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Publication Open Access 3D bioprinted organ?on?chips(Wiley, 2022) Mustafaoğlu, Nur; Zhang, Yu Shrike; Department of Mechanical Engineering; N/A; N/A; Dabbagh, Sajjad Rahmani; Sarabi, Misagh Rezapour; Birtek, Mehmet Tuğrul; 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 Üniversitesi İş Bankası Yapay Zeka Uygulama ve Araştırma Merkezi (KUIS AI)/ Koç University İş Bank Artificial Intelligence Center (KUIS AI); College of Engineering; Graduate School of Social Sciences and Humanities; Graduate School of Sciences and Engineering; N/A; N/A; N/A; 291971Organ-on-a-chip (OOC) platforms recapitulate human in vivo-like conditions more realistically compared to many animal models and conventional two-dimensional cell cultures. OOC setups benefit from continuous perfusion of cell cultures through microfluidic channels, which promotes cell viability and activities. Moreover, microfluidic chips allow the integration of biosensors for real-time monitoring and analysis of cell interactions and responses to administered drugs. Three-dimensional (3D) bioprinting enables the fabrication of multicell OOC platforms with sophisticated 3D structures that more closely mimic human tissues. 3D-bioprinted OOC platforms are promising tools for understanding the functions of organs, disruptive influences of diseases on organ functionality, and screening the efficacy as well as toxicity of drugs on organs. Here, common 3D bioprinting techniques, advantages, and limitations of each method are reviewed. Additionally, recent advances, applications, and potentials of 3D-bioprinted OOC platforms for emulating various human organs are presented. Last, current challenges and future perspectives of OOC platforms are discussed.Publication Open Access 3D-printed microneedles in biomedical applications(Elsevier, 2021) Rahbarghazi, Reza; Yetişen, Ali Kemal; N/A; Department of Mechanical Engineering; Dabbagh, Sajjad Rahmani; Sarabi, Misagh Rezapour; Sokullu, Emel; Taşoğlu, Savaş; Faculty Member; 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); Graduate School of Social Sciences and Humanities; Graduate School of Sciences and Engineering; School of Medicine; College of Engineering; N/A; N/A; 163024; 291971Conventional needle technologies can be advanced with emerging nano- and micro-fabrication methods to fabricate microneedles. Nano-/micro-fabricated microneedles seek to mitigate penetration pain and tissue damage, as well as providing accurately controlled robust channels for administrating bioagents and collecting body fluids. Here, design and 3D printing strategies of microneedles are discussed with emerging applications in biomedical devices and healthcare technologies. 3D printing offers customization, cost-efficiency, a rapid turnaround time between design iterations, and enhanced accessibility. Increasing the printing resolution, the accuracy of the features, and the accessibility of low-cost raw printing materials have empowered 3D printing to be utilized for the fabrication of microneedle platforms. The development of 3D-printed microneedles has enabled the evolution of pain-free controlled release drug delivery systems, devices for extracting fluids from the cutaneous tissue, biosignal acquisition, and point-of-care diagnostic devices in personalized medicine.Publication Open Access 3D-printed microrobots from design to translation(Nature Portfolio, 2022) Department of Mechanical Engineering; N/A; Dabbagh, Sajjad Rahmani; Sarabi, Misagh Rezapour; Birtek, Mehmet Tuğrul; Sitti, Metin; Taşoğlu, Savaş; Faculty Member; Faculty Member; Department of Mechanical Engineering; 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); Koç University Research Center for Translational Medicine (KUTTAM) / Koç Üniversitesi Translasyonel Tıp Araştırma Merkezi (KUTTAM); Graduate School of Health Sciences; Graduate School of Sciences and Engineering; School of Medicine; College of Engineering; N/A; N/A; N/A; N/A; 297104; 291971Microrobots have attracted the attention of scientists owing to their unique features to accomplish tasks in hard-to-reach sites in the human body. Microrobots can be precisely actuated and maneuvered individually or in a swarm for cargo delivery, sampling, surgery, and imaging applications. In addition, microrobots have found applications in the environmental sector (e.g., water treatment). Besides, recent advancements of three-dimensional (3D) printers have enabled the high-resolution fabrication of microrobots with a faster design-production turnaround time for users with limited micromanufacturing skills. Here, the latest end applications of 3D printed microrobots are reviewed (ranging from environmental to biomedical applications) along with a brief discussion over the feasible actuation methods (e.g., on- and off-board), and practical 3D printing technologies for microrobot fabrication. In addition, as a future perspective, we discussed the potential advantages of integration of microrobots with smart materials, and conceivable benefits of implementation of artificial intelligence (AI), as well as physical intelligence (PI). Moreover, in order to facilitate bench-to-bedside translation of microrobots, current challenges impeding clinical translation of microrobots are elaborated, including entry obstacles (e.g., immune system attacks) and cumbersome standard test procedures to ensure biocompatibility.
