Scopus İndeksli Yayınlar Koleksiyonu / Scopus Indexed Publications Collection
Permanent URI for this collectionhttps://hdl.handle.net/11147/7148
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Article Citation - WoS: 16Citation - Scopus: 18Bacterial Detection Using Bacteriophages and Gold Nanorods by Following Time-Dependent Changes in Raman Spectral Signals(Informa Healthcare, 2018) Moghtader, Farzaneh; Tomak, Aysel; Zareie, Hadi M.; Pişkin, ErhanThis study attemps to develop bacterial detection strategies using bacteriophages and gold nanorods (GNRs) by Raman spectral analysis. Escherichia coli was selected as the target and its specific phage was used as the bioprobe. Target bacteria and phages were propagated/purified by traditional techniques. GNRs were synthesized by using hexadecyltrimethyl ammonium bromide (CTAB) as stabilizer. A two-step detection strategy was applied: Firstly, the target bacteria were interacted with GNRs in suspensions, and then they were dropped onto silica substrates for detection. It was possible to obtain clear surface-enchanced Raman spectroscopy (SERS) peaks of the target bacteria, even without using phages. In the second step, the phage nanoemulsions were droped onto the bacterial-GNRs complexes on those surfaces and time-dependent changes in the Raman spectra were monitored at different time intervals upto 40 min. These results demonstrated that how one can apply phages with plasmonic nanoparticles for detection of pathogenic bacteria very effectively in a quite simple test.Article Citation - WoS: 12Citation - Scopus: 11Theoretical and Experimental Investigation of Conjugation of 1,6-Hexanedithiol on Mos2(IOP Publishing Ltd., 2018) Gül, Aytaç; Bacaksız, Cihan; Ünsal, Emre; Akbalı, Barış; Tomak, Aysel; Zareie, Hadi M.; Şahin, HasanWe report an experimental and theoretical investigation of conjugation of 1,6-Hexaneditihiol (HDT) on MoS2 which is prepared by mixing MoS2 structure and HDT molecules in proper solvent. Raman spectra and the calculated phonon bands reveal that the HDT molecules bind covalently to MoS2. Surface morphology of MoS2/HDT structure is changed upon conjugation of HDT on MoS2 and characterized by using Scanning Electron Microscope (SEM). Density Functional Theory (DFT) based calculations show that HOMO-LUMO band gap of HDT is altered after the conjugation and two-S binding (handle-like) configuration is energetically most favorable among three different structures. This study displays that the facile thiol functionalization process of MoS2 is promising strategy for obtaining solution processable MoS2.Article Citation - WoS: 36Citation - Scopus: 38Effect of Molecular Architecture on Cell Interactions and Stealth Properties of Peg(American Chemical Society, 2017) Özer, İmran; Tomak, Aysel; Zareie, Hadi M.; Baran, Yusuf; Bulmuş, VolgaPEGylation, covalent attachment of PEG to therapeutic biomolecules, in which suboptimal pharmacokinetic profiles limiting their therapeutic utility are of concern, is a widely applied technology. However, this technology has been challenged by reduced bioactivity of biomolecules upon PEGylation and immunogenicity of PEG triggering immune response and abrogating clinical efficacy, which collectively necessitate development of stealth polymer alternatives. Here we demonstrate that comb-shape poly[oligo(ethylene glycol) methyl ether methacrylate] (POEGMA), a stealth polymer alternative, has a more compact structure than PEG and self-organize into nanoparticles in a molecular weight dependent manner. Most notably, we show that comb-shape POEGMA promotes significantly higher cellular uptake and exhibits less steric hindrance imposed on the conjugated biomolecule than PEG. Collectively, comb-shape POEGMA offers a versatile alternative to PEG for stealth polymer-biomolecule conjugation applications.Article Citation - WoS: 54Citation - Scopus: 53Nitrogen Doping for Facile and Effective Modification of Graphene Surfaces(Royal Society of Chemistry, 2017) Yanılmaz, Alper; Tomak, Aysel; Akbalı, Barış; Bacaksız, Cihan; Özçeri, Elif; Arı, Ozan; Senger, Ramazan Tuğrul; Selamet, Yusuf; Zareie, Hadi M.We report experimental and theoretical investigations of nitrogen doped graphene. A low-pressure Chemical Vapor Deposition (CVD) system was used to grow large-area graphene on copper foil, using ethylene as the carbon source. Nitrogen-doped graphene (N-graphene) was prepared by exposing the graphene transferred to different substrates to atomic nitrogen plasma. The effect of varying nitrogen flow rates on doping of graphene was investigated while keeping the power and time constant during the process. The N-graphene was characterized via Raman Spectroscopy, X-ray Photoelectron Spectroscopy (XPS), Scanning Tunneling