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Elements for Innovation KAUST is intentionally designed to empower its people to aim high and investigate important questions with passion and freedom. Our students join our faculty, researchers and postdocs to think beyond the laboratory and consider how their ideas can change the world. The Cornea CAVE at KAUST is one of the highest resolution fully-immersive virtual reality environments in the world.

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ear Friends, Serving society through science and technology was a driving impetus behind the creation of KAUST. As we enter into our eighth year, this continues to motivate our people. When we launched KAUST Discovery, our goal was to engage you with our vision—to be a beacon of knowledge that bridges people and cultures. Connecting people and their ideas will not only serve society, but it will enhance our ability to make game-changing discoveries and foster innovations to improve our world. Similar to what I experienced at American science and technologies universities, the culture of excellence at KAUST percolates throughout our environment and drives our aspirations to do good things for our society. Faculty from 35 countries and students and researchers from 80 different countries are all committed to excellence through collaboration, integrity and innovation with purpose. KAUST’s environment is empowered through sustained support for our people, international partnerships with academia and industry, and the physical resources and infrastructure to help ideas go farther faster. Our ambition is realized throughout a matrix-driven organization where people move freely between disciplines to find partners in action—chemists collaborate with mathematicians, biologists learn from computer scientists and mechanical engineers equip marine scientists. In the coming pages you will read about

our research endeavors in areas ranging from photonics and photovoltaics to genetics and global climate studies. For many of them, you will discover the importance and focus we place on international partnerships. For example, you will learn more about Professor Kim Ng, who is pushing the boundaries of clean water and solar energy through MEDAD, a water desalination start-up company that stemmed from an international collaboration. Professor Carlos Duarte, director of our Red Sea Research Center and a marine scientist, is partnering with engineers and oceanog-

“The culture of excellence at KAUST percolates throughout our environment and drives our aspirations to do good things for our society.” raphers to better understand implications for global climate change by studying the unique properties of the Red Sea. Finally, the discovery of material that is physically darker than the darkest black by Professor Andrea Fratalocchi began with a fortuitous game of tennis and has led to a productive collaboration with Harvard University. Every story you’ll read in this issue has potential for societal and economic impact—and that is a good thing.

Jean-Lou Chameau President These research partnerships offer winwin solutions to all our partners by placing the focus on collaboration not competition as we jointly pursue excellence. Whether it is leveraging the talent of our students and postdocs or promoting our entrepreneurial faculty, together we are investing in science and technology with purpose and passion. Collaboration, focus, drive to be distinctive and passion for curiosity are key to innovation. If you have had the opportunity to visit KAUST you’ve experienced our culture firsthand in our laboratories, conferences and even our coffee shops. If you are curious, I invite you to join us for one of our upcoming conferences to experience KAUST for yourself. On behalf of our dedicated people, I invite you to join us as we forge ahead as a thriving global university. Yours in discovery, Jean-Lou Chameau President


HIGHLIGHTS HEALTHCARE AND GENETICS ANTIVIRALS WAITING TO BE DISCOVERED IN CORAL REEFS The Red Sea may be a treasure chest of potential new drugs.

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CATCHING A GLIMPSE OF THE DOUBLE HELIX

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Direct imaging of a single DNA molecule provides insights into fundamental biological processes.

PATHOGEN EXPERTISE BOOSTED WITH LATEST GENOMICS Expert knowledge in the field of DNA and RNA sequencing puts KAUST at the forefront of highimpact pathogen research.

NOISY CELLS PRODUCE BURSTS OF PROTEIN A new mathematical model explains how random factors affect the production of proteins within the cells.

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ADDRESSING CLIMATE CHANGE THE RED SEA MODELS THE FUTURE

BURNING A BETTER BIOFUEL

Detailed analysis of nutrient distribution and circulation in the Red Sea could provide a model for the future of the world’s oceans.

Chemical reaction modeling and combustion experiments reveal how 2-methylbutanol would behave in advanced engines.

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BUILDING BLOCKS FOR CLEAN ENERGY Novel solid-state materials may hold the key to cleaner fuels and cheap, efficient gas storage.

Seagrass genome reveals the structural and physiological adaptations needed for plants to survive and thrive in the marine environment.

WATER, WATER, EVERYWHERE

REALITY CHECK FOR RED SEA WAVE PREDICTIONS

Current models that predict ocean surface conditions overestimate wave patterns in the middle of the Red Sea.

PARTNERING FOR SUSTAINABLE FRESH WATER PRODUCTION

Combining methods for water desalination results in low-cost, highly efficient water production. 2

A CLEARER VIEW OF RAINFALL PATTERNS

Improved random modeling allows scientists to generate realistic patterns of high-frequency rainfall.


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EXPLORING THE NANO-SCALE SILVER NANOPARTICLES’ GOLD LUSTER

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An atomically precise investigation reveals close similarities between silver and gold nanoparticles.

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GRAPHENE POWERS UP WATER PURIFICATION

THE BRAIN GAMERS Novel use of gaming technology enables researchers to “step inside” the brain.

Self-cleaning graphene-coated membranes remove water pollutants while harvesting energy from microbial decomposition.

LIGHTING UP THE FUTURE SMASHING RECORDS

A SMOOTHER ROUTE TO SMART SENSORS

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Exploiting the properties of disordered, chaotic systems leads to low-cost energy harvesting and innovative microsurgery applications.

Growing highquality films of hybrid perovskite materials takes solution-processed phototransistors to new levels of performance.

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PHOTODETECTORS GAIN A SUPER-SIZED ADVANTAGE

TAKING THE HEAT OUT OF EMITTERS Semiconductor light-emitting diodes fabricated on a metal substrate are less prone to overheating.

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Integrating largearea perovskite crystals into simple circuitry leads to optical sensors with high bandwidth and sensitivity.

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KNOWN MATERIALS, NOVEL APPLICATIONS SAVING PRECIOUS WATER WITH NANOSCALE INGENUITY Biology has inspired new ways to harvest and collect water.

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ARTIFICIAL SKIN SENSORS MADE FROM STICKY NOTES

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A paper-based sensor that mimics the sensory functions of human skin has been developed for the first time from low-cost and commonly available household materials.

SENSORS FOR A LIGHT TOUCH Biocompatible tactile sensors based on magnetic hair-like structures enable new applications for touch sensors.

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Elements for Innovation At KAUST, we attract people from Saudi Arabia and around the world who want to create impact beyond their own achievements. Irrespective of their national origins, the people of KAUST are “people of the world� who share the belief that tackling global challenges by advancing science and innovation is a worthy endeavor.

Our student housing overlooks the iconic Breakwater Beacon, located on the shores of the Red Sea.

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Saving precious water with nanoscale ingenuity

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The brain gamers

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An ocean observatory for the Red Sea

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Partnering for sustainable fresh water production

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Molecular immunity from microbes

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Antivirals waiting to be discovered in coral reefs

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Pathogen expertise boosted with latest genomics

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Ready for the high seas?

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Graphene powers up water purification

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The Red Sea models the future

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From head to tail in search of piRNAs

Biology has inspired new ways to harvest and collect water.

Studies conducted at the Saudi Aramco-KAUST Marine Environmental Research Center provide new insights into the physical and biological aspects of the Red Sea.

Harnessing a bacterial system of defense can protect plants against viral pathogens.

Expert knowledge in the field of DNA and RNA sequencing puts KAUST at the forefront of high-impact pathogen research.

Self-cleaning graphene-coated membranes remove water pollutants while harvesting energy from microbial decomposition.

Small non-coding RNAs thought to be found only in testes are also present in the adult mouse brain.

Novel use of gaming technology enables researchers to “step inside” the brain.

Combining methods for water desalination results in low-cost, highly efficient water production.

The Red Sea may be a treasure chest of potential new drugs.

Seagrass genome reveals the structural and physiological adaptations needed for plants to survive and thrive in the marine environment.

Detailed analysis of nutrient distribution and circulation in the Red Sea could provide a model for the future of the world’s oceans.

DISCOVER MORE RESEARCH AT discovery.kaust.edu.sa

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A clearer view of rainfall patterns

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Brain waves in boxes

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Artificial skin sensors made from sticky notes

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Smashing records

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A picture of the artist captured in a stroke

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Sensors for a light touch

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Wireless devices tune-in to cloud power

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Noisy cells produce bursts of protein

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Miniature flexible sensor to detect heart disease

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Feeding in the moonlight

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Taking the heat out of emitters

Improved random modeling allows scientists to generate realistic patterns of high-frequency rainfall.

A paper-based sensor that mimics the sensory functions of human skin has been developed for the first time from low-cost and commonly available household materials.

A graphics technique is the first to identify people based on their sketching style.

Next-generation mobile networks can use cloud computing algorithms to manage the increasingly high data demands of users.

A new biosensor made of laser-etched electrodes on a gold-coated polymer may provide an effective and cost-efficient way to assess heart disease risk.

Semiconductor light-emitting diodes fabricated on a metal substrate are less prone to overheating.

A statistical method helps to identify abnormal signals in electroencephalograms and locate their source in the brain.

Exploiting the properties of disordered, chaotic systems leads to low-cost energy harvesting and innovative micro-surgery applications.

Biocompatible tactile sensors based on magnetic hair-like structures enable new applications for touch sensors.

A new mathematical model explains how random factors affect the production of proteins within the cells.

Consistent around the world’s ocean, the phases of the moon affect the upward migration of the world’s most abundant type of fish for feeding.

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


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Burning a better biofuel

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Faster, finer filtration

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Photodetectors gain a super-sized advantage

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Simulations blow wind tunnel tests away

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A smoother route to smart sensors

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Building Blocks for clean energy

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Making a splash

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Reality check for Red Sea wave predictions

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A new take on old materials

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Catching a glimpse of the double helix

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Silver nanoparticles’ gold luster

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Shaping rate rules to fuel the future

Chemical reaction modeling and combustion experiments reveal how 2-methylbutanol would behave in advanced engines.

Integrating large-area perovskite crystals into simple circuitry leads to optical sensors with high bandwidth and sensitivity.

Growing high-quality films of hybrid perovskite materials takes solution-processed phototransistors to new levels of performance.

Ultrafast imaging reveals the influence of even ultrasmall surface roughness on inkjet printing.

A mineral used in electrochemical devices that was thought to be a semiconductor is now identified as a metal.

An atomically precise investigation reveals close similarities between silver and gold nanoparticles.

The right blend of polymers enables rapid and molecule-selective filtering of tiny particles from water.

A simulation scheme for aerodynamic turbulence could reduce expensive wind tunnel tests.

Novel solid-state materials may hold the key to cleaner fuels and cheap, efficient gas storage.

Current models that predict ocean surface conditions overestimate wave patterns in the middle of the Red Sea.

Direct imaging of a single DNA molecule provides insights into fundamental biological processes.

Precise rate constants could provide high-fidelity combustion models for cleaner and more efficient fuels.

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Peng Wang and his colleague study their bio-inspired materials.

Saving precious water with nanoscale ingenuity

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anaging scarce water resources is problematic for many Middle East countries, and forecasts predict a more straitened situation ahead. Desalination plants are one way to manage water shortages, as more than two-thirds of the world’s desalination capacity is in this region, but processing seawater has enormous energy and environmental costs. Other approaches 8

need to be developed to achieve sustainable growth. Over the past seven years, Peng Wang and colleagues from the KAUST Biological and Environmental Science and Engineering Division have been looking for answers to these grand challenges by turning to very small science. The team specializes in producing materials and surfaces that purify, distill and catch water molecules with remarkable

efficiency thanks to nanoscale techniques, many inspired by ingenious biological tricks. “It’s amazing what nature can offer us for solving some of the problems of clean water production,” said Wang. “This field really gives you a chance to demonstrate your most creative ideas.” Wa n g e x p l a i n s t h a t h e a l w a y s approaches research with the concept of rational design in mind, which is using

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Biology has inspired new ways to harvest and collect water.


B IO LO G I CA L AN D E N V IRO NM E N TA L S C I EN C E A N D EN G IN EERIN G DIV ISION To solve this quandary, the research team coated a floating stainless steel membrane with an innovative polymer containing photo-sensitive rings. The new membrane absorbs light radiation instead of the bulk water and increases heat generation at the water surface. The researchers also mimicked the lotus leaf flower, a plant that can repair damage to its leaves by tapping into a reservoir of waxy molecules to heal any sun-based injuries to the membrane. “This device tripled the output of fresh water compared to a typical solar still,” noted Wang. Wang reveals that open cooperation and communication between scientists, postdoctoral fellows and students in his bustling lab are the key to research success. “You see lots of casual and regular meetings in a typical day,” he said. “We encourage members to share their knowledge, know-how, criticisms and concerns—this is how we work as a team” The state-of-the-art tools such as surface modification and water treatment available in Wang’s lab give researchers the chance to move into the elite ranks of scientific achievement. Since 2012, several of his papers on topics such as pH-responsive membranes that

separate oil from water or nanomaterials that efficiently generate hydrogen from water have reached the top one percent of cited articles in their fields. Two of his edited books are also expected to appear in 2016. “In our group, you need basic chemical synthesis skills, but I stress critical thinking more than anything else—you have to give defensible reasons for every step of your research,” said Wang. “Tackling relevant problems and mentoring brilliant young minds is what I find most rewarding.” The flow of water through commercial filtration membranes is limited by membrane thickness. Wang and his team are currently studying ways to accelerate this type of purification using ultrathin membranes made from stacks of graphene sheets. While the challenges of this project are intense and include making uniform pores on graphene with solution processing, the potential payoffs could be enormous. “With generous funding and fantastic support, one can focus and do amazing things with our colleagues at the University’s Water Desalination and Reuse Center,” he said. “This is really not possible anywhere else.”

