Mühendislik ve Doğa Bilimleri Fakültesi

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Citation - WoS: 12
Citation - Scopus: 15
Accurate Refinement of Docked Protein Complexes Using Evolutionary Information and Deep Learning
(Imperıal College Press, 2016) Akbal-Delibas, Bahar; Farhoodi, Roshanak; Pomplun, Marc; Haspel, Nurit
One of the major challenges for protein docking methods is to accurately discriminate native-like structures from false positives. Docking methods are often inaccurate and the results have to be refined and re-ranked to obtain native-like complexes and remove outliers. In a previous work we introduced AccuRefiner a machine learning based tool for refining protein-protein complexes. Given a docked complex the refinement tool produces a small set of refined versions of the input complex with lower root-mean-square-deviation (RMSD) of atomic positions with respect to the native structure. The method employs a unique ranking tool that accurately predicts the RMSD of docked complexes with respect to the native structure. In this work we use a deep learning network with a similar set of features and five layers. We show that a properly trained deep learning network can accurately predict the RMSD of a docked complex with 1.40 angstrom error margin on average by approximating the complex relationship between a wide set of scoring function terms and the RMSD of a docked structure. The network was trained on 35000 unbound docking complexes generated by RosettaDock. We tested our method on 25 different putative docked complexes produced also by RosettaDock for five proteins that were not included in the training data. The results demonstrate that the high accuracy of the ranking tool enables AccuRefiner to consistently choose the refinement candidates with lower RMSD values compared to the coarsely docked input structures.
Citation - WoS: 4
Citation - Scopus: 6
Agent-Based Optimization To Estimate Nash Equilibrium in Power Markets
(Taylor & Francis Inc, 2013) Yücekaya, Ahmet; Valenzuela, Jorge
In most deregulated power markets firms bid daily into a day-ahead power market. The auction mechanism supply and demand determine the equilibrium at each hour. In this environment firms aim to maximize their revenues by carefully determining their bids. This requires the development of effective computational methods that help them estimate their competitors' behaviors under incomplete information. In this article an agent-based method that uses particle swarm optimization is described to simulate the behavior of market participants. Particle swarm optimization is used in the bidding process and an agent-based model is applied to find a Nash equilibrium. Different stopping conditions are used to determine the equilibrium. Experimental results are presented for two power systems.
Citation - WoS: 1
Citation - Scopus: 2
A Bayesian Approach To Developing a Strategic Early Warning System for the French Milk Market
(Halmstad University, 2017) Bisson, Christophe; Gürpınar, Furkan
A new approach is provided in our paper for creating a strategic early warning system allowing the estimation of the future state of the milk market as scenarios. This is in line with the recent call from the EU commission for tools that help to better address such a highly volatile market. We applied different multivariate time series regression and Bayesian networks on a pre-determined map of relations between macro-economic indicators. The evaluation of our findings with root mean square error (RMSE) performance score enhances the robustness of the prediction model constructed. Our model could be used by competitive intelligence teams to obtain sharper scenarios, leading companies and public organisations to better anticipate market changes and make more robust decisions.
Citation - WoS: 14
Citation - Scopus: 16
Bayesian Compressive Sensing for Primary User Detection
(Inst Engineering Technology-IET, 2016) Başaran, Mehmet; Erküçük, Serhat; Cirpan, Hakan Ali
In compressive sensing (CS)-based spectrum sensing literature most studies consider accurate reconstruction of the primary user signal rather than detection of the signal. Furthermore possible absence of the signal is not taken into account while evaluating the spectrum sensing performance. In this study Bayesian CS is studied in detail for primary user detection. In addition to assessing the signal reconstruction performance and comparing it with the conventional basis pursuit approach and the corresponding lower bounds signal detection performance is also considered both analytically and through simulation studies. In the absence of a primary user signal the trade-off between probabilities of detection and false alarm is studied as it is equally important to determine the performance of a CS approach when there is no active primary user. To reduce the computation time and yet achieve a similar detection performance finally the effect of number of iterations is studied for various systems parameters including signal-to-noise-ratio compression ratio mean value of accumulated energy and threshold values. The presented framework in this study is important in the overall implementation of CS-based approaches for primary user detection in practical realisations such as LTE downlink OFDMA as it considers both signal reconstruction and detection.
