-quency then increased to a second peak from September to December.

Eddy size — measured in radii from its center to edge — ranged from 35km to 200km, with an average radius of 94km. While eddies may vary greatly in size, the researchers were interested to find that eddy radii was proportionate to the width of the Red Sea basin, which meant the larger eddies occurred in the sea’s wider central region.

“As the Red Sea is a relatively narrow basin, most eddies can only occupy about half of its width, providing rapid trans-port of organisms and nutrients from one coast to the other,” says Hoteit. Next steps for the team is to quantify eddy transport of heat and nutrients in the region.

“In the Red Sea, eddies profoundly affect the social and economic lives of people living in the surrounding countries.”

1. Zhan, P., A. C. Subramanian, F.

Yao, and I. Hoteit, Eddies in the Red Sea:

A statistical and dynamical study, Journal of Geophysical. Research: Oceans 119,

3909–3925 (2014)

7 7I S S U E O N E

P H Y S I C A L S C I E N C E A N D E N G I N E E R I N G D I V I S I O N #destinationKAUST#destinationKAUST

Simulations reveal the final moments of a fuel droplet as it combusts in a spray injection engine.

T

Spreading the flame

oday’s combustion engines are more efficient than ever thanks to thousands of incre-mental improvements to

engine dynamics. Yet engineers con-tinue to try for even the smallest effi-ciency gains that can provide further significant savings for airlines and freight companies.

Jaeheon Sim, Hong Im and Suk Ho Chung from KAUST have now devel-oped a numerical model that describes the precise behavior of a fuel droplet as it encounters a spreading flame1. The unprecedented detail of the simulation will help engineers understand exactly what goes on in the combustion chamber and develop even more efficient engines.

In most automotive and jet engines, fuel is injected into the combus-tion chamber as a fine spray and then ignited. The dynamics of the flame’s spread through the droplet field is one of the key parameters of perfor-mance and efficiency. “Engineers have observed that flame spread through

an array of droplets is enhanced by an effect called fuel vapor ejection as the flame approaches each droplet,” says Im. “However, it is very difficult to measure such small-scale processes inside a drop-let, so our understanding of the underly-ing mechanism had been unclear.”

Im and his team from the Clean Combustion Research Center turned to numerical simulations. “We developed a high-fidelity model that captures the detailed physical processes with proper mathematical formulations and compu-tational algorithms,” Im explains.

“The specific numerical modeling technique used for fine-scale interface dynamics was crucial to capture subtle physical processes with realism.”

The model focused on the effect of rapidly increasing temperature on the distribution of surface tension around each fuel droplet. As one side of the droplet heats up, the surface tension decreases, driving an internal convection flow in the droplet called the Marangoni effect. This motion

accelerates evaporation, resulting in the expulsion of a jet of vaporized fuel away from the advancing flame.

“One of the main implications of the study is that the internal motion within small fuel droplets can significantly modify the fuel vapor distribution and thereby overall combustion charac-teristics,” says Im. “Modeling of spray combustion must properly account for this effect.”

The researchers also believe that the Marangoni effect may determine emul-sion droplet heating and evaporation behavior. “Emulsion droplet combus-tion is of practical interest as a way to burn low-quality fuel oils efficiently and cleanly,” says Im. “We are currently work-ing to investigate Marangoni convection in such emulsion systems through similar numerical simulations.”

1. Sim, J., Im, H. G. & Chung, S. H. A computational

study of droplet evaporation with fuel vapor jet

ejection induced by localized heat sources. Physics

of Fluids 27, 053302 (2015).

KAU

ST

P ES

7 8

Researchers reveal a low-impact synthetic strategy for producing supported small nickel nanoparticles – a powerful catalytic form of the metal.

A

Softly softly approach for tiny catalyst

gentle synthetic strategy has been devised by chemists at the KAUST Catalysis Center that overcomes some prac-

tical obstacles when using nickel as a catalyst.

Nickel is highly popular as a catalyst because it is cheap and can be used for a wide range of applications. As a catalyst, it is usually employed in either its molec-ular complexes or in the form of nickel nanoparticles supported on an inert sub-strate. The smaller the nickel nanoparti-cle, the more efficient the catalysis.

Producing nickel nanoparticles of the requisite tiny size is difficult, however, because the nickel nanoparticles tend to aggregate to form clusters. Also, being so small, the particles can be damaged by the high temperatures of the treatment process.

A team lead by Professor Jean-Marie Basset has managed to overcome these challenges to produce small nickel nano-particles about one to three nanometers in diameter that are uniformly dis-tributed on inert oxide surfaces1. The researchers were able to demonstrate the effectiveness of the new tiny catalysts in the dry reforming of methane: a reaction

between carbon dioxide and methane to carbon monoxide and hydrogen.

“What is exciting about this method is the very soft control at very low tem-perature of the first step of the catalyst preparation,” says Basset. “It is important to control the elementary steps of this surface reaction because often the nano-particles used in catalysis are prepared by steps which are not fully understood.”

Using silica and alumina as inert oxide substrates, the team partially dehydrox-ylated the surfaces so they could control the number of reactive surface groups present. Then they reacted the precursor, Bis (3 allyl) nickel complex — a complex of nickel with six carbon atoms— with

the surface hydroxyl groups in a one-to-one ratio. Both steps were closely con-trolled by using infrared spectroscopy (FTIR) and solid state NMR to follow the characteristic wavelengths that cor-respond to the addition or removal of chemical groups.

Finally, the team subjected the surface nickel complexes to hydrogen gas flow at 300 degrees Celcius to produce the silica- and alumina- supported nickel nanoparticles.

The dry reforming of methane, Bas-set explains, is a very clean and selec-tive reaction when the nanoparticles of nickel catalysts are very small, like the ones produced by his team.

