Publications with Fulltext
Permanent URI for this collectionhttps://hdl.handle.net/20.500.14288/6
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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; Department of Mechanical Engineering; Alaca, Ilgım Veryeri; Başdoğan, İpek; Faculty Member; 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; Department of Mechanical Engineering; Nooranidoost, Mohammad; Izbassarov, Daulet; Muradoğlu, Metin; PhD Student; PhD Student; Faculty Member; 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; Department of Mechanical Engineering; Khavidaki, Sayed Ehsan Layegh; Lazoğlu, İsmail; Faculty Member; 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; Department of Mechanical Engineering; Küçükyılmaz, Ayşe; Sezgin, Tevfik Metin; Başdoğan, Çağatay; PhD Student; Faculty Member; Faculty Member; 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; Department of Mechanical Engineering; Department of Chemical and Biological Engineering; Özgür, Beytullah; Sayar, Mehmet; PhD Student; Faculty Member; 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 Understanding formation and structure of peptide nanofibers via steered MD simulations(Elsevier, 2012) Department of Mechanical Engineering; Department of Mechanical Engineering; Engin, Özge; Özgür, Beytullah; Sayar, Mehmet; PhD Student; Faculty Member; College of Engineering; N/A; N/A; 109820Publication Open Access Friction coefficients on surface finish of AlTiN coated tools in the milling of Ti6Al4V(Elsevier, 2017) Akgun, Ali; Yavas, Caglar; Department of Mechanical Engineering; Department of Mechanical Engineering; Akmal, Mohammad; Khavidaki, Sayed Ehsan Layegh; Lazoğlu, İsmail; PhD Student; Faculty Member; Manufacturing and Automation Research Center (MARC); College of Engineering; Graduate School of Sciences and Engineering; N/A; N/A; 179391The main constraints in high performance machining of the titanium alloys are mostly due to the friction induced thermal issues. In thermal analysis, the friction coefficient is the critical parameter for estimating the heat generation at the tool-chip interface. This paper provides a direct approach for determining the friction coefficient from slot milling of Ti6Al4V for uncoated solid carbide end-mills and AlTiN coated tools with magnetic, friction and sandblast finishing techniques. The effects of AlTiN coating and finishing techniques on friction coefficients are investigated.Publication Open Access Post-implantation shear stress assessment: an emerging tool for differentiation of bioresorbable scaffolds(Springer, 2019) Tenekecioğlu, Erhan; Torii, Ryo; Katagiri, Yuki; Chichareon, Ply; Asano, Taku; Miyazaki, Yosuke; Takahashi, Kuniaki; Modolo, Rodrigo; Al-Lamee, Rasha; Al-Lamee, Kadem; Colet, Carlos; Reiber, Johan H. C.; van Geuns, Robert; Bourantas, Christos V.; Onuma, Yoshinobu; Serruys, Patrick W.; Department of Mechanical Engineering; Department of Mechanical Engineering; Pekkan, Kerem; Faculty Member; College of Engineering; 161845Optical coherence tomography based computational flow dynamic (CFD) modeling provides detailed information about the local flow behavior in stented/scaffolded vessel segments. Our aim is to investigate the in-vivo effect of strut thickness and strut protrusion on endothelial wall shear stress (ESS) distribution in ArterioSorb Absorbable Drug-Eluting Scaffold (ArterioSorb) and Absorb everolimus-eluting Bioresorbable Vascular Scaffold (Absorb) devices that struts with similar morphology (quadratic structure) but different thickness. In three animals, six coronary arteries were treated with ArterioSorb. At different six animals, six coronary arteries were treated with Absorb. Following three-dimensional(3D) reconstruction of the coronary arteries, Newtonian steady flow simulation was performed and the ESS were estimated. Mixed effects models were used to compare ESS distribution in the two devices. There were 4591 struts in the analyzed 477 cross-sections in Absorb (strut thickness=157 mu m) and 3105 struts in 429 cross-sections in ArterioSorb (strut thickness=95 mu m) for the protrusion analysis. In cross-section level analysis, there was significant difference between the scaffolds in the protrusion distances. The protrusion was higher in Absorb (97% of the strut thickness) than in ArterioSorb (88% of the strut thickness). ESS was significantly higher in ArterioSorb (1.52 +/- 0.34Pa) than in Absorb (0.73 +/- 2.19Pa) (p=0.001). Low- and very-low ESS data were seen more often in Absorb than in ArterioSorb. ArterioSorb is associated with a more favorable ESS distribution compared to the Absorb. These differences should be attributed to different strut thickness/strut protrusion that has significant effect on shear stress distribution.Publication Open Access Tactile masking by electrovibration(Institute of Electrical and Electronics Engineers (IEEE), 2018) Güçlü, Burak; Department of Mechanical Engineering; Department of Mechanical Engineering; Başdoğan, Çağatay; Vardar, Yasemin; Faculty Member; College of Engineering; Graduate School of Sciences and Engineering; 125489; N/AFuture touch screen applications will include multiple tactile stimuli displayed simultaneously or consecutively to single finger or multiple fingers. These applications should be designed by considering human tactile masking mechanism since it is known that presenting one stimulus may interfere with the perception of the other. In this study, we investigate the effect of masking on the tactile perception of electrovibration displayed on touch screens. Through conducting psychophysical experiments with nine participants, we measured the masked thresholds of sinusoidal electrovibration bursts (125 Hz) under two masking conditions: simultaneous and pedestal. The masking signals were noise bursts, applied at five different sensation levels varying from 2 to 22 dB SL, also presented by electrovibration. For each participant, the thresholds were elevated as linear functions of masking levels for both masking types. We observed that the masking effectiveness was larger with pedestal masking than simultaneous masking. Moreover, in order to investigate the effect of tactile masking on our haptic perception of edge sharpness, we compared the perceived sharpness of edges separating two textured regions displayed with and without various types of masking stimuli. Our results suggest that sharpness perception depends on the local contrast between background and foreground stimuli, which varies as a function of masking amplitude and activation levels of frequency-dependent psychophysical channels.Publication Open Access Buckling of stiff polymers: influence of thermal fluctuations(American Physical Society (APS), 2007) Emanuel, Marc; Mohrbach, Herve; Schiessel, Helmut; Kulic, Igor M.; Department of Mechanical Engineering; Department of Mechanical Engineering; Sayar, Mehmet; Faculty Member; College of Engineering; 109820The buckling of biopolymers is a frequently studied phenomenon The influence of thermal fluctuations on the buckling transition is, however, often ignored and not completely understood. A quantitative theory of the buckling of a wormlike chain based on a semiclassical approximation of the partition function is presented. The contribution of thermal fluctuations to the force-extension relation that allows one to go beyond the classical Euler buckling is derived in the linear and nonlinear regimes as well. It is shown that the thermal fluctuations in the nonlinear buckling regime increase the end-to-end distance of the semiflexible rod if it is confined to two dimensions as opposed to the three-dimensional case. The transition to a buckled state softens at finite temperature. We derive the scaling behavior of the transition shift with increasing ratio of contour length versus persistence length.