Publications without Fulltext
Permanent URI for this collectionhttps://hdl.handle.net/20.500.14288/3
Browse
53 results
Search Results
Publication Metadata only Influence of soft segment structure, hydrogen bonding, and diisocyanate symmetry on morphology and properties of segmented thermoplastic polyurethanes and polyureas(Tubitak Scientific & Technological Research Council Turkey, 2023) Department of Chemistry; Yılgör, Emel; Yılgör, İskender; Department of Chemistry; College of SciencesA comprehensive review of the structure-morphology-property relations in segmented thermoplastic polyurethanes and polyureas (TPU) is provided. Special emphasis is given to the influence of the soft segment structure, polarity, and molecular weight, diisocyanate symmetry and the nature, extent, and strength of hydrogen bonding on the morphology and thermal and mechanical properties of TPUs. Experimental results obtained on composition-dependent TPU morphology and properties by various techniques were also compared by the morphology profiles generated by computational methods such as quantum mechanical calculations and molecular dynamics simulations.Publication Metadata only IDE-integrated microneedle arrays as fully biodegradable platforms for wearable/implantable capacitive biosensing(Institute of Electrical and Electronics Engineers Inc., 2023) Department of Electrical and Electronics Engineering; Ürey, Hakan; Mirzajani, Hadi; Department of Electrical and Electronics Engineering; Koç University Research Center for Translational Medicine (KUTTAM) / Koç Üniversitesi Translasyonel Tıp Araştırma Merkezi (KUTTAM); College of EngineeringMicroneedle biosensors have emerged as a promising tool for in situ biomarker detection due to their minimally invasive nature and ability to interface with interstitial fluid (ISF). However, most previously demonstrated ones are limited to in situ detection of small molecules and ions, employing amperometry or potentiometry measurement techniques with electrical current or voltage output metrics, respectively, which may not be suitable for detecting large molecules, such as proteins. This letter presents an innovative approach utilizing a microneedle array integrated with an interdigitated electrode (MAIDE), enabling in situ capacitive detection and quantification of protein biomarkers. Following microneedle penetration, the interdigitated electrode array establishes direct contact with the solution, enabling real-time monitoring of interfacial capacitance modulations as the result of the binding reaction, leading to the acquisition of rich molecular data. Equivalent circuit model extraction followed by impedance spectroscopy for different concentrations of bovine serum albumin (BSA) indicated the suitability of the proposed platform in tracking the interfacial capacitance variations with respect to different BSA concentrations of 100, 10, and 1 μg/mL with a detection limit of 21 ng/mL. Furthermore, the device showed satisfactory results for biodegradability experiments where it disintegrated for a duration of 10 h. In addition, in vivo experiments show stable capacitance readings with (dC/C)% deviations less than 0.5%, indicating its potential for biodegradable wearable/implantable capacitive biosensing applicationsPublication Metadata only Design and manufacturing of a hip joint motion simulator with a novel modular design approach(Springer Heidelberg, 2023) Mihcin, Senay; Department of Mechanical Engineering; Torabnia, Shams; Lazoğlu, İsmail; Department of Mechanical Engineering; Manufacturing and Automation Research Center (MARC); Graduate School of Sciences and Engineering; College of EngineeringThe study is aimed to develop a hip joint wear simulator using a modular design approach to help experimentally monitor and control critical wear parameters to validate in-silico wear models. The proper control and application of wear parameters such as the range of motion, and the applied force values while estimating the lost material due to wear are essential for thorough analysis of wear phenomena for artificial joints. The simulator's dynamics were first modeled, then dynamic loading data was used to calculate the forces, which were further used for topology optimization to reduce the forces acting on each joint. The reduction of the link weights, connected to the actuators, intends to improve the quality of motion transferred to the femoral head. The modular design approach enables topology-optimized geometry, associated gravitational and dynamic forces, resulting in a cost-effective, energy-efficient product. Moreover, this design allows integration of the subject specific data by allowing different boundary conditions following the requirements of industry 5.0. Overall, the in-vitro motion stimulations of the hip-joint prosthesis and the modular design approach used in the study might help improve the accuracy and the effectiveness of wear simulations, which could lead into the