Mühendislik ve Doğa Bilimleri Fakültesi

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Analytic Solution of the Feldtkeller Equation
(Elsevier GMBH Urban & Fischer Verlag, 2009) Şengül, Metin Y.
In every reflectance-based application like broadband matching circuit modeling etc. a nonlinear equation following from energy conservation the Feldtkeller equation must be solved in order to obtain real networks. In the literature however there is no analytic solution available but only numerical solutions. Consequently the resulting error depends on the accuracy of the numerical tools. In this paper an analytic solution is proposed which is based on the modified ABCD-parameters of a lossless reciprocal two-port network. An algorithm is presented and examples are included to illustrate the implementation of the analytical method. (C) 2008 Elsevier GmbH. All rights reserved.
Citation - WoS: 8
Citation - Scopus: 9
Antifungal Screening and in Silico Mechanistic Studies of an In-House Azole Library
(2019) Sarı, Suat; Kart, Didem; Sabuncuoğlu, Suna; Doğan, İnci Selin; Özdemir, Zeynep; Bozbey, İrem; Gencel, Melis; Eşsiz, Şebnem; Reynisson, Jóhannes; Karakurt, Arzu; Saraç, Selma; Dalkara, Sevim
Systemic Candida infections pose a serious public health problem with high morbidity and mortality. C. albicans is the major pathogen identified in candidiasis; however, non-albicans Candida spp. with antifungal resistance are now more prevalent. Azoles are first-choice antifungal drugs for candidiasis; however, they are ineffective for certain infections caused by the resistant strains. Azoles block ergosterol synthesis by inhibiting fungal CYP51, which leads to disruption of fungal membrane permeability. In this study, we screened for antifungal activity of an in-house azole library of 65 compounds to identify hit matter followed by a molecular modeling study for their CYP51 inhibition mechanism. Antifungal susceptibility tests against standard Candida spp. including C. albicans revealed derivatives 12 and 13 as highly active. Furthermore, they showed potent antibiofilm activity as well as neglectable cytotoxicity in a mouse fibroblast assay. According to molecular docking studies, 12 and 13 have the necessary binding characteristics for effective inhibition of CYP51. Finally, molecular dynamics simulations of the C. albicans CYP51 (CACYP51) homology model's catalytic site complexed with 13 were stable demonstrating excellent binding.
Citation - WoS: 1
Citation - Scopus: 3
An Approach To Evaluate Cam Software Alternatives
(TAYLOR & FRANCIS LTD, 2020) Ayağ, Zeki
The selection process for the best computer-aided manufacturing (CAM) software among a set of potential number of alternatives in market has been critical issue for most companies that aim to make their design/manufacturing-related activities automated. Because this selection process is very vital for companies because a wrong decision might put them into a difficult position in terms of economical, market share and time spent. Therefore, today's companies have used different multiple-criteria decision making (MCDM) methods for the evaluation study of CAM software alternatives to make this complex process easily applicable and not time-consuming. Among the MCDM methods in literature, the analytic hierarchy process (AHP) method has been widely used for various MCDM problems in both academic researches and industrial practices. However, in some cases, because of the vagueness and uncertainty on the judgments of decision maker(s), the crisp pair wise comparison in the conventional AHP seems to be insufficient and imprecise to capture the right judgments of decision maker(s). Therefore, a fuzzy logic method is integrated in the pair wise comparison of AHP to make up for this deficiency in the conventional AHP, called as fuzzy AHP. Moreover, the proposed approach is also realized on a case study.
