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Publication Open Access 3D bioprinted organ?on?chips(Wiley, 2022) Mustafaoğlu, Nur; Zhang, Yu Shrike; Department of Mechanical Engineering; N/A; N/A; Dabbagh, Sajjad Rahmani; Sarabi, Misagh Rezapour; Birtek, Mehmet Tuğrul; Taşoğlu, Savaş; Faculty Member; Department of Mechanical Engineering; KU Arçelik Research Center for Creative Industries (KUAR) / KU Arçelik Yaratıcı Endüstriler Uygulama ve Araştırma Merkezi (KUAR); Koç Üniversitesi İş Bankası Yapay Zeka Uygulama ve Araştırma Merkezi (KUIS AI)/ Koç University İş Bank Artificial Intelligence Center (KUIS AI); College of Engineering; Graduate School of Social Sciences and Humanities; Graduate School of Sciences and Engineering; N/A; N/A; N/A; 291971Organ-on-a-chip (OOC) platforms recapitulate human in vivo-like conditions more realistically compared to many animal models and conventional two-dimensional cell cultures. OOC setups benefit from continuous perfusion of cell cultures through microfluidic channels, which promotes cell viability and activities. Moreover, microfluidic chips allow the integration of biosensors for real-time monitoring and analysis of cell interactions and responses to administered drugs. Three-dimensional (3D) bioprinting enables the fabrication of multicell OOC platforms with sophisticated 3D structures that more closely mimic human tissues. 3D-bioprinted OOC platforms are promising tools for understanding the functions of organs, disruptive influences of diseases on organ functionality, and screening the efficacy as well as toxicity of drugs on organs. Here, common 3D bioprinting techniques, advantages, and limitations of each method are reviewed. Additionally, recent advances, applications, and potentials of 3D-bioprinted OOC platforms for emulating various human organs are presented. Last, current challenges and future perspectives of OOC platforms are discussed.Publication Open Access 3D engineered neural co-culture model and neurovascular effects of marine fungi-derived citreohybridonol(American Institute of Physics (AIP) Publishing, 2022) Polat, İrem; Özkaya, Ferhat Can; El-Neketi, Mona; Ebrahim, Weaam; Şengül, Gülgün; Department of Mechanical Engineering; Sokullu, Emel; Sarabi, Misagh Rezapour; Taşoğlu, Savaş; Faculty Member; Faculty Member; Department of Mechanical Engineering; Koç University Research Center for Translational Medicine (KUTTAM) / Koç Üniversitesi Translasyonel Tıp Araştırma Merkezi (KUTTAM); Koç Üniversitesi İş Bankası Yapay Zeka Uygulama ve Araştırma Merkezi (KUIS AI)/ Koç University İş Bank Artificial Intelligence Center (KUIS AI); KU Arçelik Research Center for Creative Industries (KUAR) / KU Arçelik Yaratıcı Endüstriler Uygulama ve Araştırma Merkezi (KUAR); School of Medicine; Graduate School of Sciences and Engineering; College of Engineering; 163024; N/A; 291971Marine-based biomolecules are emerging metabolites that have gained attention for developing novel biomaterials, drugs, and pharmaceutical in vitro platforms. Here, we developed a 3D engineered neural co-culture model via a 3D prototyped sliding frame-platform for multi-step UV lithography and investigated the neurovascular potential of citreohybridonol in neuroblastoma treatment. Citreohybridonol was isolated from a sponge-derived fungus Penicillium atrovenetum. The model was characterized by Fourier-transform infrared spectroscopy and scanning electron microscopy analysis. Human umbilical cord vein endothelial cells (HUVECs) and neuroblastoma (SH-SY5Y) cell lines were encapsulated in gelatin methacrylate (GelMA) with and without citreohybridonol. The effect of citreohybridonol on the proliferation capacity of cells was assessed via cell viability and immunostaining assays. GelMA and 3D culture characterization indicated that the cells were successfully encapsulated as axenic and mixed with/without citreohybridonol. The cytotoxic test confirmed that the 3D microenvironment was non-toxic for cultural experiments, and it showed the inhibitory effects of citreohybridonol on SH-SY5Y cells and induced the proliferation of HUVECs. Finally, immunohistochemical staining demonstrated that citreohybridonol suppressed SH-SY5Y cells and induced vascularization of HUVECs in mixed 3D cell culture.Publication Open Access A comparative study on GaSb epilayers grown on nominal and vicinal Si(100) substrates by molecular beam epitaxy(Institute of Physics (IOP) Publishing, 2020) Arpapay, Burcu; Suyolcu, Y. Eren; van Aken, Peter A.; Gülgün, Mehmet Ali; Serincan, Uğur; Çorapçıoğlu, Gülcan; n2STAR-Koç University Nanofabrication and Nanocharacterization Center for Scientifc and Technological Advanced ResearchThe direct growth of GaSb buffer layers on Si substrates is attracting considerable interest in the integration of group III-Sb based device structures on lower-cost Si substrates. Here, we present the effect of various growth