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Permanent URI for this collectionhttps://hdl.handle.net/20.500.14288/6
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Publication Open Access 3D printed personalized magnetic micromachines from patient blood-derived biomaterials(American Association for the Advancement of Science (AAAS), 2021) Ceylan, Hakan; Doğan, Nihal Olcay; Yaşa, İmmihan Ceren; Department of Mechanical Engineering; Sitti, Metin; Musaoğlu, Miraç Nur; Kulalı, Zeynep Umut; Faculty Member; Department of Mechanical Engineering; College of Engineering; School of Medicine; 297104; N/A; N/AWhile recent wireless micromachines have shown increasing potential for medical use, their potential safety risks concerning biocompatibility need to be mitigated. They are typically constructed from materials that are not intrinsically compatible with physiological environments. Here, we propose a personalized approach by using patient blood-derivable biomaterials as the main construction fabric of wireless medical micromachines to alleviate safety risks from biocompatibility. We demonstrate 3D printed multiresponsive microswimmers and microrollers made from magnetic nanocomposites of blood plasma, serum albumin protein, and platelet lysate. These micro-machines respond to time-variant magnetic fields for torque-driven steerable motion and exhibit multiple cycles of pH-responsive two-way shape memory behavior for controlled cargo delivery and release applications. Their proteinaceous fabrics enable enzymatic degradability with proteinases, thereby lowering risks of long-term toxicity. The personalized micromachine fabrication strategy we conceptualize here can affect various future medical robots and devices made of autologous biomaterials to improve biocompatibility and smart functionality.Publication Open Access Thiophene-based trimers for in vivo electronic functionalization of tissues(American Chemical Society (ACS), 2020) Mantione, Daniele; Dufil, Gwennael; Vallan, Lorenzo; Parker, Daniela; Brochon, Cyril; Cloutet, Eric; Hadziioannou, Georges; Berggren, Magnus; Stavrinidou, Eleni; Pavlopoulou, Eleni; Department of Mechanical Engineering; İstif, Emin; Faculty Member; Master Student; Department of Mechanical Engineering; College of EngineeringElectronic materials that can self-organize in vivo and form functional components along the tissue of interest can result in a seamless integration of the bioelectronic interface. Previously, we presented in vivo polymerization of the conjugated oligomer ETE-S in plants, forming conductors along the plant structure. The EDOT-thiophene-EDOT trimer with a sulfonate side group polymerized due to the native enzymatic activity of the plant and integrated within the plant cell wall. Here, we present the synthesis of three different conjugated trimers based on thiophene and EDOT or purely EDOT trimers that are able to polymerize enzymatically in physiological pH in vitro as well as in vivo along the roots of living plants. We show that by modulating the backbone and the side chain, we can tune the electronic properties of the resulting polymers as well as their localization and penetration within the root. Our work paves the way for the rational design of electronic materials that can self-organize in vivo for spatially controlled electronic functionalization of living tissue.Publication Open Access Long-term cyclic use of a sample collector for toilet-based urine analysis(Nature Publishing Group (NPG), 2021) Temirel, Mikail; Yenilmez, Bekir; Department of Mechanical Engineering; Taşoğlu, Savaş; 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); College of Engineering; 291971Urine analysis via a toilet-based device can enable continuous health monitoring, a transformation away from hospital-based care towards more proactive medicine. To enable reliable sample collection for a toilet-attached analyzer, here a novel sample collector is proposed. The applicability of the proposed sample collector is validated for long-term use. Geometric parameters of the 3D-printed sample collector are optimized. The collected and leftover volumes are quantified for a range of urination speeds and design parameters. For long-term cyclic use, the protein concentrations of samples are quantified and the effectiveness of washing the sample collector is assessed.Publication Open Access Dynamic characterization and damping control of a MEMS structure - art. no. 671509(Society of Photo-optical Instrumentation Engineers (SPIE), 2007) Department of Mechanical Engineering; Alaca, Ilgım Veryeri; Başdoğan, İpek; Faculty Member; Department of Mechanical Engineering; College of Engineering; 50569; 179940Publication Open Access A computational study of droplet-based bioprinting: effects of viscoelasticity(American Institute of Physics (AIP) Publishing, 2019) Taşoğlu, Savaş; Department of Mechanical Engineering; Nooranidoost, Mohammad; Izbassarov, Daulet; Muradoğlu, Metin; PhD Student; PhD Student; Faculty Member; Department of Mechanical Engineering; Graduate School of Sciences and Engineering; N/A; N/A; 46561Despite significant progress, cell viability continues to be a central issue in droplet-based bioprinting applications. Common bioinks exhibit viscoelastic behavior owing to the presence of long-chain molecules in their mixture. We computationally study effects of viscoelasticity of bioinks on cell viability during deposition of cell-loaded droplets on a substrate using a compound