Citation - WoS: 1
Citation - Scopus: 1
Assessing Protein-Ligand Binding Modes With Computational Tools: the Case of Pde4b
(Springer, 2017) Çifii, Gülşah; Aviyente, Viktorya; Akten, Ebru Demet; Monard, Gerald
In a first step in the discovery of novel potent inhibitor structures for the PDE4B family with limited side effects we present a protocol to rank newly designed molecules through the estimation of their IC values. Our protocol is based on reproducing the linear relationship between the logarithm of experimental IC values [(IC)] and their calculated binding free energies (). From 13 known PDE4B inhibitors we show here that (1) binding free energies obtained after a docking process by AutoDock are not accurate enough to reproduce this linear relationship
Citation - WoS: 2
Citation - Scopus: 2
Babbling Through Social Media: a Cross-Country Study Mapping Out Social Networks Using Ewom Intentions
(Springer, 2023) Zülal, İşler; Kıygı-Çallı, Meltem; El Oraiby, Maryam
This research aims to determine the factors affecting the users’ electronic word-of-mouth (eWOM) seeking and sharing intentions and to reveal the interactions among and within clusters using social network analysis (SNA). This study includes three hierarchical sub-studies conducted in two countries, Turkey and Poland. First, we develop a segmentation for social networking site (SNS) users based on the frequency of sharing product-related information on SNSs. Second, we investigate the impact of several factors that affect eWOM seeking and sharing intentions using regression analysis. In the second sub-study, we also include the identified segments developed in the first sub-study as another factor that may have differentiated eWOM intentions. Third, to understand the degree of interaction among SNS users, we apply an SNA using the forecasted eWOM intentions scores from the second sub-study, which gives us hypothetical social networks. The results of SNA present strong interactions inter- and intra-clusters in both countries. Some key findings include the identification of three SNS user segments, including “Middlers,” that may be of particular interest to brands. We also find that in terms of eWOM intentions, users in Turkey are more active than in Poland. Although some predictors of eWOM seeking and sharing intentions differ between the two countries, users intend to be more active in eWOM seeking than in eWOM sharing. The comparative study provides valuable insights for decision-makers to engage different market segments via SNSs with various proposed features using suggested information contents for selected product categories.
Citation - WoS: 12
Citation - Scopus: 10
Bound-Free Electron-Positron Pair Production in Relativistic Heavy-Ion Collisions
(Amer Physical Soc., 2009) Şengül, Metin Y.; Güçlü, Mehmet C.; Fritzsche, S.
The bound-free electron-positron pair production is considered for relativistic heavy ion collisions. In particular cross sections are calculated for the pair production with the simultaneous capture of the electron into the 1s ground state of one of the ions and for energies that are relevant for the relativistic heavy ion collider and the large hadron colliders. In the framework of perturbation theory we applied Monte Carlo integration techniques to compute the lowest-order Feynman diagrams amplitudes by using Darwin wave functions for the bound states of the electrons and Sommerfeld-Maue wave functions for the continuum states of the positrons. Calculations were performed especially for the collision of Au+Au at 100 GeV/nucleon and Pb+Pb at 3400 GeV/nucleon.
Citation - WoS: 1
Citation - Scopus: 4
Broadband Impedance Matching Via Lossless Unsymmetrical Lattice Networks
(Elsevier GMBH Urban & Fischer Verlag, 2012) Şengül, Metin Y.
In this paper a broadband impedance matching network (equalizer) design algorithm has been proposed. In the equalizer a lossless unsymmetrical lattice network has been utilized. The branch impedances of the lattice network are considered as singly terminated lossless LC networks since it is not desired to dissipate power in the equalizer. After giving the algorithm its usage has been illustrated via an example. (C) 2011 Elsevier GmbH. All rights reserved.
Citation - WoS: 5
Citation - Scopus: 7
Calculating Level Densities of Heavy Nuclei by the Shell Model Monte Carlo Method
(Academic Press Inc Elsevier Science, 2014) Alhassid, Yoram; Özen, Cem; Nakada, Hitoshi
The microscopic calculation of nuclear level densities in the presence of correlations is a difficult many-body problem. The shell model Monte Carlo method provides a powerful technique to carry out such calculations using the framework of the configuration-interaction shell model in spaces that are many orders of magnitude larger than spaces that can be treated by conventional methods. We present recent applications of the method to the calculation of level densities and their collective enhancement factors in heavy nuclei. The calculated level densities are in close agreement with experimental data.