Basset explains that the benefit of the process is two-fold — taking two envi-ronmentally harmful greenhouse gases and converting them to two products that are useful for chemical industry.

1. Li, L., Abou-Hamad, E., Anjum, D. H., Zhou, L., Laveille, P.

V., Emsley, L., & Basset, J.-M. (2014). Well-defined mono

(3-allyl) nickel complex [triple bond, length as m-dash]

MONi (3-C 3 H 5)(M= Si or Al) grafted onto silica or

alumina: a molecularly dispersed nickel precursor for

syntheses of supported small size nickel nanoparticles.

Chemical Communications 50, 7716-7719.

KAU

ST

“The benefit of the process is two-fold — taking two environmentally harmful greenhouse gases and converting them to two products that are useful for chemical industry.”

7 9I S S U E O N E


The Clean Combustion Research Center aims to develop technologies for future fuel formulations, more efficient engines and new methods for power generation.

WImproving combustion for a cleaner future

ith the effect of climate change a major global challenge for household-ers, governments and

industry, the drive to find cleaner, more efficient fuels and improve supporting technologies has never had stronger impetus. The Clean Combustion Research Center (CCRC) at KAUST draws on exper-tise from both academic and industrial sources to lead the way in new combus-tion technology design.

“The CCRC is unique for two key reasons,” says Aamir Farooq, faculty member at CCRC. “Firstly, the inter-national team here provides us with a wide-ranging and diverse knowledge

Ph.D. student, Wesley Boyette, uses a four-camera system to examine a turbulent sooting

flame, which is important in gas turbines.

8 0

P ES

base. Secondly, we have access to many state-of-the-art facilities and technolo-gies, such as high performance super-computers and laboratories where we can simulate many different real-world combustion processes.”

Inside the CCRC laboratories, researchers explore a wide variety of combustion-related fields. At the crux of many projects are dynamic collabo-rations between CCRC and other KAUST centers, as well as with industry. For instance, the CCRC takes on inquiry-driven and application-driven research into future engines, chemical kinetics in fuels, computational fluid dynamics and gas turbines for power generation, to name a few.

“The CCRC is strong in exploring vari-ous combustion processes, including fuel oxidation, pollutant formation and flame stability, in idealized conditions,” explains Farooq. “Measuring these pro-cesses in idealized environments allows us to validate predictive tools. These tools help us model combustion pro-cesses in realistic environments such as internal combustion engines.”

One example of simulation-based fuel design is the Fuel Combustion for Next Generation Engines program (FUELCOM), a collaborative project between CCRC and Saudi Aramco.Fuels used today will be unsuitable for the engines of the future; pollution mitigation and a drive for higher effi-ciency will demand fuel combustion in increasingly extreme conditions.

The FUELCOM program aims to develop new hydrocarbon-based fuels which can withstand these demands. For example, low-temperature combustion engines would require fuels that produce low emissions and have improved igni-tion. Investigations into using low grade, low cost fuel such as naphtha (volatile liquid hydrocarbon fuel) and low energy, viscous fuels are also underway.

William Roberts, director of the CCRC, is working on a project inves-tigating heavy fuel oil combustion for power generation, in collaboration with the French multinational company Alstom and the Saudi Electric Company. Over the next five years, the researchers aim to resolve pollution and particulate

issues related to the burning of heavy fuel oil. CCRC is designing new burners and plasma sources which can be used in on-site reforming to convert heavy fuel oils into higher quality, cleaner fuels for use in industrial boilers and furnaces.

Roberts and his team are also work-ing on a new thermodynamic cycle capable of dramatically improving the overall efficiency of gas turbines. Large frame gas turbines are currently the main electricity generation method in Saudi Arabia. Improving their efficiency could significantly reduce the cost of electricity and preserve crude oil for export. Their work on turbines can even be used in future airplane engines.

Future research projects will be con-ducted under three main categories: extreme combustion, future fuels and new combustion concepts.

“Extreme combustion is a long-term goal which will establish a world-lead-ing facility on combustion in extreme

conditions,” explains Farooq. “We will design and build new combustion chambers and high-pressure environ-ments in order to test diagnostic tech-niques based on ultra-fast lasers and ballistic imaging, for example. These techniques can be used to monitor fuel spray dispersion and evaporation dynamics.”

Further research will take place into fuels blended from conventional and bio sources, renewable energy sourcesand improving existing low-grade fuels. Research into computational modeling of combustion scenarios will also con-tinue. The use of plasmas, electric and magnetic fields to enhance combustion is a priority, as well as investigating thermodynamics for gas turbines and nanotechnology for flame-based mate-rial synthesis.

In line with the Center’s mission, external collaborations alongside inter-disciplinary projects within KAUST will form the backbone to future CCRC research, continuing its unique and valu-able contribution to research and devel-opment of cleaner, more efficient fuels and engines for the future. Furthermore, the Center is working closely with the Industry Engagement Office in Economic and Technology Development at KAUST to expand the Center’s offerings to lead-ing global industries.

“Inside the CCRC laboratories, researchers explore a wide variety of combustion-related fields.”

TUN

DE G

ASPA

R/KA

UST

TUN

DE G

ASPA

R/KA

UST

A green laser and camera system are used to do scattering measurements in a turbulent sooting flame.

8 1I S S U E O N E


Researchers are hoping they can use thin nanoscale films made of manganites to produce next-generation electronic devices.

THE

NAT

URA

L H

ISTO

RY M

USE

UM

/ AL

AMY

STO

CK P

HO

TO

1. Lourembam, J., Ding, J., Bera, A., Lin, W. & Wu, T.

Asymmetric electroresistance of cluster glass state in

manganites. Applied Physics Letters 104, 133508 (2014).

Nanoscale thin films containing unconventional, glass-like magnetic states can lead to the development of novel charge-spin coupled devices.

