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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 Metadata only A microstructure-sensitive model for simulating the impact response of a high-manganese austenitic steel(Asme, 2016) N/A; N/A; Department of Mechanical Engineering; Mirzajanzadeh, Morad; Canadinç, Demircan; PhD Student; Faculty Member; Department of Mechanical Engineering; Koç University Surface Science and Technology Center (KUYTAM) / Koç Üniversitesi Yüzey Teknolojileri Araştırmaları Merkezi (KUYTAM); Graduate School of Sciences and Engineering; College of Engineering; N/A; 23433Microstructurally informed macroscopic impact response of a high-manganese austenitic steel was modeled through incorporation of the viscoplastic self-consistent (VPSC) crystal plasticity model into the ANSYS LS-DYNA nonlinear explicit finite-element (FE) frame. Voce hardening flow rule, capable of modeling plastic anisotropy in microstructures, was utilized in the VPSC crystal plasticity model to predict the micromechanical response of the material, which was calibrated based on experimentally measured quasi-static uniaxial tensile deformation response and initially measured textures. Specifically, hiring calibrated Voce parameters in VPSC, a modified material response was predicted employing local velocity gradient tensors obtained from the initial FE analyses as a new boundary condition for loading state. The updated micromechanical response of the material was then integrated into the macroscale material model by calibrating the Johnson-Cook (JC) constitutive relationship and the corresponding damage parameters. Consequently, we demonstrate the role of geometrically necessary multi-axial stress state for proper modeling of the impact response of polycrystalline metals and validate the presented approach by experimentally and numerically analyzing the deformation response of the Hadfield steel (HS) under impact loading.Publication Open Access Application of stochastic flows to the sticky Brownian motion equation(Multidisciplinary Digital Publishing Institute (MDPI), 2017) Hajri, Hatem; Arnaudon, Marc; Department of Mathematics; Çağlar, Mine; Faculty Member; Department of Mathematics; College of Sciences; 105131We investigate the relationship between the levels of industry collaboration and entrepreneurial activities at universities and the employment choices of their science and engineering doctoral students. Using data from 176 U.S. universities over the period 1996-2005, we document that more interaction with industry at a university is typically associated with more of the university's doctoral students choosing industry employment. We also document a positive relationship between universities' licenses and startups and their graduates' post-doctoral study choices.Publication Open Access Attenuation constant measurements of clear glass samples at the low terahertz band(Wiley, 2020) Department of Electrical and Electronics Engineering; Yılmaz, Türker; Akan, Özgür Barış; Faculty Member; Department of Electrical and Electronics Engineering; College of EngineeringThe technical performance requirements from wireless communication networks are continuously rising. One method to satisfy the demands is increasing the carrier frequency to the millimetre wave or low terahertz band spectrum to utilise wider operation bandwidth. In order to facilitate the studies in this frequency range, the corresponding electromagnetic (EM) wave properties, channel attributes and material characteristics need to be analytically formulated. In line with these, this Letter initially presents the theoretical expressions governing the EM wave transmission across a conducting medium. Then, by using the relative S21 parameter quantities in the proposed attenuation constant (alpha) computation technique, the alpha results of the measurements performed between 260 and 350 GHz for the clear window glass samples of different thicknesses are given. This Letter concludes with the evaluation of the outcomes.Publication Open Access Bistable behavior of a two-mode Bose-Einstein condensate in an optical cavity(Maik Nauka/Interperiodica Publishing, 2013) Safaei, S.; Tanatar, B.; Department of Physics; Müstecaplıoğlu, Özgür Esat; Faculty Member; Department of Physics; College of Sciences; 1674We consider a two-component Bose-Einstein condensate in a one-dimensional optical cavity. Specifically, the condensate atoms are taken to be in two degenerate modes due to their internal hyperfine spin degrees of freedom and they are coupled to the cavity field and an external transverse laser field in a Raman scheme. A parallel laser also excites the cavity mode. When the pump laser is far detuned from its resonance atomic transition frequency, an effective nonlinear optical model of the cavity-condensate system is developed under the discrete mode approximation (DMA), while matter-field coupling has been considered beyond the rotating wave approximation. By analytical and numerical solutions of the nonlinear dynamical equations, we examine the mean cavity field and population difference (magnetization) of the condensate modes. The stationary solutions of both the mean cavity field and normalized magnetization demonstrate bistable behavior under certain conditions for the laser pump intensity and matter-field coupling strength.Publication Open Access BlockSim-Net: a network-based blockchain simulator(TÜBİTAK, 2022) Ramachandran, Prashanthi; Agrawal, Nandini; Department of Computer Engineering; Biçer, Osman; Küpçü, Alptekin; Faculty Member; Department of Computer Engineering; College of Engineering; Graduate School of Sciences and Engineering; N/A; 168060Since its proposal by Eyal and Sirer (CACM '13), selfish mining attacks on proof-of-work blockchains have been studied extensively. The main body of this research aims at both studying the extent of its impact and defending against it. Yet, before any practical defense is deployed in a real world blockchain system, it needs to be tested for security and dependability. However, real blockchain systems are too complex to conduct any test on or benchmark the developed protocols. Instead, some simulation environments have been proposed recently, such as BlockSim (Maher et al., SIGMETRICS Perform. Eval. Rev. '19), which is a modular and easy-to-use blockchain simulator. However, BlockSim's structure is insufficient to capture the essence of a real blockchain network, as the simulation of an entire network happens over a single CPU. Such a lack of decentralization can cause network issues such as propagation delays being simulated in an unrealistic manner. In this work, we propose BlockSim-Net, a modular, efficient, high performance, distributed, network-based