GCRIS

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Protein-enzyme reaction followed by vibrational spectroscopy and dft (density functional theory) characterization
(01. Izmir Institute of Technology, 2023) Öztoprak, Nazlı; Güler, Günnur; Yağmurcukardeş, Mehmet
Whey proteins are crucial for many functions of the human body. Determining the structural properties of the protein with the enzymatic hydrolysis makes it possible to improve food quality, identify allergens and better understand food poisoning. In this study, the structural alterations of β-Lactoglobulin (model whey protein) were investigated during proteolysis. Trypsin was used as a model enzyme. Digestion of β-LG by trypsin at different concentrations were measured by Fourier transform infrared (FTIR) spectroscopy as well as by Raman spectroscopy to identify the degradation of the protein and to verify the enzymatic reactions results at various temperatures in real time. Afterwards, the advanced analysis techniques, two-dimensional correlation spectroscopy (2DCOS) and curve-fitting analysis, were applied. In addition, the experimental measurements were supplemented with DFT simulations. Based on the FTIR spectroscopy results, the most notable changes take place in the amide I (1600-1700 cm-1) and in the amide II (1480-1580 cm-1) regions. FTIR spectroscopic results revealed that the structural elements of β-LG broken down and degraded during the enzymatic digestion. Moreover, the carboxylate groups (COO-) gives rise in the infrared range (1605-1580 cm-1) as released products. Raman spectroscopic results demonstrate that β-LG loses its secondary structure and the product is formed around 1425 cm-1 arising from the carboxylate groups (COO-) due to the digestion. DFT results show that the Raman spectrum of single unit arginine and lysine residues can be predicted by DFT method. Furthermore, DFT calculations give the rise at 1683 cm-1 and 3540 cm-1 caused by C-N vibrations and N-H vibrations arising from the amino groups (NH2+), respectively.
Theoretical Investigation of Structural, Vibrational, Electronic, and Elastic Properties of Ultra-Thin Anisotropic Materials
(01. Izmir Institute of Technology, 2024) Doğan, Kadir Can; Yağmurcukardeş, Mehmet; Ateş, Serkan
Dimensional reduction in materials leads to significant improvements and changes in various properties due to quantum phenomena and intense confinement of electrons. Since the separation of graphene from bulk graphite in 2004, many different materials with layered bulk structures have been experimentally introduced into the literature, including hexagonal boron nitride (BN), transition metal dichalcogenides (TMDs), and in-plane anisotropic monolayer black phosphorus (BP). Among ultra-thin materials, anisotropic materials have attracted attention due to their distinct orientation-dependent vibrational, electronic, optical, and mechanical features and have been shown to have high potential for special applications such as polarization-sensitive photodetectors, orientation-dependent optoelectronic devices, and orientation-sensitive sensors. The aim of this thesis is to predict the stable structures of ultra-thin anisotropic materials such as HfTe5, TiX5, TaX3 (X:S, Se, Te), bismuthene and magnetic MnPS3 nanoribbons and to understand their structural, magnetic, vibrational, electronic, optical and elastic properties on a physical basis by performing density functional theory (DFT)-based first-principles calculations. Preliminary data via STM images are presented for the potential experimental characterization of possible defects and oxidized structures of the single-layer HfTe5, whose predicted stable structure. The existence of stable structures of titanium-based penta-calcogenides is predicted and the direction-dependent properties of the stable phases are investigated. The dynamic stability of Ta-based trichalcogens exhibiting anisotropy different from TiS3 and ZrS3 has been investigated and their crystal-orientation dependent elastic properties are analysed. In addition, in the tilted α-bismuth known as the α phase, the identification of the external strain direction through the Raman spectrum is examined. The reduction of in-plane anisotropy to 1 dimension is studied through the edge type- and width-dependent properties in magnetic MnPS3 nanoribbons. Our findings are important for the prediction of novel anisotropic materials.
Dark Energy Mechanisms in the Context of Extra Dimensional Models
(Izmir Institute of Technology, 2011) Yağmurcukardeş, Mehmet; Erdem, Recai
Dark energy is the simplest and the most standart explanation to account for the observed accelerated expansion of the universe. In this thesis we use the term 'dark energy' in its standart meaning i.e. a field or fluid that is responsible for the cosmic acceleration in the frame work of general relativity. Meanwhile extra dimensions is an attractive framework to understand many otherwise unexplained physical phenomena in a clear, simple formulation. Therefore the study of extra dimensional cosmological models is an attractive area of study. In this thesis we have considered viability of extra dimensional cosmological models in the light of the accelerated expansion of the universe. We have confirmed the results of studies that have shown the incompatibility of a broad class of extra dimensional cosmological models with a dark energy of an equation of state close to that of cosmological constant. We have discussed also possible theoritical and vational ways to avoid the no-go theorems for extra dimensional cosmological models as well.

Master Degree / Yüksek Lisans Tezleri

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