Mühendislik ve Doğa Bilimleri Fakültesi

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Citation Count: 5
(3+3+2) warped-like product manifolds with Spin(7) holonomy
(Elsevier Science Bv, 2011) Bilge, Ayşe Hümeyra; 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 Count: 18
Absolute 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 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 Count: 0
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 Count: 1
Assessing protein-ligand binding modes with computational tools: the case of PDE4B
(Springer, 2017) Çifii, Gülşah; Aviyente, Viktorya; Akten, Ebru Demet; Monard, Gerald
In a first step in the discovery of novel potent inhibitor structures for the PDE4B family with limited side effects we present a protocol to rank newly designed molecules through the estimation of their IC values. Our protocol is based on reproducing the linear relationship between the logarithm of experimental IC values [(IC)] and their calculated binding free energies (). From 13 known PDE4B inhibitors we show here that (1) binding free energies obtained after a docking process by AutoDock are not accurate enough to reproduce this linear relationship
Citation Count: 3
Bayesian compressive sensing for ultra-wideband channel estimation: algorithm and performance analysis
(Springer, 2015) Erküçük, Serhat; 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 Count: 5
Biclustering Expression Data Based on Expanding Localized Substructures
(Springer-Verlag Berlin, 2009) Erten, Cesim; Sözdinler, Melih
Biclustering gene expression data is the problem of extracting submatrices of genes and conditions exhibiting significant correlation across both the rows and the columns of a data matrix of expression values. We provide a method LEB (Localize-and-Extract Biclusters) which reduces the search space into local neighborhoods within the matrix by first localizing correlated structures. The localization procedure takes its roots from effective use of graph-theoretical methods applied to problems exhibiting a similar structure to that of biclustering. Once interesting structures are localized the search space reduces to small neighborhoods and the biclusters are extracted from these localities. We evaluate the effectiveness of our method with extensive experiments both using artificial and real datasets.
Citation Count: 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 Count: 3
Busy tone based coexistence algorithm for WRAN and WLAN systems in TV white space
(Inst Engineering Technology-IET, 2018) Baykaş, Tunçer; 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.
Citation Count: 5
Calculating Level Densities of Heavy Nuclei by the Shell Model Monte Carlo Method
(Academic Press Inc Elsevier Science, 2014) Alhassid, Yoram; Özen, Cem; Nakada, Hitoshi
The microscopic calculation of nuclear level densities in the presence of correlations is a difficult many-body problem. The shell model Monte Carlo method provides a powerful technique to carry out such calculations using the framework of the configuration-interaction shell model in spaces that are many orders of magnitude larger than spaces that can be treated by conventional methods. We present recent applications of the method to the calculation of level densities and their collective enhancement factors in heavy nuclei. The calculated level densities are in close agreement with experimental data.
Citation Count: 18
Carboxylic acid derivatives display potential selectivity for human histone deacetylase 6: Structure-based virtual screening molecular docking and dynamics simulation studies
(Elsevier Science, 2018) Yelekçi, Kemal; 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 Count: 4
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.
Citation Count: 2
Characterization of MWCNT-TiO2 Qps and TiO2 QDs in self-assembled films
(Elsevier, 2017) Akkaya Arier, Ümit Özlem; Uysal, Bengü Özuğur
In this study the solution which includes TiO2 quantum dots (QDs) was mixed with the multi-wall carbon nanotubes (MWCNTs) to prepare MWCNT-TiO2 QDs composite films. The effect of microstructures on the structural and optical properties of MWCNT-TiO2 QDs composite films was evaluated. The activation energy for crystallite growth of TiO2 QDs which are produced in brookite phases was calculated as 20.3 kJ/mol. The properties of MWCNT-TiO2 QDs composite films were characterized by X-ray diffraction (XRD) scanning electron microscopy (SEM) atomic force microscopy (AFM) and ultraviolet-visible absorption spectroscopy (UV-vis). (C) 2017 Elsevier GmbH. All rights reserved.
Citation Count: 0
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 Count: 15
A combined fuzzy AHP-simulation approach to CAD software selection
(Taylor & Francis Ltd, 2010) Ayağ, Zeki
In this paper a combined approach where the fuzzy analytic hierarchy process (AHP) and simulation come together is presented to select the best computer-aided design (CAD) software out of the available options in the market. The fuzzy AHP is used due to the vagueness and uncertainty of the judgements of a decision maker(s) because the crisp pair-wise comparison in the conventional AHP seems to be insufficient and imprecise to capture the right judgements of the decision maker(s). In this study first the fuzzy AHP is used to reduce a possible number of alternatives for the CAD system to an acceptable level for further study simulation analysis. Secondly a simulation generator as an integrated part of the fuzzy AHP is used to try the remaining alternatives on the generated model of a real-life product organisation in which the final alternative will be used. The results of simulation experiments are obtained and then evaluated to reach to the ultimate CAD alternative.
