Mühendislik ve Doğa Bilimleri Fakültesi

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Citation - WoS: 4
Citation - Scopus: 8
Accurate Indoor Positioning With Ultra-Wide Band Sensors
(Tubitak, 2020) Arsan, Taner
Ultra-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.
Amplitude and Frequency Modulations With Cellular Neural Networks
(Springer, 2015) Tander, Baran; Özmen, Atilla
Amplitude 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.
Citation - WoS: 11
Citation - Scopus: 11
Application 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.
Citation - WoS: 2
Citation - Scopus: 3
Aryl 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) Esiyok, Peruze Ayhan; 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.
Citation - WoS: 3
Citation - Scopus: 3
Bayesian Compressive Sensing for Ultra-Wideband Channel Estimation: Algorithm and Performance Analysis
(Springer, 2015) Özgör, Mehmet; Erküçük, Serhat; Çırpan, Hakan Ali
Due to the sparse structure of ultra-wideband (UWB) channels compressive sensing (CS) is suitable for UWB channel estimation. Among various implementations of CS the inclusion of Bayesian framework has shown potential to improve signal recovery as statistical information related to signal parameters is considered. In this paper we study the channel estimation performance of Bayesian CS (BCS) for various UWB channel models and noise conditions. Specifically we investigate the effects of (i) sparse structure of standardized IEEE 802.15.4a channel models (ii) signal-to-noise ratio (SNR) regions and (iii) number of measurements on the BCS channel estimation performance and compare them to the results of -norm minimization based estimation which is widely used for sparse channel estimation. We also provide a lower bound on mean-square error (MSE) for the biased BCS estimator and compare it with the MSE performance of implemented BCS estimator. Moreover we study the computation efficiencies of BCS and -norm minimization in terms of computation time by making use of the big- notation. The study shows that BCS exhibits superior performance at higher SNR regions for adequate number of measurements and sparser channel models (e.g. CM-1 and CM-2). Based on the results of this study the BCS method or the -norm minimization method can be preferred over the other one for different system implementation conditions.
Citation - WoS: 1
Citation - Scopus: 1
Bayesian Estimation of Discrete-Time Cellular Neural Network Coefficients
(TUBITAK Scientific & Technical Research Council Turkey, 2017) Özer, Hakan Metin; Özmen, Atilla; Şenol, Habib
A new method for finding the network coefficients of a discrete-time cellular neural network (DTCNN) is proposed. This new method uses a probabilistic approach that itself uses Bayesian learning to estimate the network coefficients. A posterior probability density function (PDF) is composed using the likelihood and prior PDFs derived from the system model and prior information respectively. This posterior PDF is used to draw samples with the help of the Metropolis algorithm a special case of the Metropolis--Hastings algorithm where the proposal distribution function is symmetric and resulting samples are then averaged to find the minimum mean square error (MMSE) estimate of the network coefficients. A couple of image processing applications are performed using these estimated parameters and the results are compared with those of some well-known methods.
Citation - WoS: 2
Citation - Scopus: 2
Broadband Matching Via Reflection Function Optimization
(Wiley, 2017) Şengül, Metin Y.
In this paper a practical approach is presented for designing broadband matching networks via reflection function optimization. In the proposed algorithm the input or output reflection function of the matching network is expressed in terms of three real polynomials describing the matching network load and generator reflection coefficients. Next one of the polynomials is optimized to get minimum reflection function values in the passband. Then matching network topology and element values are obtained via the formed input reflection coefficient expression. Two examples are presented to explain the usage of the new approach. Copyright (c) 2016 John Wiley & Sons Ltd.
