Gebze Technical University
  • Gebze, Kocaeli, Turkey
Recent publications
Background Recently, biosensors have become popular analytical tools for small analytes due to their high sensitivity and wide analytical range. In the present work, development of a novel biosensing method based on tungsten disulfide quantum dots (WS2 QDs)-Au for rapidly and selectively detecting c-Met protein is introduced. As a proof of concept, M13 bacteriophage-based biosensors were used for the electrochemical detection of c-Met protein as a colon cancer biomarker. Method The M13 bacteriophage (virus), as the biorecognition element, was immobilized on glassy carbon electrodes which were modified by WS2 QDs-functionalized gold nanoparticles. The stepwise presence of the WS2 QDs, gold nanoparticles, and immobilized phage on glassy carbon electrodes were confirmed by scanning electron microscope (SEM) and square wave voltammetry (SWV) technique. Results The designed biosensor was applied to measure the amount of c-Met protein in standard solutions, and consequently the desirable detection limit of 1 pg was obtained. Finally, as a proof of concept, the developed platform was used for the evaluation of c-Met protein in serum samples of colon cancer-suffering patients and the results were compared with the results of the common Elisa kit. Conclusions As an interesting part of this study, some concentrations of the c-Met protein in colon cancer serum samples which could not be determined by Elisa, were easily analyzed by the developed bioassay system. The developed bioassay system has great potential to application in biomedical laboratories. Graphical Abstract
This study aims to elucidate the inhibitory activity of nisin alone or in combination with gilaburu (Viburnum opulus L.) against the foodborne Staphylococcus aureus. The effect of nisin and gilaburu on the growth of S. aureus was investigated under different pH (5–7) and salt concentrations (NaCl, 0.5–4.5% w/v) at 30 °C. Nisin exhibited the best antibacterial activity at pH 5 with a minimum inhibitory concentration (MIC) of 25 μg/mL, while its MIC was 50 μg/mL in all salt concentrations when the pH was kept constant at pH 7. The MIC of gilaburu was found to be 50% in all conditions studied. The minimum bactericidal concentrations (MBC) of nisin and gilaburu were 100 μg/mL and >50%, respectively. Changes in pH and salt concentrations did not affect MBC. According to checkboard assay results, a synergy was found between gilaburu and nisin (FIC = 0.25) for both 2.5% and 4.5% w/v salt concentrations at pH 5. The synergistic interaction between nisin and gilaburu was also studied using an agar disk diffusion assay where nisin concentration was kept constant at 3.125 μg/ml, while gilaburu concentration varied between 3.125 and 100%. The positive effect of gilaburu on nisin activity was further confirmed by time-kill assay, flow cytometry, and measurement of relative TTC dehydrogenase activity and conductivity as well as DNA and protein leakage. In conclusion, nisin combined with gilaburu exerted the same inhibitory effect on S. aureus at a concentration approximately 8 times lower than that of MIC of nisin alone (25 μg/mL). This study shows the potential use of nisin and gilaburu in combination to control S. aureus in food.
G protein-coupled receptors (GPCRs) induce signal transduction pathways through coupling to four main subtypes of G proteins (G s , G i , G q , and G 12/13 ), selectively. However, G protein selective activation mechanisms and residual determinants in GPCRs have remained obscure. Herein, we performed extensive phylogenetic analysis and identified specifically conserved residues for the aminergic receptors having similar coupling profiles. By integrating our methodology of differential evolutionary conservation of G protein–specific amino acids with structural analyses, we identified specific activation networks for G s , G i1 , G o , and G q . To validate that these networks could determine coupling selectivity we further analyzed G s -specific activation network and its association with G s selectivity. Through molecular dynamics simulations, we showed that previously uncharacterized Glycine at position 7x41 plays an important role in receptor activation and it may determine G s coupling selectivity by facilitating a larger TM6 movement. Finally, we gathered our results into a comprehensive model of G protein selectivity called “sequential switches of activation” describing three main molecular switches controlling GPCR activation: ligand binding, G protein selective activation mechanisms, and G protein contact.
