Mühendislik ve Doğa Bilimleri Fakültesi

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Citation Count: 5
Analysis of Mixed-Element Structures Formed With Shunt Capacitors Separated by Transmission Lines
(IEEE-Inst Electrical Electronics Engineers Inc, 2019) Şengül, Metin Y.; Çakmak, Gökhan
In 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.
Citation Count: 7
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 Count: 1
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 Count: 5
Assortment Optimization With Log-Linear Demand: Application at a Turkish Grocery Store
(Elsevier, 2019) Hekimoğlu, Mustafa; Sevim, İsmail; Aksezer, Çağlar Sezgin; Durmuş, İpek
In 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
Citation Count: 0
Audience Tracking and Cheering Content Control in Sports Events
(IEEE, 2020) Yeşilyurt, Gözdenur; Dursun, Sefa; Kumas, Osman; Çakir, Nagehan; Arsan, Taner
Swearing cheers encountered in sports competitions do not comply with sports ethics and morals. Even if this kind of cheering is a group, the entire tribune block is penalized in accordance with the current rules. This method is not preventive and individual punishment should be used. The aim of this study is to determine the individuals who cheer with swearing content. In this study, the person detection is made with the multi-task cascaded convolutional neural network. Moreover, facial landmarks representing the facial regions and the regions related to them are determined as a result of this process. The mouth region is also determined by means of these important points removed, and finally the mouth is determined according to the equation. The face recognition is carried out because the person would be in a state of yelling if the mouth opening ratio exceeds the threshold value by determining the rate of opening. Landmarks extracted from the facial regions for the face recognition are transformed into feature vectors by FaceNet, and the model is created by classifying these vectors with classifiers to use in recognition process. When evaluated in terms of industry, face recognition and detection systems find a wide field of study.
Citation Count: 0
A Comparative Study of Energy Models for Turkish Electricity Market Using Leap
(IEEE Computer Society, 2019) Massaga, Daniel Julius; Kirkil, Gökhan; Çelebi, Emre
Fossil fuel thermal power plants constitute a large part of the Turkish electricity generation capacity. Turkish government has been developing several energy policy documents to evaluate how various renewable energy sources of the country can be utilized optimally in the generation of electricity within the next 30 years. This study considers three scenarios in the transition to renewable energy for Turkey; the business as usual (BAU), energy conservation (EC) and renewable energy (REN) scenarios. EC scenario considers the use of energy-efficient appliances and imposing a carbon tax, whereas REN scenario considers increasing the share of the renewable energy sources as much as possible in the power generation mix. These scenarios were evaluated in terms of cost and environmental impact. The LEAP (Long-range Energy Alternatives Planning Model) was used in the research. The REN scenario has been shown to be the optimal energy policy option for Turkey in terms of cost and environmental impact.
Citation Count: 14
Crystallographic Structure Versus Homology Model: a Case Study of Molecular Dynamics Simulation of Human and Zebrafish Histone Deacetylase 10
(Taylor & Francis, 2020) Uba, Abdullahi İbrahim; Yelekçi, Kemal
Histone deacetylase (HDAC) 10 has been implicated in the pathology of various cancers and neurodegenerative disorders, making the discovery of novel inhibitors of the isoform an important endeavor. However, the unavailability of crystallographic structure of human HDAC10 (hHDAC10) hinders structure-based drug design effort. Previously, we reported the homology modeled structure of human HDAC10 built using the crystallographic structure of Danio rerio (zebrafish) HDAC10 (zHDAC10) (Protein Data Bank (PDB) ID; 5TD7, released on 24 May 2017) as a template. Here, in continuation with our study, both hHDAC10 and zHDAC10, and their respective complexes with trichostatin A (TSA), quisinostat, and the native ligand (in 5TD7), 7-[(3-aminopropyl)amino]-1,1,1-trifluoroheptane-2,2-diol (PDB ID; FKS) were submitted to 100 ns-long unrestrained molecular dynamics (MD) simulations. Comparative analyses of the MD trajectories revealed that zHDAC10 and its complexes displayed higher stability than hHDAC10 and its corresponding complexes over time. Nonetheless, docking of active and inactive set molecules revealed that more reliable conformations of hHDAC10 could be obtained at an extended time period. This study may shed more light on the reliability of hHDAC10 modeled structure for use in selective inhibitor design.Communicated by Ramaswamy H. Sarma.
Citation Count: 0
Design of Phase Shifters With Ladder Stubs Via Real Frequency Technique
(World Scientific, 2020) Şengül, Metin Y.
