Mühendislik ve Doğa Bilimleri Fakültesi

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Citation - WoS: 5
Citation - Scopus: 6
(3+3+2) Warped-Like Product Manifolds With Spin(7) Holonomy
(Elsevier Science Bv, 2011) Uğuz, Selman; Bilge, Ayşe Hümeyra
We 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.
Citation - WoS: 22
Citation - Scopus: 25
Absolute Configuration and Biological Profile of Pyrazoline Enantiomers as Mao Inhibitory Activity
(Wiley, 2019) Goksen, Umut Salgin; Sarıgül, Sevgi; Bultinck, Patrick; Herrebout, Wouter; Doğan, İlknur; Yelekçi, Kemal; Uçar, Gülberk; Kelekçi, Nesrin Gökhan
A 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.
Citation - WoS: 1
Citation - Scopus: 1
Across Dimensions: Two- and Three-Dimensional Phase Transitions From the Iterative Renormalization-Group Theory of Chains
(2020) Keçoğlu, İbrahim; Berker, A. Nihat
Sharp 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.
Citation - WoS: 5
Citation - Scopus: 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 - WoS: 7
Citation - Scopus: 12
An Analysis of Price Spikes and Deviations in the Deregulated Turkish Power Market
(Elsevier, 2019) Gayretli, Gizem; Yücekaya, Ahmet; Bilge, Ayşe Hümeyra
The 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.
Citation - Scopus: 88
An Analytic Network Process-Based Approach To Concept Evaluation in a New Product Development Environment
(Taylor & Francis, 2007) Ayağ, Zeki; Özdemir, Rifat Gürcan
Selecting 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.
Citation - WoS: 4
Citation - Scopus: 4
An Assessment of Mining Efficiency in Turkish Lignite Industry
(Elsevier Science, 2015) Ediger, Volkan S.; Berk, Istemi; Ersoy, Mucella
This 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.
The Association of Gvhd With Hla Dr Alleles, Ifn-Gamma, Tgf-Beta, and Mbl2 Gene Polymorphism
(Wiley, 2019) Oğuz, Rusdu; Çiftçi, Hayriye Şentürk; Gökçe, Muge; Öğret, Yeliz; Karadeniz, Sedat Tanju; Pehlivan, Sacide; Aydın, Filiz
[Abstract Not Available]
Citation - WoS: 6
Citation - Scopus: 7
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 - 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: 57
Citation - Scopus: 65
Beams: Backbone Extraction and Merge Strategy for the Global Many-To Alignment of Multiple Ppi Networks
(Oxford University Press, 2014) Alkan, Ferhat; Erten, Cesim
Motivation: Global many-to-many alignment of biological networks has been a central problem in comparative biological network studies. Given a set of biological interaction networks the informal goal is to group together related nodes. For the case of protein-protein interaction networks such groups are expected to form clusters of functionally orthologous proteins. Construction of such clusters for networks from different species may prove useful in determining evolutionary relationships in predicting the functions of proteins with unknown functions and in verifying those with estimated functions. Results: A central informal objective in constructing clusters of orthologous proteins is to guarantee that each cluster is composed of members with high homological similarity usually determined via sequence similarities and that the interactions of the proteins involved in the same cluster are conserved across the input networks. We provide a formal definition of the global many-to-many alignment of multiple protein-protein interaction networks that captures this informal objective. We show the computational intractability of the suggested definition. We provide a heuristic method based on backbone extraction and merge strategy (BEAMS) for the problem. We finally show through experiments based on biological significance tests that the proposed BEAMS algorithm performs better than the state-of-the-art approaches. Furthermore the computational burden of the BEAMS algorithm in terms of execution speed and memory requirements is more reasonable than the competing algorithms.
Citation - WoS: 12
Citation - Scopus: 17
Bidding of Price Taker Power Generators in the Deregulated Turkish Power Market
(Pergamon-Elsevier Science Ltd, 2013) Yücekaya, Ahmet; Yücekaya, Ahmet
In deregulated power markets power firms bid into the day-ahead power market either with buy offers or sell offers. The auction mechanism and competition determine the equilibrium price and quantity for each hour. If the bid price of a company is below the market clearing price then the offer of the company is accepted and rewarded with the market price. A company can be a price maker or price taker depending on the capacity it offers to the market. A price-taker unit must determine the right offer that will maximize their profit given price uncertainty and blind auction rules. This paper first examines power supply in the Turkish electricity market and bidding process. Then a marginal cost-based Monte Carlo method is developed to determine hourly and block bidding strategies of price taker units. Historical market prices are then implemented in a normal distribution to generate hourly price scenarios. A solution methodology is developed that maximizes the expected profit of each hourly and block bidding strategy over price scenarios. The generator is able to both evaluate the hourly bidding and block bidding strategies and find the best bidding strategy that will be submitted to the market using the proposed methodology. The model is illustrated for two coal units in Turkish power market and the results are presented. (C) 2013 Elsevier Ltd. All rights reserved.