Citation - WoS: 4
Citation - Scopus: 5
Broadband Equalizer Design With Commensurate Transmission Lines Via Reflectance Modeling
(IEICE-INST ELECTRONICS INFORMATION COMMUNICATIONS ENG, 2008) Şengül, Metin Y.; Yarman, Sıddık Binboğa
In this paper an alternative approach is presented to design equalizers (or matching networks) with commensurate (or equal length) transmission lines. The new method automatically yields the matching network topology with characteristic impedances of the commensurate lines. In the implementation process of the new technique first the driving point impedance data of the matching network is generated by tracing a pre-selected transducer power gain shape without optimization. Then it is modelled its it realizable bounded-real input reflection coefficient in Richard domain which ill turn yields the desired equalizer topology with line characteristic impedances. This process results in an excellent initial design for the commercially available computer aided design (CAD) packages to generate final circuit layout for fabrication. An example is given to illustrate the utilization of the new method. It is expected that the proposed design technique is employed as it front-end to commercially available computer aided design (CAD) packages which generate the actual equalizer circuit layout with physical dimensions for mass production.
Citation - WoS: 2
Citation - Scopus: 3
Broadband Matching Via Unequal Length Cascaded Transmission Lines
(World Scientific Publ Co Pte Ltd, 2017) Şengül, Metin Y.
In this paper a new approach based on the real frequency technique (RFT) has been proposed to solve broadband matching problems using cascaded unequal length transmission lines. At the end of the design process optimum characteristic impedance and delay values of transmission lines are obtained. Two examples are given to illustrate the utilization of the proposed approach.
Broadband Microwave Amplifier Design With Lumped Elements
(Walter De Gruyter Gmbh, 2016) Şengül, Metin Y.
This study introduces a broadband microwave amplifier design that utilizes the measured scattering parameters of active devices without assuming an initial topology for the matching networks or an analytic form of the system transfer function. The algorithm can be extended to design multistage broadband microwave amplifiers. An example is given to illustrate the application of the proposed method. It was found that the proposed method provides very good initials for CAD tools to further improve amplifier performance by working on the element values.
Citation - WoS: 13
Characterization of Mps Capped Cds Quantum Dots and Formation Self-Assembled Quantum Dots Thin Films on a Glass Substrate
(Natl Inst R&D Materials Physics, 2011) Koç, Kenan; Tepehan, Fatma Zehra; Tepehan, Galip Gültekin
Colloidal powdered and thin film forms of MPS capped CdS quantum dots have been produced by combination of colloidal chemistry and sol-gel method. Nanoparticles were self-assembled directly on a glass substrate using spin coating method without introducing any matrix. Colloidal powdered and thin film forms were characterised by absorbance photolimunescence XRD FT-IR HRTEM and AFM measurements. The HRTEM images give a grain size of 2.5-3.0 nm and this is in agreement with the values found in the absorbance and XRD measurement. Average size of the quantum dots increase with increasing of heat treatment temperature due to Oswald ripening.
Citation - WoS: 12
Citation - Scopus: 18
A Combined Fuzzy Ahp-Goal Programming Approach To Assembly-Line Selection
(IOS Press, 2007) Ayağ, Zeki; Özdemir, Rıfat Gürcan
In mass production assembly-line balancing (ALB) problem has been a critical and repetitive issue for companies for long time. On the other hand equipment selection for stations has also been another important problem at the design stage of an assembly-line system. In this paper both problems are handled simultaneously. Therefore first goal programming (GP) method a well-suited technique is used to develop a preemptive formulation to joint both of the problems when the nature of the problem consists of several conflicting objectives and some mathematical constraints on solutions. Second an AHP method based on fuzzy scales which is incorporated with the GP is also used due to the fact that it takes both qualitative and quantitative judgments of decision-maker(s) into consideration to rank the equipment alternatives for stations by weight. The fuzzy AHP as one of the most commonly used multiple-criteria decision making (MCDM) methods has been effectively used for more than decade in both academic research and practice and takes the vagueness and uncertainty on judgments of decision-maker(s) into consideration due to the fact that the crisp pairwise comparison in the conventional AHP seems to insufficient and imprecise to capture the right judgments of decision-maker(s). In short in this study a combined fuzzy AHP-GP approach is proposed to evaluating assembly-line design alternatives with equipment selection. An integer GP formulation is constructed which also uses the fuzzy AHP scores of equipment alternatives and employs them as one of the goals. Then the mathematical model is solved to find out the ultimate alternative in terms of the minimized equipment cost and the maximized preference measures of decision-maker(s). The proposed approach is also illustrated on a sample case study.
Citation - Scopus: 11
Competitive Intelligence and Information Technology Adoption of Smes in Turkey: Diagnosing Current Performance and Identifying Barriers
(Halmstad University, 2013) Wright, Sheila; Bisson, Christophe; Duffy, Alistair P.
