Mühendislik ve Doğa Bilimleri Fakültesi
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Article Citation Count: 0"2-pirazolin yapısındaki yeni bir bileşiğin sentezi, moleküler modellemesi ve monoaminoksidaz inhibitörü etkisinin araştırılması"(Türkiye Halk Sağlığı Kurumu, 2018) Yelekçi, Kemal; Uçar, Gülberk; Yelekçi, KemalAmaç: Nöromediatörlerin yıkımından sorumlu olan monoamin oksidaz (MAO) enziminin izoformlarının (MAO-A ve -B) birçok hastalık ile yakından ilişkili olduğu; MAO inhibitörlerinin depresyon, Parkinson ve Alzheimer hastalığı gibi hastalıkların tedavisinde kullanıldığı bilinmektedir. Grubumuzca daha etkin, tersinir ve az yan etkili yeni bir MAO inhibitörü (SH2U bileşiği) sentezlenmiş ve bu bileşiğin insan MAO enzimini (hMAO) inhibe etme yeteneği incelenmiştir. Ayrıca bu yeni bileşiğin hMAO ile etkileşimi, moleküler modelleme çalışmaları ile detaylı bir şekilde araştırılmıştır. Sentezlenen yeni bileşiğin hMAO’yu kuvvetli bir şekilde yarışmalı ve tersinir olarak inhibe ettiği bulunmuştur. Söz konusu bileşiğin Parkinson ve Alzheimer hastalıklarının tedavisinde ümit verici bir ilaç etken maddesi olabileceği düşünülmektedir. Yöntem: 3’,5’-Dikloro-2’-hidroksi asetofenon ile p-tolualdehit’in metanol içinde KOH varlığında reaksiyona girmesiyle 1-(3,5-dikloro-2-hidroksifenil)- 3-p-tolil prop-2-en-1-on (3’,5’-Dikloro-2’-hidroksi-4- metil şalkon) bileşiği sentez edilmiştir. Daha sonra elde edilen bu bileşiğin etanol içerisinde geri çeviren soğutucu altında izonikotinik asit hidrazit ile muamele edilmesiyle [3-(3,5-dikloro-2-hidroksifenil)-5-p-tolil-4,5- dihidropirazol-1-il] (piridin-4-il) metanon bileşiği sentez edilmiştir. Yapısı doğrulanan bu bileşiğin hMAO enzimi ile etkileşimi, ticari tayin kiti kullanılarak fluorometrik bir yöntemle incelenmiştir. Ayrıca, söz konusu yeni bileşik ile hMAO arasındaki etkileşimler, moleküler modelleme çalışmaları ile aydınlatılmıştır. Bulgular: Sentezlenen bileşiğin yapısı, IR, Mass, 1H-NMR ve elemental analiz yöntemleri kullanılarak doğrulanmıştır. Yapısı doğrulanan bu bileşiğin etkin, seçici, tersinir, toksik olmayan bir hMAO-B inhibitörü olduğu ve inhibisyonun yarışmalı olduğu görülmüştür. Moleküler yerleştirme programı kullanılarak bileşiğin hMAO-B enziminin aktif bölgesinde hangi amino asit yan zincirleri ile ne tür girişimleri yaptığı belirlenmiştir. Sonuç: Yeni sentezlenen SH2U bileşiği, hMAO-B enzimini kuvvetle, seçici, yarışmalı ve tersinir olarak inhibe etmiştir. Sentezlediğimiz bileşik, bilinen seçici ama tersinmez MAO-B inhibitörü olan selejilin’den daha etkin ve seçici, tersinir olarak hMAO-B enzimini inhibe etmiştir ve Parkinson ile Alzheimer hastalığı tedavisinde kullanılabilecek bir ilaç etken maddesi olarak ümit vadetmektedir.Article Citation Count: 5(3+3+2) warped-like product manifolds with Spin(7) holonomy(Elsevier Science Bv, 2011) Bilge, Ayşe Hümeyra; Bilge, Ayşe HümeyraWe consider a generalization of eight-dimensional multiply warped product manifolds as a special warped product by allowing the fiber metric to be non-block diagonal. We define this special warped product as a (3 + 3 + 2) warped-like manifold of the form M = F x B. where the base B is a two-dimensional Riemannian manifold and the fibre F is of the form F = F-1 x F-2 where the F-i(i = 1 2) are Riemannian 3-manifolds. We prove that the connection on M is completely determined by the requirement that the Bonan 4-form given in the work of Yasui and Ootsuka [Y. Yasui and T. Ootsuka Spin(7) holonomy manifold and superconnection Class. Quantum Gravity 18(2001)807-816] be closed. Assuming that the F-i are complete connected and simply connected it follows that they are isometric to S-3 with constant curvature k > 0 and the Yasui-Ootsuka solution is unique in the class of (3 + 3 + 2) warped-like product metrics admitting a specific Spin(7) structure. Crown Copyright (C) 2011 Published by Elsevier B.V. All rights reserved.Article Citation Count: 18Absolute configuration and biological profile of pyrazoline enantiomers as MAO inhibitory activity(Wiley, 2019) Yelekçi, Kemal; Sarıgül, Sevgi; Bultinck, Patrick; Herrebout, Wouter; Doğan, İlknur; Yelekçi, Kemal; Uçar, Gülberk; Kelekçi, Nesrin GökhanA new racemic pyrazoline derivative was synthesized and resolved to its enantiomers using analytic and semipreparative high-pressure liquid chromatography. The absolute configuration of both fractions was established using vibrational circular dichroism. The in vitro monoamine oxidase (MAO) inhibitory profiles were evaluated for the racemate and both enantiomers separately for the two isoforms of the enzyme. The racemic compound and both enantiomers were found to inhibit hMAO-A selectively and competitively. In particular the R enantiomer was detected as an exceptionally potent and a selective MAO-A inhibitor (K-i = 0.85 x 10(-3) +/- 0.05 x 10(-3) mu M and SI: 2.35 x 10(-5)) whereas S was determined as poorer compound than R in terms of K-i and SI (0.184 +/- 0.007 and 0.001). The selectivity of the enantiomers was explained by molecular modeling docking studies based on the PDB enzymatic models of MAO isoforms.Article Citation Count: 4Accurate