Mayda, Selma
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S. Mayda
Mayda, Selma.
Mayda, S.
Mayda, Selma.
Mayda, S.
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01. Izmir Institute of Technology
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Former Staff
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Scholarly Output
6
Articles
3
Views / Downloads
35966/2144
Supervised MSc Theses
1
Supervised PhD Theses
1
WoS Citation Count
16
Scopus Citation Count
19
Patents
0
Projects
1
WoS Citations per Publication
2.67
Scopus Citations per Publication
3.17
Open Access Source
6
Supervised Theses
2
| Journal | Count |
|---|---|
| European Physical Journal B | 1 |
| Handbook of Nanomaterials for Industrial Applications | 1 |
| Journal of Superconductivity and Novel Magnetism | 1 |
| Scientific Reports | 1 |
Current Page: 1 / 1
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6 results
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Now showing 1 - 6 of 6
Book Part Future Applications of Artificially-Synthesized Organic Molecules Containing Transition-Metal Atoms(Elsevier, 2018) Mayda, Selma; Kandemir, Zafer; Bulut, NejatArtificially-synthesized organic molecules which contain transition-metal atoms offer new possibilities for applications in the electronics, pharmaceutical, and chemical industries. Hence, developing an understanding of the electronic properties of this kind of organic molecules is important. With this purpose, here we study the electronic properties of metalloproteins, metalloenzymes, and Ru-based dye molecules as examples for this kind of organic molecules. In particular, we perform combined Hartree-Fock (HF) and quantum Monte Carlo (HF+QMC) calculations, as well as combined density functional theory (DFT) and QMC (DFT+QMC) calculations to study the electronic properties of these molecules. Our results show that new electronic states named as impurity bound states (IBS) form in metalloproteins, metalloenzymes, and Ru-based dye molecules. We show that the electron occupancy of IBS is critically important in determining the low-energy electronic properties of these molecules. In this respect, the IBS may play a central role in developing new applications based on artificially-synthesized organic molecules containing transition-metal atoms. © 2018 Elsevier Inc. All rights reserved.Article Citation - WoS: 2Citation - Scopus: 2Electronic Structure of Cyanocobalamin: Dft+qmc Study(Springer Verlag, 2017) Mayda, Selma; Kandemir, Zafer; Bulut, NejatWe study the electronic structure and the magnetic correlations of cyanocobalamin (C63H88CoN14O14P) by using the framework of the multi-orbital single-impurity Haldane-Anderson model of a transition metal impurity in a semiconductor host. Here, we first determine the parameters of the Anderson Hamiltonian by performing density functional theory (DFT) calculations. Then, we use the quantum Monte Carlo (QMC) technique to obtain the electronic structure and the magnetic correlation functions for this effective model. We find that new electronic states, which correspond to impurity bound states, form above the lowest unoccupied level of the host semiconductor. These new states derive from the atomic orbitals at the cobalt site and the rest of the molecule. We observe that magnetic moments develop at the Co(3dν) orbitals and over the surrounding sites. We also observe that antiferromagnetic correlations exist between the Co (3dν) orbitals and the surrounding atoms. These antiferromagnetic correlations depend on the filling of the impurity bound states.Master Thesis Electronic Correlations in Metalloproteins: a Quantum Monte Carlo Study(Izmir Institute of Technology, 2013) Mayda, Selma; Bulut, NejatMetalloproteins are proteins that contain a metal atom. Some metalloproteins include a transition metal such as vitamin B12 (Co) and hemoglobin (Fe) and these structures show semiconducting properties. In this thesis, as an example of metalloproteins, vitamin B12 is studied and electronic and magnetic properties of Co 3d electrons are examined by the quantum Monte Carlo method (QMC). Since vitamin B12 contains a cobalt (Co) atom and has a semiconductor gap, its electronic and magnetic properties can be described by multi-orbital Haldane-Anderson model. Haldane-Anderson model explains the electronic properties of semiconductors which contain a transition metal impurity and considers the onsite Coulomb interactions of impurity 3d orbitals. To solve this model, we use Hirsch-Fye quantum Monte Carlo algorithm (HFQMC) without making any approximations. Firstly, the occupations and intra-orbital electronic correlations of 3d orbitals are calculated. After that, the total magnetization and the inter-orbital correlations of 3d orbitals are obtained. Next, the