Recent Submissions

  • Characterization of New Cell Factory Candidate for Saudi Arabia Application

    Mei Ng, Yi; Azlin Mokhtar, Noor; Ahmad Jamhor ,Suhaiza; Archer ,John (2019-01-13) [Poster]
    Characterization of a New Cyanobacterial Cell Factory Strain for Saudi Arabia Application The use of photosynthetic cells as platform for bio-manufacturing is gaining increasing interest as it promises todeliver a sustainable, carbon neutral production system for biomass-derived chemicals, fuels and foods. SaudiArabia, in particular, is an excellent place for the deployment of photosynthetic cell factory as algal biotechnologyleverages the country’s abundant sunlight, availability of large CO2 point source emissions and access to Red Seaand Gulf waters (38 – 40 PSU). Currently a few model picocyanobacterial strain have been extensively studied forbiofuel and biochemical production, but these strains are limited to mild temperature, light and salinity conditionsthus cannot operate under Saudi Arabian climate. Therefore, in order to develop cyanobacterial cell factoryapplications for the Arabian Peninsula, there is a pressing need to discover and develop strains that can thriveunder extremely warm temperatures, high insolation and high salinity. In our study, a native unicellularSynechococcus sp. RSCCF101 strain isolated from the central Red Sea has been identified as a potential cellfactory candidate. Here we present physiological and genomic characterization of Synechococcus sp. RSCCF101to support its development as a new robust marine cell factory strain. Summary •Strain RSCCF101 is a candidate marine cyanobacterial cell factory strain isolated from the central Red Sea. It has an ovoid structure of about 1 µm length and 0.8 µm diameter (Figure 1) and 16S rRNA phylogenetic tree analysis places RSCCF101 within the Synechoccocus cluster (Figure 2). •The physiological profile showed that Synechococcus sp. RSCCF101 is both thermo- and halotolerant where it is able to grow efficiently at temperature up to 38°C and salinity between 10 PSU and 40 PSU, while remained viable at 50 PSU and 60 PSU (Figure 3A and 3B). These are desirable characteristics of a cell factory candidate as the chassis strain has to be able to survive the warm climate and intense insolation in Saudi Arabia (Nielsen, Archer et al. 2017). •Synechococcus sp. RSCCF101 is capable of producing high amount of phycocyanin under low light condition and glycogen under high light condition (Figure 4A to 4D). Phycocyanin is a valuable product for bioassay, bioimaging, pharmaceutical, food and cosmetics industry application (Chakdar and Pabbi 2016) while glycogen can be used as biofuel feedstock (Aikawa, Nishida et al. 2014). •Whole genome was successfully constructed for Synechococcus sp. RSCCF101 (Figure 5), from which a complete gene set involving in glycogen biosynthesis was identified (Figure 6). In addition, the genome contains three sets of cpcBA which encodes the alpha and beta subunits of phycocyanin (Figure 7). •Future work will include a more detailed genomic and transcriptomic profiling of RSCCF101 to establish the understanding of the physiological and molecular traits for synthetic biology purposes.
  • Synthesis of Red-Shifted Flourescent Voltage Sensors

