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Permanent URI for this collectionhttps://hdl.handle.net/20.500.14288/3

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    The impact of the vitamin D and resveratrol administration on the stiffness and elasticity of T2DM rat aorta associated with the trace element and mineral levels
    (Elsevier Inc., 2024) Anapali-Aykac, Merve; Ulutin, Turgut; Komurcu-Bayrak, Evrim; Kaya-Dagistanli, Fatma; Department of Mechanical Engineering; Ulusu, Nuriye Nuray; Aydemir, Duygu; Salman, Naveed; Karimzadehkhouei, Mehrdad; Alaca, Burhanettin Erdem; Department of Mechanical Engineering; Koç University Research Center for Translational Medicine (KUTTAM) / Koç Üniversitesi Translasyonel Tıp Araştırma Merkezi (KUTTAM); Koç University Surface Science and Technology Center (KUYTAM) / Koç Üniversitesi Yüzey Teknolojileri Araştırmaları Merkezi (KUYTAM); n2STAR-Koç University Nanofabrication and Nanocharacterization Center for Scientifc and Technological Advanced Research; School of Medicine; Graduate School of Health Sciences; College of Engineering
    Background: Type 2 diabetes mellitus (T2DM) is directly associated with increased aortic stiffness, reduced aortic elasticity, and aortic dissection, which are independent risk factors for cardiovascular death. Since Vit D and resveratrol have been reported due to their cardioprotective effects, in this study, we aim to evaluate the impact of Vit D and resveratrol treatment alone or in combination on the aortic health associated with trace element and mineral levels in a high-fructose diet/streptozotocin-induced T2DM model. Methods: We investigated biomechanical changes of the aorta samples via a custom-built stretcher, where trace element and mineral levels in aorta samples were determined via inductively coupled plasma mass spectrometry (ICP-MS) following acidic microwave digestion. Results: Vitamin D treatment ameliorated the adverse effects of T2DM on aortic stiffness, aortic elasticity, and relaxation modulus in diabetic rats. Trace element and mineral levels correlated with cardiovascular homeostasis, including Fe, Cu, Zn, Se, and Na, have been regulated upon Vit D treatment in diabetic and healthy rats. On the other hand, resveratrol treatment alone or in combination with Vit D did not show any positive effects on biomechanical properties and trace element metabolism of diabetic or healthy rats, according to our data. Conclusion: Vit D can be used in T2DM patients to protect their cardiovascular health and should be considered a promising targeted therapy approach via nanoparticles to target cardiovascular diseases in the future.
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    Mechanical properties of silicon nanowires with native oxide surface state
    (Elsevier, 2024) Department of Mechanical Engineering; Zarepakzad, Sina; Esfahani, Mohammad Nasr; Alaca, Burhanettin Erdem; Department of Mechanical Engineering; n2STAR-Koç University Nanofabrication and Nanocharacterization Center for Scientifc and Technological Advanced Research; Koç University Surface Science and Technology Center (KUYTAM) / Koç Üniversitesi Yüzey Teknolojileri Araştırmaları Merkezi (KUYTAM); Graduate School of Sciences and Engineering; College of Engineering
    Silicon nanowires have attracted considerable interest due to their wide-ranging applications in nanoelectromechanical systems and nanoelectronics. Molecular dynamics simulations are powerful tools for studying the mechanical properties of nanowires. However, these simulations encounter challenges in interpreting the mechanical behavior and brittle to ductile transition of silicon nanowires, primarily due to surface effects such as the assumption of an unreconstructed surface state. This study specifically focuses on the tensile deformation of silicon nanowires with a native oxide layer, considering critical parameters such as cross-sectional shape, length -to -critical dimension ratio, temperature, the presence of nano -voids, and strain rate. By incorporating the native oxide layer, the article aims to provide a more realistic representation of the mechanical behavior for different critical dimensions and crystallographic orientations of silicon nanowires. The findings contribute to the advancement of knowledge regarding size -dependent elastic properties and strength of silicon nanowires.