blockchain simulator that is parallelized to better reflect reality in a blockchain simulation environment.Publication Metadata only Building quadtrees for spatial data under local differential privacy(Springer Science and Business Media Deutschland Gmbh, 2023) Department of Computer Engineering; Alptekin, Ece; Gürsoy, Mehmet Emre; Department of Computer Engineering; Graduate School of Sciences and Engineering; College of EngineeringSpatial decompositions are commonly used in the privacy literature for various purposes such as range query answering, spatial indexing, count-of-counts histograms, data summarization, and visualization. Among spatial decomposition techniques, quadtrees are a popular and well-known method. In this paper, we study the problem of building quadtrees for spatial data under the emerging notion of Local Differential Privacy (LDP). We first propose a baseline solution inspired from a state-of-the-art method from the centralized DP literature and adapt it to LDP. Motivated by the observation that the baseline solution causes large noise accumulation due to its iterative strategy, we then propose a novel solution which utilizes a single data collection step from users, propagates density estimates to all nodes, and finally performs structural corrections to the quadtree. We experimentally evaluate the baseline solution and the proposed solution using four real-world location datasets and three utility metrics. Results show that our proposed solution consistently outperforms the baseline solution, and furthermore, the resulting quadtrees provide high accuracy in practical tasks such as spatial query answering under conventional privacy levels.Publication Metadata only Cell-specific and post-hoc spatial clustering tests based on nearest neighbor contingency tables(Korean Statistical Soc, 2017) Department of Mathematics; Ceyhan, Elvan; Faculty Member; Department of Mathematics; College of Sciences; N/ASpatial clustering patterns in a multi-class setting such as segregation and association between classes have important implications in various fields, e.g., in ecology, and can be tested using nearest neighbor contingency tables (NNCTs). a NNCT is constructed based on the types of the nearest neighbor (NN) pairs and their frequencies. We survey the cell-specific (or pairwise) and overall segregation tests based on NNCTs in literature and introduce new ones and determine their asymptotic distributions. We demonstrate that cell-specific tests enjoy asymptotic normality, while overall tests have chi-square distributions asymptotically. Some of the overall tests are confounded by the unstable generalized inverse of the rank-deficient covariance matrix. To overcome this problem, we propose rank-based corrections for the overall tests to stabilize their behavior. We also perform an extensive' Monte Carlo simulation study to compare the finite sample performance of the tests in terms of empirical size and power based on the asymptotic and Monte Carlo critical values and determine the tests that have the best size and power performance and are robust to differences in relative abundances (of the classes). in addition to the cell-specific tests, we discuss one(-class)-versus-rest type of tests as post-hoc,tests after a significant overall test. We also introduce the concepts of total, strong, and partial segregatioN/Association to differentiate different levels of these patterns. We compare the new tests with the existing NNCT-tests in literature with simulations and illustrate the tests on an ecological data set. (C) 2016 the Korean Statistical Society. Published by Elsevier B.V. all rights reserved.Publication Open Access CO2 absorption into primary and secondary amine aqueous solutions with and without copper ions in a bubble column(TÜBİTAK, 2022) Güler, Cansu; Uzunlar, Erdal; Department of Chemical and Biological Engineering; Erkey, Can; Yousefzadeh, Hamed; Faculty Member; Researcher; Department of Chemical and Biological Engineering; College of Engineering; 29633; N/AChemical absorption of CO2 into aqueous amine solutions using a nonstirred bubble column was experimentally investigated. The performance of CO2 absorption of four different primary and secondary amines including monoethanolamine (MEA), piperazine (PZ), 2-piperidineethanol (2PE), and homopiperazine (HPZ) were compared. The effects of initial concentration of amine, the inlet mole fraction of CO2, and solution temperature on the rate of CO2 absorption and CO2 loading (mol CO2/mol amine) were studied in the range of 0.02–1 M, 0.10–0.15, and 25–40 °C, respectively. The effect of the presence of copper ions in the amine solution on CO2 loading was also studied. By comparison of the breakthrough curves of the amines at different operational conditions, it was revealed that the shortest and longest time for the appearance of the breakthrough point was observed for MEA and HPZ solutions, respectively. CO2 loading of MEA, 2PE, PZ, and HPZ aqueous solutions at 25 °C, 0.2 M of initial concentration of amine, and 0.15 of inlet mole fraction of CO2 were 1.06, 1.14, 1.13, and 1.18 mol CO2/mol amine, respectively. By decreasing the inlet mole fraction of CO2 from 0.15 to 0.10, CO2 loading slightly decreased. As the initial concentration of amine and temperature decreased, CO2 loading increased. Also, the presence of copper ions in the absorbent solution resulted in a decrease in the CO2 loading of MEA and HPZ aqueous solutions. In case of PZ and 2PE amines, adding copper ions led to precipitation even at low copper ion concentrations.Publication Open Access Collective excitations of a laser driven atomic condensate in an optical cavity(Maik Nauka/Interperiodica Publishing, 2013) Öztop, B.; Türeci, H. E.; Department of Physics; Müstecaplıoğlu, Özgür Esat; Faculty Member; Department of Physics; College of Sciences; 1674We theoretically examine collective excitations of an optically driven atomic Bose-Einstein condensate, coupled to a high-finesse optical cavity. This open system has been recently used for the experimental demonstration of the Dicke superradiance of cavity photons, which is simultaneously and mutually triggered by spontaneous breaking of translational symmetry of the condensate into a crystalline order. We first develop a Hartree-Fock mean field dynamical model of the physical system. Using this model, we compute the dynamics of the cavity photons, the condensate density profile and the Dicke phase transition diagram. Both the imaginary-time and real-time evolution methods are used in the calculations. Collective excitations are determined by the solving Bogoliubov-de Gennes equations. The spectrum, softening of the modes and energetic hierarchy of excitations are determined.