    Deal, Parker; Al Abdullatif, Sarah; Miller, Evan (2019-01-13) [Poster]
    Synthesis of Red-Shifted Flourescent Voltage SensorsSarah Al Abdullatif; Parker Deal; Prof. Evan MillerUC Berkeley, Department of Chemistry IntroductionFluorescence imaging can be used to monitor electricalactivity in neurons by using voltage sensitive dyes (VSDs).VSDs allow the measurement of transmembrane potentialsthrough a photo-induced electron transfer (PeT) from anelectron donor through a molecular wire to a uorophore. Atresting or hyperpolarized potentials, the transmembraneelectric eld promotes PeT, quenching the excited-stateuorophore. Depolarization reverses the electric eld,decreasing the rate of PeT, and therefore leading to anincrease of uorescence. Recently we reported the development of a new class of VFsbased on isomerically pure tetramethylrhodamines. Thesenew Rhodamine Voltage Reporters, or RhoVRs, usephotoinduced electron transfer (PeT) as a trigger for voltagesensing to measure changes in membrane potential withhigh sensitivity (up to 47% F/F per 100 mV). In addition,RhoVRs possess excitation and emission proles in the greento orange region of the visible spectrum, allowing for usealongside commonly used green uorescent tools such asGFP. Modications to RhoVRPiperazine Functionalized Voltage ReportersFunctionalization of RhoVR dyes with L-cysteic acid functionalized piperazine maintains atertiary amide at the 2’ position, includes a sulfonate to aid with solubility and orientation ofthe dye in the membrane , and provides a nucleophilic handle for attachment of targetingligands.In addition to modications at the 2' position, a new RhoVR, RhoVR(Me), was synthesizedwith a less electron rich wire that is complementary dye to RhoVR(OMe) as it is muchbrighter, however less sensitive, than the parent VF. Genetic Targeting Using HaloTagRhoVRs have demonstrated the ability to record neuronal activity with good signal to noiseratio, however the dyes indiscriminately label all membranes, leading to high levels ofbackground uorescence. We have chosen to utilize HaloTag® technology as a means toaddress the limitations of RhoVRs through genetic targeting. HaloTag® is adehalogenase-based labeling system which forms a covalent linkage between a protein tagand a chemical ligand (chloroalkane). By expressing Halotag extracellularly, then addingRhoVR linked to the HaloTag® ligand via a exible linker (PEG), we hope to gain theselectivity of genetically encoded voltage indicators (GEVIs) while maintaining thefavorable photophysical properties of the small-molecule VF. PEG linkers of varying lengthwere also investigated to determine if linker length aected the voltage sensitivity of thedyes. Genetic Targeting and Voltage SensitivityThe voltage sensitivites of the RhoVR-PEGn-Halo compoundswere determined using patch-clamp electrophysiology. Allderivatives were capable of measuring membrane potential, butalso showed attenuated voltage sensitivities from the parentsarcosine-functionalized compounds. In addition theRhoVR-PEGn-HaloTag® compounds were roughly one third asbright as the parent dyes. Future WorkFuture work with RhoVR-PEG-Halos will aim to both improveupon the photophysical properties of the targeted voltage dyesas well as exploring the biological scope of HaloTag® system.Specically, this will include:1) Further investigating the relationship between linker designand voltage sensitivity2) Employing far-red voltage dyes to improve SNR andphotostability3) Genetic targeting of neuronal sub-types (excitatory,inhibitory) and sub-cellular domains (pre synaptic,post-synaptic)4) Utilization of the RhoVR-PEG-Halos in more intactpreparations (i.e. brain slice)5) Development of a HaloTag®/GCaMP6s construct to enablesimultaneous Ca2+ and voltage imaging
  • One step genome-wide association study of traits contributing to salinity stress in rice grown under controlled and field conditions

    Al-Tamimi, Nadia; Oakey, Helena; Garcia, Garcia; Berger, Bettina; Brien, Chris; Mbodj, Daouda; Manneh, Baboucarr; Tester, Mark; Negrao ,Sonia (2019-01-13) [Poster]
    One step genome-wide association study of traits contributing to salinity stress in rice grown under controlled and field conditions Background •Rice is the staple crop that feeds more than half of the world 1 •It is the most salt-sensitive cereal 2 •We need to use land that is currently unsuitable for rice production (e.g. by use of salt-tolerant rice varieties) to help address global food security •Salinity tolerance in plants is a complex quantitative trait that has various components àdissected effectively using single step GWAS models.
  • Micro Drug Delivery System for Heart Disease

