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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 3D printing of elastomeric bioinspired complex adhesive microstructures(Wiley, 2021) Dayan, Cem Balda; Chun, Sungwoo; Krishna Subbaiah, Nagaraj; Drotlef, Dirk Michael; Akolpoğlu, Mükrime Birgül; Department of Mechanical Engineering; Sitti, Metin; Faculty Member; Department of Mechanical Engineering; College of Engineering; School of Medicine; 297104Bioinspired elastomeric structural adhesives can provide reversible and controllable adhesion on dry/wet and synthetic/biological surfaces for a broad range of commercial applications. Shape complexity and performance of the existing structural adhesives are limited by the used specific fabrication technique, such as molding. To overcome these limitations by proposing complex 3D microstructured adhesive designs, a 3D elastomeric microstructure fabrication approach is implemented using two-photon-polymerization-based 3D printing. A custom aliphatic urethane-acrylate-based elastomer is used as the 3D printing material. Two designs are demonstrated with two combined biological inspirations to show the advanced capabilities enabled by the proposed fabrication approach and custom elastomer. The first design focuses on springtail- and gecko-inspired hybrid microfiber adhesive, which has the multifunctionalities of side-surface liquid super-repellency, top-surface liquid super-repellency, and strong reversible adhesion features in a single fiber array. The second design primarily centers on octopus- and gecko-inspired hybrid adhesive, which exhibits the benefits of both octopus- and gecko-inspired microstructured adhesives for strong reversible adhesion on both wet and dry surfaces, such as skin. This fabrication approach could be used to produce many other 3D complex elastomeric structural adhesives for future real-world applications.
Publication Metadata only A computational study of axial dispersion in segmented gas-liquid flow(American Institute of Physics (AIP) Publishing, 2007) Gunther, Axel; Stone, Howard A.; Department of Mechanical Engineering; Muradoğlu, Metin; Faculty Member; Department of Mechanical Engineering; College of Engineering; 46561Axial dispersion of a tracer in a two-dimensional gas-liquid flow is studied computationally using a finite-volume/front-tracking method. The effects of Peclet number, capillary number, and segment size are examined. At low Peclet numbers, the axial dispersion is mainly controlled by the convection through the liquid films between the bubbles and channel walls. In this regime, the computational results are found to be in a very good agreement with the existing model due to Pedersen and Horvath [Ind. Eng. Chem. Fundam. 20, 181 (1981)]. At high Peclet numbers, the axial dispersion is mainly controlled by the molecular diffusion, with some convective enhancement. In this regime, a new model is proposed and found to agree well with the computational results. These Peclet number regimes are shown to persist for different slug lengths. The axial dispersion is found to depend weakly on the capillary number in the diffusion-controlled regime. Finally, computational simulations are performed for the cases of six bubbles to mimic bubble trains, and results are compared with the theoretical models.Publication Open Access A computational study of two-phase viscoelastic systems in a capillary tube with a sudden contraction/expansion(American Institute of Physics (AIP) Publishing, 2016) Department of Mechanical Engineering; Izbassarov, Daulet; Muradoğlu, Metin; PhD Student; Faculty Member; Department of Mechanical Engineering; College of Engineering; N/A; 46561Two-phase viscoelastic systems are computationally studied in a pressure-driven flow with a sudden contraction and expansion using a finite-difference/front-tracking method. The effects of viscoelasticity in drop and bulk fluids are investigated including high Weissenberg and Reynolds number cases up to Wi = 100 and Re = 100. The Finitely Extensible Non-linear Elastic-Chilcott and Rallison (FENE-CR) model is used to account for the fluid viscoelasticity. Extensive computations are performed to examine drop dynamics for a wide range of parameters. It is found that viscoelasticity interacts with drop interface in a non-monotonic and complicated way, and the two-phase viscoelastic systems exhibit very rich dynamics especially in the expansion region. At high Re, the drop undergoes large deformation in the contraction region followed by strong shape oscillations in the downstream of the expansion. For a highly viscous drop, a re-entrant cavity develops in the contraction region at the trailing edge which, in certain cases, grows and eventually causes encapsulation of ambient fluid. The re-entrant cavity formation is initiated at the entrance of the contraction and is highly influenced by the viscoelasticity. Compared to the corresponding straight channel case, the effects of viscoelasticity are reversed in the constricted channel: Viscoelasticity in drop/continuous phase hinders/enhances formation of the re-entrant cavity and entrainment of ambient fluid into main drop. Encapsulation