Scopus İndeksli Yayınlar Koleksiyonu / Scopus Indexed Publications Collection
Permanent URI for this collectionhttps://hdl.handle.net/11147/7148
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Book Part Computational Approaches for Antibody-Based Drug Design(Institute of Physics Publishing, 2024) Gunes, S.; Arkca, I.; Atik, S.B.; Ulucan-Karnak, F.; Sezgin, H.T.; Uyar, A.This chapter includes various aspects of antibodies with a major emphasis on computational tools in antibody design. In this scope, current antibody databases, computational tools, and approaches for modelling antibodies and nanobodies, the structure, and interface prediction are analyzed. On the other hand, various antibody design techniques such as grafting, the significance of antibody-drug conjugates, and how computational methods contribute to the development of therapeutic antibodies are discussed with relevant strategies in the literature. Lastly, the production cost and the rising market value of antibodies are emphasized. © IOP Publishing Ltd 2023. All rights reserved.Article Citation - WoS: 6Citation - Scopus: 6Effect of the Synthesis Method and Particle Size on Bczt Electrocaloric Properties(Pergamon-elsevier Science Ltd, 2025) Temel, Helin; Avci, Tubanur; Okatan, M. Baris; Alkoy, Sedat; Misirlioglu, I. Burc; Mensur, EbruIn this study, the electrocaloric properties of BCZT ceramics fabricated through different processing methods: solid-state and sol-gel were investigated. The calcination process was done for BCZT powders obtained by sol-gel process at 900 degrees C for 2 h and by solid-state calcination method at 1200 degrees C for 6 h. BCZT-SG ceramics exhibited higher Delta T values, particularly at lower temperatures (similar to 0 degrees C-20 degrees C), and a stronger response to the electric field, suggesting a more efficient domain structure due to sol-gel processing. Notably, BCZT-SGH samples demonstrated the most complex and pronounced electrocaloric behavior, with dual Delta T peaks around 0 degrees C and 50 degrees C, and the highest Delta T of 2.5 K at 80 kV/cm and 50 degrees C, surpassing values in the literature. Especially, high Delta T results at 0 degrees C allows using this material in the extreme conditions. These results emphasize the significant role of processing techniques in tailoring the structural, dielectric, and electrocaloric properties of BCZT ceramics for high-performance energy applications.Book Part Application of Geothermal Energy in Hydrogen Production(Taylor and Francis, 2024) Ayzit, T.; Özmumcu, A.; Baba, A.Compared to other renewable resources, geothermal energy is a low-cost, technically proven, reliable, clean, and safe energy source that has been used in various fields and applications for many decades. These energy sources can be used directly or by conversion to other forms of energy. The use of geothermal energy for various purposes such as electricity, heating, cooling, greenhouses, dry food, thermal tourism, fisheries, and mineral extraction is widespread in many countries. Today’s installed geothermal capacity is dominated by the United States with about 3.7 GW, followed by Indonesia (2.1 GW), the Philippines (1.9 GW), Turkey (1.7 GW), and New Zealand. Global geothermal power generation capacity at the end of 2020 was 15.6 GW. The top ten geothermal producers account for nearly 90% of the global market, and many countries, especially Europe, plan to invest in geothermal soon. Looking at the direct use of geothermal energy for thermal applications, only four countries (China, Turkey, Iceland, and Japan) account for three-quarters of the energy consumed. Hydrogen can provide a number of benefits for future energy systems. Hydrogen can serve as storage for intermittent renewables or provide grid services. It can replace natural gas in industrial heating processes that are otherwise difficult to decarbonise. Therefore, geothermal resources can be used to produce clean hydrogen. Within this section, the importance and use of geothermal energy have been highlighted. At the same time, detailed information is given about the importance of hydrogen, its production, and its use in connection with geothermal energy. © 2025 selection and editorial matter, Mohammad Reza Rahimpour, Mohammad Amin Makarem, and Parvin Kiani.Book Part Citation - Scopus: 2Comparative Mapping(CRC Press, 2024) Frary, A.; Doganlar, S.; Ratnaparkhe, M.B.In the mid 1980s, restriction fragment length polymorphism (RFLP) analysis was first applied to plants for the purposes of creating genetic linkage maps. Using the maps developed for major crop species, the genes controlling qualitative and quantitative traits could be detected and then selected for (via closely linked molecular markers) in breeding programs. Advances in DNA marker technology