Research Outputs
Permanent URI for this communityhttps://hdl.handle.net/20.500.14288/2
Browse
11 results
Search Results
Publication Metadata only A structured mechanical risk sensitivity assessment system using red cell deformability and fragmentation parameters(Ios Press, 2021) Yalçın, Özlem; Uğurel, Elif; Göktaş, Polat; Göksel, Evrim; Çilek, Neslihan; Atar, Dila; Faculty Member; Researcher; Researcher; PhD Student; PhD Student; Undergraduate Student; School of Medicine; School of Medicine; School of Medicine; Graduate School of Health Sciences; Graduate School of Health Sciences; School of Medicine; 218440; N/A; N/A; N/A; N/A; N/AN/APublication 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 Correlation between the mechanical and histological properties of liver tissue(Elsevier, 2014) Department of Mechanical Engineering; Başdoğan, Çağatay; Yarpuzlu, Berkay; Ayyıldız, Mehmet; Tok, Olgu Enis; Aktaş, Ranan Gülhan; Faculty Member; Master Student; Faculty Member; Department of Mechanical Engineering; College of Engineering; School of Medicine; 125489; N/A; N/A; N/A; N/AIn order to gain further insight into the mechanisms of tissue damage during the progression of liver diseases as well as the liver preservation for transplantation, an improved understanding of the relation between the mechanical and histological properties of liver is necessary. We suggest that this relation can only be established truly if the changes in the states of those properties are investigated dynamically as a function of post mortem time. In this regard, we first perform mechanical characterization experiments on three bovine livers to investigate the changes in gross mechanical properties (stiffness, viscosity, and fracture toughness) for the preservation periods of 5, 11, 17, 29, 41 and 53 h after harvesting. Then, the histological examination is performed on the samples taken from the same livers to investigate the changes in apoptotic cell count, collagen accumulation, sinusoidal dilatation, and glycogen deposition as a function of the same preservation periods. Finally, the correlation between the mechanical and histological properties is investigated via the Spearman's Rank-Order Correlation method. The results of our study show that stiffness, viscosity, and fracture toughness of bovine liver increase as the preservation period is increased. These macroscopic changes are very strongly correlated with the increase in collagen accumulation and decrease in deposited glycogen level at the microscopic level. Also, we observe that the largest changes in mechanical and histological properties occur after the first 11-17 h of preservation. (C) 2013 Elsevier Ltd. All rights reserved.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 In silico analysis of elastomer-coated cerclage for reducing sternal cut-through in high-risk patients(The American Society of Mechanical Engineers (ASME), 2021) Erdoğan, Mustafa Bilge; N/A; N/A; N/A; Department of Mechanical Engineering; Department of Mechanical Engineering; Subaşı, Ömer; Oral, Atacan; Torabnia, Shams; Erdoğan, Deniz; Lazoğlu, İsmail; PhD Student; PhD Student; PhD Student; Undergraduate Student; Faculty Member; Department of Mechanical Engineering; Manufacturing and Automation Research Center (MARC); Graduate School of Sciences and Engineering; Graduate School of Sciences and Engineering; Graduate School of Sciences and Engineering; College of Engineering; College of Engineering; N/A; N/A; N/A; N/A; 179391Background: AISI 316 L stainless steel wire cerclage routinely used in sternotomy closure causes lateral cut-through damage and fracture, especially in cases of high-risk patients, which leads to postoperative complications. A biocompatible elastomer (Pellethane(R)) coating on the standard wire is proposed to mitigate the cut-through effect. Methods: Simplified peri-sternal and transsternal, sternum-cerclage contact models are created and statically analyzed in a finite element (FE) software to characterize the stress-reduction effect of the polymer coating for thicknesses between 0.5 and 1.125 mm. The performance of the polymer-coated cerclage in alleviating the detrimental cortical stresses is also compared to the standard steel cerclage in a full sternal closure FE model for the extreme cough loading scenario. Results: It was observed via the simplified contact simulations that the cortical stresses can be substantially decreased by increasing the coating thickness. The full closure coughing simulation on the human sternum further corroborated the simplified contact results. The