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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 A photonic Carnot engine powered by a spin-star network(European Physical Society (EPS), 2017) Türkpençe, Deniz; Paternostro, Mauro; Department of Physics; Altıntaş, Ferdi; Müstecaplıoğlu, Özgür Esat; Researcher; Faculty Member; Department of Physics; College of Sciences; N/A; 1674We propose a spin-star network, where a central spin-(1/2), acting as a quantum fuel, is coupled to N outer spin-(1/2) particles. If the network is in thermal equilibrium with a heat bath, the central spin can have an effective temperature, higher than that of the bath, scaling nonlinearly with N. Such temperature can be tuned with the anisotropy parameter of the coupling. Using a beam of such central spins to pump a micromaser cavity, we determine the dynamics of the cavity field using a coarse-grained master equation. We find that the central-spin beam effectively acts as a hot reservoir to the cavity field and brings it to a thermal steady state whose temperature benefits from the same nonlinear enhancement with N and results in a highly efficient photonic Carnot engine. The validity of our conclusions is tested against the presence of atomic and cavity damping using a microscopic master equation method for typical microwave cavity-QED parameters. The role played by quantum coherence and correlations on the scaling effect is pointed out. An alternative scheme where the spin-(1/2) is coupled to a macroscopic spin-(N/2) particle is also discussed. Copyright (C) EPLA, 2017Publication 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 Artificial gauge fields for the Bose-Hubbard model on a checkerboard superlattice and extended Bose-Hubbard model(Springer, 2012) Department of Physics; Işkın, Menderes; Faculty Member; Department of Physics; College of Sciences; 29659We study the effects of an artificial gauge field on the ground-state phases of the Bose-Hubbard model on a checkerboard superlattice in two dimensions, including the superfluid phase and the Mott and alternating Mott insulators. First, we discuss the single-particle Hofstadter problem, and show that the presence of a checkerboard superlattice gives rise to a magnetic flux-independent energy gap in the excitation spectrum. Then, we consider the many-particle problem, and derive an analytical mean-field expression for the superfluid-Mott and superfluid-alternating-Mott insulator phase transition boundaries. Finally, since the phase diagram of the Bose-Hubbard model on a checkerboard superlattice is in many ways similar to that of the extended Bose-Hubbard model, we comment on the effects of magnetic field on the latter model, and derive an analytical mean-field expression for the superfluid-insulator phase transition boundaries as well.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 Automatic estimation of age distributions from the first Ottoman Empire population register series by using deep learning(Multidisciplinary Digital Publishing Institute (MDPI), 2021) Department of History; Kabadayı, Mustafa Erdem; Can, Yekta Said; Faculty Member; Department of History; College of Social Sciences and Humanities; 33267; N/ARecently, an increasing number of studies have applied deep learning algorithms for extracting information from handwritten historical documents. In order to accomplish that, documents must be divided into smaller parts. Page and line segmentation are vital stages in the Handwritten Text Recognition systems; it directly affects the character segmentation stage, which in turn deter-mines the recognition success. In this study, we first applied deep learning-based layout analysis techniques to detect individuals in the first Ottoman population register series collected between the 1840s and the 1860s. Then, we employed horizontal projection profile-based line segmentation to the demographic information of these detected individuals in these registers. We further trained a CNN model to recognize automatically detected ages of individuals and estimated age distributions of people from these historical documents. Extracting age information from these historical registers is significant because it has enormous potential to revolutionize historical demography of around 20 successor states of the Ottoman Empire or countries of today. We achieved approximately 60% digit accuracy for recognizing the numbers in these registers and estimated the age distribution with Root Mean Square Error 23.61.Publication Open Access Band alignment engineers faradaic and capacitive photostimulation of neurons without surface modification(American Physical Society (APS), 2019) Department of Electrical and Electronics Engineering; N/A; Department of Chemical and Biological Engineering; Department of Molecular Biology and Genetics; Srivastava, Shashi Bhushan; Melikov, Rustamzhon; Aria, Mohammad Mohammadi; Dikbaş, Uğur Meriç; Kavaklı, İbrahim Halil; Nizamoğlu, Sedat; Researcher; PhD Student; Master Student; Faculty Member; Faculty Member; Department of Electrical and Electronics Engineering; Department of Chemical and Biological Engineering; Department of Molecular Biology and Genetics; College of Engineering; Graduate School of Sciences and Engineering; College of Sciences; N/A; N/A; N/A; N/A; 40319; 130295Photovoltaic substrates have attracted significant attention for neural photostimulation. The control of the Faradaic and capacitive (non-Faradaic) charge transfer mechanisms by these substrates are critical for safe and effective neural photostimulation. We demonstrate that the intermediate layer can directly control the strength of the capacitive and Faradaic processes under physiological conditions. To resolve the Faradaic and capacitive stimulations, we enhance photogenerated charge density levels by incorporating PbS quantum dots into a poly(3-hexylthiophene-2,5-diyl):([6,6]-Phenyl-C61-butyric acid methyl ester (P3HT:PCBM) blend. This enhancement stems from the simultaneous increase of absorption, well matched band alignment of PbS quantum dots with P3HT:PCBM, and smaller intermixed phase-separated domains with better homogeneity and roughness of the blend. These improvements lead to the photostimulation of neurons at a low light intensity level of 1 mW cm(-2), which is within the retinal irradiance level. These findings open up an alternative approach toward superior neural prosthesis.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 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.