steps on the defect types and defect density that are crucial for advancing high crystal quality GaSb buffer layer on nominal/vicinal Si substrate. As a growth step, the applied thermal annealing at an intermediate step provided a decrease in the threading dislocation (TD) density down to 1.72 x 10(8) cm(-2), indicating a more effective method compared to post-growth annealing. Additionally, the importance of period number and position of GaSb/AlSb superlattice layers inserted in GaSb epilayers is demonstrated. In the case of the GaSb epilayers grown on vicinal substrates, the APB density as low as 0.06 mu m(-1) and TD density of 1.98 x 10(8) cm(-2) were obtained for the sample grown on 4 degrees miscut Si(100) substrate.Publication Open Access Advanced materials and device architectures for magnetooptical spatial light modulators(Wiley-VCH, 2019) N/A; Department of Electrical and Electronics Engineering; Kharratian, Soheila; Onbaşlı, Mehmet Cengiz; Ürey, Hakan; Faculty Member; Faculty Member; Department of Electrical and Electronics Engineering; Graduate School of Sciences and Engineering; N/A; 258783; 8579Faraday and Kerr rotations are magnetooptical (MO) effects used for rotating the polarization of light in transmission and reflection from a magnetized medium, respectively. MO effects combined with intrinsically fast magnetization reversal, which can go down to a few tens of femtoseconds or less, can be applied in magnetooptical spatial light modulators (MOSLMs) promising for nonvolatile, ultrafast, and high-resolution spatial modulation of light. With the recent progress in low-power switching of magnetic and MO materials, MOSLMs may lead to major breakthroughs and benefit beyond state-of-the-art holography, data storage, optical communications, heads-up displays, virtual and augmented reality devices, and solid-state light detection and ranging (LIDAR). In this study, the recent developments in the growth, processing, and engineering of advanced materials with high MO figures of merit for practical MOSLM devices are reviewed. The challenges with MOSLM functionalities including the intrinsic weakness of MO effect and large power requirement for switching are assessed. The suggested solutions are evaluated, different driving systems are investigated, and resulting device architectures are benchmarked. Finally, the research opportunities on MOSLMs for achieving integrated, high-contrast, and low-power devices are presented.Publication Open Access An advanced workflow for single-particle imaging with the limited data at an X-ray free-electron laser(International Union of Crystallography, 2020) Assalauova, Dameli; Kim, Young Yong; Bobkov, Sergey; Khubbutdinov, Ruslan; Rose, Max; Alvarez, Roberto; Andreasson, Jakob; Balaur, Eugeniu; Contreras, Alice; Gelisio, Luca; Hajdu, Janos; Hunter, Mark S.; Kurta, Ruslan P.; Li, Haoyuan; McFadden, Matthew; Nazari, Reza; Schwander, Peter; Teslyuk, Anton; Walter, Peter; Xavier, P. Lourdu; Yoon, Chun Hong; Zaare, Sahba; Ilyin, Viacheslav A.; Kirian, Richard A.; Hogue, Brenda G.; Aquila, Andrew; Vartanyants, Ivan A.; Department of Molecular Biology and Genetics; Demirci, Hasan; Faculty Member; Department of Molecular Biology and Genetics; College of Sciences; 307350An improved analysis for single-particle imaging (SPI) experiments, using the limited data, is presented here. Results are based on a study of bacteriophage PR772 performed at the Atomic, Molecular and Optical Science instrument at the Linac Coherent Light Source as part of the SPI initiative. Existing methods were modified to cope with the shortcomings of the experimental data: inaccessibility of information from half of the detector and a small fraction of single hits. The general SPI analysis workflow was upgraded with the expectation-maximization based classification of diffraction patterns and mode decomposition on the final virus-structure determination step. The presented processing pipeline allowed us to determine the 3D structure of bacteriophage PR772 without symmetry constraints with a spatial resolution of 6.9 nm. The obtained resolution was limited by the scattering intensity during the experiment and the relatively small number of single hits.Publication Open Access An integrated computational-experimental hierarchical approach for the rational design of an IL/UiO-66 composite offering infinite CO2 selectivity(Wiley, 2022) Department of Chemical and Biological Engineering; Department of Chemistry; Zeeshan, Muhammad; Gülbalkan, Hasan Can; Durak, Özce; Haşlak, Zeynep Pınar; Ünal, Uğur; Keskin, Seda; Uzun, Alper; PhD Student; Faculty Member; Faculty Member; Department of Chemical and Biological Engineering; Department of Chemistry; Koç University Tüpraş Energy Center (KUTEM) / Koç Üniversitesi Tüpraş Enerji Merkezi (KÜTEM); Koç University Surface Science and Technology Center (KUYTAM) / Koç Üniversitesi Yüzey Teknolojileri