The need for SMEs to behave in a more concise and coherent competitive fashion is well recognised. This study reports on an empirical study of SMEs in Turkey. Their responses were applied to a behavioural and information technology adoption framework which enabled the identification of areas where changes would be required for these firms to begin operating at a higher level of competence. The findings revealed significant scope for improvements on all strands of the diagnostic framework: attitude gathering location technology support IT systems support and finally use of intelligence-based output by decision-makers. Through free form responses it was also possible to identify barrier to higher level adoption and performance inhibiters which were subsequently categorised and assessed for significance.
Citation - WoS: 21
Citation - Scopus: 24
Conductivity Percolation of Carbon Nanotubes (cnt) in Polystyrene (ps) Latex Film
(Canadian Science Publishing Nrc Research Press, 2010) Uğur, Şaziye; Yargı, Önder; Pekcan, Önder
In this study the effect of multiwalled carbon nanotubes (MWNT) on film formation behaviour and electrical conductivity properties of polystrene (PS) latex film was investigated by using the photon transmission technique and electrical conductivity measurements. Films were prepared by mixing PS latex with different amounts of MWNTs varying in the range between 0 and 20 wt%. After drying MWNT content films were separately annealed above the glass transition temperature (T-g) of PS ranging from 100 to 270 degrees C for 10 min. To monitor film formation behavior of PS-MWNT composites transmitted light intensity I-tr was measured after each annealing step. The surface conductivity of annealed films at 170 degrees C was measured and found to increase dramatically above a certain fraction of MWNT (4 wt%) following the percolation theory. This fraction was defined as the percolation threshold of conductivity R-c. The conductivity scales with the mass fraction of MWNT as a power law with exponent 2.27 which is extremely close to the value of 2.0 predicted by percolation theory. In addition the increase in I-tr during annealing was explained by void closure and interdiffusion processes. Film formation stages were modeled and the corresponding activation energies were measured.
Citation - WoS: 2
Citation - Scopus: 3
Corrected Panel-Reactive Antibody Positivity Rates for Hypersensitized Patients in Turkish Population With Calculated Panel-Reactive Antibody Software
(Elsevier Science Inc, 2017) Karadeniz, Sedat Tanju; Akgül, Sebahat Usta; Öğret, Yeliz; Çiftçi, Hayriye Şentürk; Bayraktar, Adem; Bakkaloğlu, Hüseyin; Çalışkan, Yaşar Kerem; Yelekçi, Kemal; Türkmen, Aydin; Aydın, Ali Emin; Oğuz, Fatma Savran; Çarin, Mahmut Nezih; Aydın, Filiz
however the rate was 86.2% using the cPRA. Discussion. cPRA shows the rate of the rejected donors according to all unacceptable antigens. The need for a list of unacceptable antigens in place of the PRA positivity rate is a real change in the sensitization-dependent calculation as cPRA positivity rate. Conclusion. In principal implementation of cPRA will encourage many centers and laboratories to adopt a standard measurement of sensitization in Turkey. It will increase the chances of better donor match particularly for hypersensitized patients by the creation of an unacceptable mismatch program using cPRA software.
Citation - WoS: 21
Citation - Scopus: 20
Critical Exponents of Kappa Carrageenan in the Coil-Helix and Helix-Coil Hysteresis Loops
(Taylor & Francis Inc, 2009) Tarı, Özlem; Kara, Selim; Pekcan, Önder
The steady-state fluorescence technique was used to study coil-helix (sol-gel) and helix-coil (gel-sol) transitions of the kappa carrageenan-water system with various carrageenan contents. Fluorescence (I) and scattered light (I-sc) intensities were measured against temperature to determine critical phase transition temperatures and exponents. It was observed that the coil-helix transition temperatures T-ch were much lower than the helix-coil (T-hc) transition temperatures due to the hysteresis of the phase transition loops. The gel fraction exponent (beta) was measured and found to be in accord with the classical Flory-Stockmayer model.
Citation - WoS: 16
Citation - Scopus: 16
Critical Exponents of Photoinitiated Gelation at Different Light Intensities
(Taylor & Francis Inc, 2009) Doğruyol, Zekeriya; Arsu, Nergis; Pekcan, Önder
A photo-differential scanning calorimetric (Photo-DSC) technique was used to study the photoinitiated radical polymerization of a 75% epoxy diacrylate (EA) and 25% tripropyleneglycoldiacrylate (TPGDA) mixture with 2-mercaptothioxanthone (TX-SH) as photoinitiator by using different light intensities. Photopolymerization reactions were carried out under identical conditions of temperature and initiator concentration. It was observed that all conversion curves during gelation at various Might intensities present good sigmoidal behavior as predicted by the percolation model. Observations around the critical time called the glass transition point (t(g)) taken for polymerization to reach the maximum rate (R-pmax) show that the gel fraction exponents beta obeyed the universal percolation picture. On the other hand R-pmax t(g) and final conversion values were found to be dependent on the UV light intensity.