2016 DGGAFG imageBROKER / Alamy Stock Photo

specific chemical and physical functions to achieve targeted results. “You have to be able to define your problem scientifically first,” he said. “We then rationally decide on what functions to impart to the surfaces or materials. In some cases, we mimic species to reach our goals.” One such example was Wang’s search for a surface that collects atmospheric fog. The hunt led the researchers to the Stenocara beetle, a native of the Namib Desert. The beetle has special wings dotted with nanoscale bumps that capture water droplets from the air. The beetle’s waxy regions slide droplets directly into the its mouth. To mimic the beetle’s wings, the team used a different bio-inspired substance— an extra-sticky dopamine-based polymer similar to natural glues used by mussel shells—to stick bumpy patterns onto a super water-repellent surface through inkjet printing techniques. Another of Wang’s projects revolves around developing point-of-use desalination devices powered by the sun. These solar stills could prove invaluable in the aftermath of natural disasters, but offer notoriously poor efficiency because it takes extended time to heat bulk quantities of water.

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Novel use of gaming technology enables researchers to “step inside” the brain.

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echnology that creates a 3-D virtual reality is best known to gamers, and it has now given researchers new insight into the structure of the brain, enabling them to inspect specific neural structures with unprecedented clarity. Photographs of cross-sections of mouse brain tissue scanned under an electron microscope were reconstructed using special software, allowing a multidisciplinary team of researchers to examine the tissue in a 3-D virtual environment1. “Aside from the excitement of being able to physically enter a 3-D microscopic model of the brain, we can see new patterns in the neural tissues,” said neurobiologist Pierre Magistretti from the Biological and Environmental Science and Engineering Division. “For instance, we could show that glycogen granules, a major source of energy in the brain, are not randomly located but accumulate around synapses, the sites of contact between neurons, which consume a lot of energy in order to work properly.” Such a detailed study on the ultrastructural localization of glycogen in the brain is new. “This is the first time that such a 3-D virtual reality analysis of brain structure has been performed at such a high level of spatial resolution,” said Corrado Cali, a postdoctoral fellow in Magistretti’s lab and first author of the paper. The research was developed by KAUST biological researchers, the University’s Visualization Lab, Germany’s Heidelberg Collaboratory for Image Processing and Switzerland’s Brain Mind Institute in Lausanne. 10

Researchers step into a three-meter cubical room that has projectors on all six sides. Using special 3-D glasses, they gain the illusion of standing within the projected 3-D image of the brain tissue. The high resolution of the images allowed them to identify and precisely locate various neural tissues as well as the locations of minute subcellular features such as glycogen granules. The team found that a significant portion of glycogen granules collected around neuron synapses close to the walls of blood vessels. This suggests that glucose entering the brain parenchyma from the blood stream is immediately converted to glycogen. Glycogen breaks down in the brain to produce lactate, which is then shuttled to neurons, playing a vital role in learning and memory. “The result was beyond our expectations,” said Magistretti. “The tool is extremely useful to help us to investigate, brainstorm and decide how to modify our analysis tool to improve our observations.” The team plans to use the same approach to study how memory is affected in animals following disturbances of glycogen metabolism. They also plan to use 3-D virtual reality environments to examine pathological brain samples, with particular emphasis on epilepsy and neurodegenerative diseases. 1. Cali, C., Baghbara, J., Boges, D. J., Holst, G. R., Kreshuk, A. et al. Three-dimensional immersive virtual reality for studying cellular compartments in 3D models from EM preparations of neural tissues. The Journal of Comparative Neurology 524, 23-38 (2016).

KAUST researchers explore nerve tissue in a 3-D immersive environment.


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he Marine Environmental Research Center established jointly by KAUST and Saudi Aramco is the first oceanic observatory capable of monitoring the Red Sea. “Marine research in the Red Sea in the past has been sporadic and often limited to easy-to-reach areas—rather like poking toothpicks into a cake to see if it is cooked,” explained Burton Jones, director of the center and KAUST professor of marine science. “Until the formation of KAUST, no one had carried out systematic, long-term research into the Red Sea’s marine and coastal environments. Now we have an oceanic observatory that will establish the baseline physical and biological aspects of this unique environment.” Established in 2013, the strategic partnership enables close collaboration between the researchers at the center and at the KAUST Red Sea Research 12

The oceanographic research considers the physical variables of the region and monitors ocean currents, the atmosphere and changes in the environment.

Center (RSRC) and with scientists from Saudi Aramco. They combine data from research conducted close to KAUST with data collected further afield in more remote parts of the Red Sea. Jones and his team have various projects underway that involve state-of-theart technology and marine monitoring systems. The projects come under two main strands of research: oceanographic monitoring and ecological assessment.

“We are interested in the cryptic diversity of coral reefs. The artificial reefs are providing a wealth of new data in this regard.” The oceanographic research considers the physical variables of the region and monitors ocean currents, the atmosphere and changes in the environment. A key aim is to create models of the Red Sea to understand the processes and influences that affect the ocean and its surroundings. Led by Ibrahim Hoteit, associate professor of earth science and engineering from the University’s Physical Science

and Engineering Division, the research focuses on the long-term monitoring and modelling of oceanic and atmospheric circulation. Knowledge of circulation patterns can prove invaluable in the event of an oil spill, for example. “To make viable predictions, we need to draw on knowledge of how the Red Sea behaves as a whole,” noted Jones. “We are developing an overview—a year in the life of the Red Sea, if you will—that will enable us to build better prediction models to examine the impact of catastrophic events and the effects of longterm climate change.” The center’s research teams collect data from networks of fixed coastal measuring systems, monitor wave patterns with radar and have the latest underwater and aerial autonomous vehicle technology at their fingertips. The autonomous vehicles have revolutionized the way oceanic research is carried out. By deploying the vehicles for a period of weeks or months, the researchers can build up a larger-scale, highly detailed picture of the Red Sea from above and below the surface. Detailed ecological assessments also form a major part of the work, with a

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Studies conducted at the Saudi Aramco-KAUST Marine Environmental Research Center provide new insights into the physical and biological aspects of the Red Sea.


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BI OLOG I CAL A ND ENVI RO NM ENTAL S C IE NC E A N D E NG I NE E RIN G D IV I S IO N

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

Data from research conducted close to KAUST is combined with data collected in more remote areas to build a comprehensive picture of the Red Sea.

particular focus on coral reefs and on the impact of new infrastructure developments along the Red Sea coast. Jones and colleagues continuously monitor the health of the Red Sea’s microenvironments, particularly in far-flung regions. There are ongoing projects to characterize the makeup of sediments and corals, checking for contaminants, toxicity and oil-related pollution. In one study led by Susana Carvalho, a research scientist in the RSRC, artificial reef structures were placed in the water for one to two years and the species that settled on them were analyzed and documented. “We are interested in the cryptic

diversity of coral reefs—those elements of the ecosystem beyond the obvious fish and coral species. The artificial reefs are providing a wealth of new data in this regard,” Jones said. This project is part of a larger international collaboration in which research teams working on artificial reefs across the globe are now sharing data to build up a more comprehensive picture of the world’s oceans. KAUST and Saudi Aramco have founded a unique oceanic observatory in the region, and, driven by the efforts of researchers working there, the initiative will continue to provide unprecedented insights into the Red Sea. ISSUE TWO

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An aerial view of the MEDAD pilot plant at KAUST.

Partnering for sustainable fresh water production Combining methods for water desalination results in low-cost, highly efficient water production.

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nnovative solutions to improve the efficiency of water desalination are a major focus in countries such as Saudi Arabia, where fresh water for industrial, agricultural and human use is scarce. A research partnership between KAUST and the National University of Singapore has won global acclaim for its unique and efficient yet low-cost method of conducting desalination called hybrid multi-effect adsorption desalination. The collaboration has resulted in two desalination pilot schemes—one at KAUST itself and the other at a second location also in Saudi Arabia—as well 14

as a spin-off company called MEDAD that will help to commercialize the hybrid desalination technology. The project is led by Kim Choon Ng from the University’s Water Desalination and Reuse Center. Ng has devoted his career to finding ways of reducing the cost of desalination through novel technologies. Traditional desalination techniques use membranes and pressure to separate salt and other minerals from seawater, but these techniques are expensive, energy intensive and inefficient. “Desalination is particularly complicated in the challenging environment of the Gulf, where high salinity, silt levels

and increased water temperatures make working with the seawater quite difficult,” Ng said. “The frequent occurrence of hazardous algal blooms has also contributed to high pre-treatment costs and severe fouling of membranes. These elements combine to considerably increase the overall unit cost of producing desalinated water.” Ng and his team recognized that the only viable option to overcome these challenges was to base their system on thermal desalination rather than membrane-based techniques. They investigated a combined technique and utilized an existing


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B IO LO G I CA L AN D E N V IRO NM E N TA L S C I EN C E A N D EN G IN EERIN G DIV ISION industrially-proven method called multi-effect distillation (MED). This involves spraying saline water over the outer surfaces of a series of tubes (or stages) arranged in a tower. At the top of the tower, saline water is fed in and heated by a steam-driven compressor. The resulting water vapor is collected while the salt is left behind. This process is repeated over subsequent stages, and the vapor from each stage is channeled through the tubes to the bottom of the tower, where it condenses to generate fresh water as it cools. Ng’s team combined MED with a thermally-driven process called adsorption desalination (AD), which uses low-cost silica gel adsorbents with a very high affinity for water vapor. The researchers adapted the last stage of MED so that the vapor uptake is carried out by AD. The water vapor is attracted to designated adsorption gel beds while the remaining gel beds undergo desorption, removing the water and preparing the silica gel for the next round. Crucially, there are no major moving parts in the AD cycle, meaning it uses far less energy than some other techniques, and it can run on waste heat from other industrial processes.

“Desalination is particularly complicated in the challenging environment of the Gulf, where high salinity, silt levels and increased water temperatures make working with the seawater quite difficult.”

Kim Choon Ng (left) explains the hybrid cycle to visitors at KAUST, including Ahmad Khowaiter from Saudi Aramco (center), Dr. Abdulrahman from the Saline Water Conversion Commission (SWCC) (right) and Dr. Ahmed Al Arifi from SWCC (far right).

producing cooling as part of the process, we can link into air-conditioning systems.” Simulations on the hybrid MEDAD system indicate that it could double or even triple desalinated water production. Experiments conducted at the pilot plant at KAUST have already increased fresh water production by more than 50 percent. This represents the highest water production ever reported for a desalination technique and earned the team a GE-Aramco “Global Innovation Challenge” award in January 2015.

The breakthrough also helps extend the lower end of the temperature range at which the system can operate, which has been a major limitation with MED in the past. “This represents a major leap forward in water production using thermallydriven cycles, and it is attributed to the excellent thermodynamic synergy between MED and AD cycles,” noted Ng. “We believe it can be developed fully to an extent where the energy efficiency of desalination can meet the target needed for sustainability.”

“The best part about AD is that it can be run at low temperatures and low pressures,” explained Ng. “In fact, we can run cycles at only 7°C and at a pressure of 2 kPa. This presents a unique opportunity to exploit the renewable energy resources that the Kingdom has— namely solar and geothermal energy— to run the system. Also, because we are ISSUE TWO

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Molecular immunity from microbes Harnessing a bacterial system of defense can protect plants against viral pathogens.

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new molecular biology tool derived from a bacterial defense system has been used for the first time by researchers to demonstrate a novel way to protect plants against viral pathogens1. Viruses are a major cause of crop disease, and infection by them results in enormous financial losses each year. They consist only of genetic material (DNA or RNA) surrounded by a protective coat. Lacking any cellular machinery of their own, they exploit the mechanisms of their host cells to replicate. In bacteria, the “CRISPR/Cas9” system provides immunity to DNA-based viruses by recognizing and disrupting their DNA. It is also rapidly gaining prominence as an effective new tool of modern molecular biology as a means to induce mutations and therefore novel characteristics in plant breeding. The KAUST team, which was led by Assistant Professor Magdy Mahfouz, introduced the Cas9 component—an enzyme capable of cleaving DNA—into tobacco plants. The team also engineered the plants to contain a short molecule known as a “sgRNA,” which is designed to complement part of the DNA sequence of the tomato yellow leaf curl virus (TYLCV). When the plants were infected with TYLCV, the sgRNA directed the Cas9 16

The tobacco plant Nicotiana benthamiana has been engineered to include the CRISPR/Cas9 system that provides resistance to tomato yellow leaf curl virus.

enzyme to attack the viral DNA, preventing it from replicating and significantly reducing disease symptoms. Protection against TYLCV, a significant scourge of tomato crops, was only the first step. The researchers next engineered plants with multiple identical sgRNAs. This process generated even stronger resistance to TYLCV, an effect they termed multiplexing. They finally inserted a new sgRNA matching the geminiviruses, a whole family of viruses, thereby providing simultaneous protection against multiple diseases. The research demonstrates that this simple microbial system can provide crop plants with a powerful defense against multiple invading viruses. The system can even be fine-tuned to defend against newly emerging viral strains simply by tweaking the sgRNA used. Mahfouz notes that the work also

provides insights into the molecular mechanisms of natural virus resistance in plants. Identifying the missing pieces in the puzzle will “help us to generate plants that are resistant to viruses while remaining free of foreign DNA,” he said. “Such engineered plants would avoid the regulatory hurdles surrounding genetic modification and be more acceptable to a GM-averse public.” The next step for the KAUST team is to modify the system to work on RNAbased as well as DNA-based viruses. Mahfouz is confident that this more difficult challenge is also surmountable. “It is only a matter of time,” he noted. 1. Ali, Z., Abulfaraj, A., Idris, A., Ali, S., Tashkandi, M., Mahfouz, M.M. CRISPR/Cas9-mediated viral interference in plants. Genome Biology 16: 238 (2015).


The sea sponge Stylissa carteri may have potential for antiviral compounds.

Antivirals waiting to be discovered in coral reefs The Red Sea may be a treasure chest of potential new drugs.