    Moussi, Khalil; Kosel, Jurgen (2019-01-13) [Poster]
    1. INTRODUCTION & MOTIVATION Ø For the last decades, Coronary Artery Disease (CAD) has been the deadliest disease in the world. Ø CAD caused 8.76 million deaths in the year 2017 according to the World Health Organization (WHO). Ø In Saudi Arabia: • CAD is the leading cause of death in the year 2016, • The number of death had a 20% increase from the year 2005 to 2016 according to WHO. Ø Existing interventions and drawbacks: • Angioplasty: - Re-narrowing of the artery within the stent - Blood clot formation - Compressed plaque - Re-narrowing in the surrounding of the stent • Coronary Artery Bypass Grafting (CABG): - Long surgery (6 - 8 hours) under general anesthetic - Risk of bleeding from the grafting area - Heart rhythm problems and blood clots which higher the risk of stroke To definitively eradicate the disease, a new treatment technique is required. 2. DESIGN & CONCEPT Ø A micro drug delivery system consisting of an electrolytic pump and drug reservoir with micro-needles is attached to a balloon catheter that pushes the micro-needles into the artery walls. Ø Actuation of the pump allows drug delivery through micro-needles to the fatty cholesterol layer. Schematic diagram of the drug delivery process inside the heart artery Schematic diagram and photographs of the drug delivery system 3. FABRICATION Interdigitated electrodes fabrication process Micro-bellows membrane fabrication process 3D-Printing drug reservoir 4. CHARACTERIZATION & TEST Penetration test of a 200 μm long microneedle into PDMS film (Scale bar 50 μm) Parylene C micro-bellows membrane expansion using electrolysis Red-dye delivery through micro-needles using water electrolysis pump 5. CONCLUSION & FUTURE WORK Ø A new treatment method for coronary artery disease has been proposed Ø Fabrication of a micro-pump for drug delivery has been achieved Ø The assembly of the drug reservoir and micro-pump has been tested successfully Ø In process: Assembly of the drug delivery system on top of the balloon catheter
  • MVApp : Multivariate analysis application for streamlined data analysis and curation

    Julkowska ,Magdalena; Saade, Stephanie; Agarwal, Gauraw; Gao, Ge; Pailles, Yveline; Morton, Mitchell; Awlia, Mariam; Tester, Mark (2019-01-13) [Poster]
    MVApp – Multivariate analysis application for streamlined data analysis and curation Mission statement: Enhanced data processing transparency Interactive and reproducible data curation Quick processing of data with/without selected outliers Increased statistical literacy across the scientific community Efficient data processing pipeline for big and small datasets Community involvement for expanding analyses included in MVApp
  • Graphene Oxide Liquid Crystal Membranes in Protic Ionic Liquid for Nanofiltration

    Mahalingam, Dinesh; Wang, Shaofei; Nunes, Suzana (2019-01-13) [Poster]
    Graphene Oxide Liquid Crystal Membranes in Protic Ionic Liquid for Nanofiltration Dinesh K Mahalingam, Shaofei Wang and Suzana P Nunes Graphene Oxide (GO) liquid crystals have been mostly reported as dispersion in water and organic solvents. They can provide highly ordered, regularly stacked nanochannels and lead ultrafast water transport and precise molecular sieving of solvated molecules. The main challenge is to obtain thin and robust layers with high water permeance and selectivity. We report GO liquid crystals from protic ionic liquid and exploit the self-assembled sheets to prepare nanofiltration membranes.
  • VSIM: Visualization and Simulation of Variants in Personal Genomes with an Application to Premarital Testing

    Althagafi, Azza; Hoehndorf, Robert (2019-01-13) [Poster]
    VSIM: Visualization and Simulation of Variants in Personal Genomes with an Application to Premarital Testing
  • Robust H_infinity Pointing Error Control for Free Space Optical Communication in a Controlled Weak Turbulence Condition

    Cai, Wenqi; Ndoye, Ibrhima (2019-01-13) [Poster]
    Robust H_∞ Pointing Error Control for Free Space Optical Communications in a Controlled Weak Turbulence Condition Wenqi Cai,1 Ibrahima Ndoye,1 Taous-Meriem Laleg 1 Estimation, Modeling and ANalysis group, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia I. MOTIVATION AND OBJECTIVE High requirement for good-alignment Affected by atmospheric turbulence. Objective-minimizing the pointing error: to maintain the center of the optical beam as close as possible to the center of the receiving aperture.
  • A Nonconvex Projection Method for Robust PCA

    Dutta, Aritra; Hanzely, Filip; Richtarik, Peter (2019-01-13) [Poster]
    A Nonconvex Projection Method for Robust PCA. -Aritra Dutta, Filip Hanzely, Peter Richtárik. Visual Computing Center, KAUST, University of Edinburgh, Moscow Institute of Physics and Technology. Robust principal component analysis (RPCA) is a well-studied problem whose goal is to decompose a matrix into the sum of low-rank and sparse components. In this paper, we propose a nonconvex feasibility reformulation of RPCA problem and apply an alternating projection method to solve it. To the best of our knowledge, this is the first paper proposing a method that solves RPCA problem without considering any objective function, convex relaxation, or surrogate convex constraints. We demonstrate through extensive numerical experiments on a variety of applications, including shadow removal, background estimation, face detection, and galaxy evolution, that our approach matches and often significantly outperforms current state-of-the-art in various ways.
  • AUC-MF: Point of Interest Recommendation with AUC Maximization