K AUST researchers have discov-ered that thin films made from manganites, a highly magnetic form of manganese oxide,

can be switched instantly and revers-ibly between conductive and insulating states using an electric field1. This new form of control could produce next-generation, more efficient transistors that boost density and speeds by tapping into both the spin and charge properties of electrons.

Unlike conventional charge-based semiconductors, materials with compet-ing electronic and magnetic properties often show exotic “phase separation” activity. For example, when manganites are cooled to frigid temperatures in a magnetic field, their electron spins can move out of alignment and “freeze” into a disordered arrangement known as a “spin glass”. Because electrical transport through spin glasses diminishes with increasing disorder, researchers are looking for easy ways to modulate these dynamic, fluid-like glassy states.

Tom Wu, associate professor in the Physical Science and Engineering Divi-sion at KAUST, and colleagues from

Glassy spin clusters shatter expectations

Nanyang Technological University in Singapore investigated whether elec-trostatic gating of ultrathin manganite films was a viable answer.

First, the team grew 40-nanometer thin layers of a praseodymium–calcium–stron-tium–manganese-oxide (PCSMO) com-pound on an atomically flat substrate. Then they patterned the film into an electric double layer transistor: a narrow PCSMO channel overlain by a “gate” elec-trode — a tiny, salty ionic liquid droplet — that can control current flow through the channel with electric fields.

Analysis of the PCSMO films showed they took on “cluster glass” attributes: a system where nanoscale regions of spin order appear inside the magnetically inhomogeneous compound.

“Glassy spin clusters in manganite films are challenging to tackle because their structures depend sensitively on

“We had to carefully design experiments to reveal their characteristics.”

the thermal and magnetic field ‘history’ they go through,” says Wu. “We had to carefully design experiments to reveal their characteristics.”

When the team modified the current flowing through the PCSMO channel using the gate electrode, they spotted a significant, low-temperature field effect — a 200 percent increase in channel resistance suitable for transistor switch-ing. This effect, which did not appear in homogenous manganite channels, appears to arise from strongly coupled charges and spins in the cluster glass. Under certain gate voltages, the electric field may “seed” the growth of more con-ductive, ordered spin phases that deac-tivate the highly resistive glassy states.

“Our work opens a new venue not only for understanding the behaviors of ‘mys-terious’ spin clusters in magnetic thin films, but also for constructing novel oxide electronic devices with inhomo-geneous materials that couple charges and spins,” says Wu.

P ES

8 2

Replacing the organic molecules surrounding atomically precise silver nanoparticles prepares them for practical applications.

A

Neat and complete nanoparticles ready for use

tomically precise noble metal nanoparticles show great potential for a broad range of applications, including catal-

ysis and solar cells. Researchers from KAUST have developed a rapid method to smooth the nanoparticle surface to increase their practical appeal.

Currently the organic molecules that cover the surface of the nanoparticles are not chemically suitable for applica-tions, which results in the nanoparticles being difficult to process. Osman Bakr and colleagues from the Solar and Pho-tovoltaics Engineering Research Center were able to replace the outer organic molecules of silver nanoparticles to produce smooth films ready for appli-cations1.

Among atomically precise noble metal nanoparticles, a useful class are the Ag44 nanocrystals, comprising exactly 44 atoms of silver. Because their structure is known down to a single atom, the properties of these nanoparticles can be easily modelled by computers. For exam-ple, their strong light absorption across a broad range of optical wavelengths

makes these particles advantageous for photovoltaic applications.

Despite such attractive properties, the chemical process used to synthesize these nanoparticles covers the silver core with a protective layer of organic molecules, known as thiolate ligands. The thiolates stabilize the nanoparticles but also hin-der their solubility, thwarting the organic solvent process needed to assemble them into thin films.

Ideally the thiolates should be replaced by other stabilizing ligands, but this, notes Bakr, has proven very difficult. “All previous attempts of ligands exchange led to either the disassociation of the nano-particles or their growth into other sizes.”

KAUST researchers developed a pro-cess by which ligands are exchanged by a chemical reaction requiring less than 30 seconds. It’s a much faster process

In the new, faster process, more than 94 percent of the ligands are exchanged, and importantly, the number of silver atoms in the Ag44 nanoparticles remains unaffected.

than comparable ligand exchange pro-cedures known for gold nanoparticles, which typically require more than 12 hours. More than 94 percent of the ligands are exchanged, and importantly, the number of silver atoms in the Ag44 nanoparticles remains unaffected.

Moreover, the process occurs in solu-tion and is easily scalable to high vol-umes. The team could also demonstrate the exchange of the original ligands by a number of different thiolates.

The new ligands significantly improve the processing of the nanoparticles and fabricating thin films from a solution of nanoparticles creates a very smooth surface which is ideal for use in appli-cations. Bakr says that his next aim is to follow up on this potential and “to explore the utility of atomically precise silver nanoparticles in photovoltaics and other optoelectronic devices.”

1. AbdulHalim, L.G., Kothalawala, N., Sinatra,

L., Dass, A. & Bakr, O.M. Neat and complete:

thiolate-ligand exchange on a silver molecular

nanoparticle. Journal of the American Chemical Society 136, 15865-15868 (2014).KA

UST

“The process occursin solution and iseasily scalable tohigh volumes.”

8 3I S S U E O N E


The ability to more precisely design an industrial material will support broad applications such as the storage of gas, including CO2.

T

Blueprint guides the shape of things to come

he functionality of a special class of porous materials known as metal–organic frameworks (MOFs) depends on their design

and diversity of application. An interna-tional team led by KAUST has developed a blueprint that can help researchers to precisely craft the MOF they seek.