Citation - WoS: 3
Citation - Scopus: 4
Busy Tone Based Coexistence Algorithm for Wran and Wlan Systems in Tv White Space
(Inst Engineering Technology-IET, 2018) Karatalay, Onur; Erküçük, Serhat; Baykaş, Tunçer
TV White Space (TVWS) refers to frequency band reserved only for licensed terrestrial TV broadcasting and is opened to unlicensed use under regulatory conditions. While regulations protect licensed systems from interference interference among unlicensed systems is left mainly to manufacturers. Consequently there is a need to develop new coexistence approaches between TVWS networks. Busy tone broadcasting is a coexistence method which can be used by TVWS networks to announce the selected frequency band is occupied. In this paper a busy tone based coexistence algorithm is proposed for IEEE 802.11af and IEEE 802.22 networks and analyzed by considering different client distributions experiencing log-normal shadowing where the exact interfering packet rate and successful packet transmission rate expressions are obtained and validated by simulations for different scenarios. The results show that with the proposed coexistence approach a WLAN can reliably detect the busy tone signal to change its frequency band and can reduce interference to WRAN. Even if there is no available frequency band for the WLAN the WRAN still maintains its enhanced successful packet transmission performance. The deployment of the proposed algorithm is important for successful coexistence between cognitive wireless networks where interference is not regulated such as in TVWS bands.
Büyük Patlama Büyük Çöküş Optimizasyon Yöntemi ile Ultra Geniş Band Sensörlerinin İç Mekân Konum Belirleme Doğruluklarının İyileştirilmesi
(Pamukkale Üniversitesi, 2018) Arsan, Taner
Ultra geniş band teknolojisi, birçok iç mekân konum belirleme sisteminde başarılı çözümler sunan, diğer yöntemlere kıyasla daha iyi performans gösteren, gelişmekte olan bir teknolojidir. Bu çalışmada, ultra geniş band (Ultra Wide Band-UWB) sensörler kullanılarak bir iç mekân konum belirleme sistemi geliştirilmiş ve kullanılan ek algoritmalarla, standart donanımların sağladığı doğruluk düzeyi arttırılırken aynı zamanda ortalama hatayı azaltmak hedeflenmiştir. Bu amaçla Büyük Patlama - Büyük Çöküş (Big Bang-Big Crunch veya BB-BC) optimizasyon yöntemi deneysel iç mekân konumlandırma sistemine uygulanmış ve ölçüm doğruluğu üzerindeki olumlu etkisi yapılan testlerle kanıtlanmıştır. Test alanı olarak 7.35 m × 5.41 m boyutlarında 39.76 m2 'lik bir alan seçilmiş ve özel olarak tasarlanmış bir tavan sistemine yerden 2.85 m yüksekliğe üç farklı UWB alıcı yerleştirilmiş ve 182 adet test noktasından 60 sn.süreyle toplam 10.920 ölçüm alınmıştır. Ölçüm sonuçları Büyük Patlama - Büyük Çöküş optimizasyon algoritması ile düzeltilerek, ortalama hatası önceki 20.72 cm değerinden 15.02 cm’ye düşürülmüş, böylelikle ölçüm sonuçlarının doğruluğu arttırılmıştır.
Citation - WoS: 4
Citation - Scopus: 6
Channel Estimation for Realistic Indoor Optical Wireless Communication in Aco-Ofdm Systems
(Springer, 2018) Özmen, Atilla; Şenol, Habib
In this paper channel estimation problem in a visible light communication system is considered. The information data is transmitted using asymmetrical clipped optical orthogonal frequency division multiplexing. Channel estimation and symbol detection are performed by the Maximum Likelihood and the Linear Minimum Mean Square Error detection techniques respectively. The system performance is investigated in realistic environment that is simulated using an indoor channel model. Two different channels are produced using the indoor channel model. Symbol error rate (SER) performance of the system with estimated channels is presented for QPSK and 16-QAM digital modulation types and compared with the perfect channel state information. As a mean square error (MSE) performance benchmark for the channel estimator Cramer-Rao lower bound is also derived. MSE and SER performances of the simulation results are presented.
Chebyshev Nets Formed by Ricci Curves in a 3-Dimensional Weyl Space
(Elsevier Science Bv, 2005) Yıldırım, Gülçin Çivi; Özdeğer, Abdülkadir
In this paper Ricci curves in a 3-dimensional Weyl space W-3(g T) are defined and it is shown that any 3-dimensional Chebyshev net formed by the three families of Ricci curves in a W-3(g T) having a definite metric and Ricci tensors is either a geodesic net or it consists of a geodesic subnet the members of which have vanishing second curvatures. In the case of in indefinite Ricci tensor only one of the members of the geodesic subnet under consideration has a vanishing second curvature. (c) 2004 Elsevier B.V. All rights reserved.