not only allowed the rapid generation of high-resolution plant genetic maps, but also facilitated detailed comparisons among species. When complementary molecular markers are mapped across related species, it is then possible to align the chromosomes of those species to create comparative linkage maps. In this way, genomic similarities between species are revealed so that genetic information about one species may be extended to others and evolutionary inferences drawn. © 2008, CRC Press. All rights reserved.Article Citation - WoS: 5Citation - Scopus: 7Targeting the Panoptosome Using Necrostatin-1 Reduces Panoptosis and Protects the Kidney Against Ischemia-Reperfusion Injury in a Rat Model of Controlled Experimental Nonheart-Beating Donor(Elsevier Science inc, 2024) Dokur, Mehmet; Uysal, Erdal; Kucukdurmaz, Faruk; Altinay, Serdar; Polat, Sait; Batcioglu, Kadir; Yeni, Sema Nur DokurPurpose. Reducing renal ischemia is crucial for the function and survival of grafts from non- heartbeat donors, as it leads to inflammatory responses and tubulointerstitial damage. The primary concern with organs from nonheartbeat donors is the long warm ischemia period and reperfusion injury following renal transplantation. This study had two main goals; one goal is to determine how Necrostatin-1 targeting the PANoptosome affects PANoptosis in the nonheartbeating donor rat model. The other goal is to fi nd out if Necrostatin-1 can protect the kidney from ischemic injury for renal transplantation surgery. Methods. Twenty-four rats were grouped randomly as control and Necrostatin-1 in this experimental animal study, and we administered 1.65 mg/kg of Necrostatin-1 intraperitoneally to the experimental group for 30 minutes before cardiac arrest. We removed the rats' left kidneys and measured various oxidative stress marker measures such as malondialdehyde, superoxide dismutase, catalase, GPx, and 8-hydroxy-2-deoxyguanosine levels. We then subjected the tissues to immunohistochemical analysis, electron microscopy, and histopathological analysis. Findings. The Necrostatin-1 group had a lower total tubular injury score (P < .001) and less Caspase-3, gasdermin D, and mixed lineage kinase domain-like protein expression. Additionally, the apoptotic index of the study group was lower (P < .001). Furthermore, the study group had higher levels of superoxide dismutase and GPx (P < .05), whereas malondialdehyde levels were reduced (P = .009). Electron microscopy also revealed a significant improvement in tissue structure in the Necrostatin-1 group. Conclusion. Necrostatin-1 protects against ischemic acute kidney injury in nonheart-beating donor rats by inhibiting PANoptosis via the blockade of RIPK1. As a result of this, Necrostatin1 may offer novel opportunities for protecting donor kidneys from renal ischemia-reperfusion injury during transplantation in patients with end-stage kidney disease requiring a renal transplantation.Article Citation - WoS: 1Citation - Scopus: 1Completeness of Energy Eigenfunctions for the Reflectionless Potential in Quantum Mechanics(Aip Publishing, 2024) Erman, Fatih; Turgut, O. TeomanThere are a few exactly solvable potentials in quantum mechanics for which the completeness relation of the energy eigenstates can be explicitly verified. In this article, we give an elementary proof that the set of bound (discrete) states together with the scattering (continuum) states of the reflectionless potential form a complete set. We also review a direct and elegant derivation of the energy eigenstates with proper normalization by introducing an analog of the creation and annihilation operators of the harmonic oscillator problem. We further show that, in the case of a single bound state, the corresponding wave function can be found from the knowledge of continuum eigenstates of the system. Finally, completeness is shown by using the even/odd parity eigenstates of the Hamiltonian, which provides another explicit demonstration of a fundamental property of quantum mechanical Hamiltonians.Article An Interior Inverse Generalized Impedance Problem for the Modified Helmholtz Equation in Two Dimensions(Wiley-v C H verlag Gmbh, 2025) Yaman, Olha Ivanyshyn; Ozdemir, GaziWe consider the inverse interior problem of recovering the surface impedances of the cavity from sources and measurements placed on a curve inside of it. The uniqueness issue is investigated, and a hybrid method is proposed for the numerical solution. The approach takes advantages of both direct and iterative schemes, such as it does not require an initial guess and has an accuracy of a Newton-type method. Presented numerical experiments demonstrate the feasibility and effectiveness of the approach.Article Citation - WoS: 5Citation - Scopus: 5Light-Induced, Liquid Crystal-Templated Fabrication of