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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 Metadata only A virtual reality toolkit for path planning and manipulation at nano-scale(IEEE Computer Soc, 2006) N/A; N/A; Department of Mechanical Engineering; Varol, Aydın; Günev, İhsan; Başdoğan, Çağatay; Master Student; Master Student; Faculty Member; Department of Mechanical Engineering; Graduate School of Sciences and Engineering; Graduate School of Sciences and Engineering; College of Engineering; N/A; N/A; 125489A virtual reality (VR) toolkit that integrates the human operator into a virtual environment by means of visual and haptic feedback has been developed to design and test manipulation strategies at nano-scale. Currently, the toolkit is capable of modeling the mechanistic interactions between an AFM tip and spherical particles on a substrate surface and generating optimum manipulation paths using a potential field approach. In addition, haptic fixtures were designed to guide the user to follow the calculated paths.Publication Metadata only Audio-driven human body motion analysis and synthesis(IEEE, 2008) Canton-Ferrer, C.; Tilmanne, J.; Bozkurt, E.; N/A; N/A; Department of Computer Engineering; Department of Computer Engineering; Department of Electrical and Electronics Engineering; Ofli, Ferda; Demir, Yasemin; Yemez, Yücel; Erzin, Engin; Tekalp, Ahmet Murat; PhD Student; Master Student; Faculty Member; Faculty Member; Faculty Member; Department of Computer Engineering; Department of Electrical and Electronics Engineering; Graduate School of Sciences and Engineering; Graduate School of Sciences and Engineering; College of Engineering; College of Engineering; College of Engineering; N/A; N/A; 107907; 34503; 26207This paper presents a framework for audio-driven human body motion analysis and synthesis. We address the problem in the context of a dance performance, where gestures and movements of the dancer are mainly driven by a musical piece and characterized by the repetition of a set of dance figures. The system is trained in a supervised manner using the multiview video recordings of the dancer. The human body posture is extracted from multiview video information without any human intervention using a novel marker-based algorithm based on annealing particle filtering. Audio is analyzed to extract beat and tempo information. The joint analysis of audio and motion features provides a correlation model that is then used to animate a dancing avatar when driven with any musical piece of the same genre. Results are provided showing the effectiveness of the proposed algorithm.Publication Metadata only Biomaterials for improving the blood and tissue compatibility of total artificial hearts (TAH) and ventricular assist devices (VAD)(Woodhead Publ Ltd, 2011) N/A; Department of Mechanical Engineering; Erbulut, Deniz Ufuk; Lazoğlu, İsmail; Researcher; Faculty Member; Department of Mechanical Engineering; School of Medicine; College of Engineering; 37661; 179391This chapter reviews biomaterials used for artificial hearts and ventricular assist devices. the chapter identifies some of the commercially available cardiac devices and the materials used within, stretching the most important polymers, metals and ceramics. It then discusses the interaction between blood/tissue and biomaterials and subsequently the way of refinement of biomaterials in order to achieve optimum performance. the chapter includes also the evaluation of biomaterials in terms of their blood and tissue compatibility and related international standards.Publication Open Access Biophotonic sensor applications based on photonic atoms - art. no. 60990Q(Society of Photo-optical Instrumentation Engineers (SPIE), 2006) Demir, Abdullah; Department of Physics; Serpengüzel, Ali; Faculty Member; Department of Physics; College of Sciences; 27855Microsphere resonators, i.e., photonic atoms, have found wide area of application in optical spectroscopy, quantum optics, cavity QED, switching, and sensing. Photonic atoms have unique optical properties such as high quality factor (Q-factor) morphology dependent resonances (MDR's), and relatively small volumes. High-Q MDR's are very sensitive to the refractive index change and microsphere uniformity. These tiny optical cavities, whose diameters vary from a few to several hundred micrometers, have resonances with reported Q-factors as large as 3x10(9). Due to their sensitivity, MDR's are also considered for biosensor applications. Binding of a protein or other biomolecules can be monitored by observing the wavelength shift of MDR's. A biosensor, based on this optical phenomenon, can even detect a single molecule, depending on the quality of the system. In this work, elastic scattering spectra from photonic atoms of different materials are experimentally obtained and MDR'S are observed. Preliminary results of unspecific binding of biomolecules are presented. Elastic light scattering spectra of MDR's for biosensor applications are calculated numerically for biomolecules such as