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Department: search.filters.department.Department of Mechanical EngineeringSubject: search.filters.subject.Biophysics

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Now showing 1 - 10 of 28
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    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; 308798
    Glucose 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.
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    Characterization of neonatal aortic cannula jet flow regimes for improved cardiopulmonary bypass
    (Elsevier Sci Ltd, 2013) Menon, Prahlad G.; Teslovich, Nikola; Chen, Chia-Yuan; Undar, Akif; Department of Mechanical Engineering; Pekkan, Kerem; Faculty Member; Department of Mechanical Engineering; College of Engineering; 161845
    During pediatric and neonatal cardiopulmonary bypass (CPB), tiny aortic outflow cannulae (2-3 mm inner diameter), with micro-scale blood-wetting features transport relatively large blood volumes (0.3 to 1.0 L/min) resulting in high blood flow velocities (2 to 5 m/s). These severe flow conditions are likely to complement platelet activation, release pro-inflammatory cytokines, and further result in vascular and blood damage. Hemodynamically efficient aortic outflow cannulae are required to provide high blood volume flow rates at low exit force. In addition, optimal aortic insertion strategies are necessary in order to alleviate hemolytic risk, post-surgical neurological complications and developmental defects, by improving cerebral perfusion in the young patient. The methodology and results presented in this study serve as a baseline for design of superior aortic outflow cannulae. In this study, direct numerical simulation (DNS) computational fluid dynamics (CFD) was employed to delineate baseline hemodynamic performance of jet wakes emanating from microCT scanned state-of-the-art pediatric cannula tips in a cuboidal test rig operating at physiologically relevant laminar and turbulent Reynolds numbers (Re: 650-2150, steady inflow). Qualitative and quantitative validation of CFD simulated device-specific jet wakes was established using time-resolved flow visualization and particle image velocimetry (PIV). For the standard end-hole cannula tip design, blood damage indices were further numerically assessed in a subject-specific cross-clamped neonatal aorta model for different cannula insertion configurations. Based on these results, a novel diffuser type cannula tip is proposed for improved jet flow-control, decreased blood damage and exit force and increased permissible flow rates. This study also suggests that surgically relevant cannula orientation parameters such as outflow angle and insertion depth may be important for improved hemodynamic performance. The jet flow design paradigm demonstrated in this study represents a philosophical shift towards cannula flow control enabling favorable pressure-drop versus outflow rate characteristics.
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    Computational modeling of vascular growth in patient-specific pulmonary arterial patch reconstructions
    (Elsevier Sci Ltd, 2021) Coban, Gursan; Kose, Banu; Salihoglu, Ece; Department of Mechanical Engineering; Department of Mechanical Engineering; Lashkarinia, Seyedeh Samaneh; Pekkan, Kerem; Researcher; Faculty Member; Department of Mechanical Engineering; College of Engineering; College of Engineering
    Recent progress in vascular growth mechanics has involved the use of computational algorithms to address clinical problems with the use of three-dimensional patient specific geometries. The objective of this study is to establish a predictive computational model for the volumetric growth of pulmonary arterial (PA) tissue following complex cardiovascular patch reconstructive surgeries for congenital heart disease patients. For the first time in the literature, the growth mechanics and performance of artificial cardiovascular patches in contact with the growing PA tissue domain is established. An elastic growing material model was developed in the open source FEBio software suite to first examine the surgical patch reconstruction process for an idealized main PA anatomy as a benchmark model and then for the patient-specific PA of a newborn. Following patch reconstruction, high levels of stress and strain are compensated by growth on the arterial tissue. As this growth progresses, the arterial tissue is predicted to stiffen to limit elastic deformations. We simulated this arterial growth up to the age of 18 years, when somatic growth plateaus. Our research findings show that the non-growing patch material remains in a low strain state throughout the simulation timeline, while experiencing high stress hot-spots. Arterial tissue growth along the surgical stitch lines is triggered mainly due to PA geometry and blood pressure, rather than due to material property differences in the artificial and native tissue. Thus, nonuniform growth patterns are observed along the arterial tissue proximal to the sutured boundaries. This computational approach is effective for the pre-surgical planning of complex patch surgeries to quantify the unbalanced growth of native arteries and artificial non-growing materials to develop optimal patch biomechanics for improved postoperative outcomes.