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he Red Sea coral reefs have long attracted visitors from around the world, but what if a cure for deadly infectious diseases were also to be found in the teeming undersea ecosystems? Now, researchers may have taken the first step towards potential new treatments for HIV using compounds naturally

produced by the sea sponge Stylissa carteri, also known as the “elephant ear” sponge.1 Their findings open a new discovery route in antiviral drugs by using naturally existing compounds that have been largely overlooked. Professor Christian Voolstra from the Red Sea Research Center at KAUST said

the coral reefs of the Red Sea are a potential treasure chest of treatments, teeming with organisms that have their own natural defense systems. “Most drugs we have are bioactives discovered from a natural source, but in the 70s and 80s there was this idea that everything could be synthesized,” he said. “Now we are realizing we have to go back to these ecosystems because they developed these molecules over millions of years and they have stood the test of time.” Voolstra noted many of the molecules had already been identified as potential cancer treatments but were abandoned when they were not successful. In their research, the team collected the elephant ear specimens from different coral reefs in the Red Sea. From these samples they characterized the antiviral mechanism for three compounds—ebromohymenialdisine (DBH), hymenialdisine (HD) and oroidin—that had already been identified, essentially taking them off the shelf for testing. Both DBH and HD suppressed some viral replication but were toxic to cells. Oroidin, on the other hand, inhibited the reverse transcription of HIV by up to 90 percent with no toxic effect on other cells, providing a promising starting point for development as an effective treatment. With more than an estimated 35.3 million people infected and living with HIV, alternative medications are in acute demand. “Our results show that we need to screen a number of compounds to find the best starting materials and go with them,” Voolstra said. Sponges are promising for investigation because they host significant levels of bacteria with great potential for these to be isolated and used for mass scale production. “Sponge is essentially an ecosystem for bacteria, as it has many crevices and cavities that make it a perfect place for bacteria to thrive,” Voolstra said. 1. O’Rourke A., Kremb S., Bader T.M., Helfer M., Schmitt-Kopplin P. et al. Alkaloids from the sponge Stylissa carteri present prospective scaffolds for the inhibition of Human Immunodeficiency Virus 1 (HIV-1). Marine Drugs 14, 28-38 (2016).

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2015 Linda Polik

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Plasmodium rosette: Pain and collaborators have recently identified Plasmodium knowlesi to be the most genetically diverse of the human malaria-causing Plasmodium species.

Pathogen expertise boosted with latest genomics

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iseases such as malaria and tuberculosis, which are caused by parasites and bacteria, respectively, significantly affect human and animal health and also impact national economies across the globe. The emergence and rapid spread of drug resistance heightens the pressing need to fully understand the origins and complex genetic diversity of pathogenic micro-organisms. The Middle East faces a particular 18

challenge: genomic descriptions of pathogens relevant to the area are historically under-represented in the scientific literature. For Arnab Pain, an expert in pathogen genomics, the opportunity to play a lead role in this science underpinned his decision to become a founding member of the faculty at KAUST. “There is a major gap in our knowledge of pathogens stemming from the Middle East and North Africa (MENA)

region,” noted Pain. “State-of-the-art genomic technologies have not been applied systematically to study pathogens affecting humans, animals and plants in this area, and samples from these countries are limited in most global genomic diversity studies.” Pain believes that KAUST can play a pivotal role in future global studies on pathogen genomics because of its location and world-class facilities. The facilities have supported his pioneering

2016 David Ferguson, Oxford University

Expert knowledge in the field of DNA and RNA sequencing puts KAUST at the forefront of high-impact pathogen research.


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“There is a major gap in our knowledge of pathogens stemming from the Middle East and North Africa.” “Understanding the DNA and RNA building blocks of these pathogenic organisms is critical to revealing how they have evolved and how they thrive,” Pain explained. “We are using the latest DNA and RNA sequencing techniques coupled with functional genomics and bioinformatics tools. A better understanding of pathogen biology could lead to new intervention strategies.” By providing insights into the genetic make-up of individual pathogens, deep sequencing techniques enable the researchers to piece together the dynamics of natural genome variation and gene functioning within a species. In a recent whole-genome study of Plasmodium knowlesi, which causes severe zoonotic malaria in Southeast Asia, Pain and his collaborators revealed that the parasite is considerably more genetically diverse than the three other human malaria-causing Plasmodium species in the world. Another of Pain’s collaborations was the first to achieve a continuous culture of P. knowlesi in human red blood

cells, providing a model to help understand how the parasite adapts to infect humans. The researchers subsequently discovered a parasite gene that determines the infectivity of P. knowlesi in human red cells. Pain and colleagues have also shown how the malaria parasites have evolved from a group of photosynthetic marine algae called chromerids. The rise of drug-resistant strains of Mycobacterium tuberculosis (Mtb) is also of grave concern, noted Pain. He is co-leading a consortium of Mtb researchers involved in studies searching for the genetic hallmarks for drug resistance in strains of Mtb, uncovering the pathogenesis of Mtb and developing global genetic variation maps. Such extensive genomic detailing of Mtb species may ultimately lead to more effective treatments and early tracking of drug resistant strains. In addition to his research on parasites and pathogenic bacteria, Pain is helping to ensure that the recent rise in use of NGS technologies in clinical settings in other parts of the world is replicated in the MENA region. “Fast, accurate and cheap pathogen detection and NGS technology is revolutionizing microbiological testing and disease monitoring,” he said. “Routine testing by NGS is rapidly being adopted in clinical laboratories, and I strongly believe that promoting its use as widely as possible in the Middle East will hold enormous benefits for the area.” Pain is collaborating with clinical laboratories in Saudi Arabia with real clinical samples using NGS and associated bioinformatic analytical tools. Such initiatives will enable real-time, accurate identification of pathogens and the monitoring of the emergence of drug resistant strains or newly-evolving pathogens. For example, Pain’s team is conducting a study to characterize pathogens circulating during the Hajj pilgrimage in collaboration with the Saudi Ministry of Health. Pain’s ambition and expertise, coupled with KAUST’s state-of-the-art technology, will ensure the MENA region becomes a significant global center for pathogen research. ISSUE TWO

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work using high throughput next-generation sequencing (NGS) technologies for research on pathogen biology. Just as important, though, Pain feels, is the considerable time he has spent over the past five years in building a global collaborative network of researchers whose combined expertise can facilitate high-impact projects. Together with his team at KAUST, Pain is currently working to reveal the biology of apicomplexan parasites— single-celled organisms that cause diseases such as malaria, toxoplasmosis and gastrointestinal illnesses. The team is also investigating mycobacteria, which cause human and animal tuberculosis.


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Ready for the high seas?

Seagrass genome reveals the structural and physiological adaptations needed for plants to survive and thrive in the marine environment.

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eagrass is the quiet achiever. The bundles of foliage often found washed up on beaches come from one of the most productive members of the plant kingdom. The long, narrow, ribbon-like leaves provide food and shelter for marine animals and mitigate coastal erosion and greenhouse gas emissions by cushioning the impact of sea waves while capturing carbon dioxide from the atmosphere. Carlos Duarte and colleagues at the KAUST Red Sea Research Center have sequenced and analyzed the genome of Zostera marina, a widespread genus of seagrass found in temperate waters of the northern hemisphere1. Their results show that seagrass ancestors underwent several major evolutionary changes before they migrated from shallow ponds back into deep seas. The work is significant because the seagrass genome is the first marine flowering plant ever to be sequenced. “It took us more than seven years to disentangle the evolutionary code contained in the genome,” said Duarte. The findings have important implications for a range of pressing issues, including food security, climate change and marine conservation. The researchers obtained a clone of Z. marina from the Archipelago Sea, which is located off the southwestern coast of Finland. They sequenced its genome using a combination of methods and identified 20,450 protein-coding genes, of which 86.6 percent were present in 20

the seagrass leaves, roots and flowers. By comparing the genome of Z. marina with that of its freshwater cousin Spirodela polyrhiza, the researchers concluded that the two genera diverged somewhere between 135 and 107 million years ago. In addition, they showed that Z. marina ancestors gave up genes that were superfluous in the marine environment—for example, genes for growing stomata (the leaf pores needed for transpiration), making terpenoids (organic compounds responsible for chemical communication, which are only useful if released in the atmosphere), detecting ethylene gas (signaling molecules essential for plant growth) and resisting ultraviolet radiation. Seagrass instead gained genes that improved tolerance to high salinity and gas and nutrient exchange across the leaves—for example, genes for strengthening cell walls, resisting osmotic stress and improving nutrient uptake in saltwater. Thanks to these evolutionary innovations, seagrass entered a world free of terrestrial competitors, insect pests, droughts, fires and weather extremities. Perhaps for these very reasons, seagrass thrived along rocky reefs, dominated all coastal waters and conquered the seven seas. Olsen, J. L., Rouzé, P., Verhelst, B., Lin, Y. C., Bayer, T. et al. The genome of the seagrass Zostera marina reveals angiosperm adaptation to the sea. Nature, 530, 331–335 (2016).


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Seagrass provides food and shelter for a wide range of marine organisms, including fish, crabs and turtles.

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Graphene powers up water purification Self-cleaning graphene-coated membranes remove water pollutants while harvesting energy from microbial decomposition.

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A new wastewater treatment system uses hollow fiber membranes coated with graphene to filter impurities from water and create hydrogen fuel.

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slight change in membrane layout can have a big “Several features in the reactor design and operation can impact on reducing biofouling in an advanced affect hydrogen production rates and fouling in the AnEMBR wastewater treatment system, a KAUST-led system, such as electrode spacing and operating voltages,” research team has found1. said Saikaly. “However, the specific cathode surface area typiMembrane bioreactors (MBRs) have become increasingly cally limits its performance, making it a key design factor popular for wastewater reclamation. MBRs use a mix of bac- for us.” teria to digest pollutants and porous membranes to sepaThe team produced two types of reactor configurations— rate bio-generated solids from clean water in a single tank. a rectangular layout where the anode faced opposite the cathode and a tubular shape where Despite the small footprint of this design, it requires significant energy the anode was stacked below the gra“The specific cathode to aerate the reactor and provide it phene membrane. Treatment trials with oxygen—an ingredient needed revealed that closely spaced rectansurface area typically for bacterial respiration and to control gular electrodes produced the highlimits its performance, the sticky fouling films that build up est amount of hydrogen bubbles and on membranes. significantly delayed membrane biomaking it a key design Krishna Katuri, Craig Werner and Pasfouling. factor for us.” To delve deeper into the reactor’s cal Saikaly from the University’s Water preference for rectangular shapes, Desalination and Reuse Center and colleagues from the KAUST Advanced Membranes & Porous the researchers used genomics to analyze any microbes Materials Center recently developed an alternative anaerobic developing on the membrane surfaces. These tools revealed electrochemical membrane bioreactor (AnEMBR) that works an abundance of methanogens on the tubular reactor that without oxygen. The device contains special electroactive bac- consumed hydrogen gas almost as fast as it was produced. teria that release electrons and protons at the anode when they Membranes in the rectangular reactors proved less hospitable digest organic matter. By driving electrons and protons to join to the micro-bugs. up into hydrogen gas at a cathode, enough clean-burning fuel Saikaly noted that these findings should help testing of real is recovered to power the entire treatment process. domestic wastewater by indicating how to optimize electrode To reduce space, the AnEMBR system contains long and configurations for low-conductivity solutions. porous hollow fibers that act as both catalytic cathodes and filtration membranes. However, the absence of oxygen in this 1. Werner, C. M., Katuri, K. P., Hari, A. R., Chen, W., Lai, Z. et al. technique made it challenging to control membrane foul- Graphene-Coated Hollow Fiber Membrane as the Cathode in Anaerobic ing. The team realized that hydrogen bubbles forming on the Electrochemical Membrane Bioreactors – Effect of Configuration and cathodes could self-scour biofilms off membrane surfaces if Applied Voltage on Performance and Membrane Fouling. Environmental gas generation rates were high enough. Science & Technology 50 (8), 4439–4447 (2016). I S S U E T W O 23


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Detailed analysis of nutrient distribution and circulation in the Red Sea could provide a model for the future of the world’s oceans.

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he health of oceanic ecosystems relies on a delicately balanced supply of nutrients, such as nitrogen and carbon distributed around the globe by oceanic, atmospheric and biological circulation. As the effects of global warming take hold, increased disruption of this precarious nutrient cycle is likely, with severe knock-on effects in the world’s oceans. Scientists at KAUST are collaborating 24

on research to understand and model nutrient cycling in the Red Sea, and aim to potentially provide a model for future healthy oceans. The Red Sea is located in an arid to semi-arid zone between Africa and Asia. With high levels of evaporation, a narrow opening to the Arabian Sea and no rivers to contribute nutrients from the surrounding land, the Red Sea is highly saline and nutrient poor—an ultra-oligotrophic environment. Organisms such as corals and photosynthetic plankton have adapted to thrive under these extreme conditions. As climate change takes hold, other ecosystems could become more like the Red Sea. “Similar oligotrophic environments are found in ocean basins—deep, isolated areas that are very difficult to reach,” said Carlos Duarte, a professor in the University’s Red Sea Research Center. “Despite

representing 70 percent of the world’s ocean environment, these systems are still poorly understood. It was only recently that we uncovered details of deep-sea carbon cycling in the Atlantic and Pacific, for example.” Duarte’s current research focuses on sources of nutrients for the Red Sea, including the role that dust from the surrounding deserts plays in propelling Red Sea productivity. Starting in early 2016, he plans to survey nutrient status in coastal habitats. Associate Professor Ibrahim Hoteit, who models oceanic and atmospheric circulation, focuses on nutrients driven by the Arabian monsoon. He has discovered that more intense monsoons, driven by global warming, could increase fertility in a warmer Red Sea thanks to an increased influx of nutrients imported from the Arabian Sea.