For the estimation of left and right-tail probabilities and the pdf of the sum of exchangeable lognormal random vectors a new conditional Monte Carlo (CMC) algorithm is developed. It removes the randomness of the sum of all input variables and is simple and fast. For estimating the left-tail probabilities the CMC algorithm is logarithmically efficient. A further improvement of the algorithm by removing also the randomness of the radius of the normal input using close to optimal one dimensional importance sampling, results in the CMC.RCMC algorithm. For the sum of independent and identically distributed (i.i.d. ) and exchangeable lognormal vectors it is the first algorithm that has bounded relative error for the left-tail probabilities. The CMC.RCMC algorithm is logarithmically efficient for the right-tail probabilities. Numerical experiments verify that it has a very good performance for all left-tail estimation problems and a good performance for the right tail for probabilities not smaller than \(10^{-10}\). When estimating the pdf the relative errors observed are all very close to those of the corresponding probability estimates.
In this study, two difluoroboradiazaindacene (BODIPY) compounds bearing diethylaminostyryl groups were synthesized in order to establish colorimetric and fluorometric paper-based pH sensors. The structures of these novel BODIPY compounds were identified by NMR (1H, 13C, 11B, and 19F), elemental analysis, MALDI-TOF, FT-IR, UV–vis and fluorescence spectroscopies as well as single-crystal X-Ray data. The DFT study was also performed to optimize of these two novel BODIPY structures. Electrochemical measurements were applied to estimate their redox potentials. Photophysical properties such as fluorescence quantum yield and lifetimes were investigated to determine the effect of acid addition in both DMSO and 1,4-dioxane solutions of the studied BODIPY derivatives. Also, pKa values of the synthesized compounds (1a and 1b) were determined from absorbance and fluorescence measurements by acid titration studies. The paper-based pH sensor behavior of these BODIPY derivatives was investigated and their performances were determined on the lemon juice samples as a real sample analysis. A simple, cost-effective, rapid, portable, colorimetric, and fluorometric paper-based BODIPY sensing platform was developed in this study for the detection of the variety of pH changes in lemon juice.
Piezoelectric fields can decrease the recombination rate of photogenerated electrons and holes in semiconductors and therewith increase their photocatalytic activities. Here, a BaTiO3/WS2 composite is synthesized and characterized, which combines piezoelectric BaTiO3 nanofibers and WS2 nanosheets. The piezo-photocatalytic effect of the composite on the persulfate activation is studied by monitoring Ofloxacin (OFL) degradation efficiency. Under mechanical forces, LED lamp irradiation, and the addition of 10 mM persulfate, the OFL degradation efficiency reaches ~90% within 75 min, which is higher than efficiencies obtained for individual BaTiO3, WS2, or TiO3, widely used photocatalysts in the field of water treatment. The boosted degradation efficiency can be ascribed to the promotion of charge carrier separation, resulting from the synergetic effect of the heterostructure and the piezoelectric field induced by the vibration. Moreover, the prepared composite displays good stability over five successive cycles of the degradation process. GC–MS analysis is used to survey the degradation pathway of OFL during the degradation process. Our results offer insight into strategies for preparing highly effective piezo-photocatalysts in the field of water purification. Piezoelectric fields can be exploited in photocatalysis to decrease the rate of photogenerated electron and hole recombination. Here, the authors demonstrate that a BaTiO3/WS2 composite is a highly effective piezo-photocatalyst for the degradation of water pollutant ofloxacin.