MOFs are three dimensional net-works that comprise two main com-ponents — metal ions or clusters and a joining organic molecule known as a linker — the choice of these components determines their chemical and physical features. The three-dimensional struc-ture of MOFs give them broad industrial applications. Bridging the gap between organic and inorganic materials, MOFs show great potential for applications in adsorption, separation, drug deliv-ery, biomedical applications, sensing, catalysis, etc. However, there needs to be improved stability and performance of current MOFs before they will be practical to replace other nanoporous materials.

While MOFs can be precisely designed, one current challenge for scientists is to predict what network structure will arise from each assembly or synthesis step.

A range of potential shapes can emerge even when combining only simple build-ing blocks. The trick is to “dial up” the right structure.

“It is crucial to be able to produce made-to-order materials for industri-ally relevant applications,” explains Mohamed Eddaoudi of the Advanced Membranes and Porous Materials Research Center. “We were looking for a careful and efficient design strategy so we can target an ideal material that would have an appropriate pore system suitable for a given application.”

Eddaoudi’s team discovered a new metal-ion cluster that they could use as a blueprint for MOFs that have a modular type of structure. This cluster, called an 18-connected net, is formed by arrang-ing organic carboxylate ligands around nine rare earth metal ion nuclei1.

They used this cluster as a molecular

building block to form a MOF in which triangular organic ligands acted as the linker between two sets of rare earth clusters. This resulted in an unprec-edented network topology called a (3,18)-connected net.

The team used this topology as a blue-print to synthesize different MOFs with a modular structure, demonstrating this by replacing the rare earth clusters with a similarly structured but larger, more open metal-organic polyhedron that also contained 18 vertices. This building block approach means the team could transpose the same (3,18)-connected net-work topology on to different MOFs with more complex building blocks.

Produced from large organic poly-hedral compounds, these MOFs form low-density materials with large pores and pore volume: a spongy structure that enables them to reversibly store a range of gases of industrial or ecological importance.

1. Guillerm, V., Weselinski, J., Belmabkhout,

Y., Cairns, A.J., D’Elia, V. et al. Discovery and

introduction of a (3,18)-connected net as an

ideal blueprint for the design of metal–organic

frameworks Nature Chemistry 6, 673–680 (2014).

“The three-dimensional structure of MOFs give them broad industrial applications.”

KAU

ST

P ES

8 4

8 5I S S U E O N E


Perfect interfaces between sheets of two-dimensional semiconductors enable advanced electronic devices.

A

Atomically flat semiconductor devices

method to grow atomically thin sheets of semiconductors to be used for two-dimen-sional electronic devices has

been developed by researchers from KAUST1.

As silicon transistors approach the point beyond which they cannot be made smaller, alternative materials are needed for future electronic devices. This demand could be met by two-dimensional semiconductor materials with the necessary fast electron trans-port capabilities and a thickness of the requisite atomic limit, such as graphene or transition metal dichalcogenides like WSe2 and MoS2.

Producing advanced electronic devices sheets of just one of these mate-rials is not sufficient, as it only allows for a limited functionality. More com-plex devices require the combination

of different two-dimensional materials, ideally so that the different materials can transport first positive and then negative electrical charges across the device area. “It is fundamentally and technically important to integrate these two-dimensional layers to form devices and circuits in a monolayer lat-eral plane,” says Lain-Jong Li from the Physical Science and Engineering Divi-sion, who led the international research team.

Individually, two-dimensional semi-conductors can already be fabricated with the right properties. The challenge lies in combining them into complex electronic devices because of difficul-ties in achieving a perfect interface at the junction where the different mate-rials meet. Any imperfections at this interface may cause losses or inferior electrical or optical properties.

The researchers solved this prob-lem by using a two-step growth tech-nique where two-dimensional sheets are grown from atomic vapor inside a furnace. In the first step, a two-dimen-sional sheet of WSe2 is fabricated. Then, MoS2 sheets are grown alongside the first WSe2 layer using a second furnace at lower temperatures suited for MoS2.

The dedicated growth procedure opti-mized for each of the materials yields a sharp and functioning interface between the two sheets, indicated by high-resolution microscopy. The junc-tion between the two materials oper-ates like an electrical diode, and devices sizes of several micrometers have been achieved. Being semiconductors, the sheets also absorb light, and therefore operate as photodetectors and solar cells. In first tests, the required photo-voltaic effect has been demonstrated.

Li says this achievement is only a first step. “There is still plenty of room for research into two-dimensional semiconductor sheets. For example, we are keen to know the possibility to use these junctions for energy harvesting, light emitting and optics, where more fundamental studies have to be done,” he notes.

The interface between the WSe2 and MoSe2 sheets is atomically perfect.

1. Li, M.-Y., Shi, Y., Cheng, C.C., Lu, L.-S., Lin, Y.C.

et al. Epitaxial growth of a monolayer WSe2-MoS2

lateral p-n junction with an atomically sharp

interface. Science 349, 524-528 (2015).

“Being semiconductors, the sheets also absorb light, and therefore operate as photodetectors and solar cells.”

KAU

ST

8 6

P ES

Producing hydrogen from water is improved by creating an orderly catalyst.

Getting more fuel from water

OO

RKA

1. Bhunia, M. K., Yamauchi, K. & Takanabe,

K. Harvesting solar light with crystalline

carbon nitrides for efficient photocatalytic

hydrogen evolution. Angewandte Chemie 53, 11001–11005 (2014).

explains Takanbe, because the synthesis of carbon nitride resulted in a non-crystalline structure.

“We have now developed a novel way to synthesize carbon nitride in a highly crystalline and organized manner that improved the photocatalytic efficiency,” he says. His team’s method begins with a process known as supramolecular aggregation, which involves combining smaller molecules into a single larger molecule. Its usefulness comes from the way it causes the molecules to align in a particular order.

