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Publication Metadata only 3D-printed micrometer-scale wireless magnetic cilia with metachronal programmability(Amer Assoc Advancement Science, 2023) Zhang, Shuaizhong; Hu, Xinghao; Li, Meng; Bozuyuk, Ugur; Zhang, Rongjing; Suadiye, Eylul; Han, Jie; Wang, Fan; Onck, Patrick; Department of Mechanical Engineering; Sitti, Metin; Department of Mechanical Engineering; College of Engineering; School of MedicineBiological cilia play essential roles in self-propulsion, food capture, and cell transportation by performing coor-dinated metachronal motions. Experimental studies to emulate the biological cilia metachronal coordination are challenging at the micrometer length scale because of current limitations in fabrication methods and ma-terials. We report on the creation of wirelessly actuated magnetic artificial cilia with biocompatibility and meta-chronal programmability at the micrometer length scale. Each cilium is fabricated by direct laser printing a silk fibroin hydrogel beam affixed to a hard magnetic FePt Janus microparticle. The 3D-printed cilia show stable actuation performance, high temperature resistance, and high mechanical endurance. Programmable meta-chronal coordination can be achieved by programming the orientation of the identically magnetized FePt Janus microparticles, which enables the generation of versatile microfluidic patterns. Our platform offers an unprecedented solution to create bioinspired microcilia for programmable microfluidic systems, biomedical en-gineering, and biocompatible implants.Publication Metadata only A front-tracking method for computational modeling of viscoelastic two-phase flow systems(Elsevier, 2015) N/A; N/A; Department of Mechanical Engineering; Izbassarov, Daulet; 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 direct numerical simulations of viscoelastic two-phase systems in which one or both phases could be viscoelastic. One set of governing equations is written for the whole computational domain and different phases are treated as a single fluid with variable material and rheological properties. The interface is tracked explicitly using a Lagrangian grid while the flow equations are solved on a fixed Eulerian grid. The surface tension is computed at the interface using the Lagrangian grid and included into the momentum equations as a body force. The Oldroyd-B, FENE-CR and FENE-MCR models are employed to model the viscoelasticity. The viscoelastic model equations are solved fully coupled with the flow equations within the front-tracking framework. A fifth-order WENO scheme is used to approximate the convective terms in the viscoelastic model equations and second-order central differences are used for all other spatial derivatives. A log-conformation method-is employed to alleviate the high Weissenberg number problem (HWNP) and found to be stable and very robust for a wide range of Weissenberg numbers. The method has been first validated for various benchmark single-phase and two-phase viscoelastic flow problems. Then it has been applied to study motion and deformation of viscoelastic two-phase systems in a pressure-driven flow through a capillary tube with a sudden contraction and expansion. The method has been demonstrated to be grid convergent with second-order spatial accuracy for all the cases considered in this paper.Publication Metadata only A support function based algorithm for optimization with eigenvalue constraints(Siam Publications, 2017) N/A; Department of Mathematics; Mengi, Emre; Faculty Member; Department of Mathematics; College of Sciences; 113760Optimization of convex functions subject to eigenvalue constraints is intriguing because of peculiar analytical properties of eigenvalue functions and is of practical interest because of a wide range of applications in fields such as structural design and control theory. Here we focus on the optimization of a linear objective subject to a constraint on the smallest eigenvalue of an analytic and Hermitian matrix-valued function. We propose a numerical approach based on quadratic support functions that overestimate the smallest eigenvalue function globally. the quadratic support functions are derived by employing variational properties of the smallest eigenvalue function over a set of Hermitian matrices. We establish the local convergence of the algorithm under mild assumptions and deduce a precise rate of convergence result by viewing the algorithm as a fixed point iteration. the convergence analysis reveals that the algorithm is immune to the nonsmooth nature of the smallest eigenvalue. We illustrate the practical applicability of the algorithm on the pseudospectral functions.Publication Metadata only A survey of energy efficiency in SDN: Software-based methods and optimization models(Elsevier, 2019) N/A; N/A; Department of Computer Engineering; Assefa, Beakal Gizachew; Özkasap, Öznur; PhD Student; Faculty Member; Department of Computer Engineering; Graduate School of Sciences and Engineering; College of Engineering; N/A; N/A; 113507Software Defined Networking (SDN) paradigm has the benefits of programmable network elements by separating the control and the forwarding planes, efficiency through optimized routing and flexibility in network management. As the energy costs contribute largely to the overall costs in networks, energy efficiency has become a significant design requirement for modem networking mechanisms. However, designing energy efficient solutions is non-trivial since they need to tackle the trade-off between energy efficiency and network performance. In this article, we address the energy efficiency capabilities that can be utilized in the emerging SDN. We provide