This work describes the compressive failure behavior and optimization of modified hierarchical re-entrant auxetic meta-materials reinforced with asymmetrical edge cells. The mechanical behavior of these metamaterials is parametrized against the width, thickness and angles of the cells. A Taguchi design (L27 (3^13)) has been performed to determine the effect of the eight geometric factors on the maximum compressive strength (specific strength), mean crushing force (MCF), specific energy absorption (SEA) and Poisson's ratio of the metamaterials. An analysis of variance (ANOVA) has been also performed to find out the relative significance and contribution percentage of each parameter from a statistical standpoint. The results show that the cell wall angle between the lateral and inclined ribs of the re-entrant unit cells has the largest effect on the compressive strength and absorbed energy of the structure that exhibits a percent variation of 82.5%, 30.0%, 85.9% and 75.1% in specific strength, MCF, SEA and Poisson's ratio, respectively. Moreover, the size of slot width and thickness, especially in the inclined struts, have a considerable effect on the mechanical performance compared to the angle of asymmetrical cells. Lastly, two samples from the optimization design table showing the best and worst mechanical responses are manufactured by using 3D printing and are tested under compression loading. The effects of the design factors on the deformation mechanisms and mechanical responses have been discussed by comparing the experimental and FE simulation results. The results show that the deformation mechanism of the asymmetrical unit cells and inclined struts play a key role in the resistance of the structures under compressive loads.
The steady, laminar, incompressible, axisymmetric stenotic blood flow is investigated with a non-polynomial solution assumption. The wall geometry of the stenosis is constructed as a fixed cosine curve. The rheology of blood is modeled as a generalized power-law fluid. The variations of the coefficients constructing both axial and radial velocity profiles through the stenotic tube are calculated with the examination of the analytical relations in closed form. The streamlines, separation and reattachment points, velocity profiles, and pressure variations are also obtained for the Newtonian cases in order to check the validation of the analytical approach. We observed that the results obtained are in good agreement with the ones that are widely available in the literature. Comparisons were made with non-Newtonian studies, which are rare for low Reynolds numbers in the literature, and with the numerical analyses performed in this study. As an important result of the analytical approach, it was concluded that the location of the separation and reattachment points and the existence of the separation-reattachment region are directly related to one of the coefficients in the non-polynomial solution assumption. Added to this, the ratio of the Reynolds number to the power-law exponent has a remarkable meaning in the characterization of the flow streamlines. Also, we introduce a rather simple formula of Reynolds number for blood-like power-law fluids.
This study presents an easy and quick method for the synthesis of graphene from graphite in a set of solvents, including n-Hexadecane (n-Hexa), dimethylsulfoxide (DMSO), sodium hydrox-ide (NaOH), 1-octanol (OCTA), perchloric acid (PA), N,N-Dimethylformamide (DMF), ethylene gly-col (EG), and ethylene diamine (ED), via microwave (MW) energy. The properties of final products were determined by X-ray diffraction spectroscopy (XRD), Fourier transform infrared spectroscopy (FTIR), ultraviolet-visible (UV-Vis) spectroscopy, and the four-point probe technique. The XRD spectra of most of the MW-assisted graphene products showed peaks at 2θ = 26.5° and 54°. Layer numbers extend from 2 and 25, and the leading comes about were gotten by having two-layered products, named as graphene synthesized in dimethylsulfoxide (G-DMSO), graphene synthesized in ethylene glycol (G-EG), and graphene synthesized in 1-octanol (G-OCTA). G-DMF has the highest electrical conductivity with 22 S/m. The electrical conductivity is higher when the dipole moment of the used solvent is between 2 and 4 Debye (D). The FTIR spectra of most of the MW-assisted graphene products are in line with commercial graphene (CG). The UV-Vis spectra of all MW-assisted graphene products showed a peak at 223 nm referring to characteristic sp2 C=C bonds and 273 nm relating to the n → π * transition of CO bonds.