Citation - WoS: 12
Citation - Scopus: 12
Blind Dockings of Benzothiazoles To Multiple Receptor Conformations of Triosephosphate Isomerase From Trypanosoma Cruzi and Human
(Wiley-VCH Verlag GmbH, 2011) Kurkcuoglu, Zeynep; Ural, Gulgun; Akten, Ebru Demet; Doruker, Pemra
We aim to uncover the binding modes of benzothiazoles which have been reported as specific inhibitors of triosephosphate isomerase from the parasite Trypanosoma cruzi (TcTIM) by performing blind dockings on both TcTIM and human TIM (hTIM). Detailed analysis of binding sites and specific interactions are carried out based on ensemble dockings to multiple receptor conformers obtained from molecular dynamics simulations. In TcTIM dimer dockings the inhibitors preferentially bind to the tunnel-shaped cavity formed at the interface of the subunits whereas non-inhibitors mostly choose other sites. In contrast TcTIM monomer binding interface and hTIM dimer interface do not present a specific binding site for the inhibitors. These findings point to the importance of the tunnel and of the dimeric form for inhibition of TcTIM. Specific interactions of the inhibitors and their sulfonate-free derivatives with the receptor residues indicate the significance of sulfonate group for binding affinity and positioning on the TcTIM dimer interface. One of the inhibitors also binds to the active site which may explain its relatively higher inhibition effect on hTIM.
Citation - WoS: 26
Citation - Scopus: 34
Broadband Decoupling and Matching of a Superdirective Two-Port Antenna Array
(IEEE-INST Electrical Electronics Engineers Inc, 2008) Volmer, Christian; Şengül, Metin Y.; Weber, Joern; Stephan, Ralf; Hein, Matthias A.
Decoupling and matching networks may be used to improve the performance of compact antenna arrays where mutual radiator coupling has caused a degradation of the diversity capabilities. A popular network consists of a 180 degrees rat-race directional coupler which decouples the antenna ports followed by impedance matching networks at each port. Researchers however usually neglect the presence of losses both within the antenna array and the decoupling and matching network. For this reason we have built various narrowband and broadband matching networks and compare their performances with the help of calibrated far-field measurement data.
Citation - WoS: 15
Citation - Scopus: 19
Campways: Constrained Alignment Framework for the Comparative Analysis of a Pair of Metabolic Pathways
(Oxford University Press, 2013) Abaka, Gamze; Biyikoglu, Turker; Erten, Cesim
Motivation: Given a pair of metabolic pathways an alignment of the pathways corresponds to a mapping between similar substructures of the pair. Successful alignments may provide useful applications in phylogenetic tree reconstruction drug design and overall may enhance our understanding of cellular metabolism. Results: We consider the problem of providing one-to-many alignments of reactions in a pair of metabolic pathways. We first provide a constrained alignment framework applicable to the problem. We show that the constrained alignment problem even in a primitive setting is computationally intractable which justifies efforts for designing efficient heuristics. We present our Constrained Alignment of Metabolic Pathways (CAMPways) algorithm designed for this purpose. Through extensive experiments involving a large pathway database we demonstrate that when compared with a state-of-the-art alternative the CAMPways algorithm provides better alignment results on metabolic networks as far as measures based on same-pathway inclusion and biochemical significance are concerned. The execution speed of our algorithm constitutes yet another important improvement over alternative algorithms.
Canonical Forms for Families of Anti-Commuting Diagonalizable Linear Operators
(Elsevier Science Inc, 2012) Kumbasar, Yalcin; Bilge, Ayşe Hümeyra
It is well known that a commuting family of diagonalizable linear operators on a finite dimensional vector space is simultaneously diagonalizable. In this paper we consider a family A = {A(a)} A(a) : V -> V a = 1... N of anti-commuting (complex) linear operators on a finite dimensional vector space. We prove that if the family is diagonalizable over the complex numbers then V has an A-invariant direct sum decomposition into subspaces V(alpha) such that the restriction of the family A to V(alpha) is a representation of a Clifford algebra. Thus unlike the families of commuting diagonalizable operators diagonalizable anti-commuting families cannot be simultaneously digonalized but on each subspace they can be put simultaneously to (non-unique) canonical forms. The construction of canonical forms for complex representations is straightforward while for the real representations it follows from the results of [A.H. Bilge S. Kocak S. Uguz Canonical bases for real representations of Clifford algebras Linear Algebra Appl. 419 (2006) 417-439]. (C) 2011 Elsevier Inc. All rights reserved.