a comprehensive and novel classification of software-based energy efficient solutions into subcategories of traffic aware, end system aware and rule placement. We propose general optimization models for each subcategory, and present the objective function, the parameters and constraints to be considered in each model. Detailed information on the characteristics of state-of-the-art methods, their advantages, drawbacks are provided. Hardware-based solutions used to enhance the efficiency of switches are also described. Furthermore, we discuss the open issues and future research directions in the area of energy efficiency in SDN.Publication Metadata only A versatile jellyfish-like robotic platform for effective underwater propulsion and manipulation(Amer Assoc Advancement Science, 2023) Wang, Tianlu; Joo, Hyeong-Joon; Song, Shanyuan; Hu, Wenqi; Keplinger, Christoph; Department of Mechanical Engineering; Sitti, Metin; Department of Mechanical Engineering; College of Engineering; School of MedicineUnderwater devices are critical for environmental applications. However, existing prototypes typically use bulky, noisy actuators and limited configurations. Consequently, they struggle to ensure noise-free and gentle inter-actions with underwater species when realizing practical functions. Therefore, we developed a jellyfish-like robotic platform enabled by a synergy of electrohydraulic actuators and a hybrid structure of rigid and soft components. Our 16-cm-diameter noise-free prototype could control the fluid flow to propel while manipulat-ing objects to be kept beneath its body without physical contact, thereby enabling safer interactions. Its against -gravity speed was up to 6.1 cm/s, substantially quicker than other examples in literature, while only requiring a low input power of around 100 mW. Moreover, using the platform, we demonstrated contact-based object ma-nipulation, fluidic mixing, shape adaptation, steering, wireless swimming, and cooperation of two to three robots. This study introduces a versatile jellyfish-like robotic platform with a wide range of functions for diverse applications.Publication Metadata only Actuation-enhanced multifunctional sensing and information recognition by magnetic artificial cilia arrays(National Academy of Sciences, 2023) Han, Jie; Dong, Xiaoguan; Yin, Zhen; Zhang, Shuaizhong; Li, Meng; Zheng, Zhiqiang; Ugurlu, Musab Cagri; Jiang, Weitao; Liu, Hongzhong; Department of Mechanical Engineering; Sitti, Metin; Department of Mechanical Engineering; College of Engineering; School of MedicineArtificial cilia integrating both actuation and sensing functions allow simultaneously sensing environmental properties and manipulating fluids in situ, which are promising for environment monitoring and fluidic applications. However, existing artificial cilia have limited ability to sense environmental cues in fluid flows that have versatile information encoded. This limits their potential to work in complex and dynamic fluid-filled environments. Here, we propose a generic actuation- enhanced sensing mechanism to sense complex environmental cues through the active interaction between artificial cilia and the surrounding fluidic environments. The proposed mechanism is based on fluid-cilia interaction by integrating soft robotic artificial cilia with flexible sen-sors. With a machine learning-based approach, complex environmental cues such as liquid viscosity, environment boundaries, and distributed fluid flows of a wide range of velocities can be sensed, which is beyond the capability of existing artificial cilia. As a proof of concept, we implement this mechanism on magnetically actuated cilia with integrated laser- induced graphene-based sensors and demonstrate sensing fluid apparent viscosity, environment boundaries, and fluid flow speed with a reconfigur-able sensitivity and range. The same principle could be potentially applied to other soft robotic systems integrating other actuation and sensing modalities for diverse environmental and fluidic applications.Publication Metadata only Adaptation strategies for MGS scalable video streaming(Elsevier, 2012) N/A; Department of Electrical and Electronics Engineering; Görkemli, Burak; Tekalp, Ahmet Murat; N/A; Faculty Member; Department of Electrical and Electronics Engineering; College of Engineering; College of Engineering; N/A; 26207An adaptive streaming framework consists of a video codec that can produce video encoded at a variety of rates, a transport protocol that supports an effective rate/congestion control mechanism, and an adaptation strategy in order to match the video source rate to the available network throughput. The main parameters of the adaptation strategy are encoder configuration, video extraction method, determination of video extraction rate, send rate control, retransmission of lost packets, decoder buffer status, and packetization method. This paper proposes optimal adaptation strategies, in terms of received video quality and used network resources, at the codec and network levels using a medium grain scalable (MGS) video codec and two transport protocols with built-in congestion control, TCP and DCCP. Key recommendations are presented to obtain the best results in adaptive video streaming using TCP or DCCP based on extensive experimental results over the Internet. (c) 2012 Elsevier B.V. All rights reserved.Publication Metadata only Adsorption, folding, and packing of an amphiphilic peptide at the air/water interface(amer Chemical Soc, 2012) N/A; Department of Mechanical Engineering; Engin, Özge; Sayar, Mehmet; Master Student; Faculty Member; Department of Mechanical Engineering; Graduate School of Sciences and Engineering, College of Engineering; N/A; 