development of better and longer-lasting joint prostheses for all. The subject-specific and society-based daily life data implemented as boundary conditions enable inclusion of the personalized effects. Next, with the results of the simulator, CEN Workshop Agreement (CWA) application is intended to cover the personalized effects for previously excluded populations, providing solution to inclusive design for all.Publication Metadata only Exploration of novel 6,8,9-trisubstituted purine analogues: synthesis, in vitro biological evaluation, and their effect on human cancer cells(Tubitak Scientific & Technological Research Council Turkey, 2024) Polat, Muhammed Fatih; Atalay, Rengul; Tuncbilek, Meral; N/A; Şahin, İrem Durmaz; Koç University Research Center for Translational Medicine (KUTTAM); School of MedicineCancer, a leading global cause of mortality, demands continuous advancements in therapeutic strategies. This study focuses on the design and synthesis of a novel series of purine derivatives, specifically 6 -(substituted phenyl piperazine)-8-(4-phenoxyphenyl)9-cyclopentyl purine derivatives (5-11). The motivation behind this endeavor lies in addressing acquired resistance mechanisms in cancer cells, a significant hurdle in current treatment modalities. The synthesis, starting from 4,6-dichloro-5-nitropyrimidine, involves a multi -step process, resulting in seven new purine derivatives. Biological evaluation against human liver, colon, and breast cancer cells (Huh7, HCT116, and MCF7, respectively) was performed using the SRB assay. Among the synthesized analogs, compounds 5 and 6, exhibited notable cytotoxic activity, surpassing clinically used positive controls 5-Fluorouracil and Fludarabine in terms of efficacy. This research underscores the potential of purine derivatives with a phenyl group at the C-8 position as a scaffold for developing compounds with improved anticancer properties. The findings offer insights for future exploration and development of novel agents in cancer pharmaceutical research.Publication Metadata only On the performance of OFDM-IM systems in the presence of CFO effects(Elsevier Inc., 2024) Besseghier, Mokhtar; Ghouali, Samir; Djebbar, Ahmed Bouzidi; Department of Electrical and Electronics Engineering; Başar, Ertuğrul; Department of Electrical and Electronics Engineering; ; College of Engineering;This study presents a comprehensive analysis of the performance degradation effects of carrier frequency offset (CFO) on orthogonal frequency division multiplexing with index modulation (OFDM-IM) systems operating over frequency-selective multipath fading channels. CFO is an impairing factor that degrades the signal-to-noise ratio (SNR) through signal attenuation and inter-carrier interference (ICI). We derive a closed-form expression to quantify the SNR degradation under CFO for OFDM-IM systems. Additionally, we formulate a very tight upper bound for the bit error rate (BER), accounting for index modulation errors, CFO distortion, and multipath fading. The presented analytical formulations capture the unique characteristics of OFDM-IM systems and facilitate precise performance evaluation. The findings yield valuable insights into mitigating CFO-induced BER degradation through appropriate system parameter selection and CFO compensation techniques. Moreover, this investigation makes significant contributions towards designing reliable OFDM-IM communication links resilient to the combined effects of index modulation, frequency offsets, and dispersive channel conditions.Publication Metadata only Switching the left and the right hearts: a novel BI-ventricle mechanical support strategy with spared native single-ventricle(Springer, 2023) Şişli, Emrah; Aka, İbrahim Başar; Tuncer, Osman Nuri; Atay, Yüksel; Özbaran, Mustafa; Department of Mechanical Engineering; Yıldırım, Canberk; Pekkan, Kerem; Department of Mechanical Engineering; Graduate School of Sciences and Engineering; College of EngineeringEnd-stage Fontan patients with single-ventricle (SV) circulation are often bridged-to-heart transplantation via mechanical circulatory support (MCS). Donor shortage and complexity of the SV physiology demand innovative MCS. In this paper, an out-of-the-box circulation concept, in which the left and right ventricles are switched with each other is introduced as a novel bi-ventricle MCS configuration for the "failing" Fontan patients. In the proposed configuration, the systemic circulation is maintained through a conventional mechanical ventricle assist device (VAD) while the venous circulation is delegated to the native SV. This approach spares the SV and puts it to a new use at the right-side providing the most-needed venous flow pulsatility to the failed Fontan circulation. To analyze its feasibility and performance, eight SV failure modes have been studied via an established multi-compartmental lumped parameter cardiovascular model (LPM). Here the LPM model is experimentally validated