droplet model. The inner droplet, which represents the cell, and the encapsulating droplet are modeled as viscoelastic liquids with different material properties, while the ambient fluid is Newtonian. The model proposed by Takamatsu and Rubinsky ["Viability of deformed cells," Cryobiology 39(3), 243-251 (1999)] is used to relate cell deformation to cell viability. We demonstrate that adding viscoelasticity to the encapsulating droplet fluid can significantly enhance the cell viability, suggesting that viscoelastic properties of bioinks can be tailored to achieve high cell viability in droplet-based bioprinting systems. The effects of the cell viscoelasticity are also examined, and it is shown that the Newtonian cell models may significantly overpredict the cell viability.Publication Open Access Offline force control and feedrate scheduling for complex free form surfaces in 5-Axis milling(Elsevier, 2012) Erdim, Hüseyin; Department of Mechanical Engineering; Khavidaki, Sayed Ehsan Layegh; Lazoğlu, İsmail; Faculty Member; Department of Mechanical Engineering; Manufacturing and Automation Research Center (MARC); College of Sciences; N/A; 179391An enhanced Force model based Feedrate Scheduling (FFS) technique for rough cutting of parts with complex free form surfaces in 5-axis machining is presented. In order to estimate the cutting forces in complex 5-axis machining an enhanced solid modeler kernel based model is developed to find the complicated engagement between cutter and workpiece for each cutter location. In this paper, cutter-workpiece engagement model is presented using the commercial Parasolid solid modeler kernel, and then cutting forces are estimated based on the developed model. In this approach, the resultant cutting forces are kept constant on a user defined threshold. The feedrate will be adjusted to keep the resultant cutting forces constant all along the tool path. Therefore, it is shown that this approach allows decreasing the cycling time drastically. The scheduled feedrate in each cutter location is carried out in NC blocks using an off-line postprocessor that can be used in commercial CAM software. Eventually, the proposed FFS technique is experimentally tested on rough machining of an impeller with free form surfaces and force validations are presented in this article.Publication Open Access Supporting negotiation behavior with haptics-enabled human-computer interfaces(Institute of Electrical and Electronics Engineers (IEEE), 2012) Department of Mechanical Engineering; Küçükyılmaz, Ayşe; Sezgin, Tevfik Metin; Başdoğan, Çağatay; PhD Student; Faculty Member; Faculty Member; Department of Mechanical Engineering; College of Engineering; N/A; 18632; 125489; N/AAn active research goal for human-computer interaction is to allow humans to communicate with computers in an intuitive and natural fashion, especially in real-life interaction scenarios. One approach that has been advocated to achieve this has been to build computer systems with human-like qualities and capabilities. In this paper, we present insight on how human-computer interaction can be enriched by employing the computers with behavioral patterns that naturally appear in human-human negotiation scenarios. For this purpose, we introduce a two-party negotiation game specifically built for studying the effectiveness of haptic and audio-visual cues in conveying negotiation related behaviors. The game is centered around a real-time continuous two-party negotiation scenario based on the existing game-theory and negotiation literature. During the game, humans are confronted with a computer opponent, which can display different behaviors, such as concession, competition, and negotiation. Through a user study, we show that the behaviors that are associated with human negotiation can be incorporated into human-computer interaction, and the addition of haptic cues provides a statistically significant increase in the human-recognition accuracy of machine-displayed behaviors. In addition to aspects of conveying these negotiation-related behaviors, we also focus on and report game-theoretical aspects of the overall interaction experience. In particular, we show that, as reported in the game-theory literature, certain negotiation strategies such as tit-for-tat may generate maximum combined utility for the negotiating parties, providing an excellent balance between the energy spent by the user and the combined utility of the negotiating parties.Publication Open Access Assembly of huntingtin headpiece into α-helical bundles(American Institute of Physics (AIP) Publishing, 2017) Department of Mechanical Engineering; Department of Chemical and Biological Engineering; Özgür, Beytullah; Sayar, Mehmet; PhD Student; Faculty Member; Department of Mechanical Engineering; Department of Chemical and Biological Engineering; Graduate School of Sciences and Engineering; College of Engineering; College of Sciences; N/A; 109820Protein aggregation is a hallmark of neurodegenerative disorders. In this group of brain-related disorders, a disease-specific “host” protein or fragment misfolds and adopts a metastatic, aggregate-prone conformation. Often, this misfolded conformation is structurally and thermodynamically different from its native state. Intermolecular contacts, which arise in this non-native state, promote aggregation. In this regard, understanding the molecular principles and mechanisms that lead to the formation of such a non-native state and