indoor positioning with ultra-wide band sensors(Tubitak, 2020) Arsan, TanerUltra-wide band is one of the emerging indoor positioning technologies. In the application phase, accuracy and interference are important criteria of indoor positioning systems. Not only the method used in positioning, but also the algorithms used in improving the accuracy is a key factor. In this paper, we tried to eliminate the effects of off-set and noise in the data of the ultra-wide band sensor-based indoor positioning system. For this purpose, optimization algorithms and filters have been applied to the raw data, and the accuracy has been improved. A test bed with the dimensions of 7.35 m x 5.41 m and 50 cm x 50 cm grids has been selected, and a total of 27,000 measurements have been collected from 180 test points. The average positioning error of this test bed is calculated as 16.34 cm. Then, several combinations of algorithms are applied to raw data. The combination of Big Bang-Big Crunch algorithm for optimization, and then the Kalman Filter have yielded the most accurate results. Briefly, the average positioning error has been reduced from 16.34 cm to 7.43 cm.Article Citation Count: 11Accurate Refinement Of Docked Protein Complexes Using Evolutionary Information And Deep Learning(Imperıal College Press, 2016) Akbal-Delibas, Bahar; Farhoodi, Roshanak; Pomplun, Marc; Haspel, NuritOne of the major challenges for protein docking methods is to accurately discriminate native-like structures from false positives. Docking methods are often inaccurate and the results have to be refined and re-ranked to obtain native-like complexes and remove outliers. In a previous work we introduced AccuRefiner a machine learning based tool for refining protein-protein complexes. Given a docked complex the refinement tool produces a small set of refined versions of the input complex with lower root-mean-square-deviation (RMSD) of atomic positions with respect to the native structure. The method employs a unique ranking tool that accurately predicts the RMSD of docked complexes with respect to the native structure. In this work we use a deep learning network with a similar set of features and five layers. We show that a properly trained deep learning network can accurately predict the RMSD of a docked complex with 1.40 angstrom error margin on average by approximating the complex relationship between a wide set of scoring function terms and the RMSD of a docked structure. The network was trained on 35000 unbound docking complexes generated by RosettaDock. We tested our method on 25 different putative docked complexes produced also by RosettaDock for five proteins that were not included in the training data. The results demonstrate that the high accuracy of the ranking tool enables AccuRefiner to consistently choose the refinement candidates with lower RMSD values compared to the coarsely docked input structures.Article Citation Count: 1Across dimensions: Two- and three-dimensional phase transitions from the iterative renormalization-group theory of chains(2020) Keçoğlu, İbrahim; Berker, A. NihatSharp two- and three-dimensional phase transitional magnetization curves are obtained by an iterative renormalization-group coupling of Ising chains, which are solved exactly. The chains by themselves do not have a phase transition or nonzero magnetization, but the method reflects crossover from temperaturelike to fieldlike renormalization-group flows as the mechanism for the higher-dimensional phase transitions. The magnetization of each chain acts, via the interaction constant, as a magnetic field on its neighboring chains, thus entering its renormalization-group calculation. The method is highly flexible for wide application.Article Citation Count: 4Agent-based Optimization to Estimate Nash Equilibrium in Power Markets(Taylor & Francis Inc, 2013) Yücekaya, Ahmet; Valenzuela, JorgeIn most deregulated power markets firms bid daily into a day-ahead power market. The auction mechanism supply and demand determine the equilibrium at each hour. In this environment firms aim to maximize their revenues by carefully determining their bids. This requires the development of effective computational methods that help them estimate their competitors' behaviors under incomplete information. In this article an agent-based method that uses particle swarm optimization is described to simulate the behavior of market participants. Particle swarm optimization is used in the bidding process and an agent-based model is applied to find a Nash equilibrium. Different stopping conditions are used to determine the equilibrium. Experimental results are presented for two power systems.Article Citation Count: 0An Alternative Approach To Design Lumped Element Delay Equalizers(Istanbul Univ Fac Engineering, 2015) Şengül, Metin Y.In this paper an algorithm has been proposed to design lumped element delay equalizers which is considered as a single block as opposed to the existing methods in literature. Then after obtaining the desired delay performance the designed delay equalizer is divided and realized as cascaded first-order and/or