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Publication Open Access 3D printed microneedles for point of care biosensing applications(Multidisciplinary Digital Publishing Institute (MDPI), 2022) Department of Mechanical Engineering; Sarabi, Misagh Rezapour; Nakhjavani, Sattar Akbar; Taşoğlu, Savaş; Faculty Member; Department of Mechanical Engineering; Koç University Research Center for Translational Medicine (KUTTAM) / Koç Üniversitesi Translasyonel Tıp Araştırma Merkezi (KUTTAM); 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); Graduate School of Sciences and Engineering; College of Engineering; N/A; N/A; 291971Microneedles (MNs) are an emerging technology for user-friendly and minimally invasive injection, offering less pain and lower tissue damage in comparison to conventional needles. With their ability to extract body fluids, MNs are among the convenient candidates for developing biosensing setups, where target molecules/biomarkers are detected by the biosensor using the sample collected with the MNs. Herein, we discuss the 3D printing of microneedle arrays (MNAs) toward enabling point-of-care (POC) biosensing applications.Publication Open Access Adaptive Q control for tapping-mode nanoscanning using a piezoactuated bimorph probe(American Institute of Physics (AIP) Publishing, 2007) Department of Mechanical Engineering; Günev, İhsan; Varol, Aydın; Karaman, Sertaç; Başdoğan, Çağatay; Master Student; Faculty Member; Department of Mechanical Engineering; College of Engineering; N/A; N/A; N/A; 125489A new approach, called adaptive Q control, for tapping-mode atomic force microscopy (AFM) is introduced and implemented on a homemade AFM setup utilizing a laser Doppler vibrometer and a piezoactuated bimorph probe. In standard Q control, the effective Q factor of the scanning probe is adjusted prior to the scanning depending on the application. However, there is a trade-off in setting the effective Q factor of an AFM probe. The Q factor is either increased to reduce the tapping forces or decreased to increase the maximum achievable scan speed. Realizing these two benefits simultaneously using standard Q control is not possible. In adaptive Q control, the Q factor of the probe is set to an initial value as in standard Q control, but then modified on the fly during scanning when necessary to achieve this goal. In this article, we present the basic theory behind adaptive Q control, the electronics enabling the online modification of the probe's effective Q factor, and the results of the experiments comparing three different methods: scanning (a) without Q control, (b) with standard Q control, and (c) with adaptive Q control. The results show that the performance of adaptive Q control is superior to the other two methods.
Publication Metadata only An electrochemical gelation method for patterning conductive PEDOT:PSS hydrogels(2019) Feig, Vivian Rachel; Tran, Helen; Lee, Minah; Liu, Kathy; Huang, Zhuojun; Mackanic, David G.; Bao, Zhenan; Department of Mechanical Engineering; Beker, Levent; Faculty Member; Department of Mechanical Engineering; College of Engineering; 308798Due to their high water content and macroscopic connectivity, hydrogels made from the conducting polymer PEDOT:PSS are a promising platform from which to fabricate a wide range of porous conductive materials that are increasingly of interest in applications as varied as bioelectronics, regen-erative medicine, and energy storage. Despite the promising properties of PEDOT:PSS-based porous materials, the ability to pattern PEDOT:PSS hydrogels is still required to enable their integration with multifunctional and multichannel electronic devices. In this work, a novel electrochemical gelation (“electrogelation”) method is presented for rapidly patterning PEDOT:PSS hydrogels on any conductive template, including curved and 3D surfaces. High spatial resolution is achieved through use of a sacrificial metal layer to generate the hydrogel pattern, thereby enabling high-performance conducting hydrogels and aerogels with desirable material properties to be introduced into increasingly complex device architecturesPublication Metadata only Development of color tunable aqueous cds-cysteine quantum dots with improved efficiency and investigation of cytotoxicity(Amer Scientific Publishers, 2010) N/A; N/A; Department of Chemistry; Department of Chemistry; Öztürk, Sinan S.; Selçukbiricik, Fatih; Acar, Havva Funda Yağcı; Master Student; N/A; Faculty Member; Department of Chemistry; Graduate School of Sciences and Engineering; College of Sciences; College of Sciences; N/A; N/A; 178902Cysteine capped aqueous CdS quantum dots with improved luminescence and excellent colloidal-luminescence stability were developed in a simple one pot aqueous method from safer precursors at low temperatures. Investigation of size and luminescence as a function of cysteine amount, pH and temperature revealed an optimum value for all these variables to maximize the quantum yield. Cysteine:Cd ratio of 2, reaction pH of 9.5 and synthesis at room temperature-30 degrees C emerged as the best conditions for the highest QY of 19%. Yet, QY can be improved up to 55% if QDs are cleaned from excess cysteine and ions and redispersed in pH 7 medium. Size of the QDs, therefore the color of luminescence, can be tuned by the reaction temperature in this simple process. Higher temperatures provide larger particles. Cell uptake and cell viability studies in a wide range of doses and different incubation times with MCF-7 and HeLa cell lines