Bovine Serum Albumin (BSA) and for Deoxyribo Nucleic Acid (DNA).Publication Metadata only Clinical validation of SERS metasurface SARS-CoV-2 biosensor(Spie-Int Soc Optical Engineering, 2022) İlgu, Müslüm; Yanık, Cenk; Çelik, Süleyman; Öztürk, Meriç; N/A; N/A; Department of Electrical and Electronics Engineering; N/A; N/A; N/A; N/A; Department of Electrical and Electronics Engineering; Bilgin, Buse; Torun, Hülya; Doğan, Özlem; Ergönül, Önder; Solaroğlu, İhsan; Can, Füsun; Onbaşlı, Mehmet Cengiz; PhD Student; PhD Student; Undergraduated Student; Faculty Member; Faculty Member; Faculty Member; Faculty Member; Faculty Member; Department of Electrical and Electronics Engineering; Koç University Research Center for Translational Medicine (KUTTAM) / Koç Üniversitesi Translasyonel Tıp Araştırma Merkezi (KUTTAM); Graduate School of Sciences and Engineering; Graduate School of Sciences and Engineering; College of Engineering; School of Medicine; School of Medicine; School of Medicine; School of Medicine; College of Engineering; Koç University Hospital; N/A; N/A; N/A; 170418; 110398; 102059; 103165; 258783The real-time polymerase chain reaction (RT-PCR) analysis using nasal swab samples is the gold standard approach for COVID-19 diagnosis. However, due to the high false-negative rate at lower viral loads and complex test procedure, PCR is not suitable for fast mass screening. Therefore, the need for a highly sensitive and rapid detection system based on easily collected fluids such as saliva during the pandemic has emerged. In this study, we present a surface-enhanced Raman spectroscopy (SERS) metasurface optimized with genetic algorithm (GA) to detect SARS-CoV-2 directly using unprocessed saliva samples. During the GA optimization, the electromagnetic field profiles were used to calculate the field enhancement of each structure and the fitness values to determine the performance of the generated substrates. The obtained design was fabricated using electron beam lithography, and the simulation results were compared with the test results using methylene blue fluorescence dye. After the performance of the system was validated, the SERS substrate was tested with inactivated SARS-CoV-2 virus for virus detection, viral load analysis, cross-reactivity, and variant detection using machine learning models. After the inactivated virus tests are completed, with 36 PCR positive and 33 negative clinical samples, we were able to detect the SARS-CoV-2 positive samples from Raman spectra with 95.2% sensitivity and specificity.Publication Open Access Estimation of fracture toughness of liver tissue: experiments and validation(Elsevier, 2012) Department of Mechanical Engineering; Gökgöl, Can; Başdoğan, Çağatay; Canadinç, Demircan; Faculty Member; Faculty Member; Department of Mechanical Engineering; Graduate School of Sciences and Engineering; College of Engineering; N/A; 125489; 23433The mechanical interaction between the surgical tools and the target soft tissue is mainly dictated by the fracture toughness of the tissue in several medical procedures, such as catheter insertion, robotic-guided needle placement, suturing, cutting or tearing, and biopsy. Despite the numerous experimental works on the fracture toughness of hard biomaterials, such as bone and dentin, only a very limited number of studies have focused on soft tissues, where the results do not show any consistency mainly due to the negligence of the puncturing/cutting tool geometry. In order to address this issue, we performed needle insertion experiments on 3 bovine livers with 4 custom-made needles having different diameters. A unique value for fracture toughness (J = 164 +/- 6 J/m(2)) was obtained for the bovine liver by fitting a line to the toughness values estimated from the set of insertion experiments. In order to validate the experimental results, a finite element model of the bovine liver was developed and its hyper-viscoelastic material properties were estimated through an inverse solution based on static indentation and ramp- and-hold experiments. Then, needle insertion into the model was simulated utilizing an energy-based fracture mechanics approach. The insertion forces estimated from the FE simulations show an excellent agreement with those acquired from the physical experiments for all needle geometries. (c) 2011 IPEM. Published by Elsevier Ltd. All rights reserved.Publication Metadata only Investigating the effect of body composition differences on seismocardiogram characteristics(IEEE Computer Soc, 2023) Tokmak, Fadime; Department of Electrical and Electronics Engineering; Gürsoy, Beren Semiz; Department of Electrical and Electronics Engineering; College of EngineeringIn seismocardiogram (SCG) analysis, inter-subject variability is observed as the medium between the heart and accelerometer consists of different tissues made of bone, muscle, fat and skin cells of which combination varies across different people. Anatomically, a similar pattern is present in the speech production system, where the vocal cord and vocal tract are