Superhydrophobic (SH) polylactic acid (PLA) surfaces were previously produced by various methods and used especially in biomedical applications and oil/water separation processes after 2008. However, the wettability of SH-PLA patterns containing micropillars has not been investigated before. In this study, PLA patterns having regular microstructured pillars with 12 different pillar diameters and pillar-to-pillar distances were prepared by hot pressing pre-flattened PLA sheets onto preformed polydimethylsiloxane (PDMS) soft molds having micro-sized pits. PDMS templates were previously prepared by photolithography using SU-8 molds. Apparent, advancing, and receding water contact angle measurements were carried out on the PLA patterns containing micropillars, and the morphology of the patterns was examined by optical and SEM microscopy. The largest contact angle obtained without the surface modification of the pure PLA pattern was 139°. Then, PLA micropatterns were hydrophobized using three types of silanes via chemical vapor deposition method, and SH-PLA patterns were obtained having θs of up to 167°. It was found that the highest θ values could be obtained when PLA pattern samples were coated with a silane containing a fluorine atom in its chemical structure. Washing and service life stability tests were also performed on the coated pattern samples and all of the silane coatings on the PLA patterns were found to be resistant over a 6 month period.
In this study, climatological properties of fog types, their association with surrounding environment and background synoptic mechanisms triggering fog formation are investigated for Turkey. For this purpose, SYNOP (surface synoptic observations) and METAR (Meteorological Aerodrome Report) codes of 105 stations are used for the period 2014‐2019. While fog types are separated to the fog, quasi‐fog and dense fog events according to horizontal visibility conditions, stations are classified as mountain, seaside, urban, and rural by considering the surrounding environment. Synoptic mechanisms causing the occurrence of springtime marine fog events over Black Sea are investigated using NCEP/NCAR Reanalysis. According to the main results, highest numbers of fog events are observed during winter, spring, fall, and summer months, respectively. Radiation fog frequently occurs in the mountainous regions (i.e. central and eastern part) of Turkey during winter. As a result of the rainfall during daytime, significant amount of moisture begins to saturation at night owing to rapid cooling processes and fog layer forms just above the surface. During spring, Black Sea‐effect marine fog events are frequently shown in the seaside stations of the Black Sea and northeastern Marmara regions. On the western Black Sea, winds from northeast enable rising of cold sea water to the surface (upwelling) and transfer it to the relatively warm land areas. Denser humid and cold air settling on the surface forces warm land air to rise. Additionally, warm air advection at 850‐hPa (low level) creates a thick inversion layer over the region. For the eastern Black Sea, relatively cold and humid sea surface transferred to the coasts by light local northwesterly winds encounters with the mountain barrier and is trapped in the region. Furthermore, southerly winds (850‐hPa) cross over the Kaçkar Mountains cause föehn effect and generate an inversion layer over the fog layer. This article is protected by copyright. All rights reserved.
In information security context, social engineering is defined as malicious activities caused by cybercriminals by means of human interactions. It is mainly a psychological manipulation technique which gets benefit of human error to reach private information. This study used machine learning algorithms to predict individuals' susceptibility to be tricked by social engineering attacks. Simulated scenarios were presented to study participants, and they were asked to identify whether each scenario was a social engineering attack or not. Different kinds of attacks related to various industries were integrated to social engineering simulations. For each participant , different types of social engineering scores were calculated according to their responses. Besides simulations, questionnaires related to demographics, technology usage, and personality traits were filled out by the participants. All of these collected data were used in building predictive classification and regression machine learning models. Through regression and classification models, it was aimed to proactively predict individuals' social engineering risk levels and classify them into different risk groups in terms of different attack types. This research revealed that it is possible to predetermine the social engineering risk levels of individuals. This important finding means that possible attacks can be prevented by raising awareness before the attack occurs. Within the scope of this study, a social engineering risk detection mobile application has also been developed to give practitioners and policy makers an idea of what kind of systems can be developed in order to determine the risk levels of individuals and then to educate them about various attacks. The ones who need to take action against social engineering attacks will get benefit from findings of this research.