Chelate Extraction of Transition Metal Ions by Ethylene Diamine Diacetic Acid With N-Substituted Octadecyl Groups
(Taylor & Francis Inc, 2002) Bıçak, Niyazi; Şungur, Şana Kutun; Tan, Nükhet; Gazi, Mustafa
An organic-soluble chelating agent NN'-di-n-octadecyl ethylenediamine-NN'-diacetic acid (DOED) has been synthesized in two steps by (i) condensation of dibromoethane with 1-amino octadecane (octadecylamine) and (ii) subsequent reaction with sodium chloro acetate in alcohol-water mixture. The chelating agent in 2-ethylhexanol-cyclohexanol (1:1) solutions shows extremely high chelating ability for Ni(II) Co(II) Cu(II) Fe(111) Cr(III) and Cd(II) ions in neutral aqueous solutions. Extractions take place by the formation of (1:1) ligand-to-metal complexes and extraction coefficients are in the range 0.74-0.99. The ligand can be regenerated almost quantitatively by washing its complexes with 1M HCl and 0.2 M NaOH solutions successively. In each extraction step the organic solution exhibits a clear-cut phase separation and does not need salting out. The chelating agent can be regenerated and recycled more than 24 times without losing its extracting ability due to nonhydrolyzability of linkages in its structure. Experiments indicate that in high metal concentrations (more than 1 M) the solvent mixture itself is able to extract appreciable amounts of metal ions (33-53%). The solubility in organic solvents induced by long aliphatic chains seems to be general and the method presented offers possibility of large scale chelate extraction of metal ions of relatively low concentrations.
Citation - WoS: 12
Citation - Scopus: 14
Compressive Sensing for Ultra-Wideband Channel Estimation: on the Sparsity Assumption of Ultra-Wideband Channels
(Wiley-Blackwell, 2014) Başaran, Mehmet; Erküçük, Serhat; Cirpan, Hakan Ali
Due to the sparse structure of ultra-wideband (UWB) multipath channels there has been a considerable amount of interest in applying the compressive sensing (CS) theory to UWB channel estimation. The main consideration of the related studies is to propose different implementations of the CS theory for the estimation of UWB channels which are assumed to be sparse. In this study we investigate the suitability of standardized UWB channel models to be used with the CS theory. In other words we question the sparsity assumption of realistic UWB multipath channels. For that we particularly investigate the effects of IEEE 802.15.4a UWB channel models and the selection of channel resolution both on channel estimation and system performances from a practical implementation point of view. In addition we compare the channel estimation performance with the Cramer-Rao lower bound for various channel models and number of measurements. The study shows that although UWB channel models for residential environments (e.g. channel models CM1 and CM2) exhibit a sparse structure yielding a reasonable channel estimation performance channel models for industrial environments (e.g. CM8) may not be treated as having a sparse structure due to multipaths arriving densely. Furthermore it is shown that the sparsity increased by channel resolution can improve the channel estimation performance significantly at the expense of increased receiver processing. Copyright (c) 2013 John Wiley & Sons Ltd.
Citation - WoS: 13
Citation - Scopus: 17
Contraction and Deletion Blockers for Perfect Graphs and H-Free Graphs
(Elsevier Science, 2018) Diner, Öznur Yaşar; Paulusma, Daniel; Picouleau, Christophe; Ries, Bernard
We study the following problem: for given integers d k and graph G can we reduce some fixed graph parameter pi of G by at least d via at most k graph operations from some fixed set S? As parameters we take the chromatic number chi clique number omega and independence number alpha and as operations we choose edge contraction ec and vertex deletion vd. We determine the complexity of this problem for S = {ec} and S = {vd} and pi is an element of{chi omega alpha} for a number of subclasses of perfect graphs. We use these results to determine the complexity of the problem for S = {ec} and S = {vd} and pi is an element of{chi omega alpha} restricted to H-free graphs. (C) 2018 Elsevier B.V. All rights reserved.
