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Publication Metadata only 10-NJ multipass-cavity femtosecond CR3+: LiCAF laser pumped by low-power single-mode diodes(Optical Society of America, 2009) Kärtner, Franz X.; Fujimoto, James G.; Demirbaş, Ümit; Department of Physics; Sennaroğlu, Alphan; Faculty Member; Department of Physics; College of Sciences; 23851We report on the generation of 9.9-nJ, 95-fs pulses at a repetition rate of 9.58 MHz from a multipass-cavity Cr3+:LiCAF laser pumped by single-mode diodes with a total absorbed pump power of only 540 mW.Publication Open Access 3D printing of elastomeric bioinspired complex adhesive microstructures(Wiley, 2021) Dayan, Cem Balda; Chun, Sungwoo; Krishna Subbaiah, Nagaraj; Drotlef, Dirk Michael; Akolpoğlu, Mükrime Birgül; Department of Mechanical Engineering; Sitti, Metin; Faculty Member; Department of Mechanical Engineering; College of Engineering; School of Medicine; 297104Bioinspired elastomeric structural adhesives can provide reversible and controllable adhesion on dry/wet and synthetic/biological surfaces for a broad range of commercial applications. Shape complexity and performance of the existing structural adhesives are limited by the used specific fabrication technique, such as molding. To overcome these limitations by proposing complex 3D microstructured adhesive designs, a 3D elastomeric microstructure fabrication approach is implemented using two-photon-polymerization-based 3D printing. A custom aliphatic urethane-acrylate-based elastomer is used as the 3D printing material. Two designs are demonstrated with two combined biological inspirations to show the advanced capabilities enabled by the proposed fabrication approach and custom elastomer. The first design focuses on springtail- and gecko-inspired hybrid microfiber adhesive, which has the multifunctionalities of side-surface liquid super-repellency, top-surface liquid super-repellency, and strong reversible adhesion features in a single fiber array. The second design primarily centers on octopus- and gecko-inspired hybrid adhesive, which exhibits the benefits of both octopus- and gecko-inspired microstructured adhesives for strong reversible adhesion on both wet and dry surfaces, such as skin. This fabrication approach could be used to produce many other 3D complex elastomeric structural adhesives for future real-world applications.Publication Open Access A diversity combination model incorporating an inward bias for interaural time-level difference cue integration in sound lateralization(Multidisciplinary Digital Publishing Institute (MDPI), 2020) N/A; Department of Computer Engineering; Mojtahedi, Sina; Erzin, Engin; Ungan, Pekcan; Faculty Member; Faculty Member; Department of Computer Engineering; Graduate School of Sciences and Engineering; College of Engineering; School of Medicine; N/A; 34503; N/AA sound source with non-zero azimuth leads to interaural time level differences (ITD and ILD). Studies on hearing system imply that these cues are encoded in different parts of the brain, but combined to produce a single lateralization percept as evidenced by experiments indicating trading between them. According to the duplex theory of sound lateralization, ITD and ILD play a more significant role in low-frequency and high-frequency stimulations, respectively. In this study, ITD and ILD, which were extracted from a generic head-related transfer functions, were imposed on a complex sound consisting of two low- and seven high-frequency tones. Two-alternative forced-choice behavioral tests were employed to assess the accuracy in identifying a change in lateralization. Based on a diversity combination model and using the error rate data obtained from the tests, the weights of the ITD and ILD cues in their integration were determined by incorporating a bias observed for inward shifts. The weights of the two cues were found to change with the azimuth of the sound source. While the ILD appears to be the optimal cue for the azimuths near the midline, the ITD and ILD weights turn to be balanced for the azimuths far from the midline.Publication Metadata only A facile synthesis of monodisperse cobalt–ruthenium alloy nanoparticles as catalysts for the dehydrogenation of morpholine borane and the hydrogenation of various organic compounds(Royal Soc Chemistry, 2022) Can, Hasan; Can, Sumeyra; Ebiri, Rustem; Department of Chemistry; Metin, Önder; Faculty Member; Department of Chemistry; College of Sciences; 46962Herein we report a novel wet-chemical protocol for the composition-controlled synthesis of monodisperse cobalt-ruthenium (CoRu) alloy NPs and their catalysis in the hydrolytic dehydrogenation of morpholine borane (MB) for chemical hydrogen storage and the hydrogenation of various organic compounds using MB as a hydrogen source. Monodisperse CoRu NPs with an average particle size of 1.7 +/- 0.6 nm at three different alloy compositions were prepared by the presented novel protocol that comprises the reduction of in situ formed ruthenium(iii) oleate complex with dicobalt octacarbonyl (Co-2(CO)(8)) in the presence of oleylamine (OAm). Next, as-synthesized CoRu alloy NPs were supported on carbon black (VC) and reduced graphene oxide (rGO) to study their catalysis in the dehydrogenation of MB and the transfer hydrogenation of various organic compouns bearing unsaturated