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 Open Access A machine learning approach for implementing data-driven production control policies(Taylor _ Francis, 2021) Department of Business Administration; N/A; Tan, Barış; Khayyati, Siamak; Faculty Member; Department of Business Administration; College of Administrative Sciences and Economics; Graduate School of Sciences and Engineering; 28600; N/AGiven the extensive data being collected in manufacturing systems, there is a need for developing a systematic method to implement data-driven production control policies. For an effective implementation, first, the relevant information sources must be selected. Then, a control policy that uses the real-time signals collected from these sources must be implemented. We analyse the production control policy implementation problem in three levels: choosing the information sources, forming clusters of information signals to be used by the policy and determining the optimal policy parameters. Due to the search-space size, a machine-learning-based framework is proposed. Using machine learning speeds up optimisation and allows utilising the collected data with simulation. Through two experiments, we show the effectiveness of this approach. In the first experiment, the problem of selecting the right machines and buffers for controlling the release of materials in a production/inventory system is considered. In the second experiment, the best dispatching policy based on the selected information sources is identified. We show that selecting the right information sources and controlling a production system based on the real-time signals from the selected sources with the right policy improve the system performance significantly. Furthermore, the proposed machine learning framework facilitates this task effectively.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 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 Open Access Advanced materials and device architectures for magnetooptical spatial light modulators(Wiley-VCH, 2019) N/A; Department of Electrical and Electronics Engineering; Kharratian, Soheila; Onbaşlı, Mehmet Cengiz; Ürey, Hakan; Faculty Member; Faculty Member; Department of Electrical and Electronics Engineering; Graduate School of Sciences and Engineering; N/A; 258783; 8579Faraday and Kerr rotations are magnetooptical (MO) effects used for rotating the polarization of light in transmission and reflection from a magnetized medium, respectively. MO effects combined with intrinsically fast magnetization reversal, which can go down to a few tens of femtoseconds or less, can be applied in magnetooptical spatial light modulators (MOSLMs) promising for nonvolatile, ultrafast, and high-resolution spatial modulation of light. With the recent progress in low-power switching of magnetic and MO materials, MOSLMs may lead to major breakthroughs and benefit beyond state-of-the-art holography, data storage, optical communications, heads-up displays, virtual and augmented reality devices, and solid-state light detection and ranging (LIDAR). In this study, the recent developments in the growth, processing, and engineering of advanced materials with high MO figures of merit for practical MOSLM devices are reviewed. The challenges with MOSLM functionalities including the intrinsic weakness of MO effect and large power requirement for switching are assessed. The suggested solutions are evaluated, different driving systems are investigated, and resulting device architectures are benchmarked. Finally, the research opportunities on MOSLMs for achieving integrated, high-contrast, and low-power devices are presented.Publication Open Access All optical control of magnetization in quantum confined ultrathin magnetic metals(Nature Publishing Group (NPG), 2021) Department of Physics; Department of Electrical and Electronics Engineering; N/A; Müstecaplıoğlu, Özgür Esat; Onbaşlı, Mehmet Cengiz; Naseem, Muhammad Tahir; Zanjani, Saeedeh Mokarian; Faculty Member; Faculty Member; Department of Physics; Department of Electrical and Electronics Engineering; College of Sciences; College of Engineering; Graduate School of Sciences and Engineering; 1674; 258783; N/A; N/AAll-optical control dynamics of magnetization in sub-10 nm metallic thin films are investigated, as these films with quantum confinement undergo unique interactions with femtosecond laser pulses. Our theoretical analysis based on the free electron model shows that the density of states at Fermi level (DOSF) and electron-phonon coupling coefficients (G(ep)) in ultrathin metals have very high sensitivity to film thickness within a few angstroms. We show that completely different magnetization dynamics characteristics emerge if DOSF and G(ep) depend on thickness compared with bulk metals. Our model suggests highly efficient energy transfer from femtosecond laser photons to spin waves due to minimal energy absorption by phonons. This sensitivity to the thickness and efficient energy transfer offers an opportunity to obtain ultrafast on-chip magnetization dynamics.