Citation - WoS: 2
Citation - Scopus: 2
Cosmic Ray Intensity Variation During a Cme
(Pergamon-Elsevier Science Ltd, 2002) Kandemir, Gulcın; Geçkinli, Melih; Fırat, Coşkun; Yılmaz, Melek; Özuğur, B
The June 6 2000 coronal mass ejection was an exceptional full halo which made it possible to measure cosmic ray (CR) decrease with a simple experimental set-up. Variation in the local secondary cosmic ray density has been investigated by means of gamma rays. The experiment site was located in Istanbul (41.1N 29.0E). CR electrons and slow gamma rays have been eliminated. The CR density has dropped drastically starting on June 8 2000. The counts have been compared with the pre-shock levels and some other cases of CMEs. During strong solar modulation the local counts of secondary CR intensity values dropped down as much as 24%. (C) 2002 Elsevier Science Ltd. All rights reserved.
Citation - WoS: 22
Citation - Scopus: 23
Critical Exponents of Gelation and Conductivity in Polyacrylamide Gels Doped by Multiwalled Carbon Nanotubes
(Taylor & Francis Ltd, 2010) Aktas, Demet Kaya; Evingür, Gülşen Akin; Pekcan, Önder
Polyacrylamide (PAM) doped by multiwalled carbon nanotube (MWNT) gels were prepared with different amounts of MWNTs varying in the range between 0.1 and 15 wt%. The PAM-MWNT composite gels were characterized by the steady state fluorescence technique (SSF). The alternative electrical conductivity (AC) of PAM-MWNT composite gels was measured by the dielectric spectroscopy technique. Observations around the gel point t(gel) for PAM-MWNTs composite gels showed that the gel fraction exponent beta obeyed the percolation result. The critical exponent r of AC electrical conductivity for the composite PAM-MWNT gel was also measured and found to be about 2.0 which agrees with a random resistor network. (C) Koninklijke Brill NV Leiden 2010
Citation - WoS: 5
Citation - Scopus: 11
A Crude Marriage: Iraq Turkey and the Kirkuk-Ceyhan Oil Pipeline
(Routledge Journals Taylor & Francis Ltd, 2017) Bowlus, John V.
Since the discovery of oil at Kirkuk in northern Iraq oil has shaped relations between Iraq and Turkey as the former needed markets and export routes to the Mediterranean and the latter reliable sources of supply. This article examines the origins of the Kirkuk-Ceyhan oil pipeline from northern Iraq to the Turkish Mediterranean coast charting the period of Iraqi-Turkish economic rapprochement in the 1960s to the construction of the pipeline in the 1970s. It also seeks to add to our collective understanding of why transnational oil pipelines in the Middle East succeed or fail by examining the pipeline's operational record.