against the corresponding pulsatile mock-up flow loop measurements of a representative 15-year-old Fontan patient employing a clinically-approved VAD (Medtronic-HeartWare). The proposed surgical configuration maintained the healthy cardiac index (3-3.5 l/min/m(2)) and the normal mean systemic arterial pressure levels. For a failed SV with low ejection fraction (EF = 26%), representing a typical systemic Fontan failure, the proposed configuration enabled a similar to 28 mmHg amplitude in the venous/pulmonary waveforms and a 2 mmHg decrease in the central venous pressure (CVP) together with acceptable mean pulmonary artery pressures (17.5 mmHg). The pulmonary vascular resistance (PVR)-SV failure case provided a similar to 5 mmHg drop in the CVP, with venous/pulmonary pulsatility reaching to similar to 22 mmHg. For the high PVR failure case with a healthy SV (EF = 44%) pulmonary hypertension is likely to occur as expected. While this condition is routinely encountered during the heart transplantation and managed through pulmonary vasodilators a need for precise functional assessment of the spared failed-ventricle is recommended if utilized in the PVR failure mode. Comprehensive in vitro and in silico results encourage this novel concept as a low-cost, more physiological alternative to the conventional bi-ventricle MCS pending animal experiments.Publication Metadata only Myocardial biomechanics and the consequent differentially expressed genes of the left atrial ligation chick embryonic model of hypoplastic left heart syndrome(Springer, 2023) Chan, Wei Xuan; Motakis, Efthymios; Ho, Sheldon; Yap, Choon Hwai; Lashkarinia, S. Samaneh; Department of Mechanical Engineering; Siddiqui, Hummaira Banu; Çoban, Mervenur; Sevgin, Börteçine; Pekkan, Kerem; Department of Mechanical Engineering; College of Engineering; Graduate School of Sciences and EngineeringLeft atrial ligation (LAL) of the chick embryonic heart is a model of the hypoplastic left heart syndrome (HLHS) where a purely mechanical intervention without genetic or pharmacological manipulation is employed to initiate cardiac malformation. It is thus a key model for understanding the biomechanical origins of HLHS. However, its myocardial mechanics and subsequent gene expressions are not well-understood. We performed finite element (FE) modeling and single-cell RNA sequencing to address this. 4D high-frequency ultrasound imaging of chick embryonic hearts at HH25 (ED 4.5) were obtained for both LAL and control. Motion tracking was performed to quantify strains. Image-based FE modeling was conducted, using the direction of the smallest strain eigenvector as the orientations of contractions, the Guccione active tension model and a Fung-type transversely isotropic passive stiffness model that was determined via micro-pipette aspiration. Single-cell RNA sequencing of left ventricle (LV) heart tissues was performed for normal and LAL embryos at HH30 (ED 6.5) and differentially expressed genes (DEG) were identified.After LAL, LV thickness increased by 33%, strains in the myofiber direction increased by 42%, while stresses in the myofiber direction decreased by 50%. These were likely related to the reduction in ventricular preload and underloading of the LV due to LAL. RNA-seq data revealed potentially related DEG in myocytes, including mechano-sensing genes (Cadherins, NOTCH1, etc.), myosin contractility genes (MLCK, MLCP, etc.), calcium signaling genes (PI3K, PMCA, etc.), and genes related to fibrosis and fibroelastosis (TGF-beta, BMP, etc.). We elucidated the changes to the myocardial biomechanics brought by LAL and the corresponding changes to myocyte gene expressions. These data may be useful in identifying the mechanobiological pathways of HLHS.Publication Metadata only Modeling and characterization of comb-actuated resonant microscanners(Iop Publishing Ltd, 2006) N/A; Department of Electrical and Electronics Engineering; Ataman, Çağlar; Ürey, Hakan; PhD Student; Faculty Member; Department of Electrical and Electronics Engineering; Graduate School of Sciences and Engineering; College of Engineering; N/A; 8579The dynamics of the out-of-plane comb-drive actuator used in a torsional resonant mode microscanner is discussed. The microscanner is fabricated using the standard SOI technology by Fraunhofer, IPMS and utilized in various display, barcode scanning, spectroscopy and other imaging applications. The device is a parametrically excited system and exhibits hysteretic frequency response, nonlinear transient response, subharmonic oscillations, multiple parametric resonances, and alternating-oscillation-frequency behavior. Analytical and numerical models are developed to predict the parametric system dynamics. The analytical model is based on the solution of the linear Mathieu equation and valid for small angular displacements. The numerical model is valid for both small and large deflection angles. The analytical and numerical models are validated with the