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Publication Metadata only 3D bioprinted glioma models(Iop Publishing Ltd, 2022) N/A; N/A; N/A; N/A; N/A; N/A; N/A; Department of Mechanical Engineering; Yığcı, Defne; Sarabi, Misagh Rezapour; Üstün, Merve; Atçeken, Nazente; Sokullu, Emel; Önder, Tuğba Bağcı; Taşoğlu, Savaş; Undergraduate Student; PhD Student; PhD Student; Researcher; Faculty Member; Faculty Member; Faculty Member; Department of Mechanical Engineering; Koç University Research Center for Translational Medicine (KUTTAM) / Koç Üniversitesi Translasyonel Tıp Araştırma Merkezi (KUTTAM); School of Medicine; Graduate School of Sciences and Engineering; Graduate School of Sciences and Engineering; N/A; School of Medicine; School of Medicine; College of Engineering; N/A; N/A; N/A; N/A; 163024; 184359; 291971Glioma is one of the most malignant types of cancer and most gliomas remain incurable. One of the hallmarks of glioma is its invasiveness. Furthermore, glioma cells tend to readily detach from the primary tumor and travel through the brain tissue, making complete tumor resection impossible in many cases. To expand the knowledge regarding the invasive behavior of glioma, evaluate drug resistance, and recapitulate the tumor microenvironment, various modeling strategies were proposed in the last decade, including three-dimensional (3D) biomimetic scaffold-free cultures, organ-on-chip microfluidics chips, and 3D bioprinting platforms, which allow for the investigation on patient-specific treatments. The emerging method of 3D bioprinting technology has introduced a time- and cost-efficient approach to create in vitro models that possess the structural and functional characteristics of human organs and tissues by spatially positioning cells and bioink. Here, we review emerging 3D bioprinted models developed for recapitulating the brain environment and glioma tumors, with the purpose of probing glioma cell invasion and gliomagenesis and discuss the potential use of 4D printing and machine learning applications in glioma modelling.Publication Open Access 3D-printed contact lenses: challenges towards translation and commercialization(Future Medicine, 2022) Yetişen, Ali K.; Department of Mechanical Engineering; Taşoğlu, Savaş; Özdalgıç, Berin; Faculty Member; PhD Student; Department of Mechanical Engineering; KU Arçelik Research Center for Creative Industries (KUAR) / KU Arçelik Yaratıcı Endüstriler Uygulama ve Araştırma Merkezi (KUAR); Koç University Research Center for Translational Medicine (KUTTAM) / Koç Üniversitesi Translasyonel Tıp Araştırma Merkezi (KUTTAM); College of Engineering; Graduate School of Sciences and Engineering; 291971; 323683NAPublication Open Access 3D-printed multi-stimuli-responsive mobile micromachines(American Chemical Society (ACS), 2020) Lee, Yun-Woo; Ceylan, Hakan; Yasa, İmmihan Ceren; Department of Mechanical Engineering; Kılıç, Uğur; Sitti, Metin; Faculty Member; Department of Mechanical Engineering; School of Medicine; College of EngineeringMagnetically actuated and controlled mobile micromachines have the potential to be a key enabler for various wireless lab-on-a-chip manipulations and minimally invasive targeted therapies. However, their embodied, or physical, task execution capabilities that rely on magnetic programming and control alone can curtail their projected performance and functional diversity. Integration of stimuli-responsive materials with mobile magnetic micromachines can enhance their design toolbox, enabling independently controlled new functional capabilities to be defined. To this end, here, we show three-dimensional (3D) printed size-controllable hydrogel magnetic microscrews and microrollers that respond to changes in magnetic fields, temperature, pH, and divalent cations. We show two-way size-controllable microscrews that can reversibly swell and shrink with temperature, pH, and divalent cations for multiple cycles. We present the spatial adaptation of these microrollers for penetration through narrow channels and their potential for controlled occlusion of small capillaries (30 μm diameter). We further demonstrate one-way size-controllable microscrews that can swell with temperature up to 65% of their initial length. These hydrogel microscrews, once swollen, however, can only be degraded enzymatically for removal. Our results can inspire future applications of 3D- and 4D-printed multifunctional mobile microrobots for precisely targeted obstructive interventions (e.g., embolization) and lab- and organ-on-a-chip manipulations.Publication Metadata only [BMIM][OAc] coating layer makes activated carbon almost completely selective for CO2(Elsevier Science Sa, 2022) N/A; N/A; Department of Chemical and Biological Engineering; Department of Chemical and Biological Engineering; Durak, Özce; Zeeshan, Muhammad; Keskin, Seda; Uzun, Alper; Master Student; PhD Student; Faculty Member; Faculty Member; Department of Chemical and Biological Engineering; 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); Graduate School of Sciences and Engineering; Graduate School of Sciences and Engineering; College of Engineering; College of Engineering; N/A; N/A; 40548; 59917Tuning the molecular affinity of porous materials towards desired gases is important to achieve superior selectivity for a target separation. Herein, we report a novel composite, prepared by coating an ordinary activated carbon (AC) with an ionic liquid (IL) (1-butyl-3-methylimidazolium acetate, [BMIM][OAc]) offering an almost complete CO2 selectivity over N-2 and CH4. Data indicated that pore blockage by the IL accompanied with the enhancement in polarity and reduction in the hydrophobic character of the surface hindered the sorption of N-2 and CH4. For CO2, on the other hand, new chemisorption and physisorption sites became available associated with the IL layer on the surface, making the composite material significantly selective. Newly formed chemisorption sites attributed to the cation's acidic C2H sites, which become available with bi-layer formation. Presence of multiple competitive sorption sites with different energies was further proven with thermal analysis and detailed spectroscopic analysis. Data showed that CO2/CH4 and CO2/N-2 ideal selectivities boosted from 3.3 to 688.3 (2.3 to 54.7) and from 15.6 to 903.7 (7.1 to 74.3) at 0.1 (1) bar and 25 degrees C, respectively, upon the deposition of IL layer. Especially at lower pressures, the IL/AC material became almost fully selective for CO2 offering ideal selectivities in the order of several tens of thousands. To the best of our knowledge, the remarkable enhancement in the ideal CO2 selectivity by a straightforward post-synthesis modification of an ordinary AC, as reported here, sets a new benchmark in high-performance and efficient gas separation for similar porous materials.