Citation - WoS: 17
Citation - Scopus: 16
Cation Effect on Slow Release From Alginate Beads: a Fluorescence Study
(Springer/Plenum Publishers, 2014) Kaygusuz, Hakan; Erim, F. Bedia; Pekcan, Önder; Evingür, Gülşen Akin
In this study spherical alginate beads containing pyranine (P-y) as a fluorescence probe were prepared by ionotropic gelation of a sodium alginate solution. The steady state fluorescence technique was used to study pyranine release from the alginate beads crosslinked with calcium barium and aluminum ions respectively. The slow release of P-y was observed with the time drive mode of the spectrophotometer at 512 nm. Fluorescence emission intensity (I-p) from P-y was monitored during the release process and the encapsulation efficiency (EE) of pyranine from the alginate beads was calculated. The Fickian Diffusion model was used to measure the release coefficients D-sl. It was seen that the slow release coefficients of pyranine from the alginate beads crosslinked with Ca2+ Ba2+ and Al3+ ions increased in the following order: D-sl (Al3+)> D-sl (Ca2+)> D-sl (Ba2+). In contrast the initial amount of pyranine and EE into the beads showed the reverse behavior.
Citation - WoS: 33
Citation - Scopus: 33
Cis-Cyclopropylamines as Mechanism-Based Inhibitors of Monoamine Oxidases
(Wiley-Blackwell, 2015) Malcomson, Thomas; Yelekçi, Kemal; Borrello, Maria Teresa; Ganesan, A.; Semina, Elena; De Kimpe, Norbert; Mangelinckx, Sven; Ramsay, Rona R.
Cyclopropylamines inhibitors of monoamine oxidases (MAO) and lysine-specific demethylase (LSD1) provide a useful structural scaffold for the design of mechanism-based inhibitors for treatment of depression and cancer. For new compounds with the less common cis relationship and with an alkoxy substituent at the 2-position of the cyclopropyl ring the apparent affinity determined from docking experiments revealed little difference between the enantiomers. Using the racemate kinetic parameters for the reversible and irreversible inhibition of MAO were determined. No inhibition of LSD1 was observed. For reversible inhibition most compounds gave high IC50 values with MAO A but sub-micromolar values with MAO B. After pre-incubation of the cyclopropylamine with the enzyme the inhibition was irreversible for both MAOA and MAOB and the activity was not restored by dilution. Spectral changes during inactivation of MAOA included bleaching at 456nm and an increased absorbance at 400nm consistent with flavin modification. These derivatives are MAOB-selective irreversible inhibitors that do not show inhibition of LSD1. The best inhibitor was cis-N-benzyl-2-methoxycyclopropylamine with an IC50 of 5nm for MAOB and 170nm for MAOA after 30min pre-incubation. This cis-cyclopropylamine is over 20-fold more effective than tranylcypromine so may be studied as a lead for selective inhibitors of MAOB that do not inhibit LSD1.
Citation - WoS: 15
Citation - Scopus: 20
A Combined Fuzzy Ahp-Simulation Approach To Cad Software Selection
(Taylor & Francis Ltd, 2010) Ayağ, Zeki
In this paper a combined approach where the fuzzy analytic hierarchy process (AHP) and simulation come together is presented to select the best computer-aided design (CAD) software out of the available options in the market. The fuzzy AHP is used due to the vagueness and uncertainty of the judgements of a decision maker(s) because the crisp pair-wise comparison in the conventional AHP seems to be insufficient and imprecise to capture the right judgements of the decision maker(s). In this study first the fuzzy AHP is used to reduce a possible number of alternatives for the CAD system to an acceptable level for further study simulation analysis. Secondly a simulation generator as an integrated part of the fuzzy AHP is used to try the remaining alternatives on the generated model of a real-life product organisation in which the final alternative will be used. The results of simulation experiments are obtained and then evaluated to reach to the ultimate CAD alternative.
Citation - Scopus: 3
Comparison of Cation Effects on Phase Transitions of Kappa and Iota Carrageenan
(European Polymer Federation, 2010) Tari, Özlem; Pekcan, Önder
Phase transitions of kappa and iota carrageenan in KCl NaCl and CaCl2 solutions were separately studied during heating and cooling processes by using fluorescence technique. Scattered light I-SC and fluorescence intensity I was monitored against temperature to determine the critical transition temperatures and exponents. Kappa and iota carrageenans with monovalent (KCl NaCl) salt system presented only coil to double helix (c-h) and double helix to coil (h-c) transitions upon cooling and heating processes respectively. Two transition regions were observed in both heating and cooling of the iota carrageenan in CaCl2 solution while in kappa carrageenan only (c-h) and (h-c) transitions was detected. During heating dimers decompose into double helices by making (d-h) transition. At the high temperature region (h-c) transition takes place. During cooling back transitions repeat themselves. A hysteresis was observed between (h-c) and (c-h) for the kappa and iota carrageenan salt system (except CaCl2) respectively. Dimer to double helix (d-h) and double helix to dimer (h-d) transitions were observed for iota carrageenan in CaCl2 salt. The gel fraction exponent beta was measured and found to be in accord with the classical Flory-Stockmayer Model for both kappa and iota carrageenan salt systems.