The researchers combined molecules of melamine and 2,4,6-triaminopy-rimidine (TAP) and then used a process called ionic melt polycondensation to rearrange the molecules and create their final material called polytriazine imide. They were able to optimize the catalyst for absorbing visible light and ensure crystallinity by varying the amount of TAP added to the mix.

Takanabe and his team confirmed the crystal structure of their polytriazine imide using X-ray analysis and solid-state nuclear magnetic resonance. They also tested the rate of the photocatalytic hydrogen evolution reaction and found it was about fourteen times faster than some previous carbon nitride catalysts.

Takanabe says efficiency still needs to be improved and hopes to achieve this by using the new molecular design with other inorganic materials.

AUST scientists have found a way to synthesize a cheap and environmentally friendly pho-tocatalyst for splitting a water

molecule into hydrogen and oxygen atoms — essential for the use of hydrogen as a green fuel.

Hydrogen is an optimal source of clean fuel due to its high energy density. Together with oxyen atoms, hydrogen can be produced by splitting a water molecule using energy from the sun and leaving only water as exhaust. Research-ers have been searching for a green and efficient catalyst to drive the water-split-ting reaction.

Now a team led by Kazuhiro Taka-nabe from the KAUST Catalysis Center has used a supramolecular-assembly

method to develop an efficient catalyst for the process1.

The ideal photocatalyst should be abun-dant, sustainable, efficient and free of any environmentally hazardous metallic substances, explains Takanabe. Materials based on carbon nitride meet all these cri-teria. “Carbon and nitrogen are both highly abundant, which has advantages for large scale application of any solar energy con-version technology,” says Takanabe.

The effectiveness of the photocatalytic reaction depends on the arrangement of the molecules in the catalyst. How the molecules are organized relative to their crystallinity plays a major role in the directional flow of electrons and there-fore on catalytic efficiency. Many previ-ous techniques have not been efficient,

Hydrogen is a clean energy source that can be produced by splitting water molecules using sunlight and the right catalyst.

K

“We have now developed a novel way to synthesize carbon nitride in a highly crystalline and organized manner that improved the photocatalytic efficiency.”

8 7I S S U E O N E


Tsunami: The importance of underwater landslides

An underwater landslide triggered by the 2011 earthquake in Japan may have exacerbated the resulting tsunami.

P ES

8 8

1. Tappin, D.R., Grilli, S.T., Harris, J.C., Geller,

R.J., Masterlark, T., Kirby, J.T., Shi, F., Ma, G.,

Thingbaijam, K.K.S., Mai. P. M. Did a submarine

landslide contribute to the 2011 Tohoku tsunami?

Marine Geology 357, (2014).

THIN

KSTO

CK

An international team of researchers including scientists at KAUST have been

modeling the tsunami triggered by the 2011 Tohoku earthquake in Japan.

our years after the devastat-ing Tohoku earthquake on Japan’s Eastern seaboard in March 2011, scientists are still deciphering the exact cause of

the extraordinary tsunami that followed. Researchers at KAUST show unequivo-cally the importance of secondary effects such as underwater landslides.

Following the mag-nitude 9.0 earthquake, the Sanriku region on Honshu Island was struck by waves measur ing 40 m high — four times the height of the tsunami in other areas. Thou-sands of people lost their lives, yet no models using earthquake-only data have been able to recreate these wave patterns.

Now an international team of scien-tists from Japan, the U.K., and the U.S., together with Martin Mai and Kiran Thingbaijam from the Division of Physi-cal Science and Engineering, have pro-duced a series of prediction models with the hypothesis that an enormous sub-marine landslide triggered by the earth-quake caused the localized heightened tsunami waves1.

“There has been great difficulty mod-eling and understanding the tsunami effects seen at Sanriku,” says Mai. “One possible cause is a submarine landslide triggered by horizontal shear-wave

motions radiated by the earthquake rup-ture process. This has not been considered before for this earthquake and is rarely included in detailed tsunami studies.”

The team faced opposition to the suggestion that the tsunami could have been exacerbated by a landslide origi-nating from the Japan Trench — part of the subduction zone which lies off Japan’s coast. They had to prove that earthquake-only ocean floor rup-tures were insufficient to trigger the extreme tsunami effects in Sanriku. The researchers conducted advanced numerical modeling to recreate the wave patterns and statistical analysis of previously published earthquake models for that day.

“Nearshore buoys along the Sanriku coast recorded the travel times of higher-frequency tsunami waves,” explains Mai. “This data helped us build a picture of ocean floor movements that would trig-ger waves of that particular height, speed and wavelength.” The detail in the data also allowed the team to work back-

wards and pinpoint the likely source.

Comparisons of pre- and post-tsunami sea-floor surveys at the predicted location 60 km north-east of the earthquake epi-center revealed that a 2 km thick sediment slab had slipped 300

m down the Japan Trench. The model suggests that the landslide, which had an estimated volume of 500-km3, occurred around two minutes after the earth-quake.

“Slope stability analysis confirmed the earthquake was sufficient to trigger a sizable landslide there,” states Mai. “This study shows the absolute neces-sity to include secondary effects, such as landslides, into future earthquake hazard studies and prediction models.”

“There has been great difficulty modeling and

understanding the tsunami effects

seen at Sanriku.”

F

8 9I S S U E O N E


S cientists have identified poly-mers that rearrange structurally in response to environmental changes. These are potentially

valuable for biomedical applications, but reproducible strategies are needed to convert these polymers into responsive nanomaterials.

Through a series of fortuitous experi-ments, Klaus-Viktor Peinemann, pro-fessor of chemical engineering in the Advanced Membranes and Porous Mate-rials Center, together with Suzana Nunes, professor of environmental science and engineering, and colleagues have iden-tified a robust approach to produce pH-sensitive particles that efficiently trap and separate protein targets1.