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The Red Sea models the future


BI OLOG I CAL A ND ENVI RO NM ENTAL S C IE NC E A N D E NG I NE E RIN G D IV I S IO N tolerance levels. Increased temperatures can reduce oxygen solubility in the water, added Duarte, which adds pressure on the marine creatures living there. There is also considerable value in understanding how photosynthetic plankton and other organisms have adapted to the extreme conditions of the Red Sea. “Low nutrient availability may actually reduce the stress generated by warming,” said Agusti. “I plan to analyze whether, by slowing the growth of photosynthetic plankton, low nutrient availability in the Red Sea provides a coping mechanism for warming. This would be disrupted if there were increased nutrient-rich influxes into the area.”

The Red Sea is highly saline with low nutrient availability, resulting in crystal clear waters. Coral reefs have adapted to thrive here, and the University’s researchers are examining these and other organisms to understand how they survive under such extreme conditions.

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Another crucial feature of the Red Sea ecosystem is the coral reefs, the research focus of Associate Professor Christian Voolstra. He investigates how the close relationship between corals and their algal and bacterial symbionts might be affected by changes in temperature and nutrient cycling. In a recent review paper, Voolstra’s team proposed that the control of nitrogen is vital to the functioning of corals. “Nitrogen is usually sparse in the Red Sea, and we think corals control their associated symbionts by restricting their nitrogen access,” Voolstra said. “With increased water temperatures and the associated influxes of nutrients, this delicate balance is disturbed, increasing coral disease and coral bleaching or the loss of the algal symbionts.” KAUST researchers are rising to the challenge of disentangling the complexities of such a dynamic system. Their efforts should pay off in providing a model of how alterations in nutrient cycling and temperature change may affect the world’s oceanic environments in the future.

KAUST is more than a premier university - we are a city that offers an exceptional quality of life.

“Model simulations provide an efficient way to investigate the link between the large-scale variability of the atmosphere and ocean and the flux of nutrients that control primary production,” Hoteit explained. “We also recently developed a 3-D-coupled physical-biological model that can simulate the pathways of dissolved inorganic nutrients, the fate of organic matter and how different groups of organisms—plankton and bacteria, for example—behave as a result.” Hoteit is also involved in a longer-term project with Duarte and Professor Susana Agusti, in which they are monitoring the effects of global warming on the Red Sea. Using 30 years of data from remote sensing satellites, the team has gathered evidence of abrupt temperature increases in surface waters since the early 1990s. Such dramatic temperature changes could push organisms beyond their current

“I plan to analyze whether, by slowing the growth of photosynthetic plankton, low nutrient availability in the Red Sea provides a coping mechanism for warming.”


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The adult mouse brain has small non-coding RNAs that help safeguard its genome stability during development.

From head to tail in search of piRNAs Small non-coding RNAs thought to be found only in testes are also present in the adult mouse brain.

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o avoid passing incorrect genetic information to their offspring, animals have evolved a number of protective mechanisms to maintain the integrity of their genomes. In particular, small non-coding RNAs known as piwi-interacting RNAs (piRNAs for short) help safeguard the genome by silencing transposable elements, mobile DNA sequences that, like 26

viruses, can alter, replicate and spread throughout the genome. Timothy Ravasi from the Biological and Environmental Science and Engineering Division and colleagues have now reported the presence of piRNAs in an unexpected place—the adult mouse brain1. Scientists first discovered piRNAs in germ cells, a type of cell found in testes

that gives rise to sperm cells. Recent studies have reported the presence of piRNAs in follicle cells of fruit fly ovaries and in the basal cells of monkey epididymides, but with the results still preliminary, these small non-coding RNAs were thought to be restricted to germ cells only. Ravasi and his team decided to look for piRNAs in mouse brain tissues at adult and two postnatal developmental stages. Using the latest sequencing technologies, the researchers could only confirm the expression of piRNAs in the adult mouse brain tissues. Further characterization revealed that mouse brains expressed piRNAs that are similar in size to those seen in mouse testes. However, the researchers could not detect the presence of mili, a certain type of piwi proteins that specifically bind mouse testicular piRNAs. In addition to the well-established role of silencing transposable elements, several studies have suggested that piRNAs may be involved in gene regulation. In light of this, the team used a novel approach that relied on RNA–target complementarity to seek out all potential targets of mouse brain piRNAs. They managed to identify 41 messenger RNA or mRNA targets, suggesting the potential involvement of mouse brain piRNAs in mRNA regulation. In mouse testes, piRNAs protect genome integrity by silencing the so-called L1 elements. Although L1 elements are active during brain development, whether or not they are silenced by piRNAs remains unanswered and warrants further investigation. The researchers believe their findings shed new light on the origin and functions of piRNAs, which is vital for the study of small non-coding RNAs. “The fact that piRNAs are expressed in adult brain cells suggests that a tight regulation of genome stability is necessary for normal development in mammals,” said Ravasi. 1. Ghosheh, Y., Seridi, L., Ryu, T., Takahashi, H., Orlando, V. et al. Characterization of piRNAs across postnatal development in mouse brain. Scientific Reports 6, 25039 (2016).

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Elements for Innovation KAUST i i o a io a c olo lo fo lic ďŹ ac a T c olo a i co loca i U i i o facili a co o a a i c olo transfer and entrepreneurship in support of economic development for the nation and the world. a i i co i f o o fac l KAUST i o i io o acc l a o al a a a a c olo i MEDAD is a water desalination start-up company founded by KAUST professor Kim Choon Ng in coordination with the National University of Singapore. The MEDAD technology offers a more efficient and sustainable solution for clean water.

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A clearer view of rainfall patterns Improved random modeling allows scientists to generate realistic patterns of high-frequency rainfall.

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thorough understanding of rainfall patterns is vital for the hydrological and agricultural models that are used to project flooding, stream flow and crop growth around the world. A study at KAUST has generated an accurate method for modeling precipitation events based on data from rain gauges in the United States1. Rainfall data are collected on different space-time scales depending on the instruments used. For example,


2016 Alamy

C O M P U TE R , E LEC TR ICAL A ND M ATH E M ATICA L S C I EN C E A N D EN G IN EERIN G DIV ISION satellites gather information on precipitation down to a resolution of around one square kilometer over days, while an individual rain gauge collects data from around one square meter as often as once every minute. The intermittent and random nature of rainfall events means that modeling a precipitation field is challenging, and the best models for simulating where and when rain might fall require a probabilistic element. Ying Sun from the University’s Computer, Electrical and Mathematical Science and Engineering Division and Michael Stein at the University of Chicago (U.S.) have developed a novel precipitation occurrence model that generates realistic patterns of rainfall events at multiple locations every 15 minutes. The researchers used high-quality

data gathered at rain gauges in Virginia, Maryland and North Carolina to develop their stochastic model. Stochastic modeling allows for random fluctuations in multiple simulations and provides a collection of possible outcomes that can help scientists understand rainfall variability across space and time. “Our model, a truncated non-Gaussian distribution, allows for areas to have zero rainfall and gives us a higher chance of simulating extreme values than in previous models,” said Sun. Sun’s model also uses a random field that connects all the sites and describes the spatial and temporal patterns, such as the tendency for one site to experience rainfall a few hours after another. “For example, if five sites out of 10 have rain, the random field model decides which five sites have

rain and how long it rains for at each site,” she said. “I used data detailing rain events at 15 minute intervals over three years to estimate the unknown parameters in my model, and I then generated multiple simulations from the estimated model,” explained Sun. “Because it includes more detail on the spatio-temporal patterns of rainfall events, our model produces more realistic rainfall occurrence patterns than other commonly used models.” The next challenge for Sun is to generate simulations of rainfall amounts for multiple sites so that model users can study the impact of both light and heavy rain. 1. Sun, Y. & Stein, M.L. A stochastic space-time model for intermittent precipitation occurrences. Annals of Applied Statistics. 9 (4), 2110-2132 (2015).

A statistical model developed by KAUST researchers enables the generation of realistic rainfall patterns that can help inform agricultural and land-use management.

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data analysis method to explore the signals from the brain generated by electroencephalograph (EEG) recordings has been developed by researchers from KAUST. “We hope to gain a better understanding of neuronal activity in the brain,� said Professor Ying Sun from the Computer, Electrical and Mathematical Science & Engineering Division at KAUST. Sun and her KAUST colleague Professor Marc Genton and co-workers led by Professor Hernando Ombao from UCI, U.S., believe their method may help clinicians detect and monitor conditions such as strokes1. An EEG uses sensors on the scalp to detect the changes in voltage caused by the electrical signals transmitted through the nerve cells in the brain. The EEG recording reveals a complex pattern of

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electrical waves of different frequencies and strengths. Changes in specific waves are associated with particular conditions such as strokes, epilepsy and tumors. Interpreting an EEG recording is challenging, especially when trying to identify significant abnormalities in the signals and the region of the brain from which they emanate. The researchers addressed the challenges using their novel functional boxplot approach. The boxplot is a classical method for analyzing complex data and depicting it graphically within boxed regions. In 2011, Sun and Genton unveiled a specific functional boxplot method suitable for analyzing large and complex sets of data (for example, from clinical settings). The KAUST team and colleagues at UCI have now shown that their method can

Figure adapted from that originally published in Ref 1Š 2015 Frontiers Media.

A statistical method helps to identify abnormal signals in electroencephalograms and locate their source in the brain.


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LEFT Pre-frontal Pre-motor Primary Motor Parietal Supplementary motor area Others Channel 197 A map of the EEG channels receiving signals from the scalp. The blue dots represent the pre-frontal channels; orange dots represent the pre-motor channels; light green dots represent the supplementary motor area; dark green dots represent the primary motor; and yellow dots represent the parietal area. The single bright orange dot is channel 197 and reflects activity roughly around the pre-motor area.

help interpret an EEG recording. The process generates spectral curves indicating the contribution from waves at different frequencies. Comparing the curves generated at different times and from different sensors can aid with identifying events in brain activity that deviate from what is expected in the normal state. The clinical significance of the deviation can then be explored. “Our colleague Steven Cramer, a

neurologist and stroke expert at the University of California, is excited about the possible use of this method in clinical research and practice,” Sun said. She explained that the method could help to monitor patients immediately after strokes. This could greatly assist in rehabilitation, helping to predict and guide the recovery of movement and other functions after strokes occur. “The analysis of other clinical data, such

as MRI scans or optical tests, could also benefit from our approach,” she added. Future work will explore other possibilities and will expand the EEG analysis to more patients to refine the procedure. 1. Ngo, D., Sun, Y., Genton, M.G., Wu, J., Srinivasan, R. et al. An exploratory data analysis of electroencephalograms using the functional boxplots approach. Frontiers in Neuroscience 9, 282 (2015).

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The flexible temperature array was made by drawing a resistor structure with a silver conductive ink pen on Post-it paper.

Artificial skin sensors made from sticky notes A paper-based sensor that mimics the sensory functions of human skin has been developed for the first time from low-cost and commonly available household materials.

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veryday materials from the kitchen drawer, such as aluminum foil, sticky note paper, sponges and tape, have been used by a team of electrical engineers to develop a low-cost sensor that can detect external stimuli, including touch, pressure, temperature, acidity and humidity. The sensor, which is called Paper Skin, performs as well as other artificial skin applications currently being developed while integrating multiple functions using cost-effective materials1. “This work has the potential to revolutionize the electronics industry and opens the door to commercializing 32

affordable high-performance sensing devices,” stated Muhammad Mustafa Hussain from the University’s Computer, Electrical and Mathematical Science and Engineering Division, where the research was conducted. Wearable and flexible electronics show promise for a variety of applications, such as wireless monitoring of patient health and touch-free computer interfaces. Current research in this direction employs expensive and sophisticated materials and processes. However, the KAUST team used sticky note paper to detect humidity, sponges and wipes to detect pressure and aluminum foil to detect motion. Coloring

a sticky note with an HB pencil allowed the paper to detect acidity levels, and aluminum foil and conductive silver ink were used to detect temperature differences. The materials were put together into a simple paperbased platform that was then connected to a device that detected changes in electrical conductivity according to external stimuli. Increasing levels of humidity, for example, increased the platform’s ability to store an electrical charge, or its capacitance. Exposing the sensor to an acidic solution increased its resistance, while exposing it to an alkaline solution decreased it. Voltage changes were detected with temperature changes. Bringing a finger closer to the platform disturbed its electromagnetic field, decreasing its capacitance. The team leveraged the various properties of the materials they used, including their porosity, adsorption, elasticity and dimensions, to develop the low-cost sensory platform. They also demonstrated that a single integrated platform could simultaneously detect multiple stimuli in real time. Several challenges must be overcome before a fully autonomous, flexible and multifunctional sensory platform becomes commercially achievable, explained Hussain. Wireless interaction with the paper skin needs to be developed. Reliability tests also need to be conducted to assess how long the sensor can last and how good its performance is under severe bending conditions. “The next stage will be to optimize the sensor’s integration on this platform for applications in medical monitoring systems. The flexible and conformal sensory platform will enable simultaneous real-time monitoring of body vital signs, such as heart rate, blood pressure, breathing patterns and movement,” Hussain said. 1. Nassar, J.M., Cordero, M.D., Kutbee, A.T., Karimi, M.A., Torres Sevillla, G.A. et al. Paper Skin Multisensory Platform for Simultaneous Environmental Monitoring. Adv. Mater. Technol., 1 (2016).

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Exploiting the properties of disordered, chaotic systems leads to low-cost energy harvesting and innovative micro-surgery applications.