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    Loop-mediated isothermal amplification-integrated CRISPR methods for infectious disease diagnosis at point of care
    (American Chemical Society, 2023) Yetisen, Ali K.; Department of Mechanical Engineering; Yığcı, Defne; Atçeken, Nazente; Taşoğlu, Savaş; Department of Mechanical Engineering; N/A; Koç University Research Center for Translational Medicine (KUTTAM) / Koç Üniversitesi Translasyonel Tıp Araştırma Merkezi (KUTTAM); KU Arçelik Research Center for Creative Industries (KUAR) / KU Arçelik Yaratıcı Endüstriler Uygulama ve Araştırma Merkezi (KUAR); School of Medicine; College of Engineering
    Infectious diseases continue to pose an imminent threat to global public health, leading to high numbers of deaths every year and disproportionately impacting developing countries where access to healthcare is limited. Biological, environmental, and social phenomena, including climate change, globalization, increased population density, and social inequity, contribute to the emergence of novel communicable diseases. Rapid and accurate diagnoses of infectious diseases are essential to preventing the transmission of infectious diseases. Although some commonly used diagnostic technologies provide highly sensitive and specific measurements, limitations including the requirement for complex equipment/infrastructure and refrigeration, the need for trained personnel, long sample processing times, and high cost remain unresolved. To ensure global access to affordable diagnostic methods, loop-mediated isothermal amplification (LAMP) integrated clustered regularly interspaced short palindromic repeat (CRISPR) based pathogen detection has emerged as a promising technology. Here, LAMP-integrated CRISPR-based nucleic acid detection methods are discussed in point-of-care (PoC) pathogen detection platforms, and current limitations and future directions are also identified.
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    Anisotropic wettability induced by femtosecond laser ablation
    (Wiley-V C H Verlag Gmbh, 2023) Yetisen, Ali K.; Department of Mechanical Engineering; Shojaeian, Mostafa; Taşoğlu, Savaş; Department of Mechanical Engineering; Koç University Research Center for Translational Medicine (KUTTAM) / Koç Üniversitesi Translasyonel Tıp Araştırma Merkezi (KUTTAM); KU Arçelik Research Center for Creative Industries (KUAR) / KU Arçelik Yaratıcı Endüstriler Uygulama ve Araştırma Merkezi (KUAR); Graduate School of Sciences and Engineering; College of Engineering
    Laser ablation has been utilized for locally and selectively modifying the surface wettability of materials in situ and enabling on-demand microfabrication. The anisotropic wettability has been observed on chemical and/or topographical patterns, such as an array of laser-inscribed strips with spacings, created on surfaces during the fabrication process. Herein, the effectiveness of the femtosecond laser ablation is evaluated in selectively modifying surface wettability. The areas processed by laser ablation exhibit anisotropic wetting behavior, even after the laser strips are overlapped. The laser-induced anisotropic surface wettability is present in space governed by laser scanning speed, scan/strip overlap, laser fluence, scan repetition, and bidirectional scanning angle. Moreover, the femtosecond laser ablation process is optimized to enhance the conventional laser inscription, leading to a modified and consistent methodology to achieve cost-effective fabrication. Herein, an approach for locally and selectively modifying surface wettability of materials in situ induced by femtosecond laser ablation is described. The laser-induced anisotropic surface wettability is found to appear in space governed by laser scanning speed, scan/strip overlap, laser fluence, scan repetition, and bidirectional scanning angle.