of ambient fluid into main droplet may be another route to produce a compound droplet in microfluidic applications. (C) 2016 AIP Publishing LLC.Publication Open Access A critical approach to the biocompatibility testing of NiTi orthodontic archwires(Vibgyor Online Publishers, 2016) Şahbazoğlu, D.; Toker, S. M.; Saher, D.; Department of Mechanical Engineering; Canadinç, Demircan; Gümüş, Berkay; Uzer, Benay; Yıldırım, Cansu; Polat-Altıntaş, Sevgi; Faculty Member; Department of Mechanical Engineering; College of Engineering; 23433; N/A; N/A; N/A; N/AThe biocompatibility of Nickel-Titanium (NiTi) archwires was investigated by simulating actual contact state of archwires around brackets, which enabled incorporation of realistic mechanical conditions into ex situ experiments. Specifically, archwires (undeformed, and bound to brackets on acrylic dental molds) were statically immersed in artificial saliva (AS) for 31 days. Following the immersion, the archwires and the immersion solutions were analyzed with the aid of variouselectron-optical techniques, and it was observed that carbon-rich corrosion products formed on both archwire sets upon immersion. The corrosion products preferentially formed at the archwire–bracket contact zones, which is promoted by the high energy of these regions and the micro-cracks brought about by stress assisted corrosion. Moreover, it is suggested that these corrosion products prevented significant Ni or Ti ion release by blocking the micro-cracks, which, otherwise, would have led to enhanced ion release during immersion. The current findings demonstrate the need for incorporating both realistic chemical and mechanical conditions into the ex situ biocompatibility experiments of orthodontic archwires, including the archwire-bracket contact.Publication Metadata only A deep etching mechanism for trench-bridging silicon nanowires(Iop Publishing Ltd, 2016) Wollschlaeger, Nicole; Österle, Werner; Leblebici, Yusuf; N/A; Department of Mechanical Engineering; Taşdemir, Zuhal; Alaca, Burhanettin Erdem; 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; 115108Introducing a single silicon nanowire with a known orientation and dimensions to a specific layout location constitutes a major challenge. The challenge becomes even more formidable, if one chooses to realize the task in a monolithic fashion with an extreme topography, a characteristic of microsystems. The need for such a monolithic integration is fueled by the recent surge in the use of silicon nanowires as functional building blocks in various electromechanical and optoelectronic applications. This challenge is addressed in this work by introducing a topdown, silicon-on-insulator technology. The technology provides a pathway for obtaining wellcontrolled silicon nanowires along with the surrounding microscale features up to a three-orderof-magnitude scale difference. A two-step etching process is developed, where the first shallow etch defines a nanoscale protrusion on the wafer surface. After applying a conformal protection on the protrusion, a deep etch step is carried out forming the surrounding microscale features. A minimum nanowire cross-section of 35 nm by 168 nm is demonstrated in the presence of an etch depth of 10 mu m. Nanowire cross-sectional features are characterized via transmission electron microscopy and linked to specific process steps. The technology allows control on all dimensional aspects along with the exact location and orientation of the silicon nanowire. The adoption of the technology in the fabrication of micro and nanosystems can potentially lead to a significant reduction in process complexity by facilitating direct access to the nanowire during surface processes such as contact formation and doping.Publication Metadata only A deformation-based approach to tuning of magnetic micromechanical resonators(2018) Yalçınkaya, Arda D.; Department of Mechanical Engineering; N/A; Department of Mechanical Engineering; Biçer, Mahmut; Esfahani, Mohammad Nasr; Alaca, Burhanettin Erdem; Researcher; PhD Student; Faculty Member; Department of Mechanical Engineering; Koç University Surface Science and Technology Center (KUYTAM) / Koç Üniversitesi Yüzey Teknolojileri Araştırmaları Merkezi (KUYTAM); College of Engineering; Graduate School of Sciences and Engineering; College of Engineering; N/A; N/A; 115108Resonance frequency tuning in magnetic micromechanical resonators remains a primary field of study for frequency reference applications. The use of magnetic micromechanical resonators for innovative timing, oscillator and sensing applications necessitates a platform for the precise control of the resonance frequency. The present work addresses a deformation based technique for tuning the resonance frequency of nickel micromechanical resonators. Frequency response is measured through magnetic actuation and optical readout. The tuning approach is based on a combination of flexural deformation and uniaxial strain. The bending deformation is achieved by using a DC current through the microbeam. This magnetomotive mechanism reduces the resonance frequency by about 13% for a maximum DC current of 80 mA. A substrate bending