Microscopy and Spectroscopy (STM and STS), and Fourier Transform Infrared spectroscopy (FTIR). Raman mapping of N-graphene was also performed to show homogeneity of nitrogen on the graphitic lattice. XPS results have revealed the presence of different nitrogen configurations in the graphitic lattice with similar doping concentrations. Density functional theory (DFT) based calculations showed that the periodic adsorption of N atoms predominantly occurs on top of the C atoms rather than through substitution of C in our N-graphene samples. Our results indicate a feasible procedure for producing N-graphene with homogenous and effective doping which would be valuable in electronic and optical applications.Article Citation - WoS: 2Citation - Scopus: 2Structural Changes in a Schiff Base Molecular Assembly Initiated by Scanning Tunneling Microscopy Tip(IOP Publishing Ltd., 2016) Tomak, Aysel; Bacaksız, Cihan; Mendirek, Gizem; Şahin, Hasan; Hür, Deniz; Görgün, Kamuran; Senger, Ramazan Tuğrul; Birer, Özgür; Peeters, François M.; Zareie, Hadi M.We report the controlled self-organization and switching of newly designed Schiff base (E)-4-((4-(phenylethynyl) benzylidene) amino) benzenethiol (EPBB) molecules on a Au (111) surface at room temperature. Scanning tunneling microscopy and spectroscopy (STM/STS) were used to image and analyze the conformational changes of the EPBB molecules. The conformational change of the molecules was induced by using the STM tip while increasing the tunneling current. The switching of a domain or island of molecules was shown to be induced by the STM tip during scanning. Unambiguous fingerprints of the switching mechanism were observed via STM/STS measurements. Surface-enhanced Raman scattering was employed, to control and identify quantitatively the switching mechanism of molecules in a monolayer. Density functional theory calculations were also performed in order to understand the microscopic details of the switching mechanism. These calculations revealed that the molecular switching behavior stemmed from the strong interaction of the EPBB molecules with the STM tip. Our approach to controlling intermolecular mechanics provides a path towards the bottom-up assembly of more sophisticated molecular machines.Article Citation - WoS: 26Citation - Scopus: 26Controlled Growth Mechanism of Poly (3-Hexylthiophene) Nanowires(IOP Publishing Ltd., 2016) Kıymaz, D.; Yağmurcukardeş, Mehmet; Tomak, Aysel; Şahin, Hasan; Senger, Ramazan Tugrul; Peeters, François M.; Zareie, Hadi M.; Zafer, CeylanSynthesis of 1D-polymer nanowires by a self-assembly method using marginal solvents is an attractive technique. While the formation mechanism is poorly understood, this method is essential in order to control the growth of nanowires. Here we visualized the time-dependent assembly of poly (3-hexyl-thiophene-2,5-diyl) (P3HT) nanowires by atomic force microscopy and scanning tunneling microscopy. The assembly of P3HT nanowires was carried out at room temperature by mixing cyclohexanone (CHN), as a poor solvent, with polymer solution in 1,2-dichlorobenzene (DCB). Both π-π stacking and planarization, obtained at the mix volume ratio of P3HT (in DCB):CHN (10:7), were considered during the investigation. We find that the length of nanowires was determined by the ordering of polymers in the polymer repetition direction. Additionally, our density functional theory calculations revealed that the presence of DCB and CHN molecules that stabilize the structural distortions due to tail group of polymers was essential for the core-wire formation.Article Citation - WoS: 45Citation - Scopus: 47Impedimetric Detection of Pathogenic Bacteria With Bacteriophages Using Gold Nanorod Deposited Graphite Electrodes(Royal Society of Chemistry, 2016) Moghtader, Farzaneh; Çongur, Gülşah; Zareie, Hadi M.; Erdem, Arzum; Pişkin, ErhanElectrochemical impedance spectroscopy (EIS) is applied for the detection of bacteria using bacteriophages as a bioprobe together with gold nanorods (GNRs). Escherichia coli-E. coli K12 was used as a model target bacteria and also for the propagation of its specific T4-phages. Gold nanorods (GNRs) were synthesized via a two-step protocol and characterized using different techniques. EIS measurements were conducted in an electrochemical cell consisting of a three electrode system. Single-use pencil graphite electrodes (PGE) were modified by the physical adsorption of GNRs to increase their interfacial conductivity and therefore sensitivity for impedimetric measurements. Therefore, interfacial charge-transfer resistance values (Rct) sharply decreased after GNRs deposition. Phages were adsorbed on these electrodes via a simple incubation protocol at room temperature, which resulted in an increase