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Article Citation - WoS: 2Citation - Scopus: 2Investigations of Ph-Dependent Dynamic Properties of Ompg-16sl, an Outer Membrane Protein G Mutant by Atr-Ftir Spectroscopy(Elsevier, 2022) Yilmaz, Irem; Korkmaz, FilizIn this paper, the dynamic properties of outer membrane protein G mutant (OmpG-16SL) are investigated with ATR-FTIR spectroscopy. While OmpG-WT has 14 beta-strands in its structure, the mutant is designed to have 16 beta-strands with the intention of creating an enlarged pore. Loop L6 is elongated by introducing six residues, two of which are negatively charged. The solvent accessibility of the OmpG-16SL mutant is compared with WT and a previously reported mutant OmpG-16S by tracking the H-1/H-2 exchange kinetics in acidic and neutral buffer conditions. The exchange kinetics and dynamics in the fast and slow exchange phases are separately investigated using the 2DCOS technique, which enables the tracking of the structural changes at each phase of the exchange process. The results suggest that the mutant OmpG-16SL is equally exposed to buffer in both acidic and neutral pH conditions. Additionally, the time range in the fast phase is very short - one-tenth of that for WT - and most of the exchange is completed in this phase. This fast exchange within minutes is also indicative of the presence of highly flexible and/or unstructured regions. In all, the fast exchange rates independent of the buffer pH justify the assumption that there is an altered interaction among the charged residues, which leads to a steadily-open pore. The role of the side-chain interactions within the pore and between the loops involving the loop L6 is also discussed.Article Citation - WoS: 8Citation - Scopus: 8Defect Characterization in Bi12geo20< Single Crystals by Thermoluminescence(Elsevier, 2021) Delice, S.; Isik, M.; Sarigul, N.; Gasanly, N. M.Bi12GeO20 single crystal grown by Czochralski method was investigated in terms of thermoluminescence (TL) properties. TL experiments were performed for various heating rates between 1 and 6 K/s in the temperature region of 300-675 K. One TL peak with peak maximum temperature of 557 K was observed in the TL spectrum as constant heating rate of 1 K/s was employed. Curve fitting, initial rise and variable heating rate methods were applied to calculate the activation energy of trap level corresponding to this TL peak. Analyses resulted in a presence of one trap center having mean activation energy of 0.78 eV. Heating rate characteristics of revealed trap center was also explored and theoretically well-known behavior that TL intensity decreases and peak maximum temperature increases with heating rates was observed for the trap level. Distribution of trapping levels was studied by thermally cleaning process for different T-stop between 425 and 525 K. Quasi-continuously distributed trapping levels were revealed with mean activation energies ranging from 0.78 to 1.26 eV. Moreover, absorption analysis revealed an optical transition taking place between a defect level and conduction band with an energy difference of 2.51 eV. These results are in good agreement for the presence of intrinsic defects above valence band in Bi12GeO20 crystals.Article Citation - WoS: 4Citation - Scopus: 5Thermoluminescence characteristics of GaSe and Ga2Se3 single crystals(Elsevier, 2022) Isik, M.; Sarigul, N.; Gasanly, N. M.GaSe and Ga2Se3 are semiconducting compounds formed from same constituent elements. These compounds have been attractive due to their optoelectronic and photovoltaic applications. Defects take remarkable attention since they affect quality of semiconductor devices. In the present paper, deep defect centers in GaSe and Ga2Se3 single crystals grown by Bridgman method were reported from the analyses of thermoluminescence measurements performed in the 350-675 K range. Experimental TL curves of GaSe and Ga2Se3 single crystals presented one and two overlapped peaks, respectively. The applied curve fitting and initial rise techniques were in good agreement about trap activation energies of 0.83 eV for GaSe, 0.96 and 1.24 eV for Ga2Se3 crystals. Crystalline structural properties of the grown single crystals were also investigated by x-ray diffraction measurements. The peaks observed in XRD patterns of the GaSe and Ga2Se3 crystals were well-consistent with hexagonal and zinc blende structures, respectively.Article Citation - WoS: 15Citation - Scopus: 16Investigation of Band Gap Energy Versus Temperature for Sns 2 Thin Films Grown by Rf-Magnetron Sputtering(Elsevier, 2020) Isik, M.; Gullu, H. H.; Terlemezoglu, M.; Surucu, O. Bayrakli; Parlak, M.; Gasanly, N. M.[No Abstract Available]Article Citation - WoS: 20Citation - Scopus: 20On Optimal Age Replacement Policy for a Class of Coherent Systems(Elsevier, 2020) Eryilmaz, Serkan; Eryılmaz, Serkan; Pekalp, Mustafa Hilmi; Eryılmaz, Serkan; Industrial Engineering; Industrial EngineeringAccording to the well-known age replacement policy, the system is replaced preventively at time t or correctively at system failure, whichever occurs first. For a coherent system consisting of components having common failure time distribution which has increasing failure rate, we present necessary conditions for the existence of the unique optimal value which minimizes the mean cost rate. The conditions are mainly based on the signature which only depends on the system's structure. The results are illustrated for linear and circular consecutive type systems. (C) 2020 Elsevier B.V. All rights reserved.Book Part Perspectives on Molecular Mimicry Between Human, Sars-Cov and Plasmodium Species Through a Probabilistic and Evolutionary Insight(Elsevier, 2024) Adiguzel,Y.; Shoenfeld,Y.This chapter examines potential molecular mimicry between similar peptide sequences and shared 6mers of five selected proteins and the proteomes of both SARS-CoV-2 and five Plasmodium species that infect humans (P. falciparum, P. malariae, P. vivax, P. knowlesi, and P. ovale). Human proteins are plasminogen receptor (KT), neutrophil collagenase (neutrophil collagenase isoform 2), myeloperoxidase precursor, mitochondrial peptide methionine sulfoxide reductase isoform a precursor, and myeloblastin precursor. The chapter eventually focuses on a probabilistic and evolutionary insight into molecular mimicry. © 2024 Elsevier B.V. All rights reserved.Article Liftable Homeomorphisms of Cyclic and Rank Two Finite Abelian Branched Covers Over the Real Projective Plane(Elsevier, 2021) Atalan, Ferihe; Medetogullari, Elif; Ozan, YildirayIn this note, we investigate the property for regular branched finite abelian covers of the real projective plane, where each homeomorphism of the base (preserving the branch locus) lifts to a homeomorphism of the covering surface. (C) 2020 Elsevier B.V. All rights reserved.
