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Review Citation - WoS: 26Citation - Scopus: 23Real-Time Biosensing Bacteria and Virus With Quartz Crystal Microbalance: Recent Advances, Opportunities, and Challenges(Taylor & Francis inc, 2023) Bonyadi, Farzaneh; Kavruk, Murat; Ucak, Samet; Cetin, Barbaros; Bayramoglu, Gulay; Dursun, Ali D. D.; Ozalp, Veli C. C.Continuous monitoring of pathogens finds applications in environmental, medical, and food industry settings. Quartz crystal microbalance (QCM) is one of the promising methods for real-time detection of bacteria and viruses. QCM is a technology that utilizes piezoelectric principles to measure mass and is commonly used in detecting the mass of chemicals adhering to a surface. Due to its high sensitivity and rapid detection times, QCM biosensors have attracted considerable attention as a potential method for detecting infections early and tracking the course of diseases, making it a promising tool for global public health professionals in the fight against infectious diseases. This review first provides an overview of the QCM biosensing method, including its principle of operation, various recognition elements used in biosensor creation, and its limitations and then summarizes notable examples of QCM biosensors for pathogens, focusing on microfluidic magnetic separation techniques as a promising tool in the pretreatment of samples. The review explores the use of QCM sensors in detecting pathogens in various samples, such as food, wastewater, and biological samples. The review also discusses the use of magnetic nanoparticles for sample preparation in QCM biosensors and their integration into microfluidic devices for automated detection of pathogens and highlights the importance of accurate and sensitive detection methods for early diagnosis of infections and the need for point-of-care approaches to simplify and reduce the cost of operation.Article Citation - WoS: 10Citation - Scopus: 11A Multi-Domain Direct Boundary Element Formulation for Particulate Flow in Microchannels(Elsevier Sci Ltd, 2021) Topuz, Alper; Baranoglu, Besim; Cetin, BarbarosIn the present study, a multi-domain boundary element formulation is developed for high surface-area-to-volume ratio problems (i.e. particulate flow in high aspect ratio microfluidic channels, in a porous medium or in microfluidic devices with repetitive structures). The solution domain is decomposed into subdomains and the variable condensation technique is implemented. The solution matrices are built for each subdomain, and the matrices are updated at each time step only for the subdomains in which the particles move at each time step. Ghost domains, which are fictitious domains encapsulating the interfaces between the subdomains, are also introduced in the formulation to treat the particles crossing the interfaces between the subdomains. The formulation reveals that the computation of the subdomain matrices is further simplified for solution domains composed of periodic structures. The results of our study revealed that speed-up values as high as 50 is achievable with the current formulation.Article Citation - WoS: 5Citation - Scopus: 5Aptamer decorated PDA@magnetic silica microparticles for bacteria purification(Springer Wien, 2024) Kavruk, Murat; Babaie, Zahra; Kibar, Gunes; Cetin, Barbaros; Yesilkaya, Hasan; Amrani, Yassine; Ozalp, V. CengizOne significant constraint in the advancement of biosensors is the signal-to-noise ratio, which is adversely affected by the presence of interfering factors such as blood in the sample matrix. In the present investigation, a specific aptamer binding was chosen for its affinity, while exhibiting no binding affinity towards non-target bacterial cells. This selective binding property was leveraged to facilitate the production of magnetic microparticles decorated with aptamers. A novel assay was developed to effectively isolate S. pneumoniae from PBS or directly from blood samples using an aptamer with an affinity constant of 72.8 nM. The capture experiments demonstrated efficiencies up to 87% and 66% are achievable for isolating spiked S. pneumoniae in 1 mL PBS and blood samples, respectively.Article Citation - WoS: 10Citation - Scopus: 11Biosensor for Atp Detection Via Aptamer-Modified Pda@poss Nanoparticles Synthesized in a Microfluidic Reactor(Springer Wien, 2024) Kibar, Gunes; Sahinoglu, O. Berkay; Kilincli, Betul; Erdem, E. Yegan; Cetin, Barbaros; Ozalp, V. CengizThis study introduces aptamer-functionalized polyhedral oligomeric silsesquioxane (POSS) nanoparticles for adenosine triphosphate (ATP) detection where the POSS nanoparticles were synthesized in a one-step, continuous flow microfluidic reactor utilizing thermal polymerization. A microemulsion containing POSS monomers was generated in the microfluidic reactor which was designed to prevent clogging by using a continuous oil flow around the emulsion during thermal polymerization. Surfaces of POSS nanoparticles were biomimetically modified by polydopamine. The aptamer sequence for ATP was successfully attached to POSS nanoparticles. The aptamer-modified POSS nanoparticles were tested for affinity-based biosensor applications using ATP as a model molecule. The nanoparticles were able to capture ATP molecules successfully with an affinity constant of 46.5 mu\documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$\upmu $$\end{document}M. Based on this result, it was shown, for the first time, that microfluidic synthesis of POSS nanoparticles can be utilized in designing aptamer-functionalized nanosystems for biosensor