further promote the formation of the critical nucleus for fiber growth is essential. In this study, the authors analyze the aggregation propensity of Huntingtin headpiece (httNT), which is known to facilitate the polyQ aggregation, in relation to the helix mediated aggregation mechanism proposed by the Wetzel group. The authors demonstrate that even though httNT displays a degenerate conformational spectrum on its own, interfaces of macroscopic or molecular origin can promote the α-helix conformation, eliminating all other alternatives in the conformational phase space. Our findings indicate that httNT molecules do not have a strong orientational preference for parallel or antiparallel orientation of the helices within the aggregate. However, a parallel packed bundle of helices would support the idea of increased polyglutamine concentration, to pave the way for cross-β structures.Publication Open Access Step-change in friction under electrovibration(Institute of Electrical and Electronics Engineers (IEEE), 2020) Delhaye, Benoit P.; Lefevre, Philippe; Department of Mechanical Engineering; Başdoğan, Çağatay; Özdamar, İdil; Alipour, Mohammad; Faculty Member; Department of Mechanical Engineering; College of Engineering; Graduate School of Sciences and Engineering; 125489; N/A; N/ARendering tactile effects on a touch screen via electrovibration has many potential applications. However, our knowledge on tactile perception of change in friction and the underlying contact mechanics are both very limited. In this article, we investigate the tactile perception and the contact mechanics for a step change in friction under electrovibration during a relative sliding between a finger and the surface of a capacitive touch screen. First, we conduct magnitude estimation experiments to investigate the role of normal force and sliding velocity on the perceived tactile intensity for a step increase and decrease in friction, called rising friction (RF) and falling friction (FF). To investigate the contact mechanics involved in RF and FF, we then measure the frictional force, the apparent contact area, and the strains acting on the fingerpad during sliding at a constant velocity under three different normal loads using a custom-made experimental set-up. The results show that the participants perceived RF stronger than FF, and both the normal force and sliding velocity significantly influenced their perception. These results are supported by our mechanical measurements; the relative change in friction, the apparent contact area, and the strain in the sliding direction were all higher for RF than those for FF, especially for low normal forces. Taken together, our results suggest that different contact mechanics take place during RF and FF due to the viscoelastic behavior of fingerpad skin, and those differences influence our tactile perception of a step change in friction.Publication Open Access Wireless MRI-powered reversible orientation-locking capsule robot(Wiley, 2021) Erin, Önder; Boyvat, Mustafa; Lazovic, Jelena; Tiryaki, Mehmet Efe; Department of Mechanical Engineering; Sitti, Metin; Faculty Member; Department of Mechanical Engineering; College of Engineering; School of Medicine; 297104Magnetic resonance imaging (MRI) scanners do not provide only high-resolution medical imaging but also magnetic robot actuation and tracking. However, the rotational motion capabilities of MRI-powered wireless magnetic capsule-type robots have been limited due to the very high axial magnetic field inside the MRI scanner. Medical functionalities of such robots also remain a challenge due to the miniature robot designs. Therefore, a wireless capsule-type reversible orientation-locking robot (REVOLBOT) is proposed that has decoupled translational motion and planar orientation change capability by locking and unlocking the rotation of a spherical ferrous bead inside the robot on demand. Such an on-demand locking/unlocking mechanism is achieved by a phase-changing wax material in which the ferrous bead is embedded inside. Controlled and on-demand hyperthermia and drug delivery using wireless power transfer-based Joule heating induced by external alternating magnetic fields are the additional features of this robot. The experimental feasibility of the REVOLBOT prototype with steerable navigation, medical function, and MRI tracking capabilities with an 1.33 Hz scan rate is demonstrated inside a preclinical 7T small-animal MRI scanner. The proposed robot has the potential for future clinical use in teleoperated minimally invasive treatment procedures with hyperthermia and drug delivery capabilities while being wirelessly powered and monitored inside MRI scanners.nd. Such an on-demand locking/unlocking mechanism is achieved by a phase-changing wax material in which the ferrous bead is embedded inside. Controlled and on-demand hyperthermia and drug delivery using wireless power transfer-based Joule heating induced by external alternating magnetic fields are the additional features of this robot. The experimental feasibility of the REVOLBOT prototype with steerable navigation, medical function, and MRI tracking capabilities with an 1.33 Hz scan rate is demonstrated inside a preclinical 7T small-animal MRI scanner. The proposed robot has the potential for future clinical use in teleoperated minimally invasive treatment procedures with hyperthermia and drug delivery capabilities while being wirelessly powered and monitored inside MRI scanners.