THE KAUST Repository is an initiative of the University Library to expand the impact of conference papers, technical reports, peer-reviewed articles, preprints, theses, images, data sets, and other research-related works of King Abdullah University of Science and Technology (KAUST). 

Theses and DissertationsResearch Publications

Files in the repository are accessible through popular web search engines and are given persistent web addresses so links will not become broken over time.

KAUST researchers: To add your research to the repository, click on Deposit your Research, log in with your KAUST user name and password, and deposit the item in the appropriate collection.

Deposit your Research

If you have any questions, please contact

  • Control of the CDC48A segregase by the plant UBX-containing (PUX) protein family

    Zhang, Junrui (2021-05) [Thesis]
    Advisor: Arold, Stefan T.
    Committee members: Blilou, Ikram; Jaremko, Lukasz
    In plants, AAA-adenosine triphosphatase (ATPase) Cell Division Control Protein 48 (CDC48) uses the force generated through ATP hydrolysis to pull, extract, and unfold ubiquitylated or sumoylated proteins from the membrane, chromatin, or protein complexes. The resulting changes in protein or RNA content are an important means for plants to control protein homeostasis and thereby adapt to shifting environmental conditions. The activity and targeting of CDC48 are controlled by adaptor proteins, of which the plant ubiquitin regulatory X (UBX) domain-containing (PUX) proteins constitute the largest and most versatile family. However, few PUX proteins have been structurally or functionally characterized and how they participate in the substrate processing of CDC48A is not fully understood. Here, we first performed a comparative bioinformatic analysis, in which we found that the PUX proteins can be functionally divided into six types. We used this classification as a guide for our experimental efforts to elucidate how PUX proteins mediate client recognition and delivery for CDC48A-mediated unfolding. As a first step in this experimental analysis, we cloned and expressed a number of PUX protein constructs, we assessed their interaction features, and obtained crystals for several PUX domains. These bioinformatic and experimental results provide a basis for the in-depth structural and functional analysis of how PUX proteins control the CDC48A segregase.
  • Controlling Electrochemically Induced Volume Changes in Conjugated Polymers by Chemical Design: from Theory to Devices

    Moser, Maximilian; Gladisch, Johannes; Ghosh, Sarbani; Hidalgo, Tania Cecilia; Ponder, James F.; Sheelamanthula, Rajendar; Thiburce, Quentin; Gasparini, Nicola; Wadsworth, Andrew; Salleo, Alberto; Inal, Sahika; Berggren, Magnus; Zozoulenko, Igor; Stavrinidou, Eleni; McCulloch, Iain (Advanced Functional Materials, Wiley, 2021-04-17) [Article]
    Electrochemically induced volume changes in organic mixed ionic-electronic conductors (OMIECs) are particularly important for their use in dynamic microfiltration systems, biomedical machinery, and electronic devices. Although significant advances have been made to maximize the dimensional changes that can be accomplished by OMIECs, there is currently limited understanding of how changes in their molecular structures impact their underpinning fundamental processes and their performance in electronic devices. Herein, a series of ethylene glycol functionalized conjugated polymers is synthesized, and their electromechanical properties are evaluated through a combined approach of experimental measurements and molecular dynamics simulations. As demonstrated, alterations in the molecular structure of OMIECs impact numerous processes occurring during their electrochemical swelling, with sidechain length shortening decreasing the number of incorporated water molecules, reducing the generated void volumes and promoting the OMIECs to undergo different phase transitions. Ultimately, the impact of these combined molecular processes is assessed in organic electrochemical transistors, revealing that careful balancing of these phenomena is required to maximize device performance.
  • Augmented Reality in Medical Practice: From Spine Surgery to Remote Assistance.

