Welcome to the Koç University Institutional Academic Repository
The Koç University Institutional Academic Repository (KUHub Research) is a state-of-the-art academic repository that consolidates all academic outputs—such as articles, conference proceedings, theses, research data, and more—produced by the university since its establishment in 1993.
KUHub Research adheres to the principles of Open Access and FAIR (Findable, Accessible, Interoperable, Reusable), providing access to the bibliographic records, research data, and full texts of research outputs. Equipped with innovative features such as Author Profile pages and enhanced tools, KUHub Research aims to enhance the visibility of researchers both nationally and internationally. KUHub Research aims to preserve and maintain Koç University's valuable academic legacy for future generations while also serving the needs of today’s researchers.
For more information or inquiries please contact openaccess@ku.edu.tr
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Recent Submissions
Mechanisms of fast CO2 fixation reaction by enoyl-CoA carboxylases/reductase
(European Synchrotron Radiation Facility, 2028-01-01) Chretien, Anaïs; Ertem Kuzucu, Fatma Betul; Summers, Jacob; Wranik, Maximilian; 0000-0001-8480-1443; 0000-0002-2144-989x; 0000-0003-3113-0353; 0000-0002-2482-0164
Carbon dioxide (CO2) is an atmospheric greenhouse gas that feeds all life, plays a critical role in global warming, and could constitute an inexpensive carbon source for future sustainable industries. While synthetic chemistry lacks suitable catalysts to functionalize carbon dioxide in mild reaction conditions, autotrophs do it constantly, and thus there is increasing interest in exploiting the CO2-fixation mechanisms offered by nature. In this exchange proposal, we propose fast time-resolved structural-dynamics studies of one of the fastest CO2-fixation enzymes, enoyl-CoA carboxylase/reductase (ECR), using ambient temperature serial X-ray crystallography on Beamline ID29, ESRF, which achieves 10μs resolution. This study will reveal details of the enzyme subunit coupling as well as the enzyme-substrate interactions to correlate the structural and functional states of the enzyme during fixation and pave the way for faster biomolecule productions using engineered C-cycling enzymes.
Mechanisms of fast CO2 fixation reaction by enoyl-CoA carboxylases/reductase
(European Synchrotron Radiation Facility, 2027-01-01) Summers, Jacob; Sanctis, Daniele; Vlahakis, Niko; Knight, Victoria; Ertem Kuzucu, Fatma Betul; Chretien, Anaïs; Nurizzo, Didier; 0000-0003-3113-0353; 0000-0003-0391-8290; 0000-0002-5092-0265; 0000-0002-2144-989x; 0000-0001-8480-1443; 0000-0002-7367-5098
Carbon dioxide (CO2) is an atmospheric greenhouse gas that feeds all life, plays a critical role in global warming, and could constitute an inexpensive carbon source for future sustainable industries. While synthetic chemistry lacks suitable catalysts to functionalize carbon dioxide in mild reaction conditions, autotrophs do it constantly, and thus there is increasing interest in exploiting the CO2-fixation mechanisms offered by nature. In this exchange proposal, we propose fast time-resolved structural-dynamics studies of one of the fastest CO2-fixation enzymes, enoyl-CoA carboxylase/reductase (ECR), using ambient temperature serial X-ray crystallography on Beamline ID29, ESRF, which achieves 10μs resolution. This study will reveal details of the enzyme subunit coupling as well as the enzyme-substrate interactions to correlate the structural and functional states of the enzyme during fixation and pave the way for faster biomolecule productions using engineered C-cycling enzymes.
Nanoscale detection of EpCAM-positive extracellular vesicles using magnetic beads and interferometric scattering microscopy
(2025-09-17) Aygün, Uğur; Yaman, Sena; Parlatan, Ugur; Durmus, Naside Gozde; Department of Electrical and Electronics Engineering; College of Engineering
Extracellular vesicles (EVs) are nanoscale biomarkers that reflect the molecular state of their cell of origin. Epithelial cell adhesion molecule (EpCAM) is frequently enriched in tumor-derived EVs, offering diagnostic and monitoring potential for epithelial cancers. We developed a label-free detection method combining magnetic bead–based molecular targeting with interferometric scattering microscopy (iSCAT) for single-particle visualization of EpCAM-positive EVs. Streptavidin-coated magnetic nanoparticles (50 nm) were conjugated with biotinylated anti-EpCAM antibodies and incubated with EVs from breast cancer (MCF-7, high EpCAM) and murine colon adenocarcinoma (MC38, low EpCAM) cell lines. Nanoparticle tracking analysis confirmed bead functionalization, and Western blotting verified differential EpCAM expression. iSCAT imaging on thin-film substrates revealed distinct scattering patterns: bare beads showed uniform profiles, high EpCAM EV–bead complexes exhibited elongated morphologies, and low EpCAM samples showed minimal change. The method requires <1 µL of sample, avoids labeling artifacts, and enables real-time, high-contrast imaging. This adaptable platform can be tailored to other EV subpopulations, providing a sensitive, label-free approach for targeted EV detection in research and clinical diagnostics.
Optimizing task generation and assignment in crowdpicking
(SAGE, 2025-08-31) Yıldız, Barış; Ovalı, Yasemin; Department of Industrial Engineering; College of Engineering
As omnichannel operations become increasingly important for meeting diverse customer expectations in retail, continuous innovation in service and business models is essential to maintain a competitive edge. While effective order fulfillment is key to omnichannel success, the manual picking process in physical stores, one of the major driver of fulfillment costs, still offers substantial opportunities for improvement. This article focuses on the crowdpicking model as an innovative approach to manage online order picking operations in physical stores by leveraging existing in-store customers, offering a business model with considerable potential. We explore the real-time assignment of orders to in-store customers using machine learning to identify effective assignment policies. These policies are combined with a task-decomposition strategy to reduce picking costs and enhance crowdpicker participation as a key resource. The proposed crowdpicking model and its real-time management framework are tested on real-world data. Our results show that a well-managed crowdpicking system can lower order picking costs by more than 20% and provide actionable insights for managers in designing such systems.
Fine tools for fine work. The form and function of ‘Small Craft Tools’ from Bronze Age Kaymakçı (Türkiye)
(Univerzita Karlova, Filozofická fakulta, 2025-08-26) Roosevelt, Christopher; Kaner, Tunç; Schaupp, Kathleen C.; Pieniążek, Magda; ANAMED (Koç University Research Center for Anatolian Civilizations); Research Center; ANAMED
Tools have always played an extremely important, defining role in human life. A closer look at Small Craft Tools (SCTs), such as drills, awls, punches, and small chisels, not only allows us an insight into the exact production techniques of artefacts but can also provide information on regional exchanges of goods and craft specializations in individual settlements. Nevertheless, these artefacts have been largely neglected in previous studies, and there seems to be no agreement among the few authors who have described such small bronze tools in more detail. The large number of middle and late Bronze Age SCTs found at Kaymakçı (Türkiye) was used as an opportunity to study their typology, characteristics, and use -wear. A total of 31 SCTs were found in only six years of excavation (2014–2021). In relation to the years of excavation, this is comparable to the number of SCTs found at Hattusa. This indicates the importance of Kaymakçı as a potential leather/textile production center. This study describes and characterizes the SCTs from Kaymakçı in detail. The authors are able to identify distinct differences between these tools and make suggestions for a more unified classification, underlining that such items are worthy of closer consideration in future studies.