Citation - WoS: 6
Citation - Scopus: 6
A Comparison of Fluorescence and Uv-Visible Spectrometry Techniques for Thermal Phase Transitions of Agarose Gels
(Springer, 2015) Arda, Ertan; Kara, Selim; Mergen, Ömer Bahadır; Pekcan, Önder
In this study thermoreversible phase transitions of high (HMP) and low (LMP) melting point agarose gels were investigated by using the UV-vis and fluorescence spectroscopy techniques. Pyranine was added to the aqueous solution of agarose as a fluorescence-probe. Transmitted light (I (tr)) and fluorescence emission (I (fl)) intensities from the gel samples with different agarose concentrations were monitored during the heating (gel-sol) and cooling (sol-gel) processes. For the both techniques gel-sol (T (gs)) and sol-gel (T (sg)) transition temperatures were determined from the first derivatives of the sigmoidal transition paths. It was observed that the critical transition temperatures obtained from UV-vis and fluorescence data slightly increased depending on the agarose type and concentration and those values were found to be in accord with each other. Transition activation energies were determined using the Arrhenius type equation and were found to be strongly correlated with the agarose content in the gel system. The produced gel-sol (Delta E (gs)) and sol-gel (Delta E (sg)) transition energies from the fluorescence data were found to be lower than that of the UV-vis data which was attributed to the temperature-dependent fluorescence quenching effect.
Citation - WoS: 16
Citation - Scopus: 17
Correlation of Experimental Liquid-Liquid Equilibrium Data for Ternary Systems Using Nrtl and Gmdh-Type Neural Network
(Amer Chemical Soc, 2017) Bekri, Sezin; Özmen, Dilek; Özmen, Atilla
In this work liquid liquid equilibrium (LLE) data for the ternary systems (water + propionic acid + solvent) were experimentally obtained at atmospheric pressure and 298.2 K. The ternary systems show type-1 behavior of LLE. Cyclopentane cyclopentanol 2-octanone and dibutyl maleate were chosen as solvent and it has been noted that there are no data in the literature on these ternary systems. The consistency of the experimental tie-line data was checked using the Hand and Othrner-Tobias correlation equations. A comparison of the extracting capabilities of the solvent was made with respect to the distribution coefficients and separation factors. The correlation of the experimental tie-line data was confirmed by the NRTL thermodynamic model. A Group Method of Data Handling (GMDH)-type neural network (NN) was also used to correlate the experimental tie-lines. It is shown that the results of the both models cohere with the experimental values.
Citation - WoS: 3
Citation - Scopus: 2
Coulomb Corrections in the Lepton-Pair Production in Ultrarelativistic Nuclear Collisions
(Amer Physical Soc., 2005) Güçlu, Mehmet C.; Kovankaya, G.; Yılmaz, Melek
We solve the perturbative electron-positron pair production exactly by calculating the second-order Feynman diagrams. We compare our result with Born methods that include Coulomb corrections. We find that a small-momentum approximation is not adequate to obtain exact Coulomb corrections and higher-order terms should also be included. We also compare the impact parameter dependence cross sections.