Citation - WoS: 18
Citation - Scopus: 19
Carboxylic Acid Derivatives Display Potential Selectivity for Human Histone Deacetylase 6: Structure-Based Virtual Screening Molecular Docking and Dynamics Simulation Studies
(Elsevier Science, 2018) Uba, Abdullahi Ibrahim; Yelekçi, Kemal
Human histone deacetylase 6 (HDAC6) has been shown to play a major role in oncogenic cell transformation via deacetylation of alpha-tubulin making it a viable target of anticancer drug design and development. The crystal structure of HDAC6 catalytic domain 2 has been recently made available providing avenues for structure-based drug design campaign. Here in our continuous effort to identify potentially selective HDAC6 inhibitors structure-based virtual screening of similar to 72 461 compounds was carried out using Autodock Vina. The top 100 compounds with calculated Delta G < -10 kcal/mol were manually inspected for binding mode orientation. Furthermore the top 20 compounds with reasonable binding modes were evaluated for selectivity by further docking against HDAC6 and HDAC7 using Autodock4. Four compounds with a carboxylic fragment displayed potential selectivity for HDAC6 over HDAC7 and were found to have good druglike and ADMET properties. Their docking complexes were then submitted to 10 ns-molecular dynamics (MD) simulation using nanoscale MD (NAMD) software to examine the stability of ligand binding modes. These predicted inhibitors remained bound to HDAC6 in the presence of water and ions and the root-mean-square deviation (RMSD) radius of gyration (Rg) and nonbond distance (protein-ligand) profiles suggested that they might be stable over time of the simulation. This study may provide scaffolds for further lead optimization towards the design of HDAC6 inhibitors with improved selectivity. (C) 2018 Elsevier Ltd. All rights reserved.
Citation - WoS: 35
Citation - Scopus: 41
Channel Estimation for Residual Self-Interference in Full-Duplex Amplify-And Two-Way Relays
(IEEE-INST Electrical Electronics Engineers Inc, 2017) Li, Xiaofeng; Tepedelenlioglu, Cihan; Şenol, Habib
Training schemes for full duplex two-way relays are investigated. We propose a novel one-block training scheme with a maximum likelihood estimator to estimate the channels between the nodes as well as the residual self-interference (RSI) channel simultaneously. A quasi-Newton algorithm is used to solve the estimator. As a baseline a multi-block training scheme is also considered. The Cramer-Rao bounds of the one-block and multi-block training schemes are derived. By using the Szego's theorem about Toeplitz matrices we analyze how the channel parameters and transmit powers affect the Fisher information. We show analytically that exploiting the structure arising from the RSI channel increases its Fisher information. Numerical results show the benefits of estimating the RSI channel.
Citation - WoS: 13
Citation - Scopus: 19
Channel Estimation for Tds-Ofdm Systems in Rapidly Time-Varying Mobile Channels
(IEEE-Inst Electrical Electronics Engineers Inc, 2018) Başaran, Mehmet; Şenol, Habib; Erküçük, Serhat; Çırpan, Hakan Ali
This paper explores the performance of time-domain synchronous orthogonal frequency-division multiplexing (TDS-OFDM) systems operated under rapidly time-varying mobile channels. Since a rapidly time-varying channel contains more unknown channel coefficients than the number of observations, the mobile channel can conveniently be modeled with the discrete Legendre polynomial basis expansion model to reduce the number of unknowns. The linear minimum mean square error (LMMSE) estimate can be exploited for channel estimation on inter-block-interference-free received signal samples owing to transmitting pseudo-noise (PN) sequences. In conventional TDS-OFDM systems, the channel estimation performance is limited due to estimating channel responses only from the beginning part of the channel. Therefore, a new system model named "partitioned TDS-OFDM system" is proposed to improve the system performance by inserting multiple PN sequences to the middle and end parts of the channel as well. In addition to providing the reconstruction error performance, Bayesian Cramer-Rao lower hound is derived analytically. Also, the LMMSE-based symbol detection is employed. To alleviate the negative effects of inter-carrier-interference (ICI) occuring in mobile channels, ICI cancellation is applied to enhance the detection performance. The simulation results demonstrate that the proposed TDS-OFDM system is superior to the conventional system and its corresponding performance is able to approach the achievable lower performance bound.
Citation - WoS: 5
Citation - Scopus: 6
Code Shift Keying Impulse Modulation for Uwb Communications
(IEEE-INST Electrical Electronics Engineers Inc, 2008) Erküçük, Serhat; Kim, Dong In; Kwak, Kyung Sup
In this paper the system performance of M-ary code shift keying (MCSK) impulse modulation is studied in detail and compared to M-ary pulse position modulation (MPPM) under single- and multi-user scenarios. For that bounds on the semi-analytic symbol-error rate (SER) expressions are derived and simulation studies are conducted. When practical implementations of MCSK and MPPM are considered it is shown that MCSK can provide about 2 dB performance gain over MPPM as it reduces the effects of multipath delays on the decision variables by randomizing locations of the transmit pulse.

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