Peinemann’s team was constructing membranes and fibers from “block copol-ymers”, molecules composed of multiple structural units with distinct chemical properties. Through their struggle to generate useful membranes from polysty-rene-b-poly(acrylic acid), or PS-b-PAA, they learned that this block copolymer had other interesting characteristics.

Over several hours, Peinemann’s team observed that PS-b-PAA in solu-tion would gradually self-assemble into sheets, ribbons and spherical forms. “It is

Nanoparticles with pores that expand and shrink could prove valuable for biochemical research and drug delivery applications.

pH-responsive particles yield a terrific trap PE

INEM

ANN

, KV

ET A

L./N

ATU

RE C

OM

MU

NIC

ATIO

NS

1. Yu, H., Qiu, X., Nunes, S.P. & Peinemann, K.V.

Biomimetic block copolymer particles with gated

nanopores and ultrahigh protein sorption capacity

Nature Communications 5, 4110 (2014).

The solid, highly-porous spheres formed by the PS-b-PAA block copolymer could prove useful for protein

analysis, purification and drug delivery.

well known that PS-b-PAA can form vesi-cles, which are tiny hollow particles,” says Peinemann. “So I was not surprised to see these structures, and probably would have stopped the experiment at this time.”

However, postdoctoral fellows Haizhou Yu and Xiaoyan Qiu continued to watch and wait until their patience was rewarded as the polymeric structures unexpectedly formed solid orbs with highly ordered net-works of pores spaced throughout. “When we cut the particles, they were not hollow but instead had a well-ordered internal structure,” says Peinemann.

His group had previously established that PS-b-PAA can aggregate into structures featuring pores that shrink at neutral or basic pH but expand in acidic conditions, and discovered that these solid nanoparticles exhibited similar properties. Porous particles are routinely used to separate proteins of

different sizes, and their PS-b-PAA par-ticles exhibited a remarkable capacity for protein purification.

Under appropriate pH conditions, the researchers could quickly separate pro-teins that differ only slightly in size. Such a task would not be possible with other existing polymers, and Peinemann believes PS-b-PAA nanoparticles could be readily adapted for high-efficiency sorting applications.

Intriguingly, these particles could also absorb tremendous amounts of protein — up to 30 times their own weight — under the appropriate pH conditions. When these conditions were reversed, the par-ticles steadily released their cargo over an extended period.

This property could prove valuable for the long-term delivery of therapeutic agents such as pharmaceutical drugs or nutrients, although Peinemann says fur-ther refinement and study will be needed. “We first have to test which drugs will be absorbed, and then we have to quantify their release behavior,” he says.

“Under appropriate pH conditions, the researchers could quickly separate proteins that differ only slightly in size.”

9 0

P ES

A fast and cost-efficient fabrication process for high-quality perovskite crystals bridges the gap to silicon.

A good solar cell will convert light into electricity with a high efficiency and in an eco-nomically viable way. Osman

Bakr and colleagues from KAUST have now developed a fabrication method for large crystals of halide perovskites — organometals that are cheaper and more efficient than silicon1.

To date, the solar cell market has been dominated by silicon both because of its high conversion efficiency and its abun-dance as a raw material. Yet fabricating silicon crystals is still a relatively expen-sive process, leading researchers to seek cheaper alternatives.

Bakr and colleagues from the Solar and Photovoltaics Engineering Research Center investigated perovskite as a potential alternative to silicon. “Per-ovskite solar cells promise to bridge the gap between high efficiency and cost-effective photovoltaic technologies,” says Bakr.

In recent years, perovskite solar cells have dramatically improved in con-version efficiency from a few percent five years ago to more than 20 percent. Similarly to silicon, the most efficient

Solar cells: a solution for better crystals

perovskite solar cells are based on pure single crystals. However, whilst silicon fabrication techniques have developed, growing suitable single perovskite crys-tals for applications remains a challenge.

The approach developed at KAUST has potential to overcome such hurdles. Current growth methods use a saturated liquid solution of a crystal’s constituents which is slowly cooled so that crystals form. However, this approach does not allow control over the crystallization process, and results in a lack of uniform-ity in the size of the crystals.

To overcome such issues, Bakr’s team used an antisolvent evaporated into the solution. The antisolvent is a compound in which the components of halide perovskites are insoluble. Adding the

antisolvent to the solution reduces its capacity to dissolve the halide perovs-kite components and encourages crystal growth.

The crystals grown using this pro-cedure are large and of high quality. Spectroscopic measurements indicates that there are fewer defects than for alternative methods. Furthermore, time-resolved measurements of the electron lifetime provided evidence that in the high-quality crystals electrons excited by the light also travel further.

The knowledge of these parameters is important for the development of high-efficiency solar cells, comments Bakr. “The determination of the ultimate carrier mobility and diffusion length provides new horizons for perovskites in solar cells and other optoelectronic devices.” The possibility to grow suffi-ciently pure crystals for perovskite solar cells is a significant step towards their commercial success.

The perovskite crystals the researchers produced are large and have fewer defects than those grown by alternative methods.

1. Shi, D., Adinolfi, V., Comin, R., Yuan, M.,

Alarousu, E., et al. Low trap-state density and long

carrier diffusion in organolead trihalide perovskite

single crystals. Science 347, 519-522 (2015).

KAU

ST

“Perovskite solar cells promise to bridge the gap between high efficiency and cost effective photovoltaic technologies.”

9 1I S S U E O N E

The fabrication of branched titanium dioxide nanomaterials enhances the connectivity in solar cells for a better performance.

E

Branching out into solar cells

lectrical contacts made of branched titanium dioxide nanowires developed by research-ers from KAUST could improve

the efficiency of solar cells.Titanium dioxide is a white pigment

used in paint and is a versatile elec-tronic material for solar cells. A cheap and abundant compound, it has similar electronic states to some light-absorb-ing compounds used in photovoltaics.