Generally at high frequencies, lumped-elements are not preferred because of their limited range of values. Therefore, in this work, a kind of phase shifter formed with ladder stubs is studied and a new approach to design phase shifter's low pass and high pass sections which are composed of series or shunt connected open-ended or short-ended stubs is proposed. In the approach, since the main focus is to form low pass and high pass two-port sections, switching process is not considered. First, the designer selects the section type and the total number of stubs in the sections; it is not necessary to fix the two-port section topologies and not necessary to derive the characteristic impedance and delay expressions for the stubs. In the example, 5-stub two-port sections of a 180∘ phase shifter are designed by means of the proposed approach.
Citation Count: 8
Determining Matchdays in Sports League Schedules To Minimize Rest Differences
(ELSEVIER, 2020) Çavdaroğlu, Burak; Atan, Tankut
Many sports leagues first announce the games to be played in each round and then determine their matchdays as the season progresses. This study focuses on the fairness criterion of minimizing the total rest difference among opposing teams to find the matchdays for an announced schedule. We show that the problem is decomposable into optimizing the rounds separately. We also provide a polynomial-time exact algorithm for canonical schedules.
Citation Count: 5
Distinctive Communication Networks in Inactive States of Beta(2)-Adrenergic Receptor: Mutual Information and Entropy Transfer Analysis
(Wiley, 2020) Soğünmez, Nuray; Akten, Ebru Demet
Mutual information and entropy transfer analysis employed on two inactive states of human beta-2 adrenergic receptor (beta(2)-AR) unraveled distinct communication pathways. Previously, a so-called "highly" inactive state of the receptor was observed during 1.5 microsecond long molecular dynamics simulation where the largest intracellular loop (ICL3) was swiftly packed onto the G-protein binding cavity, becoming entirely inaccessible. Mutual information quantifying the degree of correspondence between backbone-C(alpha)fluctuations was mostly shared between intra- and extra-cellular loop regions in the original inactive state, but shifted to entirely different regions in this latest inactive state. Interestingly, the largest amount of mutual information was always shared among the mobile regions. Irrespective of the conformational state, polar residues always contributed more to mutual information than hydrophobic residues, and also the number of polar-polar residue pairs shared the highest degree of mutual information compared to those incorporating hydrophobic residues. Entropy transfer, quantifying the correspondence between backbone-C(alpha)fluctuations at different timesteps, revealed a distinctive pathway directed from the extracellular site toward intracellular portions in this recently exposed inactive state for which the direction of information flow was the reverse of that observed in the original inactive state where the mobile ICL3 and its intracellular surroundings drove the future fluctuations of extracellular regions.
Citation Count: 0
The Effect of Data Augmentation on Adhd Diagnostic Model Using Deep Learning
(IEEE, 2019) Çiçek, Gülay; Özmen, Atilla; Akan, Aydin
Attention Deficit Hyperactivity Disorder (ADHD) is a neuro-behavioral hyperactivity disorder. It is frequently seen in childhood and youth, and lasts a lifetime unless treated.The ADHD classification model should be objective and robust. Correct diagnosis usually depends on the knowledge and experience of health professionals. In this respect, an automated method to be developed for the ADHD classification model is of great importance for clinicians. In this study, the effect of data augmentation on ADHD classification model with deep learning was investigated. For this purpose, magnetic resonance images were taken from NPIstanbul NeuroPsychiatry Hospital and ADHD-200 database. Since the images were not sufficient in terms of training, data augmentation methods were applied and by convolutional neural network (CNN) architecture, these data were classified and tried to reveal the diagnosis of the disease independently from the non-objective experiences of the health professionals.
Citation Count: 1
Effect of Temperature and Graphene Oxide on the Swelling of Paam-Go Composite Gels
(Avestia Publishing, 2019) Osma, Büşra; Akın Evingür, Gülşen; Pekcan, Önder
Graphene oxide (GO) is a two dimensional carbon material with similar one-atom thickness, and is a light material having extremely high strength and thermal stability [1]. Thus, GO is an efficient filler for the enhancement of the electrical, mechanical and thermal properties of composite materials [2]. We focused on GO as a nanofiller in polyacrylamide hydrogels and PAAm-GO composites to investigate the effect of temperature and graphene oxide on the swelling. Polyacrylamide (PAAm) hydrogels have been proposed for use as promising biomaterials in biomedical and tissue engineering. The composite gels were prepared by free radical crosslinking copolymerization with GO content varying in the range between 8 and 50 μl of GO. The effects of temperature and graphene oxide on the swelling of the composites were studied. The swelling experiment was performed in the distilled water. Decreasing in pyranine (Py) as a fluorescence probe and emission light intensity (Iem) were monitored by steady state fluorescence spectroscopy. Since the increase in Isc corresponds to the increase in turbidity of the swelling composite gel, the corrected fluorescence intensity, I was introduced to analyze the swelling processes. The Stern-Volmer equation combined with Li-Tanaka models was used to explain the behaviour of I during swelling processes. The cooperative diffusion coefficients and time constants were calculated as a function of temperature and GO, respectively.