109820Peptide oligomers play an essential role as model compounds for identifying key motifs in protein structure formation and protein aggregation. Here, we present our results, based on extensive molecular dynamics simulations, on adsorption, folding, and packing within a surface monolayer of an amphiphilic peptide at the air/water interface. Experimental results suggest that these molecules spontaneously form ordered monolayers at the interface, Adopting a beta-hairpin-like structure within the surface layer. Our results reveal that the beta-hairpin structure can be observed both in bulk and at the air/water interface. However, the presence of an interface leads to ideal partitioning of the hydrophobic and hydrophilic residues, and therefore reduces the conformational space for the molecule and increases the stability of the hairpin structure. We obtained the adsorption free energy of a single beta-hairpin at the air/water interface, and analyzed the enthalpic and entropic contributions. the adsorption process is favored by two main factors: (1) Free-energy reduction due to desolvation of the hydrophobic side chains of the peptide and release of the water molecules which form a cage around these hydrophobic groups in bulk water. (2) Reduction of the total air/water contact area at the interface upon adsorption of the peptide amphiphile. By performing mutations on the original molecule, we demonstrated the relative role of key design features of the peptide. Finally, by analyzing the potential of mean force among two peptides at the interface, we investigated possible packing mechanisms for these molecules within the surface monolayer.Publication Metadata only An ultra-compact and wireless tag for battery-free sweat glucose monitoring(Elsevier Advanced Technology, 2022) N/A; Department of Mechanical Engineering; N/A; N/A; Department of Mechanical Engineering; N/A; N/A; N/A; N/A; Department of Mechanical Engineering; Mirzajani, Hadi; Abbasiasl, Taher; Mirlou, Fariborz; İstif, Emin; Bathaei, Mohammad Javad; Dağ, Çağdaş; Deyneli, Oğuzhan; Dereli, Dilek Yazıcı; Beker, Levent; Researcher; PhD Student; PhD Student; Other; PhD Student; Faculty Member; Faculty Member; Faculty Member; Faculty Member; Department of Mechanical Engineering; Koç Üniversitesi İş Bankası Enfeksiyon Hastalıkları Uygulama ve Araştırma Merkezi (EHAM) / Koç University İşbank Center for Infectious Diseases (KU-IS CID); n2STAR-Koç University Nanofabrication and Nanocharacterization Center for Scientifc and Technological Advanced Research; Koç University Research Center for Translational Medicine (KUTTAM) / Koç Üniversitesi Translasyonel Tıp Araştırma Merkezi (KUTTAM); College of Engineering; Graduate School of Sciences and Engineering; Graduate School of Sciences and Engineering; College of 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; N/A; N/A; 171914; 179659; 308798Glucose monitoring before, during, and after exercise is essential for people with diabetes as exercise increases the risk of activity-induced hyper- and hypo-glycemic events. The situation is even more challenging for athletes with diabetes as they have impaired metabolic control compared to sedentary individuals. In this regard, a compact and noninvasive wearable glucose monitoring device that can be easily worn is critical to enabling glucose monitoring. This report presents an ultra-compact glucose tag with a footprint and weight of 1.2 cm(2) and 0.13 g, respectively, for sweat analysis. The device comprises a near field communication (NFC) chip, antenna, electrochemical sensor, and microfluidic channels implemented in different material layers. The device has a flexible and conformal structure and can be easily attached to different body parts. The battery-less operation of the device was enabled by NFC-based wireless power transmission and the compact antenna. Femtosecond laser ablation was employed to fabricate a highly compact and flexible NFC antenna. The proposed device demonstrated excellent operating characteristics with a limit of detection (LOD), limit of quantification (LOQ), and sensitivity of 24 mu M, 74 mu M, and 1.27 mu A cm(-2) mM(-1), respectively. The response of the proposed sensor in sweat glucose detection and quantification was validated by nuclear magnetic resonance spectroscopy (NMR). Also, the device's capability in attachment to the body, sweat collection, and glucose measurement was demonstrated through in vitro and in vivo experiments, and satisfactory results were obtained.Publication Metadata only Application of the numerical fractionation approach to the design of biofunctional PEG hydrogel membranes(Wiley-V C H Verlag Gmbh, 2012) N/A; Department of Chemical and Biological Engineering; Department of Chemical and Biological Engineering; Kızılel, Rıza; Kızılel, Seda; Researcher; Faculty Member; Department of Chemical and Biological Engineering; College of Engineering; College of Engineering; 114475; 28376A mathematical model is described for surface-initiated photopolymerization of PEG-DA forming crosslinked biofunctional PEG hydrogel membranes based on the NF technique. The model includes an additional monomer with biological functionality, which is a common experimental strategy for the design of ECM mimics in tissue engineering in order to direct signaling pathways, and considers concentration-dependent VP propagation and reaction diffusion termination. The influence of these features on the crosslink density of the soluble and gel phases, the progression through gelation, sol/gel fraction, and molecular weight distribution of biofunctional PEG hydrogel are studied using the NF model. This model may be useful for specific applications of tissue engineering.