second-order all-pass circuits. An example is given to illustrate the utilization of the proposed algorithm.Article Citation Count: 0Amplitude and Frequency Modulations with Cellular Neural Networks(Springer, 2015) Tander, Baran; Özmen, AtillaAmplitude and frequency modulations are still the most popular modulation techniques in data transmission at telecommunication systems such as radio and television broadcasting gsm etc. However the architectures of these individual systems are totally different. In this paper it is shown that a cellular neural network with an opposite-sign template can behave either as an amplitude or a frequency modulator. Firstly a brief information about these networks is given and then the amplitude and frequency surfaces of the generated quasi-sine oscillations are sketched with respect to various values of their cloning templates. Secondly it is proved that any of these types of modulations can be performed by only varying the template components without ever changing their structure. Finally a circuit is designed simulations are presented and performance of the proposed system is evaluated. The main contribution of this work is to show that both amplitude and frequency modulations can be realized under the same architecture with a simple technique specifically by treating the input signals as template components.Article Citation Count: 5Analysis of Mixed-Element Structures Formed With Shunt Capacitors Separated by Transmission Lines(IEEE-Inst Electrical Electronics Engineers Inc, 2019) Şengül, Metin Y.; Çakmak, GökhanIn this brief, the analysis of mixed-element structures formed with shunt capacitors separated by commensurate transmission lines is performed first time in the literature. First, a low-pass lumped-element ladder network is considered. Then the series inductors are replaced with commensurate transmission lines. As a result, a practically important mixed-element structure is obtained. Then the description of the structure by means of two frequency variables (one for shunt capacitors and one for transmission lines) is detailed: Explicit expressions for the coefficients of the descriptive two-variable polynomials in terms of the coefficients of the single variable boundary polynomials are derived for various numbers of elements, which are obtained first time in the literature. Finally, a mixed-element broadband matching network is designed to illustrate the usage of the obtained expressions. If it is preferred not to have shunt capacitors, they can be replaced with open-ended stubs via Richard's transformation. So the resultant circuit is extremely suitable for microstrip fabrication.Article Citation Count: 5An analysis of price spikes and deviations in the deregulated Turkish power market(Elsevier, 2019) Bilge, Ayşe Hümeyra; Yücekaya, Ahmet; Bilge, Ayşe HümeyraThe successful operation of a real time market is related to the planning in the day ahead market. We analyze the day ahead and real time market data for the Turkish power market for the period 2012-2015 to classify price spikes and their causes. We also focus on the levels of deviation between the day ahead market values and the real time market values. We define price deviation and load deviation ratios to measure the level of deviation both in price and demand. The analysis for the load is based on load shedding and cycling values. We analyze the mean and standard deviation in market prices and we determine the price spike as a two sigma deviation from the mean value. It is shown that 60% of the price deviation ratios are in the range of ( +/- 20%), while 44% are in the range of ( +/- 10%) and 35% are in the range of (+/- 5%). We also show that 56.9% of the spikes are due to problems in the generation of natural gas based power plants which affect the day ahead and real time prices. A total of 29.2% of the spikes are due to power plant and system failures that affect only real time prices. The share of high temperature based spikes is 13.9% which is a result of air conditioner usage.Article Citation Count: 87An analytic network process-based approach to concept evaluation in a new product development environment(Taylor & Francis, 2007) Ayağ, Zeki; Özdemir, Rifat GürcanSelecting the best product concept is one of the most critical tasks in a new product development (NPD) environment. Making decisions at this stage becomes very difficult due to imprecise and uncertain product requirements. So the evaluation process of determining the most satisfying conceptual design has been a very vital issue for companies to survive in fast-growing markets for a long time. Therefore most companies have used various methods to successfully carry out this difficult and time-consuming process. Of these methods an analytic hierarchy process (AHP) has been widely used in multiple-criteria decision-making problems (i.e. concept selection equipment evaluation). In this study however we use an analytic network process (ANP) a more general form of AHP due to the fact that AHP cannot accommodate the variety of interactions dependencies and feedback between higher and lower level