In this paper, a collocation method based on the Pell-Lucas polynomials is presented for the numerical solution of the Abel equation of the second kind. Abel equation of the second kind corresponds to a nonlinear differential equation. As a first step, the matrix forms of the Pell-Lucas polynomials and the assumed solution form are constructed. Then, the first derivative of solution, the nonlinear terms and the initial condition are introduced in matrix forms. By using the evenly spaced collocation points and the matrix relations, nonlinear problem is transformed to a system of the nonlinear algebraic equations. Consequently, the solution of this system gives the coefficients of the assumed approximate solution. In addition, the error analysis is done. Accordingly, an upper bound of the errors is stated. Besides, error estimation technique and the residual improvement technique are presented by using residual function. Moreover, the method is applied to two examples and the comparisons are made with the results of other methods in tables to show the computational efficiency of present method. The code of method and the presented graphics are constituted by using Matlab program.
Plasticised poly(lactic acid) (PLA)-based antimicrobial films were successfully produced via solvent-casting method. For this purpose, PLA copolymer-bearing quaternary ammonium salt in rate of 5 mol% was successfully fabricated through a two-step reaction procedure, i.e. combination of ring-opening copolymerization and copper(I)-catalysed azide–alkyne cycloaddition click reactions. The synthesized polymer was blended at three different amounts (5, 20 and 30% w/w) with commercial PLA which was plasticized with PEG-1000. After the blending process, antimicrobial activity of all the composite films was investigated against Gram-positive (Staphylococcus aureus) and Gram-negative (Escherichia coli) bacteria via contact-active method. It was determined that the films blended with polymer containing quaternary ammonium salt on its backbone had a highly effective antimicrobial activity against both bacteria, even at the lowest blending rate. Besides, the thermo-mechanical behaviours of obtained films were analysed. Thermal property of films was not changed significantly after blending process of antimicrobial polymer. As a result, it can be said that the film which contains antimicrobial polymer at the lowest amount provides the purpose of this work with the highly effective antimicrobial activity and better mechanical properties compared to other films.
An air-based photovoltaic-thermal (PV-T) system with a converging collector (i.e. a channel with a decreasing hydraulic diameter), to the best of authors’ knowledge for the first time, has been experimentally studied against a PV-T counterpart with the conventional thermal collector geometry (i.e. with fixed hydraulic diameter) as well as a PV module with no thermal management system. An iterative method for the calculation of the convective heat transfer coefficient (hd) introduced in the study revealed that hd for a conventional thermal collector can be easily increased up to 38 % using the idea of the converging collector with no need for any extra energy or cost. According to the measurements, this enhancement results in an increase in the net overall efficiency of the PV-T system by 12 % on average compared to a PV-T system with a conventional thermal collector. Meanwhile, the converging thermal collector results in an almost uniform temperature distribution for the PV, confirming the idea of the uniform cooling in air-based PV-T systems is possible, which has not been previously reported.
Porous cathodes are preferred to be used in lithium-sulfur (Li–S) batteries for better impregnation of the active material. On the other hand, the electrochemical performances of Li–S cells are mostly correlated with the free pore volume of the cathode hosts; however, their electrical conductivities were rarely reported in the existing literature. In this work, lightweight, 3D spongy boron-doped graphene aerogel cathodes were prepared and their electrical conductivity values were found to increase under the uniaxial compression through the vertical axis. The variation of the uniaxial compression corresponds to the fluctuations in the pressure of the springs during the assembly of Li–S cells, which resulted in the diversity of the cell performance containing the same cathode material. The electrical conductivity of the cathode was determined to be nearly constant up to a compressive strain of 60% but increased significantly from 60 to 80%. In parallel, electrical conductivity of the cathode increased with the accompanying increase of the aerogel density from 0.04 to 0.08 g·cm⁻³. In addition, the electrochemical performances of the aerogel cathodes having the same amount of active material were investigated in Li–S batteries when different uniaxial compressions were applied. It was found that the aerogel cathode having 40% uniaxial compression exhibited the best stable discharge capacity (~ 440 mAh·g⁻¹ over 100 cycles). These results indicate that both electrical conductivity and porosity properties of graphene cathodes should be considered simultaneously to obtain reliable Li–S cell performances. Graphical abstract
The novel thiophene-chalcone compound (2), phthalonitrile derivatives bearing thiophene-chalcone group (3 and 4) and their zinc (II) (ZnPcs) (3a and 4a) and magnesium (II) (MgPcs) (3b and 4b) phthalocyanine compounds were synthesized in this study. The structure of all these new compounds were elucidated by spectroscopic techniques like IR, ¹ H NMR, ¹³ C NMR (for compounds 2, 3 and 4), MALDI–TOF mass and UV-Vis. The fluorescence quantum yields and lifetimes (photophysical properties), and the singlet oxygen and photodegradation quantum yields (photochemical properties) of thiophene bearing chalcone substituted ZnPcs (3a and 4a) and MgPcs (3b and 4b) were studied in DMSO (dimethylsulfoxide) to determine if they are convenient photosensitizers for photodynamic therapy (PDT) applications.