revealed cell dependent differences. MCF-7 cells uptake more ODs but are much more viable than HeLa cells. At low doses such as 0.025 mg QD/ml all cells are viable. At 24 h incubation times MCF-7 cells demonstrate viability above 75% up to 0.15 mg QD/ml. On the other hand HeLa cells loose viability with increasing dose.Publication Open Access Enhanced sinterability, thermal conductivity and dielectric constant of glass-ceramics with PVA and BN additions(Multidisciplinary Digital Publishing Institute (MDPI), 2022) Akkasoğlu, Ufuk; Çiçek, Buğra; N/A; Department of Chemistry; Arıbuğa, Dilara; Balcı, Özge; Researcher; Department of Chemistry; Koç University AKKİM Boron-Based Materials _ High-technology Chemicals Research _ Application Center (KABAM) / Koç Üniversitesi AKKİM Bor Tabanlı Malzemeler ve İleri Teknoloji Kimyasallar Uygulama ve Araştırma Merkezi (KABAM); Graduate School of Sciences and Engineering; College of Sciences; N/A; 295531With the rapid development of the microelectronics industry, many efforts have been made to improve glass-ceramics' sinterability, thermal conductivity, and dielectric properties, which are essential components of electronic materials. In this study, low-alkali borosilicate glass-ceramics with PVA addition and glass-BN composites were prepared and successfully sintered at 770 degrees C. The phase composition, density, microstructure, thermal conductivity, and dielectric constant were investigated. It was shown that PVA addition contributes to the densification process of glass-ceramics (~88% relative density, with closed/open pores in the microstructure) and improves the thermal conductivity of glass material from 1.489 to 2.453 W/K.m. On the other hand, increasing BN addition improves microstructures by decreasing porosities and thus increasing relative densities. A glass-12 wt. % BN composite sample exhibited almost full densification after sintering and presented apparent and open pores of 2.6 and 0.08%, respectively. A high thermal conductivity value of 3.955 W/K.m and a low dielectric constant of 3.00 (at 5 MHz) were observed in this material. Overall, the resulting glass-ceramic samples showed dielectric constants in the range of 2.40-4.43, providing a potential candidate for various electronic applications.Publication Metadata only Fluorescent protein integrated white LEDs for displays(Iop Publishing Ltd, 2016) N/A; Department of Electrical and Electronics Engineering; N/A; N/A; Department of Molecular Biology and Genetics; Department of Electrical and Electronics Engineering; Press, Daniel Aaron; Melikov, Rustamzhon; Çonkar, Deniz; Karalar, Elif Nur Fırat; Nizamoğlu, Sedat; Researcher; PhD Student; PhD Student; Faculty Member; Faculty Member; Department of Molecular Biology and Genetics; Department of Electrical and Electronics Engineering; College of Engineering; Graduate School of Sciences and Engineering; Graduate School of Sciences and Engineering; College of Sciences; College of Engineering; N/A; N/A; N/A; 206349; 130295The usage time of displays (e.g., TVs, mobile phones, etc) is in general shorter than their functional life time, which worsens the electronic waste (e-waste) problem around the world. The integration of biomaterials into electronics can help to reduce the e-waste problem. In this study, we demonstrate fluorescent protein integrated white LEDs to use as a backlight source for liquid crystal (LC) displays for the first time. We express and purify enhanced green fluorescent protein (eGFP) and monomeric Cherry protein (mCherry), and afterward we integrate these proteins as a wavelength-converter on a blue LED chip. The protein-integrated backlight exhibits a high luminous efficacy of 248 lm/W-opt and the area of the gamut covers 80% of the NTSC color gamut. The resultant colors and objects in the image on the display can be well observed and distinguished. Therefore, fluorescent proteins show promise for display applications.Publication Open Access Glioma-on-a-chip models(Multidisciplinary Digital Publishing Institute (MDPI), 2021) İlçi, İrem Sultan; Department of Mechanical Engineering; N/A; N/A; Önder, Tuğba Bağcı; Taşoğlu, Savaş; Üstün, Merve; Dabbagh, Sajjad Rahmani; Faculty Member; 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); School of Medicine; College of Engineering; Graduate School of Sciences and Engineering; Graduate School of Social Sciences and Humanities; 184359; 291971; N/A; N/AGlioma, as an aggressive type of cancer, accounts for virtually 80% of malignant brain tumors. Despite advances in therapeutic approaches, the long-term survival of glioma patients is poor (it is usually fatal within 12-14 months). Glioma-on-chip platforms, with continuous perfusion, mimic in vivo metabolic functions of cancer cells for analytical purposes. This offers an unprecedented opportunity for understanding the underlying reasons that arise glioma, determining the most effective radiotherapy approach, testing different drug combinations, and screening conceivable side effects of drugs on other organs. Glioma-on-chip technologies can ultimately enhance the efficacy of treatments, promote the survival rate of patients, and pave a path for personalized medicine. In this perspective paper, we briefly review the latest developments of glioma-on-chip technologies, such as therapy applications, drug screening, and cell behavior studies, and discuss the current challenges as well as future research directions in this field.Publication Metadata only Non-invasive raman classification comparison with pXRF of