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Permanent URI for this collectionhttps://hdl.handle.net/20.500.14288/3
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Publication Metadata only Contrast improvement through a Generative Adversarial Network (GAN) by utilizing a dataset obtained from a line-scanning confocal microscope(SPIE, 2024) Department of Physics; Kiraz, Alper; Morova, Berna; Bavili, Nima; Ketabchi, Amir Mohammad; Department of Physics; Koç University Research Center for Translational Medicine (KUTTAM) / Koç Üniversitesi Translasyonel Tıp Araştırma Merkezi (KUTTAM); College of Sciences; Graduate School of Sciences and EngineeringConfocal microscopy offers enhanced image contrast and signal-to-noise ratio compared to wide-field illumination microscopy, achieved by effectively eliminating out-of-focus background noise. In our study, we initially showcase the functionality of a line-scanning confocal microscope aligned through the utilization of a Digital Light Projector (DLP) and a rolling shutter CMOS camera. In this technique, a sequence of illumination lines is projected onto a sample using a DLP and focusing objective (50X, NA=0.55). The reflected light is imaged with the camera. Line-scanning confocal imaging is accomplished by synchronizing the illumination lines with the rolling shutter of the sensor, leading to a substantial enhancement of approximately 50% in image contrast. Subsequently, this setup is employed to create a dataset comprising 500 pairs of images of paper tissue. This dataset is employed for training a Generative Adversarial Network (cGAN). Roughly 45% contrast improvement was measured in the test images for the trained network, in comparison to the ground-truth images.Publication Metadata only Optimization of argon-air DBD plasma-assisted grafting of polyacrylic acid on electrospun POSS-PCUU(Pergamon-Elsevier Science Ltd, 2023) Salehi, Roya; Mahkam, Mehrdad; Siahpoush, Vahid; Rahbarghazi, Reza; l; Abbasi, Farhang; Gargari, Ziba Zakeri; Sokullu, Emel; Koç University Research Center for Translational Medicine (KUTTAM) / Koç Üniversitesi Translasyonel Tıp Araştırma Merkezi (KUTTAM); School of MedicineIt is accepted that significant interfacial reactions take place in engineered tissues between biomaterial surfaces and the host's tissue in the body. The lack of appropriate functional groups limits long-term biocompatibility and successful biological response of biomaterials. Therefore, the cell-biomaterial affinity should be increased by functional groups grafting to the surface of biomaterials which provide the basic properties of the desired tissue. For the first time in this study, PAAc grafting was performed using two-step argon-air DBD plasma at atmospheric pressure in a few seconds of exposure time, to modify the surface of POSS-PCUU nanofibers to selectively in-crease their superficial properties while maintaining the required mechanical properties. The Response Surface Methodology was used for experimental design to optimize the operating conditions of carboxylic acid grafting at the electrospun POSS-PCUU surface. Nanofiber surface modification was confirmed using ATR-FTIR, FE-SEM, AFM, WCA, and tensile test. The grafting of PAAc to the nanofiber surface was proved by the presence of a broad hydroxyl band in ATR-FTIR spectrum, the morphological changes observed in the SEM and AFM images, and the reduction of the water contact angle. The stress-strain behavior at the optimum point also showed an acceptable reduction in tensile strength. Furthermore, the effects of two variables, plasma processing time and plasma copolymerization time were optimized and investigated using the CCD method at five levels of carboxylic acid grafting density. The grafting of PAAc onto the nanofiber surface (73.69 +/- 2.1 mu g/cm2) produced at reaction conditions displayed great agreement with the predicted results by the model. Results showed that the modified PAAc-POSS-PCUU nanofibers will be a desirable surface for the immobilization of various ECM proteins with high potential in small-diameter vascular graft applications.Publication Metadata only Collision-induced state-changing rate coefficients for cyanogen backbones NCN 3Σ− and CNN 3Σ− in astrophysical environments(Royal Society of Chemistry, 2023) González-Sánchez, Lola; de la Fuente, Jorge Alonso; Sanz-Sanz, Cristina; Wester, Roland; Gianturco, Francesco A.; Department of Chemistry; Department of Chemistry; College of SciencesWe report quantum calculations involving the dynamics of rotational energy-transfer processes, by collision with He atoms in interstellar environments, of the title molecular species which share the presence of the CN backbone and are considered of importance in those environments. The latter structural feature is taken to be especially relevant for prebiotic chemistry and for its possible role in the processing of the heterocyclic rings of RNA and DNA nucleobases in the interstellar space. We carry out ab initio calculations of their interaction potentials with He atoms and further obtain the state-to-state rotationally inelastic cross sections and rate coefficients over the relevant range of temperatures. The similarities and differences between such species and other similar partners which have been already detected are analyzed and discussed for their significance on internal state populations in interstellar space for the two title molecular radicals.Publication Metadata only Temporal evolution of entropy and chaos in low amplitude seismic wave prior to an earthquake(Pergamon-Elsevier Science Ltd, 2023) Akilli, Mahmut; Ak, Mine; Department of Physics; Yılmaz, Nazmi; Department of Physics; College of SciencesThis study investigates the temporal changes of entropy and chaos in low-amplitude continuous seismic wave data prior to two moderate-level earthquakes. Specifically, we examine seismic signals before and during the Istanbul-Turkey