Nonlinear panel flutter and post-flutter behavior of wing-like, taper, and skew plates made of functionally graded (FG) multilayered graphene platelet-reinforced polymer composite (GPL-RPC) are investigated in this study. Using two types of geometrical non-uniformity, skew and taper, the flutter boundary, limit cycle oscillations, and bifurcation plots of functionally graded GPL-RPC plates are reported. The graphene platelet (GPL) nanofillers are assumed to be dispersed uniformly or non-uniformly in the matrix and in the thickness direction. All GPL distribution patterns of UD, FG-O, FG-X, and FG-A are considered. The modified Halpin–Tsai micro-mechanical model and the rule of mixture are utilized to determine the effective material characteristics of GPL-RPC layers. In order to obtain the nonlinear mathematical model for the non-uniform plates, Von-Karman kinematic strains descriptions are used along with the virtual work principle and Hamilton’s expression. To generalize the structural model, a first-order shear deformation theory (FSDT) is used. The well-recognized first-order piston theory is also utilized to account for the aerodynamic loading description. In the end, governing differential equations of motion are projected to their equivalent algebraic representation by means of the generalized differential quadrature method (GDQM), which is then followed by a time integration using the Newmark’s average acceleration scheme. The goal of current research is to find how the GPL weight fraction affects the flutter instability margins and post-flutter behavior for FG GPL-RPC cantilevered plates at several proposed distribution patterns.
Membrane technology is an outstanding alternative for treating complex textile wastewaters. However, difficulties in the management of the resultant concentrate are the main disadvantage of these membrane technologies. This study is focused on the development of integrative management for membrane concentrate of textile effluent under the principle of discharge regulations that aim to achieve zero-liquid discharge (ZLD). Thus, biologically treated textile wastewater (BTTW) is fed to nanofiltration (NF) and reverse osmosis (RO) membranes with ultrafiltration (UF) pre-treatment, separately. NF concentrates (NFC) and RO concentrates (ROC) are further treated with electrocoagulation (EC) and electro-Fenton (EF) to remove COD and color. After the EC and EF steps, the electrodialysis (ED) method is used for ion removal. Operational costs of each process are calculated. Through the NF of BTTW > 65% COD and 92% color removals were achieved, whereas with the RO process, > 65% COD and 98% color removals were obtained. For NFC, > 80% COD and 91% color removal efficiencies were achieved with EC + ED processes and 57% COD and almost total color removal was achieved with EF + ED processes. For ROC, 71% COD and 85% color removals were obtained with EC + ED processes and 85% COD and 98% color removal was observed with EF + ED processes. Additionally, efficient treatment and concentrate management options were investigated for textile effluent. Graphical abstract
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3,237 members
Hulya Akdemir
  • Department of Molecular Biology and Genetics
Elif Okutan
  • Department of Chemistry
Oleg A. (Aleksandrovich) Tretyakov
  • Department of Electronics Engineering
Çayırova, 41400, Gebze, Kocaeli, Turkey
Head of institution
Prof. Dr. Muhammed Hasan Aslan
+90 (262) 605 10 00
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