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ost researchers actively try to suppress disordered states such as background static, as they lead to unpredictable experimental results. However, recent findings from researchers at KAUST reveal that the built-up energy inside chaotic systems can be tapped using optical waves and nanofabrication. This approach has led to producing the darkest material ever seen on Earth—a T-shaped nanoparticle with record-setting potential to store and release light energy. “Sometimes our research is described as complex, but it is actually quite simple,” explained Andrea Fratalocchi, assistant professor of electrical engineering at KAUST. “We just follow the evolution of nature and what we see around us.” In this manner, white beetles of the genus Cyphochilus and natural thermodynamic phenomena became the inspiration behind the discovery of an advanced light trapping material. Fratalocchi leads a team that seeks to understand and design three-dimensional systems that automatically optimize their energy trapping. As an example, he discusses the problem of delivering a precise microgram quantity of a drug powder. “Too much and the patient dies, a little less and it has no effect. If there is no scale capable of weighing such a small amount precisely, what would you do?” The answer, he explains, is to dissolve the powder in water and use the natural tendency of molecules to move via random Brownian motion uniformly throughout the liquid. A volume containing the exact dosage can then be extracted. This diffusion process makes this system’s entropy—a parameter that quantifies thermodynamic disorder—increase irreversibly towards its maximum value. “This is an extremely powerful effect that works every time regardless of the size and shape of a container,” Fratalocchi noted. “It’s so ubiquitous we think of

it as simple, but it is actually based on very complex chaotic dynamics.” Chaotic energy harvesting, he continued, can function the same way. “Think of the powder as being light and the container is an optical resonator, or a cavity that stores light energy,” he said. The team’s resonators make photons move wildly and irreparably so that the system’s entropy increases and condenses the maximum amount of scattered light within a single second. Fratalocchi and the team combined theoretical simulations and polystyrene microspheres to put their strategy into

“We had an idea based on a beetle that uses extremely white scales to reflect light as a form of camouflage,” Fratalocchi said. “By reversing this effect with chaotic structures, we could harvest a lot of energy and create an ultra-dark material.” Liu’s simulations revealed that the nanosphere–nanorod structures had near ideal scattering behavior, and when the team dispersed them in water the liquid turned completely black—so dark, in fact, that 99 percent of incoming light was captured. The black body turned into a new source of monochromatic light following laser excitation.

“We had an idea based on a beetle that uses extremely white scales to reflect light as a form of camouflage.” practice. They discovered that by deforming the microspheres with mechanical pressure, light could scatter chaotically for significantly enhanced energy harvesting—the device held over 600 percent more energy than a similarly sized classical system. The researchers’ next target was to fabricate a perfect black body, a material that absorbs and emits large quantities of radiation. This technology could lead to new light and thermal energy sources, but the team’s early designs relied on complex structures that were extremely difficult to fabricate. One day, however, a tennis match between Changxu Liu from Fratalocchi’s lab and Jianfeng Huang, a chemist working with KAUST professor Yu Han, turned out to be more than just a sociable workout. Discussing their research as they played, the students realized that new particles synthesized by Huang consisting of nanospheres attached to nanorods might be used for a simpler bio-inspired approach to creating a black body device.

Another successful collaboration, although this one a bit more intentionally developed, involves Frederico Capaso from Harvard University. Together, Fratalocchi and Capaso are working on new types of plasmonic materials. The ultimate goal of improved energy harvesting has several applications from solar energy to commercial paint. Finally, dielectric metamaterials that manipulate light are another target for Fratalocchi’s group. He and his team developed the concept of rogue wavebased devices that arrange photonic crystals into stadium-shaped arrangements on a microchip. Chaotic waves in these devices can build up until they release a localized waveform with exceptional amplitude, an energy localization akin to natural events such as hurricanes. “This can permanently change how we look at catastrophic events,” Fratalocchi said. “Imagine if we develop a system where we can transport energy in extremely large quantities like a tsunami wave, or where we create anomalous giant amplitude waves localized at the nanoscale for extremely precise microsurgery and new imaging techniques. These ideas are not fiction but fully possible science.” I S S U E T W O 35


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A picture of the artist captured in a stroke A graphics technique is the first to identify people based on their sketching style.

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novel method can break down sketches into individual strokes and mathematically calculate the frequency of each kind of stroke to identify the sketch’s author. Called stroke authorship recognition (SAR), the technique could prove useful in detecting fraudulent artwork and in assessing the progress of artists-intraining. KAUST researchers used a widely available graphics design software tool to decompose sketches into strokes to form a dictionary of basic strokes 1. Their method takes a sketch, decomposes it to strokes and then identifies the frequency with which various strokes from the dictionary are used. The various frequencies are depicted in a histogram. Because artists use 36

different types of strokes with different frequencies, each histogram is unique to a specific artist. The team commissioned sketches by 10 professional artists specifically for the study. They also asked nine of the artists to imitate the sketches of the tenth to simulate sketch fraud. In an online survey, 2,000 participants were shown some of the sketches and told to whom each belonged. Then they were shown an additional sketch and asked to identify which artist drew it. Answers chosen completely at random give an average accuracy of 10 percent. The survey respondents were able to recognize the correct sketch author with an average accuracy of 29 percent. SAR was able to identify the correct artist with an accuracy of 56 percent.

SAR also did much better than 25 experienced artists in recognizing fraudulent from original sketches. “The results show that SAR can significantly outperform humans in discriminating sketch style and detecting fraudulent sketches,” stated Bernard Ghanem from the University’s Visual Computing Center. In addition to detecting art fraud, the method could also be used to assess the progress of artists-in-training. Artists working in large corporations like the Walt Disney Company are often trained to emulate a specific drawing style. SAR could help trainers assess how well trainees are progressing in emulating the desired drawing style. The team has made SAR’s code openly available to encourage further research they say is needed to improve the method’s accuracy. The team next aims to analyze how artists generate strokes by tracking their hand movements while sketching. “We believe this will provide us with more information about an artist’s sketching style,” Ghanem said. 1. Shaheen, S., Rockwood, A., Ghanem, B. SAR: Stroke authorship recognition. Computer Graphics Forum 0, 1-15 (2015).

2015 KAUST

Sketches by three of the 10 artists commissioned for the study.


2015 KAUST

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Sensors for a light touch Biocompatible tactile sensors based on magnetic hair-like structures enable new applications for touch sensors.

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ighly sensitive tactile sensors that can mimic the touch sensitivity of human skin have been developed by researchers from KAUST. Tactile sensors can be used in a range of applications from artificial skins to energy generation. Typically they are made out of materials that change their electrical resistance or create an electrical voltage when touched. However, these materials often lack the minute sensitivity and dynamic range needed for more advanced applications. These high sensitivities can be achieved through sensors that mimic the function of cilia, which are small hairlike structures that line the human inner ear and that insects have on their legs to sense vibrations. “The bio-inspired sensors feature hairlike structures that are implemented in a compact design and operate with ultralow power consumption,” said Associate Professor Jürgen Kosel1. The tactile sensors developed by Ph.D. student Ahmed Alfadhel and Kosel consist of iron magnetic

The tactile sensors consist of iron nanowires embedded in an elastic polymer matrix that is shaped to form the hairs.

nanowires embedded in an elastic polymer matrix that is shaped to form the hairs. If the hairs are bent, these nanowires change the relative orientation to the substrate to which the hairs are anchored. This also shifts the orientation of the nanowire magnetic field. A magnetic sensor that is embedded into the substrate detects these orientation changes and converts them into an electrical signal. Unlike previous tactile sensor designs, the magnetic fields do not require an electrical connection to the individual hairs. In addition, the sensors are able to pick up tiny changes in the magnetic field, giving these sensors the potential for acute sensitivity, although the sensitivity of the devices and the forces that they can detect depends on their design. Some of the devices have been shown to react to small perturbations equivalent

to the detection of a small fly landing on skin. As the sensors operate by remote sensing of the magnetic fields, their power consumption is extremely low at only about 0.08 microWatts. The sensors can be fabricated on flexible substrates to be used, for example, as artificial skins. They work in air and in liquids, and the biocompatibility of both the polymer and the iron nanowires means the sensors can also be used for applications inside the body, Kosel explained. The researchers plan to envelop a surgical instrument with the tactile sensor so surgeons will be able to “feel” tissue as they move the instrument through an artery. 1. Alfadhel, A. & Kosel, J. Magnetic Nanocomposite Cilia Tactile Sensor. Advanced Materials 27 (47), 7888–7892 (2015)

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Wireless devices tune-in to cloud power Next-generation mobile networks can use cloud computing algorithms to manage the increasingly high data demands of users.

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ifth-generation (5G) cellular technologies will provide gigabits-per-second connection speeds to customers and innovative infrastructure such as self-driving cars. KAUST researchers have now developed a platform that coordinates 5G data traffic more efficiently using cloud-radio access networks (CRANs)1. The CRAN concept fundamentally restructures the way network resources are allocated. Current radio access networks use computers at each antenna station to assign resource blocks for data transfer—a setup that produces


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Norbert-Zsolt Suto / Alamy Stock Photo

A cloud-based algorithm for moving data between users and base-station (BS) antennas could yield gigabit-per-second download speeds.

interference when different base-stations re-use the same spectrum. With CRANs, algorithms for resource block assignment and power allocation are implemented via a central cloud-based server that uses shared processing power to boost data transmission across the entire network. One challenge with CRANs lies in coordinating cloud-based problem solving with the substantial communication volumes that stream across “backhaul” links connecting cell sites to the core network. Ahmed Douik, Tareq Al-Naffouri and Mohamed-Slim Alouini from KAUST and Hayssam Dahrouj from Effat University investigated an alternative CRAN that uses the cloud to solve a particular allocation problem—how to schedule users to resource blocks and simultaneously optimizing transmitter power while giving base-stations control over other radio resources, such as signal processing.

To avoid searching all possible userto-resource blocks assignments, the researchers modeled the associations between users, base-stations and power levels as interconnected points, or vertices, on a graph. By assigning different weights to the vertices using a sum benefits analysis and accounting for practical physical constraints, they created a program that quickly scopes out the essential features of a CRAN and solves the joint scheduling and power control problem with efficient algorithms. “These algorithms are centralized in nature and require strong computing processors, which make the cloud a necessity,” said Dahrouj. “The cloud provides the right platform for graph-theoretical based computations and helped us find the jointly global optimal solution for the first time.”

Surprisingly, the team observed an appreciable gain in data throughput by solving the network problem jointly. Previous simulations that calculated parameters separately and then iterated back and forth between solutions could not discern the true advantages of the global optimum. “The wireless communications industry is at a critical inflection point where mobile internet enabled by smart phones and mobile computing devices is driving data usage higher and higher,” noted Dahrouj. “Our graph theoretical approach can be reformulated to solve several resource allocation problems in CRANs, such as channel assignment and antenna selection.” 1. Douik, A., Dahrouj, H., Al-Naffouri, T.Y., Alouini, M-S. Coordinated Scheduling and Power Control in Cloud-Radio Access Networks. IEEE Transactions on Wireless Communications 15(4): 2523-2536 (2016).

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A new mathematical model explains how random factors affect the production of proteins within the cells.

Study lead author Xin Gao from the University’s Computational Bioscience Research Center works on the new mathematical model at KAUST.

AUST researchers have developed a new mathematical model that makes the complex process of synthesizing proteins from the genes that encode them more predictable. The multi-step synthesis pathway, which is mediated by RNA molecules, can be affected by random events, creating bursts of protein production. The KAUST model captures the factors that make this “noise” in protein production and that may provide insights into how genes are controlled and how they evolved1. Protein synthesis consists of two main stages: transcription of the genetic code into messenger RNA (mRNA) molecules and translation of the mRNA into proteins. Study lead author Xin Gao from the University’s Computational Bioscience Research Center (CBRC) explained that this is a stochastic process that “leads to variability in the abundance of gene products (RNAs or proteins) in a single cell through time or among genetically identical cells,” he said.

This variability can have far-reaching effects on the evolution and function of cells such as cancer cells and microbial pathogens—including their capacity for drug resistance. “Bursts” of translation are thought to be the main cause of variability, especially in simple organisms like bacteria, where there are often only small amounts of mRNA. However, translation itself comprises multiple steps, including initiation, elongation and termination. Previous models treated initiation as the only rate-limiting step in protein production, but this may not always be realistic. “Our study was inspired by recent research showing that translational efficiency can be strongly affected by the elongation steps under stress conditions, such as when drugs are applied to pathogens,” noted Gao. The KAUST team responded by developing the more sophisticated model that has the capacity to handle more general situations, including internal and external influences on translation. The model allows them to explore the different

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mechanisms regulating protein production and showed that the distribution of the translational burst can have a strong impact on the features and fitness of a cell. The team anticipates that their model might provide insights into cells’ responses to stress, which rely on changes in protein abundance. “We had planned to analyze the association between stress and gene expression noise using experimental data, but we found we needed the theoretical model that is more general than previous models,” Gao said. The research might also be applicable to more complex organisms. “Recent studies have shown that stress conditions can have strong effects on translation in yeast and plants, and so protein burst size distributions could have effects on their protein abundance levels,” stated Gao. 1. Kuwahara, H., Arold, S.T. & Gao, X. Beyond initiation-limited translational bursting: the effects of burst size distributions on the stability of gene expression. Integrative Biology 7, 1622-1632 (2015).

2016 KAUST

Noisy cells produce bursts of protein


C O M P U TE R , E LEC TR ICAL A ND M ATH E M ATICA L S C I EN C E A N D EN G IN EERIN G DIV ISION

A new biosensor made of laser-etched electrodes on a goldcoated polymer may provide an effective and cost-efficient way to assess heart disease risk.