applications. The integration of POSS in biosensing technologies not only exemplifies the versatility and efficacy of these nanoparticles but also marks a significant contribution to the field of biorecognition and sample preparation.Article Citation - WoS: 2Citation - Scopus: 3Microfluidic Rapid Isolation and Electrochemical Detection of S. Pneumonia Via Aptamer-Decorated Surfaces(Elsevier, 2025) Babaie, Zahra; Kibar, Gunes; Yesilkaya, Hasan; Amrani, Yassine; Dogan, Soner; Tuna, Bilge G.; Cetin, Barbaros; Özalp, Veli CengizBackground: S. pneumoniae is widely recognized as a leading cause of respiratory infections worldwide, often resulting in high mortality rates. However, the advent of microfluidic technologies has brought significant advancements, including the simplified, sensitive, cost-effective, and rapid approach to pneumococcal bacteremia detection. In this study, a microfluidic magnetic platform is presented for rapid isolation, and an electrode array is utilized for the electrochemical detection of S. pneumoniae. Aptamer-decorated surfaces were employed for both isolation and detection. For isolation, silica magnetic microparticles were synthesized and decorated with aptamer. Results: Isolation performance was assessed for phosphate-buffered saline (PBS) and blood samples for different concentrations of S. pneumoniae. Electrical impedance spectroscopy (EIS) with fabricated gold interdigitated electrodes (IDEs) decorated with aptamer was implemented for the detection of S. pneumoniae at different bacteria concentrations. The microfluidic platform performed bacteria isolation at comparable isolation efficiency with batch systems but at a much faster rate (isolation took about a minute, and the aptamer-decorated electrode array exhibited a limit of detection (LOD) at 962 CFU/mL and linear range between 104 and 107CFU/mL. Significance: Our method represents a significant advancement compared to previous reports. Our microfluidic platform can efficiently isolate 60 mu L of the bacteria sample within about one minute. The entire process takes about two minutes including the detection step. Furthermore, our method achieves a notable improvement in the detection limit for S. pneumoniae compared to conventional ELISA and magnetic microfluidics ELISA.Article Citation - WoS: 5Citation - Scopus: 6Isogeometric Boundary Element Formulation for Cathodic Protection of Amphibious Vehicles(Elsevier Sci Ltd, 2024) Gumus, Ozgur Can; Atak, Kaan; Cetin, Baris; Baranoglu, Besim; Cetin, BarbarosIn this study, we propose an isogeometric boundary element formulation for the cathodic protection (CP) modeling for amphibious vehicles which includes the treatment of non-linear boundary conditions. Half-space Green's functions are utilized which leads to the discretization of the hull surface only. Non-Uniform Rational B splines (NURBS) are employed to represent both geometry and field variables to obtain higher accuracy where discontinuous collocation points are utilized to make multi-patch implementation easier. Variable condensation technique is applied to manipulate system matrices in a such way that the solution is iterated only on the surfaces where non-linear boundary conditions are assigned which results in reduced computational cost. The computational performance of the formulation is assessed with different solvers for a representative hull geometry.Article Citation - WoS: 13Citation - Scopus: 13Semi-Analytical Source (sas) Method for 3-D Transient Heat Conduction Problems With Moving Heat Source of Arbitrary Shape(Pergamon-elsevier Science Ltd, 2021) Cetin, Barbaros; Kuscu, Yigit F.; Cetin, Baris; Tumuklu, Ozgur; Cole, Kevin D.In this study, the semi-analytical source method, which has recently developed by the authors, is implemented for a 3-D fully-transient heat conduction problem with a moving heat source. The method utilizes the exact Green's function for a diffusion problem with a piecewise constant heat source meaning that the heat source term is defined as the superposition of piece-wise constant contributions in each time interval and in each spatial interval. This approach allows the modeling of any arbitrary spatial distribution of heating with time varying power. Moreover, the method is not limited to straight-line motion of the heat source, and can include internal heating as well as surface heating. One important aspect of the method is that spatial discretization is required only on the path of the heating source and at the observation locations of interest, consequently the discretization of the entire domain is not required as in the case of fully-numerical methods. To verify the semi-analytical source method, an experimental setup was constructed and experiments were conducted with a fiber laser, and satisfactory agreement is achieved. Several case studies are also demonstrated with a Gaussian heat source. The semi-analytical source method is particularly well-suited for parallel computing. To explore this aspect, the parallelization of the method is explored using the Message Passing Interface (MPI) and domain decomposition with up to 800 processors on Stampede2. The parallelization results reveal that semi-analytical method is very suitable for parallel computation. For a strong scaling, the method shows an ideal linear scaling with increasing number of processors with a proper load balance. The weak scaling reveals that the parallelization performance exponentially increases with the increasing time domain due to convolution nature of the method in time. (C) 2020 Elsevier Ltd. All rights reserved.