    Han, Peng; Shang, Shuo; Sun, Aixin; Zhao, Peilin; Zheng, Kai; Kalnis, Panos (2019-01-13) [Poster]
    AUC-MF: Point of Interest Recommendation with AUC Maximization Location-based social networks (LSBNs) allow users to check in and share their experiences when they visit a point of interest (POI), such as a museum or a restaurant. With the development and popularity of various LSBN (Fig. 1) platforms e.g., BrightKite, Foursquare, and Gowalla, user check-in data is growing at an unprecedented pace. For instance, Foursquare had more than 50 million active users and more than 8 billion check-ins made by 2016. The availability of abundant amount of user check-in data, enables many studies on recommender systems to further enhance user experiences. POI recommendation aims at finding unvisited locations that a user may be interested in, by learning from users check-in history and other related factors. POI recommendation is challenging for many reasons. One of the most important reasons is that user check-in data is extremely sparse .
  • Approximate Computing with Stochastic Transistors' Voltage Over-scaling

    Li, Ren; Naous, Rawan; Salama, Khaled; Fariborzi, Hossein (2019-01-13) [Poster]
    Approximate Computing with Stochastic Transistors’ Voltage Over-scaling Introduction Approximate computing is a promising technique for error resilient applications. The intrinsic variability of the transistor (reflectedonVTH)is a concern for traditional designs. Thisworkaddresses the variation as the source of performance shaping in approximate computing. StochasticTransistorModel The physical variations are summed up into threshold voltage(VTH)variability; The variation is modeled by adding a thermal noise to the gate voltage. The added variability ensures Enoughdata points within a single transient simulation; The full spectrum of the Gaussian distribution is captured. Approximate Computing The worst-case scenario is guaranteed by assigning the obtained value “x” to the counterpart of its correct value. Voltageover-scaling scheme explores the designs pace of approximate full adder (FA) up to 16-bit. Designconsideration includes: Technology node Operating frequency Energy and delay Process corner Temperature Quantification on Approximate Adder Mean Error Distance (MED) describes the actual value of error. Mean Relative Error Distance (MRED) describes the deviation from the expected value. Image Compression Using Approximate Adder saves up to 90% energy while preserving relative quality. Conclusion The IoT (Internet of Things) operations which consist of numerous error resilient applications can benefit from this work. In conclusion, it Embraces and models the variability of the transistor; Adopts the inherent stochasticity in approximate computing; Provides design space and improved energy efficiency References R. Li, R. Naous, H. Fariborzi, and K. N. Salama, “Approximate Computing with Stochastic Transistors’ Voltage Over-scaling,” IEEE Access, 2018. DOI: 10.1109/ACCESS.2018.2889747 P. Weckx, et al, “Defect-centric perspective of combined BTI and RTN time-dependent variability,” in 2015 IEEE International Integrated Reliability Workshop (IIRW), pp. 21–28.
  • A comparison study of Eddy Dissipation Concept and Partially Stirred Reactor using a Stochastic Reactor Model

    Quadarella, Erica; Stagni, Alessandro; Cuoci, Alberto; Parente, Alessandro; Im, Hong; Faravelli, Tiziano (2019-01-13) [Poster]
  • Driving Policy Transfer via Modularity and Abstraction

    Mueller, Matthias; Dosovitskiy, Alexey; Ghanem, Bernard; Koltun, Vladlen (2019-01-13) [Poster]
    Driving Policy Transfer via Modularity and Abstraction Summary ➢We transfer driving policies from simulation to reality via modularity and abstraction. ➢The driving policy is encapsulated such that it is not directly exposed to raw perceptual input or low-level vehicle dynamics. ➢We evaluate our approach in simulated urban environments and in various real-world conditions in two different continents. Simulation ➢We use CARLA, an open-source simulator for urban driving. ➢The simulator provides access to sensor data from the ego-vehicle, as well as detailed privileged information about the ego-vehicle and the environment. ➢CARLA provides access to two towns: Town 1 and Town 2 which differ in their layout, size, and visual style. ➢CARLA also provides multiple environmental conditions (combinations of weather and lighting). ➢We use two of these in our experiments: clear daytime and cloudy daytime after rain. ➢The two towns and environmental conditions used in our experiments are illustrated on the right. Physical World ➢We use a modified 1/5 scale Traxxas Maxx truck as vehicle. ➢At runtime, given an image, the onboard computer predicts the waypoints and uses a PID controller to convert them to low-level control commands. ➢While the car is driving, the driving policy can be guided by high-level command inputs through a switch on the remote control.
  • Heavy Fuel combustion model