Citation Count: 32
Effects of Gnp Addition on Optical Properties and Band Gap Energies of Pmma Films
(Wiley, 2019) Mergen, Ömer Bahadır; Arda, Ertan; Kara, Selim; Pekcan, Önder
In this study the effects of graphene nanoplatelet (GNP) doping on the optical parameters (absorption coefficient alpha and extinction coefficient k) and the optical transition energies (optical band gap and Urbach energies) of poly(methyl methacrylate)/graphene nanoplatelet (PMMA/GNP) composite films were studied. PMMA/GNP composite films with various GNP mass fractions were prepared by spin coating technique. The absorbance (A) changes of the prepared composites were measured by using UV-Vis technique. The alpha and k values of the composites were obtained from UV-Vis data. The observed rapid increase in A values in UV-region were associated with the optical transitions of GNP electrons from valence to conduction band. The direct (E-d) and indirect (E-i) optical band gap energies of the composites were determined by using Tauc method. Both of the band gap energies were decreased when the GNP content in the PMMA matrix is increased. The decrease in the band gap energies was interpreted as evidence of increased conductivity of the composites. Additionally energies of the band tails (Urbach energy) were calculated. It was seen that the Urbach energy levels were increased with GNP content. POLYM. COMPOS. 40:1862-1869 2019. (c) 2018 Society of Plastics Engineers
Citation Count: 1
Evaluation of the Fractal Dimension of Polyacrylamide During Gelation and Swelling
(Elsevier, 2021) Arda, Ertan; Kara, Selim; Pekcan, Önder; Gülşen, Akın-Evingür
[Abstract Not Available]
Citation Count: 14
A Farewell To King Coal: Geopolitics, Energy Security, and the Transition To Oil, 1898–1917
(Cambridge Univ Press, 2019) Ediger, Volkan S.; Bowlus, John V.
Interest in energy transitions has accelerated in recent years due to rising concerns about global warming and resource scarcity but the drivers of these phenomena are not well understood. To date scholars have primarily focused on commercial and technological factors highlighting that oil was 'better' than coal - more powerful cheaper cleaner and more practical to use - and that the internal combustion engine made it more advantageous to use in transportation. Yet oil was also a strategic commodity that powerful states sought to acquire for military reasons. This article contends that geopolitics military decision-making and energy security hastened the transition from oil to coal prior to the First World War. It argues that Britain Germany and the United States sought to transition their naval fleets from coal to oil to gain a military advantage at sea which created for the first time the problem of oil-supply security. Through government-led initiatives to address oil-supply security vast new supplies of oil came online and prices fell the ideal environment for oil to eclipse coal as the dominant source in the global energy system.
Citation Count: 2
Fluorescence and Photon Transmission Techniques for Studying Film Formation From Ps/Go Nanocomposites
(SPRINGER, 2020) M. Selin, Sunay; Şaziye, Uğur; Pekcan, Önder
Steady-state fluorescence and UV-Vis techniques were used to study the film formation behavior of composites consisting of pyrene (P)-labeled polystyrene (PS) latex and graphene oxide (GO) in terms of PS latex/GO volume fraction. PS/GO composite films were prepared on glass substrates with different volume fractions of PS and GO using the drop casting method at room temperature. The film formation behavior of these composites was studied by annealing them at a temperature range of 100-300 degrees C and monitoring the scattered light intensity (I-sc), fluorescence intensity (I-P) from P and transmitted light intensity (I-tr) through the films after each annealing step. The optical results indicate that PS/GO composites showed complete film formation independent of GO volume fraction. The morphological changes in the films were also found to be in consistent with these results.