Large-Area Pure Nanoporous Gold Films With High-Density Plasmonic Cavities(Amer Chemical Soc, 2024) Orhan, Ozan Baran; Polat, Nahit; Demir, Seren; Balci, Fadime Mert; Balci, SinanNanoporous gold (NPG) films are three-dimensional gold (Au) frameworks characterized by a uniform distribution of nanoscale irregular pores. Typically produced via a dealloying process, where the less noble silver (Ag) is selectively etched out, NPG films offer a large surface area, excellent chemical stability, remarkable catalytic activity, unique optical properties, and biocompatibility. These attributes make them invaluable for applications in catalysis, plasmonics, biosensors, and nanophotonics. However, the presence of residual Ag from the dealloying process can limit their performance in certain applications. In this study, we report a novel method for the fabrication of ultrapure, large-area NPG films (several cm2) using a light-induced and liquid crystal-templated method. A hexagonal lyotropic liquid crystal containing a strong acid and a nonionic surfactant is combined with an aqueous solution of HAuCl4, followed by the photochemical synthesis of gold nanoparticles (NPs) within the liquid crystal. After calcination of the Au NP-containing liquid crystal film at high temperature, pure NPG films are produced. We demonstrate surface-enhanced Raman spectroscopy (SERS) of Rhodamine 6G (R6G) molecules adsorbed on the NPG films and detect extremely low concentrations (below 10-6 M) of R6G. Additionally, we thoroughly investigated the formation and optical properties of the NPG films. The results reveal that the ultrapure NPG films contain high-density plasmonic nanocavities, where substantial electromagnetic fields are generated, leading to significant enhancement of optical processes at nanoscale dimensions.Article Citation - WoS: 4Citation - Scopus: 4Tailored Bodipy-Based Fluorogenic Probes for Phosgene Detection: a Comparative Evaluation of Recognition Sites(Royal Soc Chemistry, 2024) Dartar, Suay; Kaya, Beraat Umur; Yayak, Yanki Oncu; Vural, Ezgi; Emrullahoglu, MustafaWe constructed two novel boron-dipyrromethene (BODIPY)-based fluorescent probes, BOPD and BOBA, each equipped with the phosgene specific recognition units o-phenylenediamine (OPD) and o-aminobenzylamine (OBA) at the 2-position of the BODIPY core. BOPD and BOBA represent rare examples of BODIPY-based probes that operate by modulating an intramolecular charge transfer process (ICT), as validated by computational studies. We systematically compared the analytic performance of those recognition units while focusing on selectivity, fluorescence turn-on ratios and response times. Probe BOBA, equipped with OBA as the recognition unit, demonstrated a remarkably low detection limit (i.e., 1.40 nM) and a rapid response time (<10 s) for triphosgene. By comparison, BOPD, featuring an OPD unit, showed superior selectivity towards triphosgene, with a detection limit of 93 nM and a response time of up to 30 s. A portable sensing platform was developed by loading BOPD onto test strips made of TLC plates, nonwoven materials and small-headed cotton swabs, which were assessed for their effectiveness in detecting phosgene. We additionally performed the first successful application of a fluorescent probe, namely BOPD, for monitoring the accumulation of phosgene in plants.Article Citation - WoS: 2Citation - Scopus: 2Stabilization of the First-Order Phase Transition Character and Enhancement of the Electrocaloric Effect by Na<sub>0.5</Sub>bi<sub>0.5< Substitution in Batio<sub>3</Sub> Ceramics(Royal Soc Chemistry, 2024) Karakaya, Merve; Gurbuz, Irem; Fulanovic, Lovro; Adem, UmutThe electrocaloric properties of BaTiO3-based Pb-free ferroelectric materials are widely investigated. One approach to achieving a large electrocaloric response is making use of the substantial polarization change associated with the first-order phase transition at the Curie temperature. To make use of this approach, we have investigated the electrocaloric response of (1 - x)BaTiO3-xNa0.5Bi0.5TiO3 (BT-NBT) ceramics for x = 0.05, 0.10, 0.20 and 0.30. For this BT-rich part of the solid solution, it is established that increasing the NBT content increases the tetragonality of the BaTiO3. We show that this increase in tetragonality with NBT substitution helps to maintain the first-order nature of the phase transition in BaTiO3 and correspondingly a large electrocaloric response, despite the simultaneous enhancement of relaxor ferroelectric character with the NBT substitution. A significantly larger effective electrocaloric temperature change (Delta Teff) of 1.65 K was obtained for the x = 0.20 sample under 40 kV cm-1, using the direct measurement of the electrocaloric effect, which is in reasonable agreement with the indirect measurements.