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flexible device that can be used as a biosensing tool has been developed by researchers at KAUST. The low-cost method for manufacturing the tool involves sputtering a 600-nanometer layer of gold on to a small sheet made of a common plastic known as polyethylene terephthalate (PET)1. The gold layer is etched by laser to make parallel gold electrodes across the PET surface. The sheet is then coated to insulate and protect it from moisture. This gold interdigitated electrode array (IDE) was made in an inexpensive setup without the use of clean room facilities. Antibodies specific to C-reactive protein (CRP), a protein made in the liver

Shilpa Sivashankar and Ulrich Buttner depositing CRP on their biosensor chip and testing it under the microscope using an electrical probe station.

in reaction to tissue injury and inflammation, were then spread in a thin film across the IDE and attached to the surface of tiny beads, allowing more sites for the CRP to connect to. Postdoctoral fellow Shilpa Sivashankar from the Computer, Electrical and Mathematical Science and Engineering Division, said this was the first time that beads were used to improve the performance of gold IDEs. The team, led by principal investigator Khaled Salama, found that the sensor was able to quantify various amounts of CRP in serum. When the CRP interacted with the antibody, a change of capacitance was detected that increased with higher levels of CRP. Salama pointed to the example of commonly used biosensors, such as pregnancy tests and diabetic monitoring devices. “Having access to cheap, easyto-use sensors is important,” he said. “If we can extend the range of devices to include other biomarkers, we could help improve the healthcare spectrum. There is still room to improve the miniaturization and sensitivity of detection

of various biomarkers that are known to be associated with certain diseases,” he added. Research has shown that CRP serum concentrations can be used to assess the risk for cardiac disease where CRP concentrations above 3 mg per liter of blood indicate a high risk. “The hope is to have these devices used in the field or at the point of care directly,” noted Salama. The team has filed to patent their flexible capacitive sensor. They also have seed funding to explore its use as a gas sensor. “Similar to biomarkers, there are chemical materials that are sensitive and selective to specific gases. Coating our sensor with these materials should allow us to detect volatile organic gases that may be hazardous,” explained coauthor Ulrich Buttner, a KAUST research scientist. 1. Sivashankar, S., Sapsanis, C., Buttner, U. & Salama, K.N. Flexible low-cost cardiovascular risk marker biosensor for point-of-care applications. Electronics Letters 51, 1746–1748 (2015).

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2015 KAUST

Miniature flexible sensor to detect heart disease


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Feeding in the moonlight Consistent around the world’s ocean, the phases of the moon affect the upward migration of the world’s most abundant type of fish for feeding.

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coustic data from the Malaspina research expedition, which circumnavigated the earth’s oceans between December 2010 and July 2011, shows that a full moon causes fish to stay at deeper levels. Data analyzed by KAUST doctoral student Perdana Prihartato showed that the effect was consistent around the globe despite changes in environmental conditions and varying types of species in different parts of each ocean1.

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Acoustic data showed that the fish were deepest at 75 percent or more full moon, although the mean depths were not significantly different across the four moon phases.

Previous research indicated that fish that occupy the mesopelagic zone (between 200 to 1000 meters) will avoid feeding on plankton available in relatively shallower waters on moonlit nights, possibly to avoid being eaten themselves by larger marine animals. Yet the effect was not a linear one, explained Marine Scientist Stein Kaartvedt. Contrary to their initial expectations, the team did not find the shallowest distribution of mesopelagic fish during the darkest night at new moon. The researchers identified a threshold. “The distribution of organisms is unaffected by moonlight until a critical value is reached—about 70 percent full moon— after which they dive so as not to be seen by predators,” explained Kaartvedt. The study illustrates the benefits of interdisciplinary research between statisticians and, in this case, marine

scientists, said Marc Genton, professor of statistics. “Statisticians get access to very unique datasets that may trigger the development of new statistical methodologies, and the marine scientists get more robust and reliable results from the data they collect,” he explained. The data was collected using echosounders, which produce sound waves similar to those used by submarines to see through the ocean. Mesopelagic fish are so abundant that they produce what looks like a layer in the ocean waters. This layer moves upwards as the fish migrate towards the surface to feed or downwards to hide from predatory creatures. This movement and feeding contribute to bringing carbon dioxide from the surface to deeper layers, supplying food for deeper-living organisms and storing it away from the Earth’s atmosphere.

“It is important to know how such a significant component of the ecosystem distributes and behaves in order to understand the functions of the oceans,” said Professor of Marine Science Xabier Irigoien. Team members from the KAUST Red Sea Research Center are currently analyzing acoustic data from the same expedition regarding the potential impact of oxygen on the daytime distribution of mesopelagic fish. Their future research will analyze the effect of water clarity on the distribution of mesopelagic fish, especially as it relates to oxygen-depleted zones in the world’s oceans. 1. Prihartato, P.K., Irigoien, I., Genton, M.G., Kaartvedt, S. Global effects of moon phase on nocturnal acoustic scattering layers. Marine Ecology Progress Series 544, 65–75 (2016).

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Molecular beam epitaxy was used to lay down titanium and then titanium nitride on a molybdenum substrate.

Taking the heat out of emitters

Semiconductor light-emitting diodes fabricated on a metal substrate are less prone to overheating.

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icrometer-scale light emitters that can be incorporated into electronic chips could enable faster computation and communication systems in compact devices. Researchers at KAUST have developed a simple technique for fabricating optically active semiconductors on a metal substrate, showing that the devices work at room temperature and do not overheat. The success of the modern electronics industry rests on the ability to fabricate thousands of electronic components on a single silicon chip. Optical devices could 44

benefit in the same way from such an integrated-circuit approach, enabling a cheaper platform for optical communications or portable optical sensors. However, silicon is not the ideal material for optical applications, so an alternative material is required. Chao Zhao, TienKhee Ng, Boon Ooi and colleagues from the Computer, Electrical and Mathematical Science and Engineering Division used the semiconductor gallium nitride to develop a platform for high-power light emission1. “Nitride-based materials have been intensively studied for photonics

applications such as solid-state lighting and displays because the alloys have direct bandgaps that cover the entire visible spectrum,” explained Zhao. Gallium nitride-based structures have been created on silicon, sapphire and glass substrates. These materials are flawed, however, because they impair heat flow out of the device, causing a rise in temperature that eventually leads to malfunction. The KAUST team fabricated galliumnitride nanowires on a metal substrate instead; this substrate has better thermal properties. They started with a molybdenum substrate on which they laid down titanium and then titanium nitride using a technique called molecular beam epitaxy. The light-emitting region itself was built up of alternating layers of gallium nitride and indium gallium nitride. This material self-assembled into vertical nanowires with diameters between 40 and 110 nanometers and 300 nanometers long. Each light-emitting diode incorporated many of these nanowires in a cylinder 200 micrometers across. With better thermal properties than previously studied substrates, molybdenum can also act as the bottom electrical contact required to power the devices. This simplified the construction of the final devices. The red light emitting diode worked at room temperature and exhibited no signs of overheating. For example, the researchers observed no drop in operation efficiency (known as thermal droop) as the current through the device increased. The emission color from the device also did not shift. “Our work revolutionizes the semiconductor crystal growth technology and also realizes a practical platform for high-power nanowires light-emitters,” stated Zhao. “This uncovers new applications in high-power optoelectronics, high-speed and power electronics, display technology, energy conversion and green technologies.” 1. Zhao, C., Ng, T. K., Wei, N., Prabaswara, A., Alias, M. S. et al. Facile formation of high-quality InGaN/ GaN quantum-disks-in-nanowires on bulk-metal substrates for high-power light-emitters. Nano Letters 16, 1056-1063 (2016).

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Elements for Innovation KAUST has a distinctly global DNA that bridges people, ideas and traditions from around the world. We come from over 100 different countries and collaborate with academic communities across the globe. Together, we make discoveries for the welfare of society and are committed o a a c of ci iďŹ c o l i a cial foc o i o a i a a of lo al i iďŹ ca c foo a a io

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Burning a better biofuel Chemical reaction modeling and combustion experiments reveal how 2-methylbutanol would behave in advanced engines.

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A high-pressure shock tube more than 13 meters long can reveal how fuels burn at very high pressures.

next-generation biofuel has promising combustion properties that could make it a viable replacement for conventional fossil fuels, suggests a modeling study by researchers from KAUST1. Burning traditional liquid fuels such as gasoline produces the greenhouse gas carbon dioxide and particles and nitrogen oxide gases that can harm human health. Fuels containing oxygen atoms can reduce these emissions if they are produced from renewable resources—by fermenting plant sugars into ethanol, for example—they can further offset carbon dioxide emissions. Ethanol, however, is a short-chain alcohol, which leads to practical problems. It has a relatively low energy density and can be difficult to store because it readily absorbs water. “Longer-chain alcohols could significantly increase the biofuel content in blended fuels due to their higher energy content, better engine compatibility and lower water solubility,” noted Mani Sarathy of the University’s Clean Combustion Research Center. Sarathy’s team studied the combustion of a longer-chain bio-derived alcohol called 2-methylbutanol to reveal how it would burn in clean, fuel-flexible and efficient engines that operate at higher pressures than today’s engines. The researchers measured 2-methylbutanol’s laminar flame speed, which indicates how quickly the fuel mixture burns after ignition, and found similar results to conventional liquid fuels. They also burned 2-methylbutanol in a high-pressure shock tube that can heat and compress a mixture of fuel and air almost instantaneously. They tested three

different fuel concentrations at pressures of 20 bar and 40 bar and temperatures from 477 to 977 degrees Celsius. At intermediate temperatures, the time delay between compression and ignition was similar to another longer-chain alcohol called isopentanol. Ignition was faster, however, at higher temperatures, suggesting that 2-methylbutanol would be suitable for use in compression-ignition engines similar to those that burn diesel. The team also created a computational model of all the chemical reactions involved in combustion that contained 469 different molecules and 2504 reactions. “We need this comprehensive set of chemical reactions and their rates to be able to accurately predict the rate of energy release, soot and pollutant formation, ignition behavior and flame characteristics,” said Sarathy. “This can represent how next-generation fuels behave in internal combustion engines.” The model identified a particularly significant low-temperature reaction between molecular oxygen and a reactive “radical” called -hydroxypentyl, which forms a stable aldehyde molecule and hydroperoxy radicals. Changes in this reaction’s rate had the most marked effect on the ignition delay. Having proved the value of the model, Sarathy hopes to adapt it to study the combustion properties of other biofuels under various engine conditions. 1. Park, S., Mannaa, O., Khaled, F., Bougacha, R., Mansour, M. S. et al. A comprehensive experimental and modeling study of 2-methylbutanol combustion. Combustion and Flame 162, 2166-2176 (2015).

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Faster, finer filtration

The right blend of polymers enables rapid and molecule-selective filtering of tiny particles from water.

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method of fabricating polymer membranes with nanometer-scale holes that overcomes some practical challenges has been demonstrated by KAUST researchers1,2. Porous membranes can filter pollutants from a liquid, and the smaller the holes, the finer the particles the membrane can remove. The KAUST team developed a block copolymer membrane with pores as small as 1.5 nanometers


P H YS ICAL S C IE N C E A ND E N G IN EERIN G DIVI SI ON

“We hope to optimize membranes for protein separation and other applications by changing the copolymer composition, synthesizing new polymers and mixing with additives.”

2016 KAUST

Professors Suzana Nunes and Klaus-Viktor Peinemann led the block copolymer studies.

but with increased water flux, the volume processed per hour by a membrane of a certain area. A nanofilter needs to be efficient at rejecting specific molecules, be producible on a large scale, filter liquid quickly and be resistant to fouling or the buildup of removed micropollutants on the surface. Block copolymers have emerged as a viable material for this application. Their characteristics allow them to

self-assemble into regular patterns that enable the creation of nanoporous materials with pores as small as 10 nanometers. However, reducing the size further to three nanometers has only been possible by post-treating the membrane (depositing gold, for example). Moreover, smaller holes usually reduce the water flux. Klaus-Viktor Peinemann from the Advanced Membranes and Porous Materials Center and Suzana Nunes from the Biological and Environmental Science and Engineering Division formed a multidisciplinary team to find a solution. “We mixed two block copolymers in a casting solution, tuning the process by choosing the right copolymer systems, solvents, casting conditions,” explained Haizhou Yu, a postdoctoral fellow in Peinemann’s group. This approach is an improvement on alternatives because it doesn’t require material post-treatment. Peinemann and colleagues blended polystyrene-b-poly(acrylic acid) and polystyrene-b-poly(4-vinylpyridine) in a ratio of six to one. This created a sponge-like layer with a 60 nanometer film on top. Material analysis showed that nanoscale pores formed spontaneously without the need for direct patterning. The researchers used their nanofiltration material to filter the biological molecule protoporphyrin IX from water. The

filter simultaneously allowed another molecule, lysine, to pass through, demonstrating its molecular selectivity. The researchers were able to filter 540 liters per hour for every square meter of membrane, which is approximately 10 times faster than commercial nanofiltration membranes. The groups teamed up with Victor Calo from the University’s Physical Science and Engineering Division to develop computer models to understand the mechanism of pore formation. They showed that the simultaneous decrease in pore size and increase in flux was possible because, while the pores are smaller, the pore density in the block copolymer is higher. “In the future, we hope to optimize membranes for protein separation and other applications by changing the copolymer composition, synthesizing new polymers and mixing with additives,” said Nunes. 1. Yu, H., Qiu, X., Moreno, N., Ma, Z., Calo, V. M., Nunes, S. P. & Peinemann, K.-V. Self-assembled asymmetric block copolymer membranes: Bridging the gap from ultra- to nanofiltration. Angewandte Chemie International Edition 54, 13937–13941 (2015). 2. Yu, H., Qiu, X., Nunes, S. P. & Peinemann, K.-V. Self-assembled isoporous block copolymer membranes with tuned pore sizes. Angewandte Chemie International Edition 53, 10072–10076 (2014).

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Solar conversion efficiencies can be further boosted by a simple method to improve the growth of crystals.

Photodetectors gain a super-sized advantage Integrating large-area perovskite crystals into simple circuitry leads to optical sensors with high bandwidth and sensitivity.