    Guida, Paolo (2019-01-13) [Poster]
    •Large portion of Heavy Fuel Oils (HFOs) are burned to meet the energy demand in Saudi Arabia. It is a relatively cheap and widely available fuel. •The combustion processes associated to HFOs present numerous complications from both the environmental and technical point of view. •Several aspects concerning the combustion behavior and the physics of the fuel itself are not known. A numerical description of physical and chemical phenomena involving HFOs is very challenging. •The methodologies developed for HFOs are suitable to describe other relatively heavy fuels involved in chemical processes like crude-oil and bio-fuels. •Various fuel modifications, such as different asphaltene percentages and emulsions, are studied to improve the combustion performance as well as reduce the environmental impact, a correct prediction of these phenomena would save the costs associated to the experiments.
  • Wafer scale quasi single crystalline MoS2 realized by epitaxial phase conversion

    Xu, Xiangming; Wang, Zhenwei; Lopatin, Sergei; A. Quevedo-Lopez, Manuel; N. Alshareef, Husam (2019-01-13) [Poster]
    Wafer scale quasi single crystalline MoS2 realized by epitaxial phase conversion Recent Technological Demands: The fabrication of large-scale, single-crystalline, silicon wafers has enabled the modern electronics industry. Wafer-scale, single-crystalline, 2D graphene was first fabricated in 2014 Until Now, wafer scale MoS2 film has been realized, but all with polycrystalline structure, which limit the reliability of MoS2 based integrated circuit device. Develop a new fabrication process for fabricating single crystalline MoS2 film at wafer scale is significant and necessary
  • TIN OXIDE MODIFIED SILICON NANOWIRES ON SILICON CHIP AS AMMONIA SENSOR

    Yuvaraja, Saravanan; Dhasmana, Hrishikesh; Kumar, Amit; Kumar, Vivek; Verma, Abhishek; Kumar Jain, Vinod; Nabil Salama, Khaled (2019-01-13) [Poster]
    Title: TIN OXIDE MODIFIED SILICON NANOWIRES ON SILICON CHIP AS AMMONIA SENSOR Authors: Saravanan Yuvaraja1,2, Hrishikesh Dhasmana2, Amit Kumar2, Vivek Kumar2, Abhishek Verma2, V. K. Jain2 and Khaled Salama1. Section 1: HOW YOU ARE EXPOSED TO AMMONIA ? Section 2: HOW AMMONIA AFFECTS YOUR HEALTH ? Section 3: WE CAN SAVE YOU FROM AMMONIA EXPOSURE Level 1: Synthesis Level 2: Performance analysis Level 3: Prototype demonstration Attention: Both Synthesis process flow and Gas sensing mechanism concept of the reported device architecture is presented in the video
  • Multibit Storage devices

    wasef, shaik (2019-01-13) [Poster]
  • SST Measurements in the Red Sea

    Shellem, Claire (2019-01-13) [Poster]
    Accuracy of satellite SST measurements compared to in-situ SST measurements in the central Red Sea: implications for coral bleaching studies
  • Shark Strike in the Northern Red Sea