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    Stencil-based selective surface functionalization of silicon nanowires in 3D device architectures for next-generation biochemical sensors
    (American Chemical Society, 2024) Esfahani, Mohammad Nasr; Leblebici, Yusuf; Department of Mechanical Engineering; Ali, Basit; Özkan, Sena Nur; Akıncı, Seçkin; Öztürk, Ece; Alaca, Burhanettin Erdem; Department of Mechanical Engineering; Koç University Research Center for Translational Medicine (KUTTAM) / Koç Üniversitesi Translasyonel Tıp Araştırma Merkezi (KUTTAM); n2STAR-Koç University Nanofabrication and Nanocharacterization Center for Scientifc and Technological Advanced Research; Koç University Surface Science and Technology Center (KUYTAM) / Koç Üniversitesi Yüzey Teknolojileri Araştırmaları Merkezi (KUYTAM); Graduate School of Sciences and Engineering; Graduate School of Health Sciences; College of Engineering; School of Medicine
    Surface functionalization of 1D materials such as silicon nanowires is a critical preparation technology for biochemical sensing. However, existing nonselective functionalization techniques result in nonlocal binding and contamination, with potential device damage risks. Associated risks are further exacerbated for next-generation devices of a 3D nature with challenging topographies. Such 3D devices draw inspiration from the out-of-plane evolution of planar transistors to FinFETs and to today's gate-all-around transistors. This study is the first reported technological work addressing stencil-based surface decoration and selective functionalization of a suspended silicon nanowire building block embedded within such a device that involves two-order-of-magnitude thicker features compared to the nanowire critical dimensions. A gold pattern resolution of 3.0 mu m atop the silicon nanowires is achieved with a stencil aperture critical dimension of 2.2 mu m, accompanied by a die-level registration accuracy of 1.2 +/- 0.3 mu m. Plasma-enhanced chemical vapor deposition-based silicon nitride stencil membranes as large as 300 x 300 mu m2 are used to define the apertures without any membrane fracture during fabrication and membrane cleaning. The pattern-blurring aspect as a resolution-limiting factor is assessed by using 24 individual nanowire devices. Finally, gold-patterned silicon nanowires are functionalized using thiolated heparin and employed for selective attachment and detection of the human recombinant basic fibroblast growth factor (FGF-2). With the potential involvement in angiogenesis, the process of new blood vessel formation crucial for tumor growth, FGF-2 can serve as a potential prognostic biomarker in oncology. Demonstrated selectively on nanowires with high pattern resolution, the proposed functionalization approach offers possibilities for parallel sensing using vast nanowire arrays embedded in 3D device architectures developed for next-generation biochemical sensors in addition to serving various encapsulation and packaging needs.
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    Glioma- on-a-chip platform
    (Mary Ann Liebert, Inc, 2023) Department of Mechanical Engineering; Üstün, Merve; Birtek, Mehmet Tuğrul; Sokullu, Emel; Taşoğlu, Savaş; Department of Mechanical Engineering; Graduate School of Sciences and Engineering; School of Medicine; College of Engineering
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    Wound healing strategies based on nanoparticles incorporated in hydrogel wound patches
    (Royal Soc Chemistry, 2023) Dam, Paulami; Celik, Merve; Ustun, Merve; Saha, Sayantan; Saha, Chirantan; Kacar, Elif Ayse; Kugu, Senanur; Karagulle, Elif Naz; Tasoglu, Savas; Buyukserin, Fatih; Mondal, Rittick; Roy, Priya; Macedo, Maria L. R.; Franco, Octavio L.; Cardoso, Marlon H.; Altuntas, Sevde; Mandal, Amit Kumar; Department of Mechanical Engineering; Üstün, Merve; Taşoğlu, Savaş; Department of Mechanical Engineering; Graduate School of Sciences and Engineering; College of Engineering
    The intricate, tightly controlled mechanism of wound healing that is a vital physiological mechanism is essential to maintaining the skin's natural barrier function. Numerous studies have focused on wound healing as it is a massive burden on the healthcare system. Wound repair is a complicated process with various cell types and microenvironment conditions. In wound healing studies, novel therapeutic approaches have been proposed to deliver an effective treatment. Nanoparticle-based materials are preferred due to their antibacterial activity, biocompatibility, and increased mechanical strength in wound healing. They can be divided into six main groups: metal NPs, ceramic NPs, polymer NPs, self-assembled NPs, composite NPs, and nanoparticle-loaded hydrogels. Each group shows several advantages and disadvantages, and which material will be used depends on the type, depth, and area of the wound. Better wound care/healing techniques are now possible, thanks to the development of wound healing strategies based on these materials, which mimic the extracellular matrix (ECM) microenvironment of the wound. Bearing this in mind, here we reviewed current studies on which NPs have been used in wound healing and how this strategy has become a key biotechnological procedure to treat skin infections and wounds.
