PubMed
Permanent URI for this collectionhttps://acikarsiv.thk.edu.tr/handle/123456789/2549
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Publication A comparison of peptide amphiphile nanofiber macromolecular assembly strategies(SPRINGER, 2019) Dana, Aykutlu; Tekinay, Ayse B.; Tekin, E. Deniz; Tekin, Emine Deniz; Stanford University; Turk Hava Kurumu University; Turkish Aeronautical Association.Supramolecular peptide nanofibers that are composed of peptide amphiphile molecules have been widely used for many purposes from biomedical applications to energy conversion. The self-assembly mechanisms of these peptide nanofibers also provide convenient models for understanding the self-assembly mechanisms of various biological supramolecular systems; however, the current theoretical models that explain these mechanisms do not sufficiently explain the experimental results. In this study, we present a new way of modeling these nanofibers that better fits with the experimental data. Molecular dynamics simulations were applied to create model fibers using two different layer models and two different tilt angles. Strikingly, the fibers which were modeled to be tilting the peptide amphiphile molecules and/or tilting the plane were found to be more stable and consistent with the experiments.Publication A new and effective method for human retina optic disc segmentation with fuzzy clustering method based on active contour model(2020) Abdullah AS; Abdullah AS, Rahebi J, Özok YE, Aljanabi M.Publication A new triphenylphosphonium-conjugated amphipathic cationic peptide with improved cell-penetrating and ROS-targeting properties(2022) Ishkaeva RA; Ishkaeva RA, Salakhieva DV, Garifullin R, Alshadidi R, Laikov AV, Yergeshov AA, Kamalov MI, Abdullin TI.Publication A novel method for retinal optic disc detection using bat meta-heuristic algorithm(2018) Abdullah AS; Abdullah AS, Özok YE, Rahebi J.Publication A numerical study on indentation properties of cortical bone tissue: influence of anisotropy(2015) Demiral M; Demiral M, Abdel-Wahab A, Silberschmidt V.Publication Alkaline Phosphatase-Mimicking Peptide Nanofibers for Osteogenic Differentiation(AMER CHEMICAL SOC, 2015) Gulseren, Gulcihan; Yasa, I. Ceren; Ustahuseyin, Oya; Tekin, E. Deniz; Tekinay, Ayse B.; Guler, Mustafa O.; Tekin, Emine Deniz; Ihsan Dogramaci Bilkent University; Turk Hava Kurumu University; Turkish Aeronautical AssociationRecognition of molecules and regulation of extracellular matrix synthesis are some of the functions of enzymes in addition to their catalytic activity. While a diverse array of enzyme-like materials have been developed, these efforts have largely been confined to the imitation of the chemical structure and catalytic activity of the enzymes, and it is unclear whether enzyme-mimetic molecules can also be used to replicate the matrix-regulatory roles ordinarily performed by natural enzymes. Self-assembled peptide nanofibers can provide multifunctional enzyme-mimetic properties, as the active sequences of the target enzymes can be directly incorporated into the peptides. Here, we report enhanced bone regeneration efficiency through peptide nanofibers carrying both catalytic and matrix-regulatory functions of alkaline phosphatase, a versatile enzyme that plays a critical role in bone formation by regulating phosphate homeostasis and calcifiable bone matrix formation. Histidine presenting peptide nanostructures were developed to function as phosphatases. These molecules are able to catalyze phosphate hydrolysis and serve as bone-like nodule inducing scaffolds. Alkaline phosphatase-like peptide nanofibers enabled osteogenesis for both osteoblast-like and mesenchymal cell lines.Publication Publication Comment on "Einstein-Gauss-Bonnet Gravity in Four-Dimensional Spacetime"(2020) Gürses M; Gürses M, Þiþman TÇ, Tekin B.Publication Comparison of Two Different Distraction Methods Affecting the Level of Pain and Anxiety during Extracorporeal Shock Wave Lithotripsy: A Randomized Controlled Trial(2018) Gezginci E; Gezginci E, Iyigun E, Yalcin S, Bedir S, Ozgok IY.Publication Construction of an Exudative Age-Related Macular Degeneration Diagnostic and Therapeutic Molecular Network Using Multi-Layer Network Analysis, a Fuzzy Logic Model, and Deep Learning Techniques: Are Retinal and Brain Neurodegenerative Disorders Related?