functional groups (nitro, nitrile and carbonyl) using MB as a hydrogen source, respectively. VC-CoRu nanocatalysts exhibited a higher catalytic activity in hydrogen generation from the hydrolysis of MB with an initial turnover frequency (TOF) of 95 mol H-2*(mol (Co + Ru) min)(-1) while rGO-CoRu nanocatalysts showed better catalytic performance in the transfer hydrogenation reactions. All tested unsatured organic compounds (30 examples in total) are converted into corresponding hydrogenated products with the yields reaching up to 99% under mild conditions.Publication Metadata only A genome-wide functional screen identifies enhancer and protective genes for amyloid beta-peptide toxicity(Multidisciplinary Digital Publishing Institute (MDPI), 2023) Picon-Pages, Pol; Bosch-Morato, Monica; Subirana, Laia; Rubio-Moscardo, Francisca; Guivernau, Biuse; Fanlo-Ucar, Hugo; Herrera-Fernandez, Victor; Vicente, Ruben; Fernandez-Fernandez, Jose M.; Garcia-Ojalvo, Jordi; Oliva, Baldomero; Posas, Francesc; de Nadal, Eulalia; Munoz, Francisco J.; N/A; N/A; N/A; Department of Computer Engineering; Department of Computer Engineering; Zeylan, Melisa Ece; Şenyüz, Simge; Gürsoy, Attila; Keskin, Özlem; PhD Student; Master Student; Faculty Member; Faculty Member; Department of Computer Engineering; Graduate School of Sciences and Engineering; Graduate School of Sciences and Engineering; College of Engineering; College of Engineering; N/A; N/A; 8745; 26605Alzheimer's disease (AD) is known to be caused by amyloid beta-peptide (A beta) misfolded into beta-sheets, but this knowledge has not yet led to treatments to prevent AD. To identify novel molecular players in A beta toxicity, we carried out a genome-wide screen in Saccharomyces cerevisiae, using a library of 5154 gene knock-out strains expressing A beta(1-42). We identified 81 mammalian orthologue genes that enhance A beta(1-42) toxicity, while 157 were protective. Next, we performed interactome and text-mining studies to increase the number of genes and to identify the main cellular functions affected by A beta oligomers (oA beta). We found that the most affected cellular functions were calcium regulation, protein translation and mitochondrial activity. We focused on SURF4, a protein that regulates the store-operated calcium channel (SOCE). An in vitro analysis using human neuroblastoma cells showed that SURF4 silencing induced higher intracellular calcium levels, while its overexpression decreased calcium entry. Furthermore, SURF4 silencing produced a significant reduction in cell death when cells were challenged with oA beta(1-42), whereas SURF4 overexpression induced A beta(1-42) cytotoxicity. In summary, we identified new enhancer and protective activities for A beta toxicity and showed that SURF4 contributes to oA beta(1-42) neurotoxicity by decreasing SOCE activity.Publication Open Access A micropatterned human-specific neuroepithelial tissue for modeling gene and drug-induced neurodevelopmental defects(Wiley, 2021) Sahni, Geetika; Chang, Shu-Yung; Meng, Jeremy Teo Choon; Tan, Jerome Zu Yao; Fatien, Jean Jacques Clement; Bonnard, Carine; Utami, Kagistia Hana; Chan, Puck Wee; Tan, Thong Teck; Altunoglu, Umut; Pouladi, Mahmoud; Toh, Yi-Chin; Kayserili, Hülya; Reversade, Bruno; Faculty Member; School of Medicine; 7945; N/AThe generation of structurally standardized human pluripotent stem cell (hPSC)-derived neural embryonic tissues has the potential to model genetic and environmental mediators of early neurodevelopmental defects. Current neural patterning systems have so far focused on directing cell fate specification spatio-temporally but not morphogenetic processes. Here, the formation of a structurally reproducible and highly-organized neuroepithelium (NE) tissue is directed from hPSCs, which recapitulates morphogenetic cellular processes relevant to early neurulation. These include having a continuous, polarized epithelium and a distinct invagination-like folding, where primitive ectodermal cells undergo E-to-N-cadherin switching and apical constriction as they acquire a NE fate. This is accomplished by spatio-temporal patterning of the mesoendoderm, which guides the development and self-organization of the adjacent primitive ectoderm into the NE. It is uncovered that TGF beta signaling emanating from endodermal cells support tissue folding of the prospective NE. Evaluation of NE tissue structural dysmorphia, which is uniquely achievable in the model, enables the detection of apical constriction and cell adhesion dysfunctions in patient-derived hPSCs as well as differentiating between different classes of neural tube defect-inducing drugs.Publication Open Access A near-infrared benzothiazole-based chemodosimeter for rapid and selective detection of hydrogen sulfide(Turkish Chemical Society / Türkiye Kimya Derneği, 2021) Department of Chemistry; Kölemen, Safacan; Faculty Member; Department of Chemistry; Koç University Surface Science and Technology Center (KUYTAM) / Koç Üniversitesi Yüzey Teknolojileri Araştırmaları Merkezi (KUYTAM); Koç University Boron and Advanced Materials Application and Research Center (KUBAM) / Koç Üniversitesi Bor ve İleri Malzemeler Uygulama ve Araştırma Merkezi (KUBAM); College of Sciences; 272051Hydrogen sulfide (H2S) is a biologically relevant gaseous molecule, which involves in a wide variety of physiological