total magnetic susceptibility and magnetic susceptibilities between the 3d orbitals are calculated. Finally, we discuss the physical meaning of the QMC calculations.Article Citation - WoS: 2Citation - Scopus: 2Electronic Structure and Correlations of Vitamin B12 Studied Within the Haldane-Anderson Impurity Model(Springer Verlag, 2016) Kandemir, Zafer; Mayda, Selma; Bulut, NejatWe study the electronic structure and correlations of vitamin B12 (cyanocobalamine) by using theframework of the multi-orbital single-impurity Haldane-Anderson model of atransition-metal impurity in a semiconductor host. The parameters of the effectiveHaldane-Anderson model are obtained within the Hartree-Fock (HF) approximation. Thequantum Monte Carlo (QMC) technique is then used to calculate the one-electron andmagnetic correlation functions of this effective model. We observe that new states forminside the semiconductor gap found by HF due to the intra-orbital Coulomb interaction atthe impurity 3d orbitals. In particular, the lowest unoccupiedstates correspond to an impurity bound state, which consists of states from mainly the CNaxial ligand and the corrin ring as well as the Co eg-like orbitals. We alsoobserve that the Co (3d) orbitals can develop antiferromagneticcorrelations with the surrounding atoms depending on the filling of the impurity boundstates. In addition, we make comparisons of the HF+QMC data with the density functionaltheory calculations. We also discuss the photoabsorption spectrum of cyanocobalamine.Doctoral Thesis Magnetic Effect in the Biological Functioning of Hemoglobin: Dft+qmc Approach Within an Effective Multi-Orbital Anderson Impurity Model(Izmir Institute of Technology, 2019) Mayda, Selma; Bulut, Nejat; Demir, Mustafa MuammerHemoglobin corresponds to O2 transportation from lungs to the tissues and exhibits high-spin to low-spin transition by binding of O2 to Fe. In this thesis, we study the electronic and magnetic properties of the deoxy and the oxy forms of the human adult hemoglobin (HbA) to investigate the mechanism of the spin transition. We use an effective multi-orbital Anderson model and the parameters of this model are determined by the density functional theory (DFT) calculations. Then, this model is solved by using a quantum Monte Carlo (QMC) algorithm. The DFT+QMC results show that new electronic states named as the impurity bound states (IBS) exist in both deoxy-HbA and oxy-HbA.We also observe that as the temperature decreases, a magnetic gap is opened at the Fermi level for oxy-HbA. This gap arises from the Fe-O2 charge transfer. We find that both the IBS and the opening of the magnetic gap are responsible for the spin transition in hemoglobin. In addition, the DFT+QMC calculations show that antiferromagnetic (AF) correlations between the Fe(3d) and the surrounding orbitals exist in both deoxy-HbA and oxy-HbA. For deoxy-HbA, the anomalous magnetic circular dichrosim signal in the UV region is experimental evidence for these AF correlations. In the light of these magnetic measurements, we propose some explanations for the Bohr effect and the cooperativity which are the fundemental functional properties of the hemoglobin. The results presented in this thesis show that the magnetic effects play a crucial role in the funtioning of the hemoglobin.Article Citation - WoS: 12Citation - Scopus: 15Magnetic Mechanism for the Biological Functioning of Hemoglobin(Nature Publishing Group, 2020) Mayda, Selma; Kandemir, Zafer; Bulut, Nejat; Maekawa, SadamichiThe role of magnetism in the biological functioning of hemoglobin has been debated since its discovery by Pauling and Coryell in 1936. The hemoglobin molecule contains four heme groups each having a porphyrin layer with a Fe ion at the center. Here, we present combined density-functional theory and quantum Monte Carlo calculations for an effective model of Fe in a heme cluster. In comparison with these calculations, we analyze the experimental data on human adult hemoglobin (HbA) from the magnetic susceptibility, Mossbauer and magnetic circular dichroism (MCD) measurements. In both the deoxygenated (deoxy) and the oxygenated (oxy) cases, we show that local magnetic moments develop in the porphyrin layer with antiferromagnetic coupling to the Fe moment. Our calculations reproduce the magnetic susceptibility measurements on deoxy and oxy-HbA. For deoxy-HbA, we show that the anomalous MCD signal in the UV region is an experimental evidence for the presence of antiferromagnetic Fe-porphyrin correlations. The functional properties of hemoglobin such as the binding of O-2, the Bohr effect and the cooperativity are explained based on the magnetic correlations. This analysis suggests that magnetism could be involved in the functioning of hemoglobin.