Citation - WoS: 11
Citation - Scopus: 11
Derivation of the Optical Constants of Spin Coated Ceo2-Tio2 Thin Films Prepared by Sol-Gel Route
(Pergamon-Elsevier Science Ltd, 2011) Ghodsi, Farhad E.; Tepehan, Fatma Zehra; Tepehan, Galip Gültekin
Ternary thin films of cerium titanium zirconium mixed oxide were prepared by the sol-gel process and deposited by a spin coating technique at different spin speeds (1000-4000 rpm). Ceric ammonium nitrate ce(NO3)(6)(NH4)(2) titanium butoxide Ti[O(CH2)(3)CH3](4) and zirconium propoxide Zr(OCH2CH2CH3)(4) were used as starting materials. Differential calorimetric analysis (DSC) and thermogravimetric analysis (TGA) were carried out on the CeO2-TiO2-ZrO2 gel to study the decomposition and phase transition of the gel. For molecular structural elemental and morphological characterization of the films Fourier Transform Infrared (FTIR) spectral analysis X-ray diffraction (XRD) energy dispersive X-ray spectroscopy (EDS) cross-sectional scanning electron microscopy (SEM) and atomic force microscopy (AFM) were carried out. All the ternary oxide thin films were amorphous. The optical constants (refractive index extinction coefficient band gap) and thickness of the films were determined in the 350-1000 nm wavelength range by using an nkd spectrophotometer. The refractive index extinction coefficient and thickness of the films were changed by varying the spin speed. The oscillator and dispersion energies were obtained using the Wemple-DiDomenico dispersion relationship. The optical band gap is independent of the spin speed and has a value of about E-g approximate to 2.82 +/- 0.04 eV for indirect transition. (C) 2011 Published by Elsevier Ltd.
Design and Synthesis of Novel 2-Pyrazoline Analogues and Their Hmao Inhibitory Activities
(Wiley-Blackwell, 2015) Uçar, Gülberk; Evranos-Aksoz, Begum; Yabanoglu-Çiftçi, Samiye; Yelekçi, Kemal
[Abstract Not Available]
Citation - WoS: 3
Citation - Scopus: 4
Design of Broadband Microwave Amplifiers With Mixed-Elements Via Reflectance Data Modeling
(Elsevier GMBH Urban & Fischer Verlag, 2008) Şengül, Metin Y.; Yarman, Sıddık Binboğa
A practical method is introduced to design single-stage broadband microwave amplifiers with mixed lumped and distributed elements via modeling the reflectance data obtained from lumped-element input and output matching network prototypes. The same transducer power gain level is obtained by using less number of lumped-elements in the mixed-element amplifier than that of the lumped-element amplifier prototype. A mixed-element amplifier design is presented to exhibit the utilization of the method. It is expected that the method will be employed to design microwave amplifiers for broadband communication systems. (C) 2007 Elsevier GmbH. All rights reserved.
Citation - WoS: 5
Citation - Scopus: 7
Design of Broadband Single Matching Networks
(Elsevier GMBH Urban & Fischer Verlag, 2009) Şengül, Metin Y.
In general commercially available software tools are preferred to design broadband matching networks for wireless communication systems. But they need a properly selected matching network topology with good initial element values. Therefore in this paper a new real frequency technique is presented to generate broadband single matching networks with suitable initial element values. In the proposed method load impedance is written in terms of ABCD-parameters of the desired matching network and the source resistor. Then free parameters are optimized which in turn yields the desired matching network with initial element values. It is not needed to select a circuit topology for the matching network which is the natural consequence of the matching processes. Also there is no need to select the desired transducer power gain level , the proposed technique naturally provides a gain curve fluctuating around the final available level. Eventually the initial design is improved by optimizing the performance of the matched system employing the commercially available computer-aided design (CAD) packages. An algorithm and two examples are given to illustrate the utilization of the proposed technique. (C) 2007 Elsevier GmbH. All rights reserved.
Citation - WoS: 11
Design of Distributed-Element Rf Filters Via Reflectance Data Modeling
(Elsevier GMBH Urban & Fischer Verlag, 2008) Şengül, Metin Y.; Yarman, Sıddık Binboğa; Volmer, Christian; Hein, Matthias A.
A reflectance-based modeling method is presented to obtain the distributed-element counterpart of a lumped-element network which is described by measured or computed reflectance data at a set of frequencies. Numerical generation of the scattering parameters forms the basis of this modeling tool. It is not necessary to select a circuit topology for the distributed-element model which is the natural consequence of the modeling process. Our approach supplements the known interpolation methods by a simple technique that does not involve complicated cascaded circuit topologies and whose numerical convergence is proven. To illustrate the utilization of the proposed method a lumped-element low-pass Chebyshev filter is transformed to its distributed-element counterpart. The filter designed for a frequency band around 1 GHz was fabricated and experimentally characterized. We find excellent agreement between measured and simulated transducer power gain over the entire frequency band. (c) 2007 Elsevier GmbH. All rights reserved.

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