Citation Count: 3
Fractal Dimension and Phase Transition of Graphene Oxide (go) Doped Polyacrylamide
(ELSEVIER SCI LTD, 2020) Evingür, Gülşen Akın; Pekcan, Önder
Graphene Oxide (GO)- Polyacrylamide composites prepared between 5 and 50 mu l GO were performed by Fluorescence Spectroscopy. The phase transition performed on the composites was measured by calculating the critical exponents, beta and gamma, respectively. In addition, fractal analysis of the composites was calculated by a fluorescence intensity of 427 nm. The geometrical distribution of GO in the composites was calculated based on the power law exponent values using scaling models. While the gelation proceeded GO plates first organized themselves into a 3D percolation cluster with the fractal dimension (D-f) of the composite, D-f = 2.63, then After it goes to diffusion limited clusters with D-f = 1.4, its dimension lines up to a Von Koch curve with a random interval of D-f = 1.14.
Citation Count: 9
Homology Modeling Andin Silicodesign of Novel and Potential Dual-Acting Inhibitors of Human Histone Deacetylases Hdac5 and Hdac9 Isozymes
(2020) Elmezayen, Ammar D.; Yelekçi, Kemal
Histone deacetylases (HDACs) are a group of enzymes that have prominent and crucial effect on various biological systems, mainly by their suppressive effect on transcription. Searching for inhibitors targeting their respective isoforms without affecting other targets is greatly needed. Some histone deacetylases have no crystal structures, such as HDAC5 and HDAC9. Lacking proper and suitable crystal structure is obstructing the designing of appropriate isoform selective inhibitors. Here in this study, we constructed human HDAC5 and HDAC9 protein models using human HDAC4 (PDB:2VQM_A) as a template by the means of homology modeling approach. Based on the Z-score of the built models, model M0014 of HDAC5 and model M0020 of HDAC9 were selected. The models were verified by MODELLER and validated using the Web-based PROCHECK server. All selected known inhibitors displayed reasonable binding modes and equivalent predicted Ki values in comparison to the experimental binding affinities (Ki/IC50). The known inhibitor Rac26 showed the best binding affinity for HDAC5, while TMP269 showed the best binding affinity for HDAC9. The best two compounds, CHEMBL2114980 and CHEMBL217223, had relatively similar inhibition constants against HDAC5 and HDAC9. The built models and their complexes were subjected to molecular dynamic simulations (MD) for 100 ns. Examining the MD simulation results of all studied structures, including the RMSD, RMSF, radius of gyration and potential energy suggested the stability and reliability of the built models. Accordingly, the results obtained in this study could be used for designing de novo inhibitors against HDAC5 and HDAC9. Communicated by Ramaswamy H. Sarma
Citation Count: 25
Homology Modeling of Human Histone Deacetylase 10 and Design of Potential Selective Inhibitors
(Taylor & Francis Inc, 2019) Uba, Abdullahi Ibrahim; Yelekçi, Kemal
Histone deacetylases (HDACs) are implicated in the pathology of various cancers, and their pharmacological blockade has proven to be promising in reversing the malignant phenotypes. However, lack of crystal structures of some of the human HDAC isoforms (e.g., HDAC10) hinders the design of the isoform-selective inhibitor. Here, the recently solved X-ray crystal structure of Danio rerio (zebrafish) HDAC10 (Protein Data Bank (PDB) ID; 5TD7, released on 24 May 2017) was retrieved from the PDB and used as a template structure to model the three-dimensional structure of human HDAC10. The overall quality of the best model (M0017) was assessed by computing its z-score-a measure of the deviation of the total energy of the structure with respect to an energy distribution derived from random conformations and by docking of known HDAC10 inhibitors to its catalytic cavity. Furthermore, to identify potential HDAC10-selective inhibitor ligand-based virtual screening was carried out against the ZINC database. The free modeled structure of HDAC10 and its complexes with quisinostat and the highest-ranked compound ZINC19749069 were submitted to molecular dynamics simulation. The comparative analysis of root-mean-squared deviation, root-mean-squared fluctuation, radius of gyration (Rg), and potential energy of these systems showed that HDAC10-ZINC19749069 complex remained the most stable over time. Thus, M0017 could be potentially used for structure-based inhibitor against HDAC10, and ZINC19749069 may provide a scaffold for further optimization. Communicated by Ramaswamy H. Sarma
Citation Count: 0
Hybrid Mems-Based Molecular Communication System
(Institute of Electrical and Electronics Engineers Inc., 2019) Erküçük, Serhat; Baykaş, Tunçer; Zeshan, Arooba; Pusane, Ali Emre
In this paper, we consider a molecular communication link integrated in a micro-electro mechanical system (MEMS) based environment. We apply acoustic tweezing techniques to the molecular communication system to increase communication reliability. We use finite element methods to simulate this hybrid system. By deriving the symbol error rate as the performance metric, we show that the proposed system facilitates reliable communication in the presence of fluid flow and its performance is robust against external factors, such as temperature.

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