earthquake of September 26, 2019 (M = 5.7), and the Duzce-Turkey earthquake of November 17, 2021 (M = 5.2), which occurred near the Marmara Sea region on the north-Anatolian fault line. We aim to identify changes in complexity and chaotic characteristics in the pre-earthquake seismic waves and explore the possibility of earthquake forecasting minutes before an earthquake. To accomplish this, we utilize windowed scalogram entropy and sample entropy methods and compared the results with Lyapunov exponents and windowed scale index. Our findings indicate that measuring the temporal change of entropy using windowed scalogram entropy is sensitive to the change in complexity due to the frequency shifts during the weak ground motion approaching an earthquake.On the other hand, Lyapunov exponents and sample entropy appear more effective in their response to the change in complexity and chaotic characteristics due to the change in the signal amplitude. Additionally, the windowed scale index can detect temporal fluctuations in the aperiodicity of the signal. Overall, our results suggest that all four methods can be valuable in characterizing complexity and chaos in short-time pre -earthquake seismic signals, differentiating earthquakes, and contributing to the development of earthquake forecasting techniques.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 Liquid metal microdroplet-initiated ultra-fast polymerization of a stimuli-responsive hydrogel composite(Wiley-V C H Verlag Gmbh, 2023) Zhang, Jianhua; Liao, Jiahe; Liu, Zemin; Zhang, Rongjing; Department of Mechanical Engineering; Sitti, Metin; Department of Mechanical Engineering; College of Engineering; School of MedicineRecent advances in composite hydrogels achieve material enhancement or specialized stimuli-responsive functionalities by pairing with a functional filler. Liquid metals (LM) offer a unique combination of chemical, electrical, and mechanical properties that show great potential in hydrogel composites. Polymerization of hydrogels with LM microdroplets as initiators is a particularly interesting phenomenon that remains in its early stage of development. In this work, an LM-hydrogel composite is introduced, in which LM microdroplets dispersed inside the hydrogel matrix have dual functions as a polymerization initiator for a polyacrylic acid-poly vinyl alcohol (PAA/PVA) network and, once polymerized, as passive inclusion to influence its material and stimuli-responsive characteristics. It is demonstrated that LM microdroplets enable ultra-fast polymerization in approximate to 1 min, compared to several hours by conventional polymerization techniques. The results show several mechanical enhancements to the PAA/PVA hydrogels with LM-initiated polymerization. It is found that LM ratios strongly influence stimuli-responsive behaviors in the hydrogels, including swelling and ionic bending, where higher LM ratios are found to enhance ionic actuation performance. The dual roles of LM in this composite are analyzed using the experimental characterization results. These LM-hydrogel composites, which are biocompatible, open up new opportunities in future soft robotics and biomedical applications. A composite hydrogel embedded with liquid metal (LM) microdroplets is introduced, where the LM microdroplets have dual roles of initiating ultra-fast polymerization and passive inclusion. The physical effects of LM on polymerization and stimuli-responsive behaviors are analyzed, including swelling and ionic actuation due to osmotic pressure differences. Their benefits to the LM-hydrogel functionalities, such as robot locomotion, are demonstrated.Publication Metadata only Machine learning-based shear optimal adhesive microstructures with experimental validation(Wiley-V C H Verlag Gmbh, 2023) Dayan, Cem Balda; Son, Donghoon; Aghakhani, Amirreza; Wu, Yingdan; Demir, Sinan Ozgun; Department of Mechanical Engineering; Sitti, Metin; Department of Mechanical Engineering; College of Engineering; School of MedicineBioinspired fibrillar structures are promising for a wide range of disruptive adhesive applications. Especially micro/nanofibrillar structures on gecko toes can have strong and controllable adhesion and shear on a wide range of surfaces with residual-free, repeatable, self-cleaning, and other unique features. Synthetic dry fibrillar adhesives inspired by such biological fibrils are optimized in different aspects to increase their performance. Previous fibril designs for shear optimization are limited by predefined standard shapes in a narrow range primarily based on human intuition, which restricts their maximum performance. This study combines the machine learning-based optimization and finite-element-method-based shear mechanics simulations to find shear-optimized fibril designs automatically. In addition, fabrication limitations are integrated into the simulations to have more experimentally relevant results. The computationally discovered shear-optimized structures are fabricated, experimentally validated, and compared with the simulations. The results show that the computed shear-optimized fibrils perform better than the predefined standard fibril designs. This design optimization method can be used in future real-world shear-based gripping or nonslip surface applications, such as robotic pick-and-place grippers, climbing robots, gloves, electronic devices, and medical and wearable devices. This study combines the machine learning-based optimization and finite-element-method-based shear mechanics simulations to find shear-optimized fibril designs automatically. The results show that the computed optimal fibrils perform better than the predefined standard fibril designs. This design optimization framework can be used in future nonslip surface applications in grippers, robots, gloves, and electronic, medical, and wearable devices.Publication Metadata only Magnetic putty as a reconfigurable, recyclable, and