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    An analytical-atomistic model for elastic behavior of silicon nanowires
    (IOP Publishing Ltd, 2024) Esfahani, Mohammad Nasr; Department of Mechanical Engineering; Zarepakzad, Sina; Alaca, Burhanettin Erdem; Department of Mechanical Engineering; Koç University Surface Science and Technology Center (KUYTAM) / Koç Üniversitesi Yüzey Teknolojileri Araştırmaları Merkezi (KUYTAM); n2STAR-Koç University Nanofabrication and Nanocharacterization Center for Scientifc and Technological Advanced Research; Graduate School of Sciences and Engineering; College of Engineering
    Silicon nanowires entail significant potential as sensors in nanoelectromechanical systems. Despite its crucial impact in such applications, inconsistent trends in mechanical behavior reported in computational and experimental studies remain unexplained. Hence, scale effect in even the most fundamental elastic properties requires clarification. This work introduces a multiscale model to bridge the existing gap between atomistic simulations and experimental observations encountered around a critical dimension of 10 nm. The combined approach of this work is based on molecular dynamics and modified core-shell model and captures the scale effect over a substantial size range. The evolution of the modulus of elasticity is thus studied and linked to nanowire critical dimension through the parameterization of surface inhomogeneity. The developed method is also validated through an analysis of native oxide revealing an average modulus of elasticity of 75 GPa. The method's applicability can be extended to similar one-dimensional structures with unique surface states.
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    Effects of kinematic hardening of mucus polymers in an airway closure model
    (Elsevier Sci Ltd, 2024) Erken, Oguzhan; Izbassarov, Daulet; Romano, Francesco; Grotberg, James B.; Department of Mechanical Engineering; Fazla, Bartu; Muradoğlu, Metin; Department of Mechanical Engineering; Graduate School of Sciences and Engineering; College of Engineering
    The formation of a liquid plug inside a human airway, known as airway closure, is computationally studied by considering the elastoviscoplastic (EVP) properties of the pulmonary mucus covering the airway walls for a range of liquid film thicknesses and Laplace numbers. The airway is modeled as a rigid tube lined with a single layer of an EVP liquid. The Saramito-Herschel-Bulkley (Saramito-HB) model is coupled with an Isotropic Kinematic Hardening model (Saramito-HB-IKH) to allow energy dissipation at low strain rates. The rheological model is fitted to the experimental data under healthy and cystic fibrosis (CF) conditions. Yielded/unyielded regions and stresses on the airway wall are examined throughout the closure process. Yielding is found to begin near the closure in the Saramito-HB model, whereas it occurs noticeably earlier in the Saramito-HB-IKH model. The kinematic hardening is seen to have a notable effect on the closure time, especially for the CF case, with the effect being more pronounced at low Laplace numbers and initial film thicknesses. Finally, standalone effects of rheological properties on wall stresses are examined considering their physiological values as baseline.
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    Characterization and comparative evaluation of polysulfone and polypropylene hollow fiber membranes for blood oxygenators
    (Wiley, 2024) Teber, Oguz Orhun; Altinay, Aysegul Derya; Naziri Mehrabani, Seyed Ali; Zeytuncu, Bihter; Ates-Genceli, Esra; Dulekgurgen, Ebru; Yildiz, Yahya; Koyuncu, Ismail; Department of Mechanical Engineering; Köse, Tansu Gölcez; Pekkan, Kerem; Department of Mechanical Engineering; Graduate School of Sciences and Engineering; College of Engineering
    Blood oxygenators are used to saturate oxygen levels and remove carbon dioxide from the body during cardiopulmonary bypass. Although the natural lung is hydrophilic, commercially used oxygenator materials are hydrophobic. Surface hydrophobicity weakens blood compatibility, as long-term contact with the blood environment may lead to different degrees of blood activity. Polysulfone may be considered an alternative hydrophilic material in the design of oxygenators. Therefore, it may be directed toward developing hydrophilic membranes. This study aims to investigate the feasibility of achieving blood gas transfer with a polysulfone-based microporous hollow fiber membrane and compare it with the commercially available polypropylene membranes. Structural differences in the membrane morphology, surface hydrophilicity, tortuosity, mass transfer rate, and material properties under different operation conditions of temperature and flow rates are reported. The polysulfone membrane has a water contact angle of 81.3 degrees, whereas a commercial polypropylene membrane is 94.5 degrees. The mass transfer resistances (s/m) for the polysulfone and polypropylene membranes are calculated to be 4.8 x 104 and 1.5 x 104 at 25 degrees C, respectively. The module made of polysulfone was placed in the cardiopulmonary bypass circuit in parallel with the commercial oxygenator, and pH, pO2, pCO2 levels, and metabolic activity were measured in blood samples. Preparation steps of the blood oxygenator.image