considered as the source and medium, respectively. For observing the change of the vocal tract filter while voicing different sounds, linear predictive analysis has been used for years. Thus, it was hypothesized that the medium characteristics of the human thorax would also have a filtering effect on the SCG signals and the differences in the filtering effects would be observed in the respiration (<1 Hz), vibration (1-20 Hz) and acoustic (>20 Hz) characteristics of the SCG signals. To that aim, three different binary classification tasks representing the body composition differences were defined: (i) whether the metabolic age of the subject is more than the real age of the subject, (ii) whether the BMI of the subject is bigger than 25, and (iii) whether the subject is male or female. To understand the metabolism-induced changes in the respiration, vibration and acoustic components, classification experiments were conducted using different frequency bands of the SCG signal. In each case, linear predictive coefficients were extracted and used to train individual classification models for the aforementioned scenarios. With the vibration components (120 Hz), all of the tasks resulted in high performance (0.86, 0.93, 0.93) for age, BMI and gender classification tasks, respectively. This study reveals that the vibration components of SCG make a stable and informative contribution to selected classification tasks, and due to its high generalizability, it is suitable for various practical applications.Publication Metadata only Liposomes under shear: structure, dynamics, and drug delivery applications(Wiley-VCH, 2023) Department of Chemical and Biological Engineering; N/A; Şenses, Erkan; Karaz, Selcan; Faculty Member; Master Student; Department of Chemical and Biological Engineering; College of Engineering; Graduate School of Sciences and Engineering; 280298; N/AThe targeted delivery to specific locations while not causing damage to healthy tissues efficiently remains a challenge in drug delivery systems. Through addressing this issue, stimuli-responsive materials have been under investigation. As one of the fundamental forces associated with blood flow, shear stress is taken as an advantage to design shear-sensitive drug carriers. Although blood flow is modeled as laminar flow under normal conditions, in case of constrictions caused by endothelial shear stress, cardiovascular diseases, or angiogenesis due to tumor formation, local shear stress can dramatically increase. To date, shear-sensitive materials have been investigated under two main categories: shear-disaggregated and shear-deformed nanoparticles based on their structural mechanism after exposure to high-shear stress. Among them, liposomes are promising materials with their soft and deformable structure, high biocompatibility, controlled-release properties, and sensitivity to shear stress. Herein, in this review, the effects of shear stress on liposomes in terms of their structural changes, flow regimes, rheological properties, and drug delivery applications are discussed. It is believed that this work provides a basis for designing more effective drug delivery systems considering the complexity of the human body.Publication Open Access Microsphere-based optical system for biosensor applications(Society of Photo-optical Instrumentation Engineers (SPIE), 2004) Department of Physics; Department of Electrical and Electronics Engineering; İşçi, Şenol; Bilici, Temel; Serpengüzel, Ali; Kurt, Adnan; Faculty Member; Teaching Faculty; Department of Physics; Department of Electrical and Electronics Engineering; College of Sciences; N/A; N/A; 27855; 194455Optical microsphere resonators have been recently utilized in quantum optics, laser science, spectroscopy, and optoelectronics and attracted increasing interest due to their unique optical properties. Microspheres possess high quality factor (Q-factor) optical morphology dependent resonances, and have relatively small volumes. High-Q morphology dependent resonances are very sensitive to the refractive index change and microsphere uniformity. These tiny optical cavities, whose diameters may vary from a few to several hundred micrometers, have resonances with reported Q-factors as large as 3 x 10(9). Due to their sensitivity, morphology dependent resonances of microspheres are also considered for biosensor applications. Binding of a protein or other biomolecules can be monitored by observing the wavelength shift of morphology dependent resonances. A biosensor, based on this optical phenomenon, can even detect a single molecule, depending on the quality of the system design. In this work, elastic scattering spectra from the microspheres of different materials are experimentally obtained and morphology dependent resonances are observed. Preliminary results of unspecific binding of biomolecules onto the microspheres are presented. Furthermore, the morphology dependent resonances of the microspheres for biosensor applications are analyzed theoretically both for proteins such as bovine serum albumin.