and pathological processes. Thus, detection of H2S is highly valuable in order to clarify its complex roles. In this study, a new benzothiazole-based donor-acceptor type H 2S selective chemodosimeter (HP-1) was synthesized and its H2S detection capabilities were investigated in aqueous solutions. HP-1 exhibited a red-shifted absorption signal at 530 nm and a near-infrared (NIR) fluorescence peak at 680 nm as a result of enhanced intramolecular charge transfer (ICT) in the presence of H2S, which enabled a selective and very rapid ratiometric fluorescent detection. HP-1 was also showed to be highly sensitive toward H2S with a very low limit of detection value.Publication Open Access A promising catalyst for the dehydrogenation of perhydro-dibenzyltoluene: Pt/Al2O3 prepared by supercritical CO2 deposition(Multidisciplinary Digital Publishing Institute (MDPI), 2022) Modisha, Phillimon; Garidzirai, Rudaviro; Rommel, Sarshad; Uzunlar, Erdal; Aindow, Mark; Bessarabov, Dmitri; Department of Chemical and Biological Engineering; Bozbağ, Selmi Erim; Erkey, Can; Güneş, Hande; Researcher; Faculty Member; Department of Chemical and Biological Engineering; Koç University Tüpraş Energy Center (KUTEM) / Koç Üniversitesi Tüpraş Enerji Merkezi (KÜTEM); College of Engineering; N/A; 29633; N/APt/Al2O3 catalysts prepared via supercritical deposition (SCD), with supercritical CO2, wet impregnation (WI) methods and a selected benchmark catalyst, were evaluated for the dehydrogenation of perhydro-dibenzyltoluene (H18-DBT) at 300 degrees C in a batch reactor. After ten dehydrogenation runs, the average performance of the catalyst prepared using SCD was the highest compared to the benchmark and WI-prepared catalysts. The pre-treatment of the catalysts with the product (dibenzyltoluene) indicated that the deactivation observed is mainly due to the adsorbed H0-DBT blocking the active sites for the reactant (H18-DBT). Furthermore, the SCD method afforded a catalyst with a higher dispersion of smaller sized Pt particles, thus improving catalytic performance towards the dehydrogenation of H18-DBT. The particle diameters of the SCD- and WI-prepared catalysts varied in the ranges of 0.6-2.2 nm and 0.8-3.4 nm and had average particle sizes of 1.1 nm and 1.7 nm, respectively. Energy dispersive X-ray spectroscopy analysis of the catalysts after ten dehydrogenation runs revealed the presence of carbon. In this study, improved catalyst performance led to the production of more liquid-based by-products and carbon material compared to catalysts with low catalytic performance.Publication Metadata only A statistical approach to control particle size of poly(acrylic acid) stabilized iron oxide nanoparticles(Routledge, 2006) N/A; N/A; Department of Chemistry; Department of Chemistry; Acar, Havva Funda Yağcı; Demirer, Miray; Faculty Member; Undergraduate Student; Department of Chemistry; College of Sciences; College of Sciences; 178902; N/APoly(acrylic acid) coated superparamagnetic iron oxide nanoparticles were prepared in aqueous solutions of iron salts with in situ coating of poly(acrylic acid). Influence of reaction variables, namely, iron concentration, reactive(COOH)/iron mole ratio, base (NH4OH) amount and polymer molecular weight, primarily on hydrodynamic size and stability of the particles was investigated. Also, size and stability of washed particles (no excess coating material) and magnetization as a function of these variables were studied. In order to design best set of experiments and correlate the results to variables, statistics programs Design Expert 7.0 and Minitab14 were used. Results will be discussed in this paper.Publication Open Access A tissue adhesion-controllable and biocompatible small-scale hydrogel adhesive robot(Wiley, 2022) Lee, Y.W.; Chun, S.; Son, D.; Hu, X.; Schneider, M.; Department of Mechanical Engineering; Sitti, Metin; Faculty Member; Department of Mechanical Engineering; College of Engineering; School of Medicine; 297104Recently, the realization of minimally invasive medical interventions on targeted tissues using wireless small-scale medical robots has received an increasing attention. For effective implementation, such robots should have a strong adhesion capability to biological tissues and at the same time easy controlled detachment should be possible, which has been challenging. To address such issue, a small-scale soft robot with octopus-inspired hydrogel adhesive (OHA) is proposed. Hydrogels of different Young's moduli are adapted to achieve a biocompatible adhesive with strong wet adhesion by preventing the collapse of the octopus-inspired patterns during preloading. Introduction of poly(N-isopropylacrylamide) hydrogel for dome-like protuberance structure inside the sucker wall of polyethylene glycol diacrylate hydrogel provides a strong tissue attachment in underwater and at the same time enables easy detachment by temperature changes due to its temperature-dependent volume change property. It is finally demonstrated that the small-scale soft OHA robot can efficiently implement biomedical functions owing to strong adhesion and controllable detachment on biological tissues while operating inside the body. Such robots with repeatable tissue attachment and detachment possibility pave the way for future wireless soft miniature robots with minimally invasive medical interventions.