    McIvor, Ashlie (2019-01-13) [Poster]
    A KAUST seaglider was attacked by a shark at approximately 09:10 Arabian Standard Time at a depth of 56.39m off the coast of Duba, Saudi Arabia. Seagliders are long-range autonomous underwater vehicles (AUVs) that can profile the ocean for many months at a time at a fraction of the cost of traditional methods. Shark attacks are a threat to the integrity of the data recorded by AUVs. This study quantifies the damage inflicted on the seaglider, as well as discussing the strike mechanics and potential attack motivation. Bite profiles were used to compare the inflicted damage on the Seaglider to the known pelagic species inhabiting the Red Sea. This included a tooth fragment and bite location on the Seaglider. Seaglider 213 was deployed from 5th October 2015 until an emergency recovery on the 14th November 2015, 70km offshore of Duba. During this time, communications with the glider had been challenging, where buoyancy and direction of the Seaglider were near impossible (blue spirals). The Seaglider had been struck twice. This created an ingress of water, severed oxygen sensor and removed a wing of the Seaglider (pink circle) causing difficulties in control. A second glider was struck during the summer of 2018. Heavy fishing in the Red Sea has reduced prey items. Pelagic sharks tend to display territorial behavior. Sharks are curious and test with their mouths; the color, noise, and biofouling could attract attention. The only records of shark attacks on AUVs have been from white sharks, which are not found in the Red Sea. Potential species include the Oceanic Whitetip and the Shortfin Mako. Future studies should focus on Artificial Intelligence software that can be developed to learn the normal patterns of vertical velocity, pitch, and roll of seagliders. Sharp and jagged movements are abnormal and could be interpreted as a shark strike to alert the Seaglider pilot in order to abort the mission. To identify the potential species of the attacks, pelagic baited remote underwater video surveys (BRUVS) should be conducted at the site of attack after a mission has been aborted due to a shark strike.
  • Wind Resource Assessment and Characterization of Arabian Peninsula with Electrical Generation Estimation for Saudi Arabia

    Ilton De Oliveira Filho, Jose; Ombao, Hernando (2019-01-13) [Poster]
    Wind Resource Assessment and Characterization of Arabian Peninsula with Electrical Generation Estimation for Saudi Arabia SAUDI Arabia is a fast-growing country, with a stunning increased of Gross Domestic Product (GDP). To sustain this fast-growing rates, Saudi Arabia has continuously expanded its energy power plants. KSA has great potential for Wind Farms, but dust storms can be a major problem as it can increase the maintenance costs drastically. It was used two datasets to this project, the first dataset is from 89 weather stations across Saudi Arabia provided by the National Oceanic and Atmospheric Administration (NOAA) of the Integrated Surface Data (ISD) program. The second is from the weather forecast model produced by the National Centers for Environmental Prediction (NCEP). We also utilized the data presented in the work from 1, 2, 3 about the dust storm over middle East. From their work, we analyzed the Shamal wind current that affects Saudi Arabia with sessional dust storms and also the sources of dust in the Arabian Peninsula. The wind turbine generate electricity by transforming the kinectenergy provided by the wind on its blades. The Eolic energy can be observed as the theoretic energy potential of the site, and the power density of the wind can be express as: Where W(vb) is the estimated probability distribution made by Weibull distribution: As the data are acquired at 10m above ground level and the turbines are in different altitudes we used the exponential law for wind to extrapolate the airflow speed〖v〗_h. The annual energy production can be calculated by: The two figures below presents the overall mean direction (left) and wind speed for the Arabian peninsula with spatial resolution of 50km (right). By analyzing the regions with great wind speed average (>4.133m/s) at 10m hub-height above ground level (AGL), proximity to load centers, distance from dust storm path and long-term (>10 years) data available we ended up with two regions, Wejhand Prince Salman Bin Abdulaziz(PSBA) airport regions. The figure on the left shows the wind rose map for Wejh(region 1) and on the right for PSBA (region 2). Region2 presents 52.3% more power generation than Region 1 at a hub height of 112 meters. The power that can be generated by this region using only one turbine (16320 MW/a) is capable to power 3547 houses (using for this calculation the same power consumption of a normal house in UK) or 1395 houses (using for this calculation the same power consumption of a normal house in US). As a wind power farm has usually 50turbines, a wind farm installed in Region 2 could power 69750 residences using US standards of consumption. Thus, both regions combined, with a 50 turbine wind farm in each, could power 115540 houses (US standards of consumption). In thiswork we conducted the analyses of the wind pattern over Saudi Arabia with additional work on its surroundings, the Arabian Peninsula. By crossing results with previous works, we have observed that the North East and Central East of the country, despite showing good wind patternsfor this application, as it was presented on works 4-5, are not suitableregions to build wind farms, due to the incidence of sand storms.

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