Citation - WoS: 15
Citation - Scopus: 17
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 - WoS: 6
Citation - Scopus: 8
The Design of Potent Hiv-1 Integrase Inhibitors by a Combined Approach of Structure-Based Virtual Screening and Molecular Dynamics Simulation
(Taylor & Francis Ltd, 2018) Samorlu, Augustine S.; Yelekçi, Kemal; Uba, Abdullahi Ibrahim
Bu araştırmanın amacı, AIDS olarak bilinen insan bağışıklık sistemine etki eden, duraksamayan ve depresif bir hastalığa neden olan HIV-1'in tedavisi için potansiyel inhibitörleri elde etmektir. HIV-1 integraz inhibitörleri, HIV-1 enfeksiyonunun tedavisinde çok önemlidir. İntegraz enziminin (IN) inhibe edilmesi HIV-1 virüsünün çoğalma işleminin sonlandırılmasına neden olur. Böylece yaşam döngüsüne son verir. Bu inhibitörleri elde etmek için bilgisayar destekli in silico yaklaşım kullanılmıştır. Temelde, Otava Kimya Kütüphanesi tarandı ve inhibitör tasarımında kullanılan sistematik yaklaşımlar uygulandı, böylece dört güçlü integraz inhibitörü bulundu. İnhibitörlerin enzime bağlanma değerleri PyRx ve AutoDock 4.2 doklama programları kullanılarak gerçekleştirildi. Çalışmada bir kimyasalın güçlü bir inhibitör olabilmesi için hesaplanan serbest bağ enerjisi = -8.00 kcal / mol veya daha az olması ve integrazın aktif bölgesinde bulunan 3 önemli amino asidinden herhangi biri ile de etkileşimde bulunması kriterine uyulmuştur. Discovery Studio Visualizer, inhibitörlerin yapısını çizmekte, inhibitörü komplekslerinin resimlerini üretmekte, enzim ve inhibitör arasındaki etkileşimin türünü belirlememizi sağlayan 2D ve 3D yapıları görüntülemek için kullanıldı. Elde edilen dört güçlü inhibitörden, kendimizin tasarladığı moleküllerden (Ki= 652.83 nanomolar bir ve bağlanma serbest enerjisi -8.44kcal / mol), kalan üç inhibitörde, Otava Kimya Kütüphanesi'nde tarandı ve Otava koduyla parantez içerisinde listelenmiştir. Bunların inhibisyon sabiti ve bağlanma enerjileri sırasıyla; 107320240, Ki=131.7nm, -9.39kcal/ mol; 109750115, Ki= 44.19nm, -10.03kcal / mol; 111150115 Ki = 395.19nm, -8.74kcal / mol olarak bulunmuştur.
Citation - WoS: 6
Citation - Scopus: 11
Design, Synthesis and Hmao Inhibitory Screening of Novel 2-Pyrazoline Analogues
(Bentham Science Publ Ltd, 2017) Evranos-Aksöz, Begüm; Uçar, Gülberk; Yelekçi, Kemal
Aim and Objective: MAO inhibitors have a significant effect on the nervous system since they act in regulation of neurotransmitter concentrations. Neurotransmitter levels are critical for a healthy nervous system. MAO inhibitors can be used in the treatment of neurological disorders such as depression, Parkinson's disease and Alzheimer's disease, as the increase or decrease of some neurotransmitter concentrations is associated with these neurological disorders. This study was conducted to discover new and active MAO inhibitor drug candidates. Materials and Methods: New pyrazoline derivatives have been designed with the molecular docking approach and interactions of our compounds with the MAO enzyme have been investigated using the Autodock 4.2 program. The designed pyrazoline derivative compounds were synthesized by the reaction of the chalcones and hydrazides in ethanol. hMAO inhibitory activities of the newly synthesized compounds were investigated by fluorimetric method. In vitro cytotoxicity of five most potent inhibitors were tested in HepG2 cells. Results: (3-(5-bromo-2-hydroxyphenyl)-5-(4-methoxyphenyl)-4,5-dihydropyrazol-1-yl)(phenyl) methanone (5i) and (3-(2-hydroxy-4-methoxy phenyl)-5-p-tolyl-4,5-dihydropyrazol-1-yl)(phenyl) methanone (5l) inhibited hMAO-A more potently than moclobemide (Ki values are 0.004 +/- 0.001 and 0.005 +/- 0.001, respectively). The same two compounds, 5i and 5l, inhibited hMAO-A more selectively than moclobemide (SI values are 5.55x10(-5) and 0.003, respectively). Both of these compounds were found non toxic at 1 mu M, 5 mu M and 25 mu M concentrations. Conclusion: Two of the newly synthesized compounds, (3-(5-bromo-2-hydroxyphenyl)-5-(4-methoxyphenyl)- 4,5-dihydropyrazol-1-yl)(phenyl) methanone and (3-(2-hydroxy-4-methoxy phenyl)5- p-tolyl-4,5-dihydropyrazol-1-yl)(phenyl) methanone were found to be promising MAO-A inhibitors due to their high inhibitory potency, high selectivity and low toxicity.

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