accessible soft robotic material(Wiley-V C H Verlag Gmbh, 2023) Li, Meng; Pal, Aniket; Byun, Junghwan; Gardi, Gaurav; Department of Mechanical Engineering; Sitti, Metin; Department of Mechanical Engineering; College of Engineering; School of MedicineMagnetically hard materials are widely used to build soft magnetic robots, providing large magnetic force/torque and macrodomain programmability. However, their high magnetic coercivity often presents practical challenges when attempting to reconfigure magnetization patterns, requiring a large magnetic field or heating. In this study, magnetic putty is introduced as a magnetically hard and soft material with large remanence and low coercivity. It is shown that the magnetization of magnetic putty can be easily reoriented with maximum magnitude using an external field that is only one-tenth of its coercivity. Additionally, magnetic putty is a malleable, autonomous self-healing material that can be recycled and repurposed. The authors anticipate magnetic putty could provide a versatile and accessible tool for various magnetic robotics applications for fast prototyping and explorations for research and educational purposes. Permanent magnetic particles embedded in a viscoelastic putty matrix result in a self-healing soft magnetic material with both high remanence and low coercivity, providing hard-magnetic performance without the need for inaccessible strong magnetic fields. Programmable and reconfigurable magnetization, frequency-dependent force output, and easy to shape and assemble, magnetic putty can be a versatile tool in research prototyping and inspire future explorations.Publication Metadata only Liquid metal actuators: a comparative analysis of surface tension controlled actuation(Wiley-V C H Verlag Gmbh, 2023) Liao, Jiahe; Majidi, Carmel; Department of Mechanical Engineering; Sitti, Metin; Department of Mechanical Engineering; College of Engineering; School of MedicineLiquid metals, with their unique combination of electrical and mechanical properties, offer great opportunities for actuation based on surface tension modulation. Thanks to the scaling laws of surface tension, which can be electrochemically controlled at low voltages, liquid metal actuators stand out from other soft actuators for their remarkable characteristics such as high contractile strain rates and higher work densities at smaller length scales. This review summarizes the principles of liquid metal actuators and discusses their performance as well as theoretical pathways toward higher performances. The objective is to provide a comparative analysis of the ongoing development of liquid metal actuators. The design principles of the liquid metal actuators are analyzed, including low-level elemental principles (kinematics and electrochemistry), mid-level structural principles (reversibility, integrity, and scalability), and high-level functionalities. A wide range of practical use cases of liquid metal actuators from robotic locomotion and object manipulation to logic and computation is reviewed. From an energy perspective, strategies are compared for coupling the liquid metal actuators with an energy source toward fully untethered robots. The review concludes by offering a roadmap of future research directions of liquid metal actuators. This review summarizes the operation and design principles of surface tension-controlled actuation by liquid metals and discusses their performance and functionalities. Theoretical pathways toward higher performances, thanks to the unique scaling law of surface tension, are analyzed and compared to other popular soft actuators. The review concludes by offering a roadmap for future research directions.Publication Metadata only Nanodiamond-enhanced magnetic resonance imaging(Wiley-V C H Verlag Gmbh, 2023) Lazovic, Jelena; Goering, Eberhard; Wild, Anna-Maria; Schuetzenduebe, Peter; Shiva, Anitha; Loeffler, Jessica; Winter, Gordon; Department of Mechanical Engineering; Sitti, Metin; Department of Mechanical Engineering; College of Engineering; School of MedicineNanodiamonds (ND) hold great potential for diverse applications due to their biocompatibility, non-toxicity, and versatile functionalization. Direct visualization of ND by means of non-invasive imaging techniques will open new venues for labeling and tracking, offering unprecedented and unambiguous detection of labeled cells or nanodiamond-based drug carrier systems. The structural defects in diamonds, such as vacancies, can have paramagnetic properties and potentially act as contrast agents in magnetic resonance imaging (MRI). The smallest nanoscale diamond particles, detonation ND, are reported to effectively reduce longitudinal relaxation time T1 and provide signal enhancement in MRI. Using in vivo, chicken embryos, direct visualization of ND is demonstrated as a bright signal with high contrast to noise ratio. At 24 h following intravascular application marked signal enhancement is noticed in the liver and the kidneys, suggesting uptake by the phagocytic cells of the reticuloendothelial system (RES), and in vivo labeling of these cells. This is confirmed by visualization of nanodiamond-labeled macrophages as positive (bright) signal, in vitro. Macrophage cell labeling is not associated with significant increase in pro-inflammatory cytokines or marked cytotoxicity. These results indicate nanodiamond as a novel gadolinium-free contrast-enhancing agent with potential for cell labeling and tracking and over periods of time. The presence of paramagnetic centers in nanodiamonds drives effective reduction in longitudinal relaxation time (T1) and relaxation of neighboring water molecules, resulting in bright appearance on T1-weighted magnetic resonance images. , Using in vivo chicken embryos, it is confirmed nanodiamonds can provide high contrast to noise ratio for tracking and cell labeling over periods of time using magnetic resonance imaging (MRI).