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ow-cost photodetectors that have quick response times and high sensitivity have been produced by researchers at KAUST by adapting classical chemistry techniques to transform metal and organic atoms into extended near-perfect crystal films1. Inorganic–organic compounds that crystallize into so-called “perovskite” structures have gained attention because they can be solution-processed into

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photovoltaic devices. Recent fabrication strategies and materials have helped boost perovskite solar conversion efficiencies to levels that rival silicon cells. Researchers anticipate even higher efficiencies if crystal defects can be minimized during the growth process. Osman Bakr from the Solar & Photovoltaics Engineering Research Center and colleagues realized that to make perovskite crystals arrange in an orderly way into a film, they had to find

a way to control the growth kinetics. To do so, they turned to antisolvent crystallization. The technique, which is widely used to purify proteins and other bio-compounds, begins by dissolving a compound in a compatible liquid. Then, adding the antisolvent—a liquid in which the molecule is poorly soluble—causes the particle to precipitate. The team first dissolved precursors for a perovskite called methylammonium lead bromide into an organic solvent and then poured the mixture into a sealed dish containing a substrate like silicon. By diffusing in a chlorinated antisolvent through a small opening in the dish’s lid, they gradually crystallized millimeter-scale perovskite films on their substrate at room temperature. Critical to this procedure was constant stirring of the liquid; the continuous movement helped to nucleate the growth on the surface instead of in solution. Mobility measurements revealed the new film could move charges 100 times faster than normal polycrystalline perovskite films and defect densities were a million times lower. “This was very exciting for us—we had a film that could grow over large areas and behave much like a single crystal,” Bakr said. “It inspired us to try and make the crystals useful for devices.” The team fabricated a simple photodetector by evaporating metal electrodes onto a perovskite-coated silicon wafer, and its amplification and response time was comparable to cutting-edge semiconductor transistors. Furthermore, the device combined rapid detection with high sensitivity, a rare combination for solution-processed photodetectors. “Using the stirring force approach to force perovskites to crystallize on a substrate makes them really easy to handle,” noted Bakr. “We’d like to expand the spectrum of these photodetectors to multiple wavelengths and explore other photovoltaic devices, because with this type of crystallinity, we can compete with traditional semiconductors.” 1. Saidaminov, M. I., Adinolfi, V., Comin, R., Abdelhady, A. L., Peng, W. et al. Planar-integrated single-crystalline perovskite photodetectors. Nature Communications 6, 8724 (2015).

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Aerodynamic flow field showing separation of the boundary layer and the formation of an eddy.

Simulations blow wind tunnel tests away A simulation scheme for aerodynamic turbulence could reduce expensive wind tunnel tests.

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t high speeds, air flow becomes increasingly turbulent and its interaction with surfaces becomes difficult to predict. Due to the extreme complexity of such chaotic turbulent flows, aerodynamic engineers designing everything from aircraft wings to golf balls rely on wind tunnel tests to understand how their designs will stand up in practical and sometimes life-or-death situations. Unfortunately, wind tunnel tests are expensive and time-consuming, making it a challenge to iteratively refine a design for better performance. Ravi Samtaney from KAUST and colleagues Wan Cheng and Dale Pullin from Caltech have developed a simulation code that accurately reproduces experimentally observed turbulence fields for high-speed applications1. “Turbulent flows across surfaces are most accurately modelled by direct numerical simulation,” explained Samtaney. “However, such simulations are computationally intensive and will not

be practical for highly turbulent flows for many decades to come.” The team’s new simulation code combines a numerical simulation scheme called large eddy simulation (LES) to resolve large scales of turbulent motion with mathematical models describing small-scale features and the ultrathin but important viscous flow layer that forms in contact with the moving surface. In this way, the researchers simplify the simulation by many orders of magnitude while maintaining high fidelity with experimental observations. One of the most important physical features of aerodynamic flow is the separation of the flow-field from the surface, which produces a separation vortex and a significant increase in drag. Over a wing, the expansion of such turbulent boundary layer separation can suddenly and significantly reduce lift, but may only appear at certain air speeds. In less critical applications, this same effect can alter the trajectory and flight of a golf ball. “Our simulations can accurately

predict flow separation and reattachment points along a wall as well as skin friction, and the results are in excellent agreement with two different reference experiments,” noted Samtaney. “Such a close match with experimental measurements has not been achieved previously for such flows.” Accurate prediction of turbulent boundary separation by simulation can ease the engineer’s reliance on expensive wind tunnel tests. The low computational cost of this LES-based method means that conducting such simulations at the high-speed air flows of engineering interest is now possible. “Our simulation code overcomes a major roadblock that has prevented expansion of our present predictive capability for engineering fluid dynamics simulation,” Samtaney said. 1. Cheng, W., Pullin, D. I., & Samtaney, R. Largeeddy simulation of separation and reattachment of a flat plate turbulent boundary layer. Journal of Fluid Mechanics 785, 78–108 (2015).

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A smoother route to smart sensors 52

Growing high-quality films of hybrid perovskite materials takes solution-processed phototransistors to new levels of performance.


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Solar technology will benefit from innovation in phototransistors.

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ow-light cameras and optoelectronic devices stand to benefit from an innovative photoactive thin film developed by KAUST researchers1. The technology uses a simple and effective deposition procedure that turns hybrid organic–inorganic light-harvesting crystals into low-cost phototransistors with

super-fast response rates and significant current amplification. Phototransistors are designed to generate large amounts of charge carriers— either negatively charged electrons or positively charged holes—when exposed to light. These devices can amplify initial signals up to hundreds of thousands of times with very little background noise by controlling how these carriers move through a channel using a gate electrode. Phototransistors with the highest amplification factors, however, are among the most expensive to manufacture. Tom Wu and colleagues from the Physical Science and Engineering Division at KAUST investigated an alternative approach based on methylammonium lead halide compounds. These organic– inorganic materials can be dissolved into liquids and then cast into thin films using a straightforward spin coating technique. A low-temperature treatment then crystallizes the film into a “perovskite”-type structure that can photogenerate numerous charge carriers with high mobility and long lifetimes. Spin-coated films usually have a rough surface that leaves devices with sub-optimal mobility and weak gate tuning effects. “The perovskite film quality is the key to achieving high performance in phototransistors,” noted Wu. The researchers used a two-step vapor-assisted process to improve film deposition. First, they spin-coated a lead halide precursor solution onto a silicon

substrate and then exposed the material to methylammonium iodide gas at temperatures of 150 degrees Celsius. This reaction led to perovskite-structure films with smooth and defect-free surfaces and uniform crystal grain sizes— all ideal characteristics for light-based sensing. After coating the perovskite film with a protective polymer coating, Wu and his team tested the device charge transport characteristics under dark and illuminated conditions. The high-quality film structure had a striking impact—light detection occurred within 10 microseconds, charge carrier mobility increased considerably over previous attempts and the current produced per Watt of incident light energy proved to be among the largest values ever reported for phototransistors. Intriguingly, the organolead film could transport both electrons and holes through its gate-modulated channel, which could enable device designers to integrate complementary circuits. The team could also tweak device mobility by altering channel lengths or incorporating different halides into the perovskite structure. “These findings open doors for employing such solution-processed perovskites in a wide range of optoelectronic applications,” added Wu. 1. Li, F., Ma, C., Wang, H., Hu, W., Yu, W. et al. Ambipolar solution-processed hybrid perovskite phototransistors. Nature Communications 6, 8238 (2015).

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2015 KAUST

“The perovskite film quality is the key to achieving high performance in phototransistors.”


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Building blocks for clean energy Novel solid-state materials may hold the key to cleaner fuels and cheap, efficient gas storage.

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aterials developed by researchers at KAUST have the potential to improve the quest for green energy, including the search for cleaner fuels and the means to store various gases. In recent years, there has been a surge of interest in a group of fabricated materials known as metal-organic frameworks (MOFs). These materials are entirely synthetic and are created from preselected molecular building units into networks of metal ions connected by organic linkers. Their flexible structures can be manipulated for a multitude of highly specific applications. KAUST is fortunate to have the services of a leading expert in MOFs. Professor Mohamed Eddaoudi from the Physical Science and Engineering Division has devoted his career to designing and building MOFs. The University’s Advanced Membranes and Porous Materials Center, where he conducts his research, was purpose-built to support the KAUST ambition of the University becoming a world-class center for research into sustainable clean energy and power. “The energy costs associated with the separation and purification of industrial commodities such as gases, fine chemicals and fresh water currently represent around 15 percent of global energy production, and the demand for 54


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such commodities is projected to triple by 2050,” Eddaoudi said. “The ongoing challenge is to develop effective separation and purification technologies that have much smaller energy footprints.” There is also a pressing need to find ways of storing gases—either to remove CO2 from the atmosphere or to enable the storage of cleaner fuels such as hydrogen and methane (CH4) for power. Functional solid-state materials like MOFs could fill this gap in technology. MOFs are designed from the molecular level up, rather like custom-building with nanoscale bricks. Eddaoudi described how he has developed various design strategies based on the molecular building block approach for the construction of MOFs. “We select particular metal ions (either individual ions or clusters of two or more together) and then design the organic ligands to bridge the ions/clusters together prior to the MOF fabrication process,” he said. “By doing this, we can control the MOF assembly and determine their nanoscale structure for pre-defined purposes.” Eddaoudi hopes that improving the processes used to create MOFs will lead to materials being scaled up for use on an industrial scale. Two recent projects by Eddaoudi and his team highlight the promise of MOFs for gas storage and fuel separation. The first study, which was led by Eddaoudi’s colleague Dr. Youssef Belmabkhout and Ph.D. student Dalal Alezi, used novel aluminum-based MOFs to store CH4, a cheaper and cleaner alternative to existing fuels. The researchers settled on a “soctopology” MOF design, a structure based on linking square and octrahedral-shaped building units. The resultant soc-MOF structure encloses channels and cubic-shaped cages with eight metal ion clusters on the vertices of the cage. The team designed a rectangular

organic linker that would help in the automatic formation of clusters of three aluminum ions. The resulting “Al-socMOF” showed exceptional porosity, with the highest-ever recorded CH4 uptake at pressures of 35 bar and above, fulfilling the U.S. Department of Energy’s target for CH4 storage. The same Al-soc-MOFs also showed high storage capacity for CO2 and O2. This suggests that if the MOFs could be scaled up, they could provide solutions for fuel storage, CO2 reduction and improvements to medical devices requiring O2 storage. “Another of our projects explores how MOFs may help in the separation of light hydrocarbons, one of the most energy-intensive and demanding process in the gas, oil and fuel industries,” said Eddaoudi. “Our team recently succeeded in developing new, cost-effective and energy-efficient adsorbent materials for sieving—and therefore separating—paraffins.” Branched paraffins are valuable in gasoline production because they create a more efficient fuel. Similarly, normal paraffins are highly prized in diesel fuel. The research team led by Ph.D. student Ayalew Assen under Belmabkhout’s supervision created an MOF based on rare earth metal ions and replaced longer linkers with shorter, dicarboxylate-based organic ligands called fumarate. The fine-tuning of the size of triangular-shaped apertures in the MOFs allowed for the complete molecular sieving of paraffins. The normal paraffins pass through the holes and the branched paraffins are excluded. “The MOF materials synthesized at KAUST show great promise to reduce the prominent energy footprint associated with existing technologies,” Eddaoudi noted. “Once we are able to scale-up MOF production, there is no end to the potential of this technology.” I S S U E T W O 55

2015 Eric Bakken

KAUST Professor Mohamed Eddaoudi shows off model MOFs at the University.


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The tiniest bumps on a smooth surface can form a ring of microbubbles when a drop hits the surface.

Making a splash Ultrafast imaging reveals the influence of even ultrasmall surface roughness on inkjet printing. 56


Reproduced with permission from ref 1© 2015 Cambridge University Press.

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Frames from an ultra-high-speed video show the air bubbles trapped under a water droplet impacting on a glass surface. The imaging is through the glass.

ring of small microbubbles underneath a droplet1. “The drop can distinguish between a 10 nanometer glass roughness and perfectly smooth mica. This is quite surprising,” stated Sigurdur Thoroddsen, lead of the research team at the University. Studying drop dynamics is relevant to applications ranging from inkjet printing to industrial coatings to the fabrication of mobile phone displays that use printed organic electronic circuits.

The advantage of using laser beams is to provide a depth measurement through interference fringes that are visible in the recorded images. The camera images show the effect of roughness on the bubble formation with more bubbles formed on rough glass than on smooth. In the extreme limit of mica, which has atomically smooth surfaces, no such ring of microbubbles formed during the droplet impact. Even small surface imperfections

“The problem of microbubble formation is greater

for drops of higher viscosity, where a larger number of bubbles are entrained. This is our next target.”

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he impact of drops on a glass surface has been captured at ultrafast time scales by researchers at KAUST. Using a high-speed video camera, the researchers discovered that even minute surface roughness leads to the formation of a

The inkjet printing processes are technologically challenging, because the drops hitting the surface experience large deceleration forces equivalent to 300,000 times that of gravity. At such speeds, air is trapped underneath the drops during deposition, and, as the researchers observed, this creates a ring of minuscule bubbles at the fringes of the droplets. The bubbles reduce the uniformity of the deposits and can reduce printing quality. The researchers studied the formation of the microbubbles using a high-speed camera that can record clips at a rate of five million images per second, or at an imaging resolution of 200 nanoseconds. The camera is placed underneath the glass and laser beams are used as a flash during exposure. The superfast recording speed necessitates a different laser diode for each individual image frame, requiring an array of 180 separate lasers.

leave a clear signature on the bubble distribution. Microbubbles form even on glass surfaces with a roughness of only around 10 nanometers, which is about 500 times smaller than the size of the microbubbles that are created and 500,000 times smaller than the drop, presenting severe problems for numerical simulations. The evolution of the drops also depends on other parameters, which will be the next area of study, noted Thoroddsen. “The problem of microbubble formation is greater for drops of higher viscosity, where a larger number of bubbles are entrained. This is our next target; we would like to see how bubbles are entrained for higher viscosity drops,” he said. 1. Li, E.Q., Vakarelski, I.U. & Thoroddsen, S.T. Probing the nanoscale: the first contact of an impacting drop. Journal of Fluid Mechanics 785, R2 (2015).