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    Conformation and aggregation of peptides at interfaces
    (Cell Press, 2014) Department of Mechanical Engineering; Sayar, Mehmet; Faculty Member; Department of Mechanical Engineering; College of Engineering; 109820
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    Designing covalent organic framework-based light-driven microswimmers towards therapeutic applications
    (Wiley, 2023) Sridhar, Varun; Yıldız, Erdost; Rodríguez-Camargo, Andrés; Lyu, Xianglong; Yao, Liang; Wrede, Paul; Aghakhani, Amirreza; Akolpoglu, Birgul M.; Podjaski, Filip; Lotsch, Bettina V.; Department of Mechanical Engineering; Sitti, Metin; Faculty Member; Department of Mechanical Engineering; College of Engineering; 297104
    While micromachines with tailored functionalities enable therapeutic applications in biological environments, their controlled motion and targeted drug delivery in biological media require sophisticated designs for practical applications. Covalent organic frameworks (COFs), a new generation of crystalline and nanoporous polymers, offer new perspectives for light-driven microswimmers in heterogeneous biological environments including intraocular fluids, thus setting the stage for biomedical applications such as retinal drug delivery. Two different types of COFs, uniformly spherical TABP-PDA-COF sub-micrometer particles and texturally nanoporous, micrometer-sized TpAzo-COF particles are described and compared as light-driven microrobots. They can be used as highly efficient visible-light-driven drug carriers in aqueous ionic and cellular media. Their absorption ranging down to red light enables phototaxis even in deeper and viscous biological media, while the organic nature of COFs ensures their biocompatibility. Their inherently porous structures with ≈2.6 and ≈3.4 nm pores, and large surface areas allow for targeted and efficient drug loading even for insoluble drugs, which can be released on demand. Additionally, indocyanine green (ICG) dye loading in the pores enables photoacoustic imaging, optical coherence tomography, and hyperthermia in operando conditions. This real-time visualization of the drug-loaded COF microswimmers enables unique insights into the action of photoactive porous drug carriers for therapeutic applications.
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    Detection of human kappa-opioid antibody using microresonators with integrated optical readout
    (Elsevier advanced Technology, 2010) N/A; N/A; N/A; N/A; Department of Mechanical Engineering; Department of Chemical and Biological Engineering; Department of Electrical and Electronics Engineering; Department of Mechanical Engineering; Timurdoğan, Erman; Özber, Natali; Nargül, Sezin; Yavuz, Serhat; Kılıç, M. Salih; Kavaklı, İbrahim Halil; Ürey, Hakan; Alaca, Burhanettin Erdem; PhD Student; Master Student; PhD Student; Master Student; Resercher; Faculty Member; Faculty Member; Faculty Member; Department of Chemical and Biological Engineering; Department of Electrical and Electronics Engineering; Department of Mechanical Engineering; Graduate School of Sciences and Engineering; Graduate School of Sciences and Engineering; Graduate School of Sciences and Engineering; Graduate School of Sciences and Engineering; College of Engineering; College of Engineering; College of Engineering; College of Engineering; N/A; N/A; N/A; N/A; N/A; 40319; 8579; 115108
    Label-free detection of the interaction between hexahistidine-tagged human kappa-opioid receptor membrane protein and anti-His antibody is demonstrated in liquid by an optical microelectromechanical system utilizing electromagnetically actuated microresonators Shift in resonance frequency due to accretion of mass on the sensitive surface of microresonators is monitored via an integrated optical readout a frequency resolution of 2 Hz is obtained Together with a sensitivity of 7 ppm/(ng/ml)) this leads to a minimum detectable antibody concentration of 57 ng/ml for a 50-kHz device the measurement principle is shown to impart immunity to environmental noise, facilitate operation in liquid media and bring about the prospect for further miniaturization of actuator and readout leading to a portable biochemical sensor.
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    Digital monitoring of the microchannel filling flow dynamics using a non-contactless smartphone-based nano-liter precision flow velocity meter
    (Elsevier Advanced Technology, 2024) Xu, Weiming; Köydemir, Hatice Ceylan; Department of Mechanical Engineering; Atik, Abdulkadir Yasin; Beker, Levent; Department of Mechanical Engineering; Graduate School of Sciences and Engineering; College of Engineering
    Microfluidic systems find widespread applications in diagnostics, biological research, chemistry, and engineering studies. Among their many critical parameters, flow rate plays a pivotal role in maintaining the functionality of microfluidic systems, including droplet-based microfluidic devices and those used in cell culture. It also significantly influences microfluidic mixing processes. Although various flow rate measurement devices have been developed, the challenge remains in accurately measuring flow rates within customized channels. This paper presents the development of a 3D-printed smartphone-based flow velocity meter. The 3D-printed platform is angled at 30 degrees to achieve transparent flow visualization, and it doesn't require any external optical components such as external lenses and filters. Two LED modules integrated into the platform create a uniform illumination environment for video capture, powered directly by the smartphone. The performance of our platform, combined with a customized video processing algorithm, was assessed in three different channel types: uniform straight channels, straight channels with varying widths, and vessel-like channel patterns to demonstrate its versatility. Our device effectively measured flow velocities from 5.43 mm/s to 24.47 mm/s, with video quality at 1080p resolution and 60 frames per second, for which the measurement range can be extended by adjusting the frame rate. This flow velocity meter can be a useful analytical tool to evaluate and enhance microfluidic channel designs of various lab-on-a-chip applications.