stress reduction effect was found to be more prominent in the transsternal contacts in comparison to peri-sternal contacts. Conclusions: Bearing in mind the promising numerical simulation results, it is put forth that a standard steel wire coated with Pellethane will majorly address the cut-through complication.Publication Metadata only Integrating molecular simulations with machine learning guides in the design and synthesis of [bmim][bf(4)]/mof composites for co(2)/n(2) separation(American Chemical Society, 2023) N/A; N/A; N/A; N/A; Department of Chemical and Biological Engineering; Department of Chemical and Biological Engineering; Harman, Hilal Dağlar; Gülbalkan, Hasan Can; Habib, Nitasha; Durak, Özce; Uzun, Alper; Keskin, Seda; PhD Student; PhD Student; PhD Student; Undergraduate Student; Faculty Member; Faculty Member; Department of Chemical and Biological Engineering; Koç University Tüpraş Energy Center (KUTEM) / Koç Üniversitesi Tüpraş Enerji Merkezi (KÜTEM); Koç University Surface Science and Technology Center (KUYTAM) / Koç Üniversitesi Yüzey Teknolojileri Araştırmaları Merkezi (KUYTAM); Graduate School of Sciences and Engineering; Graduate School of Sciences and Engineering; Graduate School of Sciences and Engineering; Graduate School of Sciences; College of Engineering and Engineering; College of Engineering; N/A; N/A; N/A; N/A; 59917; 40548Considering the existence of a large number and variety of metal-organic frameworks (MOFs) and ionic liquids (ILs), assessing the gas separation potential of all possible IL/MOF composites by purely experimental methods is not practical. In this work, we combined molecular simulations and machine learning (ML) algorithms to computationally design an IL/MOF composite. Molecular simulations were first performed to screen approximately 1000 different composites of 1-n-butyl-3-methylimidazolium tetrafluoroborate ([BMIM][BF4]) with a large variety of MOFs for CO2 and N2 adsorption. The results of simulations were used to develop ML models that can accurately predict the adsorption and separation performances of [BMIM][BF4]/MOF composites. The most important features that affect the CO2/N2 selectivity of composites were extracted from ML and utilized to computationally generate an IL/MOF composite, [BMIM][BF4]/UiO-66, which was not present in the original material data set. This composite was finally synthesized, characterized, and tested for CO2/N2 separation. Experimentally measured CO2/N2 selectivity of the [BMIM][BF4]/UiO-66 composite matched well with the selectivity predicted by the ML model, and it was found to be comparable, if not higher than that of all previously synthesized [BMIM][BF4]/MOF composites reported in the literature. Our proposed approach of combining molecular simulations with ML models will be highly useful to accurately predict the CO2/N2 separation performances of any [BMIM][BF4]/MOF composite within seconds compared to the extensive time and effort requirements of purely experimental methods.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 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 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.Publication Open Access Oscillator noise analysis(American Institute of Physics (AIP) Publishing, 2005) Department of Electrical and Electronics Engineering; Demir, Alper; Faculty Member; Department of Electrical and Electronics Engineering; College of Engineering; 3756Oscillators are key components of many kinds of systems, particularly electronic and opto-electronic systems. Undesired perturbations, i.e. noise, that exist in practical systems adversely affect the spectral and timing properties of the signals generated by oscillators resulting in phase noise and timing jitter. These are key performance limiting factors, being major contributors to bit-error-rate (BER) of RF and optical communication systems, and creating synchronization problems in clocked and sampled-data electronic systems. In noise analysis for oscillators, the key is figuring out how the various disturbances and noise sources in the oscillator end up as phase fluctuations. In doing so, one first computes transfer functions from the noise sources to the oscillator phase, or the sensitivity of the oscillator phase to these noise sources. In this paper, we first provide a discussion explaining the origins and the proper definition of this transfer or sensitivity function, followed by a critical review of the various numerical techniques for its computation that have been proposed by various authors over the past fifteen years.