    Cofano, Fabio; Di Perna, Giuseppe; Bozzaro, Marco; Longo, Alessandro; Marengo, Nicola; Zenga, Francesco; Zullo, Nicola; Cavalieri, Matteo; Damiani, Luca; Boges, Daniya J; Agus, Marco; Garbossa, Diego; Calì, Corrado (Frontiers in surgery, Frontiers Media SA, 2021-04-16) [Article]
    Background: While performing surgeries in the OR, surgeons and assistants often need to access several information regarding surgical planning and/or procedures related to the surgery itself, or the accessory equipment to perform certain operations. The accessibility of this information often relies on the physical presence of technical and medical specialists in the OR, which is increasingly difficult due to the number of limitations imposed by the COVID emergency to avoid overcrowded environments or external personnel. Here, we analyze several scenarios where we equipped OR personnel with augmented reality (AR) glasses, allowing a remote specialist to guide OR operations through voice and $\textit{ad-hoc}$ visuals, superimposed to the field of view of the operator wearing them. Methods: This study is a preliminary case series of prospective collected data about the use of AR-assistance in spine surgery from January to July 2020. The technology has been used on a cohort of 12 patients affected by degenerative lumbar spine disease with lumbar sciatica co-morbidities. Surgeons and OR specialists were equipped with AR devices, customized with P2P videoconference commercial apps, or customized holographic apps. The devices were tested during surgeries for lumbar arthrodesis in a multicenter experience involving author's Institutions. Findings: A total number of 12 lumbar arthrodesis have been performed while using the described AR technology, with application spanning from telementoring (3), teaching (2), surgical planning superimposition and interaction with the hologram using a custom application for Microsoft hololens (1). Surgeons wearing the AR goggles reported a positive feedback as for the ergonomy, wearability and comfort during the procedure; being able to visualize a 3D reconstruction during surgery was perceived as a straightforward benefit, allowing to speed-up procedures, thus limiting post-operational complications. The possibility of remotely interacting with a specialist on the glasses was a potent added value during COVID emergency, due to limited access of non-resident personnel in the OR. Interpretation: By allowing surgeons to overlay digital medical content on actual surroundings, augmented reality surgery can be exploited easily in multiple scenarios by adapting commercially available or custom-made apps to several use cases. The possibility to observe directly the operatory theater through the eyes of the surgeon might be a game-changer, giving the chance to unexperienced surgeons to be virtually at the site of the operation, or allowing a remote experienced operator to guide wisely the unexperienced surgeon during a procedure.
  • Antennal transcriptome sequencing and identification of candidate chemoreceptor proteins from an invasive pest, the American palm weevil, Rhynchophorus palmarum.

    Gonzalez, Francisco; Johny, Jibin; Walker, William B; Guan, Qingtian; Mfarrej, Sara; Jakše, Jernej; Montagné, Nicolas; Jacquin-Joly, Emmanuelle; Alqarni, Abdulaziz A; Al-Saleh, Mohammed Ali; Pain, Arnab; Antony, Binu (Scientific reports, Springer Science and Business Media LLC, 2021-04-16) [Article]
    For decades, the American palm weevil (APW), Rhynchophorus palmarum, has been a threat to coconut and oil palm production in the Americas. It has recently spread towards North America, endangering ornamental palms, and the expanding date palm production. Its behavior presents several parallelisms with a closely related species, R. ferrugineus, the red palm weevil (RPW), which is the biggest threat to palms in Asia and Europe. For both species, semiochemicals have been used for management. However, their control is far from complete. We generated an adult antennal transcriptome from APW and annotated chemosensory related gene families to obtain a better understanding of these species' olfaction mechanism. We identified unigenes encoding 37 odorant-binding proteins (OBPs), ten chemosensory proteins (CSPs), four sensory neuron membrane proteins (SNMPs), seven gustatory receptors (GRs), 63 odorant receptors (ORs), and 28 ionotropic receptors (IRs). Noticeably, we find out the R. ferrugineus pheromone-binding protein and pheromone receptor orthologs from R. palmarum. Candidate genes identified and annotated in this study allow us to compare these palm weevils' chemosensory gene sets. Most importantly, this study provides the foundation for functional studies that could materialize as novel pest management strategies.
  • Modulation of electronic and magnetic properties of monolayer chromium trihalides by alloy and strain engineering

    Wang, Qian; Han, Nannan; Zhang, Xuyang; Zhang, Chenhui; Zhang, Xixiang; Cheng, Yingchun (Journal of Applied Physics, AIP Publishing, 2021-04-16) [Article]
    Monolayer CrI3 is a rare ferromagnetic semiconductor with intrinsic long-range magnetic order, which makes it a great potential material in spintronic devices [Song et al., Science 360, 1214 (2018)]. To extend the applications of monolayer CrI3 in flexible devices, the modulation of its electronic and magnetic properties is important. Here, we investigated the combined effect of strain and alloy on the properties of monolayer CrI3 by first-principles calculations. Br is chosen as the alloyed element due to the similar atomic configuration and property of CrX3 (X = Br, I), and the strain is applied by simultaneously changing the in-plane lattice constants (a and b). We find that the bandgap of monolayer Cr2I6−xBrx can be tuned greatly, while the magnetic moment of monolayer Cr2I6−xBrx is regulated very little under different strain and Br concentration. This unique property of monolayer Cr2I6−xBrx under strain makes it a good candidate for the flexible spintronic devices.

View more