monochrome and related qing porcelains: lead-rich-, lead-poor-, and alkali-based glazes(Multidisciplinary Digital Publishing Institute (MDPI), 2024) Colomban, Philippe; Gallet, Xavier; Fournery, Nicolas; Quette, Béatrice; Franci, Gülsu Şimşek; Koç University Surface Science and Technology Center (KUYTAM) / Koç Üniversitesi Yüzey Teknolojileri Araştırmaları Merkezi (KUYTAM)Chinese porcelain with an optically clear colored glaze, imported to Europe from the Kangxi period (1662–1722, Qing Dynasty) onwards was highly collected by the French Elite of the 18th century. The bright colors with a clear, shiny glaze were unlike anything produced in Europe at that time. The colors of enamelled artifacts (on biscuits or already glazed porcelain) can be fully monochrome or consist of associations of large monochromatic areas with or without application of gilding. Non-invasive portable XRF and mobile Raman analyses have previously shown their effectiveness in the characterization of (colored) glassy silicates. In this study, we compare the Raman signatures of twenty-one Chinese artifacts fully—or with major monochrome area (sancai)—decorated with blue, turquoise (or celectian blue), honey-yellow, green, eggplant, and red color. Different types of glazes are identified and confirmed by pXRF: lead-rich, lead-poor-alkali, lead-doped alkali, and alkali-based compositions. However, an unexpected low level of lead is observed in the turquoise glazes, likely to optimize the gloss. Raman spectroscopy appears more reliable to compare the Pb content than pXRF. This work presents Raman spectral signatures of glazes that can potentially be used for non-invasive object classification and counterfeit detection.Publication Open Access Optimum folding pathways of proteins: their determination and properties(American Institute of Physics (AIP) Publishing, 2006) Department of Chemical and Biological Engineering; Güner, Pınar Tatar; Arkun, Yaman; Erman, Burak; Teaching Faculty; Faculty Member; Faculty Member; Department of Chemical and Biological Engineering; College of Engineering; 188227; 108526; 179997We develop a dynamic optimization technique for determining optimum folding pathways of proteins starting from different initial configurations. A coarse-grained Go model is used. Forces acting on each bead are (i) the friction force, (ii) forces from bond length constraints, (iii) excluded volume constraints, and (iv) attractive forces between residue pairs that are in contact in the native state. An objective function is defined as the total attractive energy between nonbonded residues, which are neighbors in the native state. The objective function is minimized over all feasible paths, satisfying bond length and excluded volume constraints. The optimization problem is nonconvex and contains a large number of constraints. An augmented Lagrangian method with a penalty barrier function was used to solve the problem. The method is applied to a 36-residue protein, chicken villin headpiece. Sequences of events during folding of the protein are determined for various pathways and analyzed. The relative time scales are compared and scaled according to experimentally measured events. Formation times of the helices, turn, and the loop agree with experimental data. We obtain the overall folding time of the protein in the range of 600 ns-1.2 mu s that is smaller than the experimental result of 4-5 mu s, showing that the optimal folding times that we obtain may be possible lower bounds. Time dependent variables during folding and energies associated with short- and long-range interactions between secondary structures are analyzed in modal space using Karhunen-Loeve expansion.Publication Metadata only Roadmap for clinical translation of mobile microrobotics(Wiley-V C H Verlag Gmbh, 2024) Bozuyuk, Ugur; Wrede, Paul; Yildiz, Erdost; Department of Mechanical Engineering; Sitti, Metin; Department of Mechanical Engineering; College of Engineering; School of MedicineMedical microrobotics is an emerging field to revolutionize clinical applications in diagnostics and therapeutics of various diseases. On the other hand, the mobile microrobotics field has important obstacles to pass before clinical translation. This article focuses on these challenges and provides a roadmap of medical microrobots to enable their clinical use. From the concept of a "magic bullet" to the physicochemical interactions of microrobots in complex biological environments in medical applications, there are several translational steps to consider. Clinical translation of mobile microrobots is only possible with a close collaboration between clinical experts and microrobotics researchers to address the technical challenges in microfabrication, safety, and imaging. The clinical application potential can be materialized by designing microrobots that can solve the current main challenges, such as actuation limitations, material stability, and imaging constraints. The strengths and weaknesses of the current progress in the microrobotics field are discussed and a roadmap for their clinical applications in the near future is outlined. The clinical use of medical microrobots gets closer to reality with the rapidly growing biomedical research on them. However, the clinical translation of microrobots has several challenges and obstacles, including scalability, biocompatibility, and imaging. In this review article, a realistic roadmap for medical microrobots is conceptualized with the collaborative efforts of microrobot researchers and clinicians.