elements. Briefly in this paper an ANP-based approach is presented to evaluate a set of conceptual design alternatives in order to reach to the best concept satisfying the needs and expectations of both customers and company. In addition a numerical example is presented to illustrate the proposed approach.Article Citation Count: 0Analytic 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.Article Citation Count: 7Antifungal 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, SevimSystemic 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.Article Citation Count: 10Application of epidemic models to phase transitions(Taylor & Francis Ltd, 2012) Bilge, Ayşe Hümeyra; Pekcan, Önder; Gürol, M. V.The Susceptible-Infected-Recovered (SIR) and Susceptible-Exposed-Infected-Recovered (SEIR) models describe the spread of epidemics in a society. In the typical case, the ratio of the susceptible individuals fall from a value S-0 close to 1 to a final value S-f, while the ratio of recovered individuals rise from 0 to R-f = 1 - S-f. The sharp passage from the level zero to the level R-f allows also the modeling of phase transitions by the number of "recovered" individuals R(t) of the SIR or SEIR model. In this article, we model the sol-gel transition for polyacrylamide-sodium alginate (SA) composite with different concentrations of SA as SIR and SEIR dynamical systems by solving the corresponding differential equations numerically and we show that the phase transitions of "classical" and "percolation" types are represented, respectively, by the SEIR and SIR models.Article Citation Count: 1An approach to evaluate CAM software alternatives(TAYLOR & FRANCIS LTD, 2020) Ayağ, ZekiThe 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.Article Citation Count: 2Aryl butenoic acid derivatives as a new class of histone deacetylase inhibitors: synthesis in vitro evaluation and molecular docking studies(Scientific Technical Research Council Turkey-Tubitak, 2014) Yelekçi, Kemal; Seven, özlem; Eymur, Guluzar; Tatar, Gamze Bora; Erden, Didem Dayangaç; Yelekçi, Kemal; Yurter, Hayat; Demir, Ayhan S.New aryl butenoic acid derivatives have been synthesized by combining hydroxy- or methoxy-substituted phenyl rings as the capping group with a double bond in the short linker as well as metal binding groups enoic ester and salts bearing either methyl or morpholine. These compounds have been shown to possess promising histone deacetylase inhibition activities via in vitro fluorometric assay and molecular docking studies.Article Citation Count: 1Assessing protein-ligand binding modes with computational tools: the case of PDE4B(Springer, 2017) Çifii, Gülşah; Aviyente, Viktorya; Akten, Ebru Demet; Monard, GeraldIn 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 relationshipArticle Citation Count: 4An assessment of mining efficiency in Turkish lignite industry(Elsevier Science, 2015) Ediger, Volkan S.; Berk, Istemi; Ersoy, MucellaThis article focuses on the mining activities of Turkish Coal Enterprises (TKI) the major lignite supplier in Turkey. First we analyzed the lignite production and overburden removal activities of TKI from a historical perspective and then employed the Principle Component Analysis to build a mining efficiency index of TKI and investigated its historical development since the establishment of the company. We found that labor productivity and operational structure have been the most important factors positively affecting the index. The current article makes two important contributions: (1) by using the most comprehensive data set available on TKI for the first time and (2) by developing a Mining Efficiency Index (MEI) which can be used to analyze productivity in lignite mining activities in different countries. (C) 2015 Elsevier Ltd. All rights reserved.Article Citation Count: 5Assortment optimization with log-linear demand: Application at a Turkish grocery store(Elsevier, 2019) Hekimoğlu, Mustafa; Sevim, İsmail; Aksezer, Çağlar Sezgin; Durmuş, İpekIn retail sector product variety increases faster than shelf spaces of retail stores where goods are presented to consumers. Hence assortment planning is an important task for sustained financial success of a retailer in a competitive business environment. In this study we consider the assortment planning problem of a retailer in Turkey. Using empirical point-of-sale data a demand model is developed and utilized in the optimization model. Due to nonlinear nature of the model and integrality constraint we find that it is difficult to obtain a solution even for moderately large product sets. We propose a greedy heuristic approach that generates better results than the mixed integer nonlinear programming in a reasonably shorter period of time for medium and large problem sizes. We also proved that our method has a worst-case time complexity of O(n 2 )while other two well-known heuristics’ complexities are O(n 3 )and O(n 4 ). Also numerical experiments reveal that our method has a better performance than the worst-case as it generates better results in a much shorter run-times compared to other methods. © 2019 Elsevier Ltd