This match ensures that electrical charges are efficiently funnelled away from the active region of a solar cell into the titanium dioxide and from there towards the electrical contacts of the device. “It is the most success-ful electron transporting material in hybrid organic/inorganic photovolta-ics,” explains research leader Aram Amassian of the Solar and Photovoltaics Engineering Research Center.

To ensure good contact between the titanium dioxide and the solar cell mate-rial, the titanium dioxide needs a very large surface area to maximize capture of electrical charges. The surface area can be expanded by using nanostruc-tured materials such as meshes made from nanowires. These meshes have not been able to effectively transport the

electrical charges across the nanowires.Different architectural structures

could help improve charge transport — for instance, branched structures would have a much stronger electrical connec-tion. Established techniques for growing such branched structures are inefficient, however, and produce nanostructures with many impurities and defects.

KAUST researchers have now estab-lished an efficient two-stage process to fabricate branched titanium dioxide materials. The first step is to deposit nanofibers using an electrospinning tech-nique, where a narrow jet of a titanium dioxide solution is ejected from a needle using electrostatic charges, resulting in

a network of electron highways. “Elec-trospinning of metal oxide nanofibers has emerged as a potentially low-cost, rapid and useful technique to grow one-dimensional nanostructures on a variety of substrates,” says Amassian.

In the second step, these structures are heated further, which results in the hydrothermal growth of branched nanostructures. The hyperbranched materials perform better than conven-tional nanofibers in solar cells, which indicates their potential viability in other devices such as batteries, or in catalytic applications.

The team reduced the processing tem-perature substantially — down to 300 degrees Celsius — but the demand for a high processing temperature remains a practical barrier to the technology, says Amassian. “Future work to halve this temperature could help implement hyper-branched electron transport materials for solar cell fabrication on flexible and stretchable plastic or textile substrates.”

1. Mahmood, K., Swain, B. S. & Amassian,

A. Highly efficient hybrid photovoltaics

based on hyperbranched three-dimensional

TiO2 electron transporting materials.

Advanced Materials 27, 2814 (2015).

“Electrospinning of metal oxide nanofibers has emerged as a potentially low cost, rapid and useful technique to grow one-dimensional nanostructures on a variety of substrates.”

P ES

9 2

Schematic of the low-cost fabrcation of titanium dioxide nanomaterials by electrospinning.

2015

WIL

EYP H Y S I C A L S C I E N C E A N D E N G I N E E R I N G D I V I S I O N

9 3I S S U E O N E

Efficiently extracting the charge required by quantum dot solar cells can be controlled by chemically configuring molecules.

ETET ETET

N NN N

N NN N

NN

NN

-N

-N

N-

N-

N-

-NN-

-N

ISCISC

ISCISC

A

On-off switches forquantum devices

chemical “on-off switch” that could improve the efficiency of solar cells as well as other elec-tronic devices has been devel-

oped by researchers from KAUST.The efficiency of solar cell devices

depends not just on the active region where sunlight is converted into elec-tricity, but also on the efficiency of the interface between the active regions and the device.

Studying devices based on small semi-conductor nanocrystals, also known as quantum dots, a team from the Solar and Photovoltaics Engineering Research Center has shown that chemical sub-groups in the molecules that couple to these quantum dots can be used to switch the flow of electrical charges on and off1. “We can tune the electron injection into the quantum dot interface from zero to very efficient,” says Omar F. Mohammed, who led the research.

Quantum dot devices such as solar cells can be highly efficient and cost effective. The best way to connect to quantum dots is via porphyrin organic molecules — these are flat molecules with ring-like structures at each of their four corners. The different groups on the corners can be deliberately chemically synthesized to have a positive electrical polarization at their ends, which then attract negative charges from the environment.

The researchers found that the trans-port of electrical charges from the por-phyrin molecules through to quantum dots is greatly dependent on the number and position of the charged corners. If all four corners are electrically charged, then the transport of charges to quan-tum dots is suppressed. If, however, two neighboring corners are charged and the other two not, then the transport of charges through the quantum dots is very efficient and ultrafast.

The efficiency of the charge transport from the quantum dot (green and orange schematic atoms) can be controlled by the electrical chargesof the corners of porphyrin molecules (light gree/blue).

“The discovery is a big step toward the exploitation of an efficient charge transfer.”

The efficiency of this charge transport has been demonstrated using state-of-the-art equipment that can measure the dynamics of electrons at a broad range of energies with ultrafast time resolu-tion of less than a millionth of a mil-lionth of a second. These measurements confirm that the porphyrin variant with two neighboring charged corners shows a high efficiency and is also one of the fastest transports of electrical charges for such solar cells.

This information has implications for the design of quantum dot devices, says Mohammed. “The novel insights reported in this study provide a pro-found understanding of the key vari-ables involved in the nanoassembly of devices,” he says.

Mohammed says the discovery is a big step toward the exploitation of an efficient charge transfer, an essential breakthrough for optimal device performance.

1. Aly, S.M., Ahmed, G.H., Shaheen, B.S., Sun, J. &

Mohammed, O.F. Molecular-structure control of

ultrafast electron Injection at cationic porphyrin-

CdTe quantum dot interfaces. Journal of Physics and Chemistry Letters 6, 791-795 (2015).

REPR

OD

UCE

D W

ITH

PER

MIS

SIO

N 2

014

AMER

ICAN

CH

EMIC

AL S

OCI

ETY

9 4

The emergence of two volcanic islands in the Red Sea suggests a larger underlying event linked to African Arabian plate separation.

T

Plate separation births two volcanic islands

he appearance of two new volcanic islands in the Zubair archipelago of the southern Red Sea gave researchers from

KAUST the opportunity to study the rare emergence of new islands on a mid-ocean ridge system1.