in Rct values, which was concluded to be as a result of nonconductive phage layers. These phage-carrying GNRs-PGEs were used for impedimetric detection of the target bacteria, E. coli. Significant increases at the Rct values were observed which were attributed to the insulation effects of the adsorbed bacterial layers. This increase was even more when the bacterial concentrations were higher. In the case of the non-target bacteria Staphylococcus aureus (S. aureus), conductivity noticeable decreases (due to nonspecific adsorption). However, in the case of E. coli, the Rct value increase is time dependent and reaches maximum in about 25-30 min, then decreases gradually as a result of bacterial lysis due to phage invasion on the electrode surfaces. In contrast, there were no time dependent changes with the non-target bacteria S. aureus (no infection and no lytic activity). It is concluded that the target bacteria could be detected using this very simple and inexpensive detection protocol with a minimum detection limit of 103 CFU mL-1 in approximately 100 μL bacterial suspension.Article Citation - WoS: 3Citation - Scopus: 3Gold Nanorod Encapsulated Bubbles(Royal Society of Chemistry, 2015) Tomak, Aysel; Zareie, Hadi M.A simple method has been described for synthesizing gold nanorods (GNRs) encapsulated bubbles in a controlled manner. The method involves the use of nitrogen gas in the seed-mediated synthesis method routinely used for synthesis of GNRs. Control over the morphology of the nanostructures was achieved by nitrogen gas flow. The synthesized structures were examined by UV-Vis Spectroscopy, Scanning Electron Microscopy (SEM) and Atomic Force Microscopy (AFM). New structures of this type could conceivably serve as plasmonic biosensors, nanodevices and photothermal theranostics with dual modality imaging functionality. © The Royal Society of Chemistry 2015.Article Citation - Scopus: 1Charging of Gold/Metal Oxide/Gold Nanocapacitors in a Scanning Electron Microscope(IOP Publishing Ltd., 2014) Coutts, Michael J.; Zareie, Hadi M.; Cortie, Michael B.; McDonagh, Andrew MichaelTriangular parallel-plate nanocapacitors were fabricated by a combination of microsphere lithography and physical vapor deposition. The devices were comprised of a 20 nm layer of dielectric material sandwiched between two 20 nm layers of gold. Dielectric materials with a range of relative permittivities were investigated. Charging of the capacitors was probed in a scanning electron microscope (SEM) by monitoring the change in brightness of the images of the devices as a function of time. The time constants, RC, associated with the charging of the capacitors, were extracted from the SEM grayscale data. The resulting average RC values were 248 ± 27 s for SiO2, 70 ± 8 s for Al2O3, 113 ± 80 s for ZnO and 125 ± 13 s for HfO2. These values are consistent with the anticipated RC values based on the resistivities and permittivities of the materials used in the devices and importantly, were measured without the need to attach any wires or leads.Article Citation - WoS: 33Citation - Scopus: 33Folic Acid Modified Clay/Polymer Nanocomposites for Selective Cell Adhesion(Royal Society of Chemistry, 2014) Barlas, Fırat Barış; Ağ Şeleci, Didem; Özkan, Melek; Demir, Bilal; Şeleci, Muharrem; Aydın, Muhammed; Taşdelen, M. A.; Zareie, Hadi M.; Timur, Suna; Özçelik, Serdar; Yağcı, YusufA folic acid (FA) modified poly(epsilon-caprolactone)/clay nanocomposite (PCL/MMT-(CH2CH2OH)2-FA) resulting in selective cell adhesion and proliferation was synthesized and characterized as a cell culture and biosensing platform. For this purpose, first the FA modified clay (MMT-(CH2CH2OH)2-FA) was prepared by treating the organo-modified clay, Cloisite 30B [MMT-(CH2CH 2OH)2] with FA in chloroform at 60°C. Subsequent ring opening polymerization of ε-caprolactone in the presence of tin octoate (Sn(Oct)2) using MMT-(CH2CH2OH)2-FA at 110°C resulted in the formation of MMT-(CH2CH 2OH)2-FA with an exfoliated clay structure. The structures of intermediates and the final nanocomposite were investigated in detail by FT-IR spectral analysis and DSC, TGA, XRD, SEM and AFM measurements. The combination of FA, PCL and clay provides a simple and versatile route to surfaces that allows controlled and selective cell adhesion and proliferation. FA receptor-positive HeLa and negative A549 cells were used to prove the selectivity of the modified surfaces. Both microscopy and electrochemical sensing techniques were applied to show the differences in cell adherence on the modified and pristine clay platforms. This approach is expected to be adapted into various bio-applications such as 'cell culture on chip', biosensors and design of tools for targeted diagnosis or therapy.