Citation Count: 0
Comparison of cation effects on phase transitions of kappa and iota carrageenan
(European Polymer Federation, 2010) Tari, Özlem; Pekcan, Önder
Phase transitions of kappa and iota carrageenan in KCl NaCl and CaCl2 solutions were separately studied during heating and cooling processes by using fluorescence technique. Scattered light I-SC and fluorescence intensity I was monitored against temperature to determine the critical transition temperatures and exponents. Kappa and iota carrageenans with monovalent (KCl NaCl) salt system presented only coil to double helix (c-h) and double helix to coil (h-c) transitions upon cooling and heating processes respectively. Two transition regions were observed in both heating and cooling of the iota carrageenan in CaCl2 solution while in kappa carrageenan only (c-h) and (h-c) transitions was detected. During heating dimers decompose into double helices by making (d-h) transition. At the high temperature region (h-c) transition takes place. During cooling back transitions repeat themselves. A hysteresis was observed between (h-c) and (c-h) for the kappa and iota carrageenan salt system (except CaCl2) respectively. Dimer to double helix (d-h) and double helix to dimer (h-d) transitions were observed for iota carrageenan in CaCl2 salt. The gel fraction exponent beta was measured and found to be in accord with the classical Flory-Stockmayer Model for both kappa and iota carrageenan salt systems.
Citation Count: 6
A comparison of fluorescence and UV-visible spectrometry techniques for thermal phase transitions of agarose gels
(Springer, 2015) Arda, Ertan; Kara, Selim; Mergen, Ömer Bahadır; Pekcan, Önder
In this study thermoreversible phase transitions of high (HMP) and low (LMP) melting point agarose gels were investigated by using the UV-vis and fluorescence spectroscopy techniques. Pyranine was added to the aqueous solution of agarose as a fluorescence-probe. Transmitted light (I (tr)) and fluorescence emission (I (fl)) intensities from the gel samples with different agarose concentrations were monitored during the heating (gel-sol) and cooling (sol-gel) processes. For the both techniques gel-sol (T (gs)) and sol-gel (T (sg)) transition temperatures were determined from the first derivatives of the sigmoidal transition paths. It was observed that the critical transition temperatures obtained from UV-vis and fluorescence data slightly increased depending on the agarose type and concentration and those values were found to be in accord with each other. Transition activation energies were determined using the Arrhenius type equation and were found to be strongly correlated with the agarose content in the gel system. The produced gel-sol (Delta E (gs)) and sol-gel (Delta E (sg)) transition energies from the fluorescence data were found to be lower than that of the UV-vis data which was attributed to the temperature-dependent fluorescence quenching effect.
Citation Count: 11
Compressive sensing for ultra-wideband channel estimation: on the sparsity assumption of ultra-wideband channels
(Wiley-Blackwell, 2014) Erküçük, Serhat; 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 Count: 5
Conformal and generalized concircular mappings of Einstein-Weyl manifolds
(2010) Özdeğer, Abdülkadir
In this article after giving a necessary and sufficient condition for two Einstein-Weyl manifolds to be in conformal correspondence we prove that any conformal mapping between such manifolds is generalized concircular if and only if the covector field of the conformal mapping is locally a gradient. Using this fact we deduce that any conformal mapping between two isotropic Weyl manifolds is a generalized concircular mapping. Moreover it is shown that a generalized concircularly flat Weyl manifold is generalized concircular to an Einstein manifold and that its scalar curvature is prolonged covariant constant. © 2010 Wuhan Institute of Physics and Mathematics.
Citation Count: 10
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 Count: 9
Contraction Blockers for Graphs with Forbidden Induced Paths
(Springer-Verlag Berlin, 2015) Diner, Öznur Yaşar; Paulusma, Daniel; Picouleau, Christophe; Ries, Bernard
We consider the following problem: can a certain graph parameter of some given graph be reduced by at least d for some integer d via at most k edge contractions for some given integer k? We examine three graph parameters: the chromatic number clique number and independence number. For each of these graph parameters we show that when d is part of the input this problem is polynomial-time solvable on P-4-free graphs and NP-complete as well as W[1]-hard with parameter d for split graphs. As split graphs form a subclass of P-5-free graphs both results together give a complete complexity classification for P-l-free graphs. The W[1]-hardness result implies that it is unlikely that the problem is fixed-parameter tractable for split graphs with parameter d. But we do show on the positive side that the problem is polynomial-time solvable for each parameter on split graphs if d is fixed i.e. not part of the input. We also initiate a study into other subclasses of perfect graphs namely cobipartite graphs and interval graphs.

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