method is used for applying uniaxial strain to increase the resonance frequency by about 8%. A bidirectional frequency modulation is thus demonstrated by utilizing both deformation techniques. The interpretation of results is carried out by finite element analysis and electromechanical analogy in an equivalent circuit. Using deformation techniques, this study provides a rigorous approach to control the resonance frequency of magnetic micromechanical resonators.Publication Metadata only A front tracking method for direct numerical simulation of evaporation process in a multiphase system(Academic Press Inc Elsevier Science, 2017) N/A; N/A; Department of Mechanical Engineering; Irfan, Muhammad; Muradoğlu, Metin; PhD Student; Faculty Member; Department of Mechanical Engineering; Graduate School of Sciences and Engineering; College of Engineering; N/A; 46561A front-tracking method is developed for the direct numerical simulation of evaporation process in a liquid-gas multiphase system. One-field formulation is used to solve the flow, energy and species equations in the framework of the front tracking method, with suitable jump conditions at the interface. Both phases are assumed to be incompressible; however, the divergence-free velocity field condition is modified to account for the phase-change/mass-transfer at the interface. Both temperature and species gradient driven evaporation/phase-change processes are simulated. For the species gradient driven phase change process, the Clausius-Clapeyron equilibrium relation is used to find the vapor mass fraction and subsequently the evaporation mass flux at the interface. A number of benchmark cases are first studied to validate the implementation. The numerical results are found to be in excellent agreement with the analytical solutions for all the studied cases. The methods are then applied to study the evaporation of a static as well as a single and two droplets systems falling in the gravitational field. The methods are demonstrated to be grid convergent and the mass is globally conserved during the phase change process for both the static and moving droplet cases.Publication Metadata only A front-tracking method for computation of interfacial flows with soluble surfactants(Academic Press Inc Elsevier Science, 2008) Tryggvason, Gretar; Department of Mechanical Engineering; Muradoğlu, Metin; Faculty Member; Department of Mechanical Engineering; College of Engineering; 46561A finite-difference/front-tracking method is developed for computations of interfacial flows with soluble surfactants. The method is designed to solve the evolution equations of the interfacial and bulk surfactant concentrations together with the incompressible Navier-Stokes equations using a non-linear equation of state that relates interfacial surface tension to surfactant concentration at the interface. The method is validated for simple test cases and the computational results are found to be in a good agreement with the analytical solutions. The method is then applied to study the cleavage of drop by surfactant-a problem proposed as a model for cytokinesis [H.P. Greenspan, On the dynamics of cell cleavage, J. Theor. Biol. 65(l) (1977) 79; H.P. Greenspan, On fluid-mechanical simulations of cell division and movement, J. Theor. Biol., 70(l) (1978) 125]. Finally the method is used to model the effects of soluble surfactants on the motion of buoyancy-driven bubbles in a circular tube and the results are found to be in a good agreement with available experimental data.Publication Metadata only A magnetically actuated resonant mass sensor with integrated optical readout(Ieee-Inst Electrical Electronics Engineers Inc, 2008) N/A; N/A; Department of Electrical and Electronics Engineering; N/A; Department of Electrical and Electronics Engineering; Department of Chemical and Biological Engineering; Department of Mechanical Engineering; Öztürk, Alibey; Ocaklı, Hüseyin İlker; Özber, Natali; Ürey, Hakan; Kavaklı, İbrahim Halil; Alaca, Burhanettin Erdem; Master Student; Researcher; Master Student; Faculty Member; Faculty Member; Faculty Member; Department of Electrical and Electronics Engineering; Department of Chemical and Biological Engineering; Department of Mechanical Engineering; Graduate School of Sciences and Engineering; College of Engineering; Graduate School of Sciences and Engineering; College of Engineering; College of Engineering; College of Engineering; N/A; N/A; N/A; 8579; 40319; 115108Nickel cantilevers with integrated diffraction gratings are used as resonant mass sensors with a resolution of 500 femtograms. Their applicability to biosensing is demonstrated with human opioid receptors. The device is fabricated through a single-mask lithographic process. The microoptical readout provides a simple measurement platform with one external photodiode. Thanks to its ac operation principle, the device is immune to environmental noise and entails a high tolerance to fabrication defects. Obtained signal-to-noise ratio is comparable to that of a high-end Doppler vibrometer. The device with these aspects for systems integration and microarray technology is a candidate for low-cost portable sensors.