experimental results under various ambient pressures and excitation schemes and successfully predict the dynamics of the parametric nature of the microscanner. As many as four parametric resonances are observed at 30 mTorr. The models developed in this paper can be used to optimize the structure and the actuator.Publication Metadata only Novel fenestration designs for controlled venous flow shunting in failing fontans with systemic venous hypertension(Wiley, 2013) Albal, Priti G.; Menon, Prahlad G.; Kowalski, William; Undar, Akif; Turkoz, Riza; Department of Mechanical Engineering; Pekkan, Kerem; Faculty Member; Department of Mechanical Engineering; College of Engineering; 161845The Fontan procedure is employed as the final-stage palliation in single-ventricle congenital heart patients and results in diversion of venous blood directly to the pulmonary arteries. Fontan patients have been known to suffer from postoperative systemic venous hypertension, which in turn is associated with pleural effusions and protein losing enteropathy, leading to a decreased duration and quality of life. Despite the ongoing debate on its benefits, a circular fenestration hole (typically 4?mm) establishing a venous shunt to the common atrium is traditionally employed to relieve venous pressure in the Fontan conduit and improve early postoperative Fontan hemodynamics. However, these improvements come at the cost of reduced oxygen saturation due to excessive right-to-left shunting if the fenestration is permanent. The ideal selective fenestration would therefore limit or eliminate shunt flow at tolerable systemic venous pressures and allow increased flow at high pressures. The objective of this study is to introduce new fenestration designs that exhibit these desirable pressure-flow characteristics. Novel plus-shaped and S-shaped fenestration designs with leaflets are introduced as alternatives to the traditional circular fenestration, each having identical effective orifice areas at the fully open states. In vitro steady leakage flow tests were performed for physiological flow-driving pressures in order to obtain pressure-drop versus flow-rate characteristics. In addition, the leaflet opening kinematics of the plus-shaped fenestration was investigated computationally using finite element simulation. Fluid-structure interaction analysis was performed to determine leaflet displacements and pressure-flow characteristics at low pressures. Further, a lumped parameter model of the single-ventricle circuit was created to simulate pulsatile flow conditions For the plus-shaped fenestration, the flow rate was found to increase nonlinearly with increased driving systemic venous pressures at high physiological-pressure drops which did not cause the leaflets to fully open, and linearly for low driving pressures. These results indicate that leaflets of the plus-shaped fenestration design activated passively after a critical systemic venous pressure threshold. This feature is ideal for minimizing undesirable excessive venous shunting. A large variability in shunting flow rate may be obtained by changing the shape, thickness, size, and material of the fenestration to suit requirements of the patient, which can further limit shunt flow in a controlled manner.Publication Metadata only A novel orthogonal frequency division multiplexing with index modulation waveform with carrier frequency offset resistance and low peak-to-average power ratio(Wiley, 2022) Kucukyavuz, Defne; Onat, Furuzan Atay; N/A; Department of Electrical and Electronics Engineering; Gürol, İlter Erol; Başar, Ertuğrul; PhD Student; Faculty Member; Department of Electrical and Electronics Engineering; Graduate School of Sciences and Engineering; College of Engineering; N/A; 149116In this paper, we propose a novel orthogonal frequency division multiplexing (OFDM) scheme with high carrier frequency offset (CFO) resistance and low peak-to-average power ratio (PAPR). In this scheme, we consider a hybrid model with two subblock types, namely, pilot subblocks and standard subblocks. In pilot subblocks, active subcarriers are utilized for PAPR reduction while inactive carriers generated by the index modulation (IM) are utilized for the coarse CFO estimation. For standard subblocks, we consider unique subcarrier activation patterns (SAPs) with high-diversity IM to enhance the bit error performance of the overall system. Additionally, the inactive data tones in standard subblocks are utilized for fine CFO estimation, which enhances the CFO estimation quite significantly. Furthermore, in this paper, we show that proposed hybrid OFDM-IM (H-OFDM-IM) scheme can outperform conventional OFDM-IM and classical OFDM both in CFO estimation and PAPR reduction without requiring transmission of any side information. Finally, we show both mathematically and through computer simulations that proposed H-OFDM-IM can achieve a satisfactory bit error rate (BER) performance under high CFO scenarios.