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Reality check for Red Sea wave predictions Current models that predict ocean surface conditions overestimate wave patterns in the middle of the Red Sea.

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mproved modelling of wind and waves by KAUST scientists will enhance simulations of oceansurface conditions in the Red Sea. Mathematical wind-wave models are used to illustrate past and future ocean surface conditions. They are important for coastal oceanographic studies, coastal management activities, ocean engineering and maritime activities. While satisfactorily accurate for open oceans, these models have been inadequate for conditions on enclosed seas. Predicting conditions in the Red Sea is particularly challenging because of the Red Sea’s long and narrow shape. “This makes the local conditions extremely sensitive to even minor changes in the direction of the driving wind fields,” explained Ibrahim Hoteit from the Physical Science and Engineering Division. The Red Sea basin is bordered by mountain ranges on both sides, transforming it into a wind tunnel. In the winter months, winds blow in a south-easterly direction from the 58

Warm northwesterly winds meet cold southeasterly winds in the Red Sea’s convergence zone. The warm winds flow on top of the cold winds, trapping them and forcing them to reverse at a higher altitude. This creates a cloudy zone, unusual for the sunny Red Sea.

Mediterranean and a north-westerly direction from the Gulf of Aden. These two opposing wind systems meet in the so-called “Red Sea convergence zone,” producing complicated wave patterns that depend on small details in the driving winds. A team of scientists from KAUST and the Institute of Marine Sciences in Italy compared predictions of WAVEWATCH III, a widely used state-of-the-art wave model, with actual data from satellites and meteooceanographic buoys in the Red Sea1. Their results suggested that current inputs to the model do not properly represent the evolution of wind-wave patterns, especially in the convergence zone. Even with correct or underestimated wind conditions, the model tended to overestimate the wave conditions, particularly in the convergence zone. By modifying details in the model’s equations, the team managed to improve the wave-model simulation under opposing wind and wave conditions. “Precise knowledge of sea-state

information and its climatology would be highly beneficial to marine activities ranging from conventional fishing to transportation of goods and crude oil,” said KAUST Ph.D. student Sabique Langodan. “This study developed an accurate representation of wave fields in the Red Sea…[and] provided a unique opportunity to study the evolution of two wave systems of similar amplitude and frequency propagating in opposite directions.” The study can be considered an important contribution to future developments of wave models, he explained. The team is currently studying how wind and wave patterns in the Red Sea have varied over time. They are also characterizing wind and wave energy resources to identify the Red Sea’s potential as a renewable energy source. 1. Langodan, S., Cavaleri, L., Viswanadhapalli, Y., Hoteit, I. Wind-wave source functions in opposing seas. Journal of Geophysical Research Oceans 120, 6751–6768 (2015).


Alshareef and colleagues testing semiconductors in the lab.

A new take on old materials

A mineral used in electrochemical devices that was thought to be a semiconductor is now identified as a metal.

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iegenite has strong potential to be used in devices that can generate and store energy, but a detailed characterization by researchers at KAUST shows it might not be what it seems1. Metals can efficiently carry an electrical current because electrons are free to roam through the material. Semiconductors, on the other hand, have a so-called ‘bandgap’ that prevents electrons from flowing at low temperature, which means that they only conduct at higher temperatures or when impurities are introduced. This property

is central to the operation of electronic devices that have revolutionized information and telecommunications systems. Professor Husam Alshareef, his student Chuan Xia and their colleagues have discovered that a mineral known as siegenite, which was originally thought to be a semiconductor, is in fact a metal. This helps to explain its remarkable electrochemical performance. First identified more than 160 years ago, siegenite, or nickel cobalt sulfide, has attracted renewed interest because of its encouraging performance as

electrodes in energy devices such as solar cells, supercapacitors and fuel cells. Its good performance in these devices has been attributed mostly to the electrochemical activity of the transition metal cations cobalt and nickel. Siegenite is a member of a class of materials known as chalcogenides, which are predominantly semiconductors. Because of this, it was assumed that siegenite was also a semiconductor. Alshareef and his colleagues combined numerous experimental and theoretical techniques to assess the structural and electrical properties of their siegenite2. They measured a room temperature resistivity of around 103 microohm-centimeters and showed that this increased with temperature. They also showed that the carrier density, or the number of electrical charges in a particular volume, was 3.18×1022 per cubic centimeter. The material also exhibited a very low thermopower of around 5 microvolts per Kelvin. These properties, together with first-principles calculations, indicate a metal rather than a semiconductor. “Having an electrochemically active electrode material with metallic conductivity means that efficient electron transfer takes place during electrochemical reactions, resulting in significantly improved performance,” said Alshareef. Checking the chemical composition of their sample was vital. The team used a technique called Raman spectroscopy to create a spectral signature associated with a specific atomic arrangement. The spectrum, which was measured in an inert argon environment, matched a mathematically simulated one. The team explained differences in their results from those reported previously as being a result of oxygen in the environment that compromised the previously reported Raman spectra. 1. Xia, C., Li, P., Gandi, A.N., Schwingenschlögl, U. & Alshareef, H.N. Is NiCo2S4 Really a Semiconductor? Chem. Mater., 27 (19), 6482–6485 (2015). 2. Chen, W., Xia, C. & Alshareef, H.N. One-step electrodeposited nickel cobalt sulfide nanosheet arrays for high-performance asymmetric supercapacitors. ACS Nano 8, 9531–9541 (2014).

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2016 KAUST

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Catching a glimpse of the double helix Direct imaging of a single DNA molecule provides insights into fundamental biological processes.

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lthough the structure of DNA was first unraveled more than 60 years ago, a direct image of DNA’s detail has remained elusive. Researchers at KAUST have now developed a technique that allows them to visualize individual DNA molecules in real time1. 60

DNA has always been a slippery customer because of the low-contrast elements of which it is made and the fragile structure of the helical molecule. An international team has now perfected a preparation technique that fixes the unstable structure and an imaging process that minimizes its degradation.

According to Professor Enzo Di Fabrizio from the University’s Physical Science and Engineering Division, this opens potential to investigate molecular phenomena from DNA modification by mutation to DNAprotein interactions. “Single molecule interactions are crucial for the understanding of many


2015 KAUST

P H YS ICAL S C IE N C E A ND E N G IN EERIN G DIVI SI ON

Using a high-resolution transmission electron microscope, the researchers were able to produce an image of a single DNA molecule.

fundamental biological mechanisms,” he said. The new process involves suspending single DNA molecules within a framework of minute silicon pillars. The DNA is then viewed with a high-resolution transmission electron microscope (HRTEM) that fires beams of electrons

through it to produce a perfect image. This method enabled the researchers to take key measurements of the DNA helix, including its diameter, the distance between the building blocks of the molecule (called “bases”) and the depth of the so-called “grooves” of the helix that provide a measure of its shape. In other

words, said Di Fabrizio, “how the molecule is coiled.” They could also determine the length of bonds between the two helices of DNA, which may indicate its level of methylation (a chemical effect that can alter gene activity) and pinpoint errors in base-pairing that may cause mutations and disease. Di Fabrizio suggests that HRTEM images will be invaluable in figuring out exactly how DNA interacts with proteins in the cellular environment. He is focusing in particular on how repair proteins “dock” on to DNA to fix errors in the genetic code. “Until now, this has not been seen at such a high resolution,” he said. “In the future, this will help scientists understand in detail how DNA repair occurs under both normal and pathological conditions.” This is a rapidly-developing field— already there are cameras that are 100 times more sensitive than the one used in this work. The team intends to combine their approach with a freezing technique known as cryoEM to achieve even greater detail and to extend it to imaging the structure of cell membranes. 1. Marini, M., Falqui, A., Moretti, M., Limongi, T., Allione, M. et al. The structure of DNA by direct imaging. Science Advances 1, e1500734 (2015).

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Structure of the nanoparticles containing exactly 25 silver atoms and surrounding stabilizing components.

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Silver nanoparticles’ gold luster

2015 KAUST

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An atomically precise investigation reveals close similarities between silver and gold nanoparticles.

n atomically precise silver nanoparticle that is almost identical to gold nanoparticles has been synthesized by researchers from KAUST1. This offers an alternative candidate for potential industrial use as well as the opportunity to address an age-old question of fundamental differences between silver and gold. Nanoparticles with an atomically precise number of constituent atoms are of interest for applications such as catalysis, in which they enhance a diverse range of chemical reactions. The particular number of atoms of each individual nanoparticle lends them properties similar to atoms; for example, energetic states. Having a precise number of atoms also makes these types of nanoparticles relevant for fundamental research, said Associate Professor Osman Bakr, who led the research team. “They help provide answers to fundamental questions, such as how atomic properties manifest themselves as the number of interacting atoms increases,” said Bakr. “Because their structure is precise and known, they can be computationally modeled and their properties predicted with high precision.” Previous research has produced a wide variety of known atomically precise nanoparticles made from different quantities of gold atoms. Gold nanoparticles are desirable for their good catalytic properties, but they are also an expensive resource, and the high cost is a drawback for their commercial potential. The researchers wanted to know whether atomically precise nanoparticles made from comparable elements such as silver

could produce similar properties to gold. Comparison of the properties of gold and silver nanoparticles requires them to have not only the same number of atoms, but also to have the same chemical structures on their surfaces used to stabilize the particles in their environment. Unfortunately, there are only a few known types of atomically precise silver nanoparticles compared to gold nanoparticles. Careful design and nanoparticle synthesis has enabled the researchers to synthesize silver nanoparticles containing precisely 25 atoms each and with the same surrounding molecules as gold nanoparticles having the same number of atoms. Comparison of nanoparticles shows their structure and properties to be remarkably similar, although there are subtle differences in the angles of the chemical bonds between the metal atoms and the length of the bonds. The optical properties of the two types of nanoparticles are also nearly identical, with only small differences in the color of their optical absorption spectra. Exploring their practical potential will be the next step, said Bakr. “It will be interesting to see how these similarities and differences are correlated to their properties such as catalytic activity and nobility of their constituent atoms,” he noted. 1. Joshi, C.P., Bootharaju, M.S., Alhilaly, M.J. & Bakr, O.M. [Ag25(SR)18]¯: The ‘Golden’ Silver Nanoparticle. Journal of the American Chemical Society. 137, 11578–11581 (2015).

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Shaping rate rules to fuel the future

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he performance of future engines could soon be predicted with greater accuracy thanks to research by KAUST scientists to find high-efficiency and low-emission solutions in the fight against climate change. Engine design and optimization depend on combustion chemistry models consisting of multiple elementary reactions. In particular, reactions between hydrocarbons and hydroxyl (OH) radicals play a central role in the breakup of fuel components during combustion. Few researchers, however, have directly measured rate constants for high-temperature reactions between OH and large alkanes comprising more than five carbon atoms; these prevail in gasoline and diesel. To shed light on this, Aamir Farooq and colleagues from the KAUST Clean Combustion Research Center have established “rate rules,” or site-specific rate constants, for the OH-mediated hydrogen removal from alkanes at 64

Shown is the end section of a shock tube. A green laser beam passes through the optical ports of the shock tube.

carbons bearing two and three functional groups1. In this approach, they evaluated the rate constants for the high-temperature reactions between large linear and branched alkanes and OH radicals. “We carefully selected seven alkanes varying in structure to derive rate rules applicable to alkanes not covered in this study,” Farooq noted. The researchers conducted their measurements in a shock tube, an ideal reactor for high-temperature kinetic studies. A supersonic wave traveled through the test gas mixture, heating it to temperatures ranging between 880 and 1440 K almost instantly. Farooq explained that a large pressure discontinuity is created between the test gas mixture and an inert gas (such as helium) using a diaphragm. The diaphragm bursts when the inert gas pressure increases, producing the supersonic wave. Test gas mixtures combined a specific alkane, a clean thermal OH radical source called tert-butyl-hydroperoxide and argon as a thinner. At high temperature, tert-butyl-hydroperoxide decomposed in a few microseconds to generate the radicals, which then reacted with the alkane.

The researchers determined the rate constants by monitoring the OH radical decay using an ultraviolet laser system. Measured rate constants for n-hexane and 2,2-dimethyl-butane closely matched previous assessments, supporting the researchers’ approach. The value calculated using the rate rules also agreed with experimental data for the reaction involving 2-methyl-heptane. “This gives us confidence that our rate rules are suitable for other classes of alkanes,” said Farooq. These measurements were also in line with estimates obtained by earlier prediction methods. The rate constants and rate rules are now implemented in new combustion models developed at KAUST and at other international universities. “These models are used by our collaborators from Saudi Aramco and other institutes in high-fidelity engine simulations to improve engine efficiency and reduce emissions,” Farooq added. 1. Badra, J., Elwardany, A. & Farooq, A. Shock tube measurements of the rate constants for seven large alkanes + OH, Proceedings of the Combustion Institute 35, 189–196 (2015).

2015 KAUST

Precise rate constants could provide highfidelity combustion models for cleaner and more efficient fuels.


Elements for Innovation Our people and their academic and industry partners conduct experimental research in a i l i a o i ica io i c olo icall a a c o Laboratories offer our scientists, engineers and collaborators a comprehensive and competitive advantage in an easily accessible University setting.

The Shaheen supercomputer is ranked among the top ten most powerful supercomputers in the world.

www.kaust.edu.sa


Elements for Innovation KAUST’s integrated academic structure creates an interdisciplinary and collaborative learning environment for our students. Our three Academic Divisions encompass multiple disciplines and 11 a icall co c ac o o o c io i i a oal o i research. Our faculty, researchers and students are encouraged to be entrepreneurial and are empowered to aim high in order to translate their science into discoveries and new technologies. Three professors - each from a different academic division, discuss their work with the KAUST community at one of the monthly science cafes.

www.kaust.edu.sa

KAUST Discovery - Issue 2  

From curiosity to innovation

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