Between 2011 and 2013 two vol-canic islands named Sholan and Jadid appeared in the Zubair archipelago’s mid-ocean ridge system. The eruptions from which they were formed were accompanied by a series of earthquakes, and the seismic and volcanic activity caused visible disturbance to the land-scape on neighboring islands.

Sigurjón Jónsson from the Physi-cal Science and Engineering Program recalled hearing of the islands’ forma-tion in December 2011, along with his-colleagues Wenbin Xu and Joel Ruch. “Given the rarity of such an event, we immediately wanted to learn from it,” Jónsson says.

“However, the islands belong to Yemen and are basically out of reach for field-work, so our observations were limited to satellite images and seismic data.”

Xu and Ruch used high-resolution

satellite optical and radar imag-ing techniques to study both how the islands developed as well as how the land deformed on other islands in the archipelago. They detected a previously unrecognized yet significant period of magmatic activity connected with the separation of the African and Arabian continental plates.

Xu used this information to simu-late the two eruptions and pinpoint the likely underground triggers for the vol-canic activity. Each eruption was fed by a dike — an intrusion of magma push-ing towards the surface through exist-ing rock layers. The model suggests both dikes run along a larger, existing North-South fracture system which cuts through the Zubair area.

“We realized the two eruptions were

likely part of a larger sequence of events — a so-called rifting episode,” explains Jónsson. “Rifting episodes occur on boundaries where continen-tal plates are moving apart — a large amount of magma enters the crust from below, and meter-scale spreading of the plates can occur in just a few years. More often than not, this happens on the sea floor, where it’s almost impos-sible to study.”

Many decades of limited activity can pass between rifting episodes in any one particular place. The last period of rifting in the southern Red Sea was probably in the 19th century. The recent events present a valuable opportunity to advance understanding of plate diver-gence, particularly as they are visible on the Earth’s surface.

“We will continue studying this island-building event and its possible influences on future activity in the area,” states Jónsson.

The emergence of two new volcanic islands in the southern Red Sea points to a larger rifting event linked to the African-Arabian plate divergence.

1. Xu, W., Ruch, J. & Jónsson, S. Birth

of two volcanic islands in the southern

Red Sea. Nature Communications 6,

7104 (2015).

XU E

T AL

.

“We realized the two eruptions were likely part of a larger sequence of events — a so-called rifting episode.”

9 5I S S U E O N E

Stable air layers that wrap around liquid drops can retain their remarkable geometries a thousand times longer than theory predicts.

N

Antibubbles make a splash

atural processes, including cloud formation and soil ero-sion, and technology such as inkjet printers are based

on interactions between droplets and surfaces. One area of investigation for climate scientists and engineers is low velocity impacts — for example, sec-ondary splashes that occur after the primary contact, or drops ejected from a boiling interface. These types of col-lisions are hard to predict, as they involve complex physical interactions.

KAUST Research Scien-tist Erqiang Li and Professor of Mechanical Engineering Sigurdur Thoroddsen from the University’s Physical Science and Engineering Division, along with col-laborators in France and the Netherlands, used advanced video cameras to study drop impacts between different liquids.

At low velocities, drops tend to either bounce away or enter into target liquids on a thin, hemispherical air cushion that eventu-ally ruptures into micro-bubbles. The team realized that they might be able to control the geometry of these air sheets if they used droplets that are more viscous.

To experiment, the researchers placed a syringe filled with thick, viscous silicone oil a few millimeters above a pool containing lower-vis-cosity oil. By gradually

increasing droplet viscosity, air sheets began to envelop the heavy liquids as they fell into the light oil. After analyz-ing several thousand video clips, the

team mapped out the parameters needed to produce seldom-seen spherical anti-bubbles on demand.

At the upper limits of viscosity, the droplets stay connected to the syringe nozzle along long, thin threads of oil during the initial impact. When the droplet and its long tail enter into the pool, air sheets also wrap around these structures and produce cylindrical films of air that are stable for thou-

sands of times longer than expected.

When the team used laser-based interferometry to scrutinize the cylinders, they were surprised to see the films can become nar-rower than 100 nanom-eters before breaking. At these scales, stability theory predicts their disin-tegration in a few micro-seconds through the same mechanism that breaks up the water stream running out of faucets.

“Soap molecules could stabilize the layers, but there are no surfactants involved here,” said Thoroddsen. “Our results suggest the stabilization force is the viscous lubrication forces within the submicron air layer. This shines new light on thin film instability and also introduces many more questions.”

When a viscous oil droplet enters into another liquid, an air cushion wraps around its long tail and eventually breaks off - creating free-floating cylinders of air with surprisingly long lifetimes.

1. Beilharz, D., Guyon, A., Li, E. Q.,

Thoraval, M.-J. & Thoroddsen, S.

T. Antibubbles and fine cylindrical

sheets of air. Journal of Fluid Mechanics 779, 87–115 (2015).

KAU

ST

“Soap molecules could stabilize the layers, but there are no surfactantsinvolved here.”

9 6

P ES

KAUSTofficial @kaust_newskausteduKAUSTkaustofficial

Get socialwith KAUSTFollow us on social media

KAUST students are empowered and encouraged to aim highand investigate important questions with passion.

As a truly global university, KAUST fosters excellence in curiosity-driven and goal-oriented research that willbuild a better world of tomorrow.

Discover the possibilities and apply for yourM.S. or Ph.D. degree at kaust.edu.saAll admitted students receive the benefits of the KAUST Fellowship, which includes: full tuition support, competitive monthly living allowance, private medical and dental coverage, housing, and relocation support.

Choose

KAUSTas your destination

ISSUE O

NE - 2015

DISCO

VERY.KA

UST.ED

U.SA

Documents

KAUST Discovery Issue 1