Araştırmaları Merkezi (KUYTAM); College of Engineering; College of Sciences; Graduate School of Sciences and Engineering; N/A; N/A; N/A; N/A; 42079; 40548; 59917Owing to the possibility of generating theoretically unlimited numbers of ionic liquid (IL)-metal-organic framework (MOF) combinations, experimental studies on IL/MOF composites for gas separation applications are mostly conducted on a trial-and-error basis. To address this problem, an integrated computational-experimental hierarchical approach is presented for selecting the best IL-MOF combination for a target gas separation application. For this purpose, UiO-66 and pyrrolidinium-based ILs are chosen as the parent MOF and IL family, respectively, and three powerful computational tools, Conductor-like Screening Model for Realistic Solvents calculations, density functional theory calculations, and grand canonical Monte Carlo simulations, are integrated to identify the most promising IL-UiO-66 combination as 1-n-butyl-1-methylpyrrolidinium dicyanamide/UiO-66, [BMPyrr][DCA]/UiO-66. Then, this composite is synthesized, characterized in deep detail, and tested for CO2/N-2, CO2/CH4, and CH4/N-2 separations. Results demonstrate that [BMPyrr][DCA]/UiO-66 offers an extraordinary gas separation performance, with practically infinite CO2 and CH4 selectivities over N-2 at 15 degrees C and at low pressures. The integrated hierarchical approach proposed in this work paves the way for the rational design and development of novel IL/MOF composites offering exceptional performance for any desired gas separation application.Publication Open Access Automatic CNN-based Arabic numeral spotting and handwritten digit recognition by using deep transfer learning in Ottoman population registers(Multidisciplinary Digital Publishing Institute (MDPI), 2020) Department of History; Kabadayı, Mustafa Erdem; Can, Yekta Said; Faculty Member; Department of History; College of Social Sciences and Humanities; 33267; N/AHistorical manuscripts and archival documentation are handwritten texts which are the backbone sources for historical inquiry. Recent developments in the digital humanities field and the need for extracting information from the historical documents have fastened the digitization processes. Cutting edge machine learning methods are applied to extract meaning from these documents. Page segmentation (layout analysis), keyword, number and symbol spotting, handwritten text recognition algorithms are tested on historical documents. For most of the languages, these techniques are widely studied and high performance techniques are developed. However, the properties of Arabic scripts (i.e., diacritics, varying script styles, diacritics, and ligatures) create additional problems for these algorithms and, therefore, the number of research is limited. In this research, we first automatically spotted the Arabic numerals from the very first series of population registers of the Ottoman Empire conducted in the mid-nineteenth century and recognized these numbers. They are important because they held information about the number of households, registered individuals and ages of individuals. We applied a red color filter to separate numerals from the document by taking advantage of the structure of the studied registers (numerals are written in red). We first used a CNN-based segmentation method for spotting these numerals. In the second part, we annotated a local Arabic handwritten digit dataset from the spotted numerals by selecting uni-digit ones and tested the Deep Transfer Learning method from large open Arabic handwritten digit datasets for digit recognition. We achieved promising results for recognizing digits in these historical documents.Publication Open Access Biocompatible quantum funnels for neural photostimulation(American Chemical Society (ACS), 2019) N/A; Department of Chemical and Biological Engineering; N/A; Department of Electrical and Electronics Engineering; Department of Molecular Biology and Genetics; N/A; Jalali, Houman Bahmani; Doğru-Yüksel, Itır Bakış; Eren, Güncem Özgün; Nizamoğlu, Sedat; Karatüm, Onuralp; Melikov, Rustamzhon; Dikbaş, Uğur Meriç; Kavaklı, İbrahim Halil; Sadeghi, Sadra; Yıldız, Erdost; Ergün, Çağla; Şahin, Afsun; PhD Student; Faculty Member; PhD Student; Master Student; Faculty Member; PhD Student; PhD Student; Faculty Member; Department of Chemical and Biological Engineering; Department of Electrical and Electronics Engineering; Department of Molecular Biology and Genetics; Koç University Research Center for Translational Medicine (KUTTAM) / Koç Üniversitesi Translasyonel Tıp Araştırma Merkezi (KUTTAM); Graduate School of Sciences and Engineering; College of Engineering; College of Sciences; School of Medicine; N/A; N/A; N/A; 130295; N/A; N/A; N/A; 40319; N/A; N/A; N/A; 171267Neural photostimulation has high potential to understand the working principles of