(2023) Latifi-Navid H; Latifi-Navid H, Barzegar Behrooz A, Jamehdor S, Davari M, Latifinavid M, Zolfaghari N, Piroozmand S, Taghizadeh S, Bourbour M, Shemshaki G, Latifi-Navid S, Arab SS, Soheili ZS, Ahmadieh H, Sheibani N.Publication Correction to: A new and effective method for human retina optic disc segmentation with fuzzy clustering method based on active contour model(2020) Abdullah AS; Abdullah AS, Rahebi J, Özok YE, Aljanabi M.Publication Diagnosing and differentiating viral pneumonia and COVID-19 using X-ray images(2022) Kör H; Kör H, Erbay H, Yurttakal AH.Publication Drying municipal sewage sludge with v-groove triple-pass and quadruple-pass solar air heaters along with testing of a solar absorber drying chamber(2020) Khanlari A; Khanlari A, Sözen A, Afshari F, Þirin C, Tuncer AD, Gungor A.Publication Effect of glottic geometry on breathing: three-dimensional unsteady numerical simulation of respiration in a case with congenital glottic web(2016) Gökcan MK; Gökcan MK, Günaydinoðlu E, Kurtuluþ DF.Publication Elasticity-based mechanism for the collective motion of self-propelled particles with springlike interactions: a model system for natural and artificial swarms(2013) Ferrante E; Ferrante E, Turgut AE, Dorigo M, Huepe C.Publication End-To-End Computerized Diagnosis of Spondylolisthesis Using Only Lumbar X-rays(2021) Varçýn F; Varçýn F, Erbay H, Çetin E, Çetin Ý, Kültür T.Publication Forecast combination approach with meta-fuzzy functions for forecasting the number of immigrants within the maritime line security project in Turkey(Springer Science and Business Media LLC, 2023-01-05) Fatma Carman Cevik; Basak Gever; Nihat Tak; Tahir Khaniyev; Ekinci, Başak GeverPublication Fractal-Fractional Mathematical Model Addressing the Situation of Corona Virus in Pakistan(2020) Shah K; Shah K, Arfan M, Mahariq I, Ahmadian A, Salahshour S, Ferrara M.Publication Graphene as a Reversible and Spectrally Selective Fluorescence Quencher(Springer Science and Business Media LLC, 2016-09-22) Omer Salihoglu; Nurbek Kakenov; Osman Balci; Sinan Balci; Coskun KocabasAbstractWe report reversible and spectrally selective fluorescence quenching of quantum dots (QDs) placed in close proximity to graphene. Controlling interband electronic transitions of graphene via electrostatic gating greatly modifies the fluorescence lifetime and intensity of nearby QDs via blocking of the nonradiative energy transfer between QDs and graphene. Using ionic liquid (IL) based electrolyte gating, we are able to control Fermi energy of graphene in the order of 1 eV, which yields electrically controllable fluorescence quenching of QDs in the visible spectrum. Indeed, our technique enables us to perform voltage controllable spectral selectivity among quantum dots at different emission wavelengths. We anticipate that our technique will provide tunable light-matter interaction and energy transfer that could yield hybrid QDs-graphene based optoelectronic devices with novel functionalities and additionally, may be useful as a spectroscopic ruler, for example, in bioimaging and biomolecular sensing. We propose that graphene can be used as an electrically tunable and wavelength selective fluorescence quencher.Publication Investigation of human β-defensins 1, 2 and 3 in human saliva by molecular dynamics(SPRINGER, 2022) Tekin, E. Deniz; Calisir, Metin; Tekin, Emine Deniz; Turkish Aeronautical Association; Turk Hava Kurumu University; Adiyaman UniversityHuman beta-defensins present in saliva have a broad spectrum of antimicrobial activities that work against infections in oral cavity. To provide a better understanding of these molecules' properties and functions at the molecular level, we have investigated and compared the important structural properties of human beta-defensin-1, -2 and -3 using molecular dynamics simulations. Our results have shown that human beta-defensin-3 has a more flexible structure in water than the other two because of its high hydrophilicity, low beta-sheet content and high repulsive forces between its charged residues. Moreover, we found that the location of the salt bridges is important in protein's stability in water.