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    Effect of asymmetry on finite element model of cervical spine
    (The American Society of Mechanical Engineers (ASME), 2013) N/A; Department of Mechanical Engineering; Department of Mechanical Engineering; N/A; Zafarparandeh, Iman; Erbulut, Deniz Ufuk; Lazoğlu, İsmail; Özer, Ali Fahir; PhD Student; Researcher; Faculty Member; Faculty Member; Department of Mechanical Engineering; Graduate School of Sciences and Engineering; College of Engineering; College of Engineering; School of Medicine; N/A; 37661; 179391; 1022
    The cervical region of spinal column has been known as a frequent site of injuries. The major causes of injuries are vehicle accidents and sports. Clinical instability is known as one of the important topics in cervical spine research. It clarifies the relation between the mechanical dysfunction of the spine and the neurologic dysfunction and pain. From the clinical point of view, if the spinal segment exhibits abnormal large increase in rotational or translational displacements under physiological load, it is considered as unstable. There are different biomechanical models available to understand the underlying mechanisms of injury and dysfunction. Finite element (FE) models have been used as a strong tool to provide the basic insights into the workings of the cervical spine system. Furthermore, they have been clinically useful in the development of the definition of clinical instability and of diagnostic guidelines.
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    Effect of preservation period on the viscoelastic material properties of soft tissues with implications for liver transplantation
    (Asme, 2010) N/A; N/A; N/A; Department of Mechanical Engineering; Department of Mechanical Engineering; Öcal, Sina; Özcan, Mustafa Umut; Başdoğan, İpek; Başdoğan, Çağatay; Master Student; Master Student; Faculty Member; Faculty Member; Department of Mechanical Engineering; Graduate School of Sciences and Engineering; Graduate School of Sciences and Engineering; College of Engineering; College of Engineering; N/A; N/A; 179940; 125489
    The liver harvested from a donor must be preserved and transported to a suitable recipient immediately for a successful liver transplantation. In this process, the preservation period is the most critical, since it is the longest and most tissue damage occurs during this period due to the reduced blood supply to the harvested liver and the change in its temperature. We investigate the effect of preservation period on the dynamic material properties of bovine liver using a viscoelastic model derived from both impact and ramp and hold experiments. First, we measure the storage and loss moduli of bovine liver as a function of excitation frequency using an impact hammer. Second, its time-dependent relaxation modulus is measured separately through ramp and hold experiments performed by a compression device. Third, a Maxwell solid model that successfully imitates the frequency- and time-dependent dynamic responses of bovine liver is developed to estimate the optimum viscoelastic material coefficients by minimizing the error between the experimental data and the corresponding values generated by the model. Finally, the variation in the viscoelastic material coefficients of bovine liver are investigated as a function of preservation period for the liver samples tested 1 h, 2 h, 4 h, 8 h, 12 h, 24 h, 36 h, and 48 h after harvesting. The results of our experiments performed with three animals show that the liver tissue becomes stiffer and more viscous as it spends more time in the preservation cycle.
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    Effect of solution and post-mortem time on mechanical and histological properties of liver during cold preservation
    (IOS Press, 2014) N/A; N/A; Department of Mechanical Engineering; Ayyıldız, Mehmet; Aktaş, Ranan Gülhan; Başdoğan, Çağatay; PhD Student; Faculty Member; Faculty Member; Department of Mechanical Engineering; Graduate School of Sciences and Engineeringg; School of Medicine; College of Engineering; N/A; 137519; 125489
    Background: In liver transplantation, the donor and recipient are in different locations most of the time, and longer preservation periods are inevitable. Hence, the choice of the preservation solution and the duration of the preservation period are critical for the success of the transplant surgery. Objective: In this study, we examine the mechanical and histological properties of the bovine liver tissue stored in Lactated Ringer's (control), HTK and UW solutions as a function of preservation period. Methods: The mechanical experiments are conducted with a shear rheometer on cylindrical tissue samples extracted from 3 bovine livers and the change in viscoelastic material properties of the bovine liver is characterized using the fractional derivative Kelvin-Voigt Model. Also, the histological examinations are performed on the same liver samples under a light microscope. Results: The results show that the preservation solution and period have a significant effect on the mechanical and histological properties of the liver tissue. The storage and loss shear moduli, the number of the apoptotic cells, the collagen accumulation, and the sinusoidal dilatation increase, and the glycogen deposition decreases as the preservation period is longer. Conclusions: Based on the statistical analyses, we observe that the liver tissue is preserved well in all three solutions for up to 11 h. After then, UW solution provides a better preservation up to 29 h. However, for preservation periods longer than 29 h, HTK is a more effective preservation solution based on the least amount of change in mechanical properties. on the other hand, the highest correlation between the mechanical and histological properties is observed for the liver samples preserved in UW solution.