complex neural networks and develop novel therapeutic methods for neurological disorders. A key issue in the light-induced cell stimulation is the efficient conversion of light to bioelectrical stimuli. In photosynthetic systems developed in millions of years by nature, the absorbed energy by the photoabsorbers is transported via nonradiative energy transfer to the reaction centers. Inspired by these systems, neural interfaces based on biocompatible quantum funnels are developed that direct the photogenerated charge carriers toward the bionanojunction for effective photostimulation. Funnels are constructed with indium-based rainbow quantum dots that are assembled in a graded energy profile. Implementation of a quantum funnel enhances the generated photoelectrochemical current 215% per unit absorbance in comparison with ungraded energy profile in a wireless and free-standing mode and facilitates optical neuromodulation of a single cell. This study indicates that the control of charge transport at nanoscale can lead to unconventional and effective neural interfaces.Publication Open Access Broadband enhancement of Faraday effect using magnetoplasmonic metasurfaces(Springer, 2020) N/A; Department of Electrical and Electronics Engineering; Kharratian, Soheila; Ürey, Hakan; Onbaşlı, Mehmet Cengiz; Faculty Member; Faculty Member; Department of Electrical and Electronics Engineering; Graduate School of Sciences and Engineering; College of Engineering; N/A; 8579; 258783Magnetooptical Faraday effect enables ultrafast photonic devices based on nonreciprocal polarization rotation; however, the intrinsic weakness of Faraday effect prevents miniaturization and practical applications of nonreciprocal photonic devices. Magnetoplasmonics offers new mechanisms for enhancing magnetooptical effects using surface plasmon resonances, which generally have narrow bandwidths. Using finite-difference time-domain modeling, we demonstrate a magnetoplasmonic metasurface, which remarkably enhances the Faraday effect in a wide spectral range. While Faraday rotation in a bare bismuth-substituted yttrium iron garnet film is below 0.02 degrees in the studied range of 600-1600 nm, the proposed metasurface yields few degrees of rotation in a broad band with a maximum exceeding 6.5 degrees, which indicates about three orders of magnitude enhancement. We also show that by optimizing the configuration of the system including the geometry and excitation parameters, the metasurface response and operation band can be tuned further, and rotation values higher than 20 degrees can be achieved. Finally, we present guidelines for designing magnetoplasmonic metasurfaces.Publication Open Access Bulk-heterojunction photocapacitors with high open-circuit voltage for low light intensity photostimulation of neurons(Royal Society of Chemistry (RSC), 2021) Department of Electrical and Electronics Engineering; Department of Molecular Biology and Genetics; N/A; Department of Chemical and Biological Engineering; N/A; Srivastava, Shashi Bhushan; Melikov, Rustamzhon; Yıldız, Erdost; Dikbaş, Uğur Meriç; Sadeghi, Sadra; Kavaklı, İbrahim Halil; Şahin, Afsun; Nizamoğlu, Sedat; Researcher; PhD Student; PhD Student; Master Student; PhD Student; Faculty Member; Faculty Member; Faculty Member; Department of Electrical and Electronics Engineering; Department of Molecular Biology and Genetics; Department of Chemical and Biological Engineering; Koç University Research Center for Translational Medicine (KUTTAM) / Koç Üniversitesi Translasyonel Tıp Araştırma Merkezi (KUTTAM); Graduate School of Sciences and Engineering; College of Engineering; College of Sciences; School of Medicine; N/A; N/A; N/A; N/A; N/A; 40319; 171267; 130295High-level transduction control of light to bioelectricity is an important goal for the realization of superior neuron-device interfaces that can be used for regulating fundamental cellular processes to cure neurological disorders. In this study, a single-junction, wireless, and capacitive-charge-injecting optoelectronic biointerface with negligible faradaic reactions by using a high open-circuit voltage (0.75 V) bulk heterojunction of PTB7-Th:PC71BM is designed and demonstrated. The biointerface generates a 2-fold higher photocurrent in comparison with P3HT:PC61BM having an open-circuit voltage of 0.55 V. Furthermore, we observed that light intensity is logarithmically correlated with the open-circuit voltage of solar cells, and the photovoltage of the biointerfaces varies the switching speed of capacitive charge-transfer. Finally, pulse trains of capacitive stimuli at a low light intensity of 20 mW cm−2elicit action potential generation in primary hippocampal neurons extracted from E15-E17 Wistar Albino rats. These findings show the great promise of high open-circuit voltage bulk heterojunction biointerfaces for non-genetic, all-optical and safe modulation of neurons.