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 computational multicriteria optimization approach to controller design for pysical human-robot interaction(Institute of Electrical and Electronics Engineers (IEEE), 2020) Tokatlı, Ozan; Patoğlu, Volkan; Department of Mechanical Engineering; Aydın, Yusuf; Başdoğan, Çağatay; Faculty Member; Department of Mechanical Engineering; Graduate School of Sciences and Engineering; College of Engineering; N/A; 125489Physical human-robot interaction (pHRI) integrates the benefits of human operator and a collaborative robot in tasks involving physical interaction, with the aim of increasing the task performance. However, the design of interaction controllers that achieve safe and transparent operations is challenging, mainly due to the contradicting nature of these objectives. Knowing that attaining perfect transparency is practically unachievable, controllers that allow better compromise between these objectives are desirable. In this article, we propose a multicriteria optimization framework, which jointly optimizes the stability robustness and transparency of a closed-loop pHRI system for a given interaction controller. In particular, we propose a Pareto optimization framework that allows the designer to make informed decisions by thoroughly studying the tradeoff between stability robustness and transparency. The proposed framework involves a search over the discretized controller parameter space to compute the Pareto front curve and a selection of controller parameters that yield maximum attainable transparency and stability robustness by studying this tradeoff curve. The proposed framework not only leads to the design of an optimal controller, but also enables a fair comparison among different interaction controllers. In order to demonstrate the practical use of the proposed approach, integer and fractional order admittance controllers are studied as a case study and compared both analytically and experimentally. The experimental results validate the proposed design framework and show that the achievable transparency under fractional order admittance controller is higher than that of integer order one, when both controllers are designed to ensure the same level of stability robustness.Publication Metadata only A containerized proof-of-concept implementation of LightChain system(Ieee, 2020) N/A; N/A; Department of Computer Engineering; N/A; Department of Computer Engineering; Department of Computer Engineering; Hassanzadeh-Nazarabadi, Yahya; Nayal, Nazir; Hamdan, Shadi Sameh; Özkasap, Öznur; Küpçü, Alptekin; PhD Student; Faculty Member; Master Student; Faculty Member; Faculty Member; Department of Computer Engineering; Graduate School of Sciences and Engineering; College of Engineering; Graduate School of Sciences and Engineering; College of Engineering; College of Engineering; N/A; N/A; N/A; 113507; 168060LightChain is the first Distributed Hash Table (DHT)-based blockchain with a logarithmic asymptotic message and memory complexity. In this demo paper, we present the software architecture of our open-source implementation of LightChain, as well as a novel deployment scenario of the entire LightChain system on a single machine aiming at results reproducibility.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 diversity combination model incorporating an inward bias for interaural time-level difference cue integration in sound lateralization(MDPI, 2020) N/A; N/A; Department of Computer Engineering; N/A; Mojtahedi, Sina; Erzin, Engin; Ungan, Pekcan; PhD Student; 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 lab-scale manufacturing system environment to investigate data-driven production control approaches(Elsevier Sci Ltd, 2021) N/A; N/A; Department of Business Administration; Khayyati, Siamak; Tan, Barış; PhD Student; Faculty Member; Department of Business Administration; Graduate School of Sciences and Engineering; College of Administrative Sciences and Economics; N/A; 28600Controlling production and release of material into a manufacturing system effectively can lower work-inprogress inventory and cycle time while ensuring the desired throughput. With the extensive data collected from manufacturing systems, developing an effective real-time control policy helps achieving this goal. Validating new control methods using the real manufacturing systems may not be possible before implementation. Similarly, using simulation models can result in overlooking critical aspects of the performance of a new control method. In order to overcome these shortcomings, using a lab-scale physical model of a given manufacturing system can be beneficial. We discuss the construction and the usage of a lab-scale physical model to investigate the implementation of a data-driven production control policy in a production/inventory system. As a datadriven production control policy, the marking-dependent threshold policy is used. This policy leverages the partial information gathered from the demand and production processes by using joint simulation and optimization to determine the optimal thresholds. We illustrate the construction of the lab-scale model by using LEGO Technic parts and controlling the model with the marking-dependent policy with the data collected from the system. By collecting data directly from the lab-scale production/inventory system, we show how and why the analytical modeling of the system can be erroneous in predicting the dynamics of the system and how it can be improved. These errors affect optimization of the system using these models adversely. In comparison, the datadriven method presented in this study is considerably less prone to be affected by the differences between the physical system and its analytical representation. These experiments show that using a lab-scale manufacturing system environment is very useful to investigate different data-driven control policies before their implementation and the marking-dependent threshold policy is an effective data-driven policy to optimize material flow in manufacturing systems.