Citation - WoS: 1
Citation - Scopus: 1
The Critical Point of a Sigmoidal Curve
(Babeș-Bolyai University, 2020) Bilge, Ayşe Hümeyra; Özdemir, Yunus
Let y(t) be a monotone increasing curve with lim(t ->+/-infinity) y((n))(t) = 0 for all n and let t(n) be the location of the global extremum of the nth derivative y((n))(t). Under certain assumptions on the Fourier and Hilbert transforms of y(t), we prove that the sequence {t(n)} is convergent. This implies in particular a preferred choice of the origin of the time axis and an intrinsic definition of the even and odd components of a sigmoidal function. In the context of phase transitions, the limit point has the interpretation of the critical point of the transition as discussed in previous work [3].
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 - Scopus: 1
Determination of Growth Kinetics and Size Dependent Structural Morphological Optical Characteristics of Sol-Gel Derived Silica Nanoparticles in Silica Matrix
(De Gruyter Poland Sp Zoo, 2019) Uysal, Bengü Özuğur; Tepehan, Fatma Zehra
Nanocomposite silica thin films made using the sol-gel method were studied. The nano-silica films were prepared using a mixture of tetraethyl orthosilicate (TEOS) deionized water ethanol and ammonia solution. To control the growth of the particles inside the film the nanocomposite silica film was prepared using a mixture of the nano-silica sol and the silica sol. The change in the particle size with the heat treatment temperature ranging from 450 degrees C to 1100 degrees C was investigated. X-ray diffraction (XRD) atomic force microscopy (AFM) scanning electron microscopy (SEM) NKD (refractive index-N extinction coefficient-K and thickness-D) and ultraviolet-visible (UV-Vis) spectrophotometry were used for characterization purposes. The XRD studies showed that the nano-silica thin films were amorphous at all annealing temperatures except for 1100 degrees C. The alpha-cristobalite crystal structure formed at the annealing temperature of 1100 degrees C. Optical parameters such as refractive indices and extinction coefficients were obtained using the NKD analyzer with respect to the annealing temperature of the films. The activation energy and enthalpy of the nanocomposite silica film were evaluated as 22.3 kJ/mol and 14.7 kJ/mol respectively. The cut-off wavelength values were calculated by means of extrapolation of the absorbance spectra estimated using the UV-Vis spectroscopy measurements. A red shift in the absorption threshold of the nanocomposite silica films indicated that the size of the silica nanoparticles increased with an increase of the annealing temperatures from 450 degrees C to 900 degrees C and this confirms the quantum confinement effect in the nanoparticles.
Citation - WoS: 12
Citation - Scopus: 14
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 - WoS: 6
Citation - Scopus: 6
Effect of Calcium Ion Concentration on Small Molecule Desorption From Alginate Beads
(Taylor & Francis Inc, 2014) Evingür, Gülşen Akin; Kaygusuz, Hakan; Erim, F. Bedia; Pekcan, Önder
Spherical alginate beads were prepared by ionotropic gelation of sodium alginate through the use of calcium ions. Pyranine (Py) was added to the alginate solution as a small molecule probe for fluorescence studies. Desorption of Py in water from the alginate beads cross-linked with calcium ions was studied by using the steady state fluorescence technique. The fluorescence emission intensity (I) from Py was monitored during the desorption process at 512 nm using the time drive mode of the spectrofluorometer. The increase in I was attributed to Py release from the beads. The Fickian diffusion model was used to calculate the desorption coefficients D which were found to be increased up to 3% (w/v) CaCl2 concentration in the beads and then decreased with a further increase of CaCl2 content. On the other hand the encapsulation efficiency of Py in the calcium alginate beads presented the reverse behavior compared to D. It was observed that when the content of CaCl2 was increased the incubation time t(0) for the start of desorption increased.
Citation - WoS: 3
Citation - Scopus: 4
Elasticity Study of Paam-Kappa C Composite Prepared in Various Kappa C Content and Measured at Several Temperatures
(Polish Acad Sciences Inst Physics, 2015) Evingür, Gülşen Akin; Pekcan, Önder
Polyacrylamide (PAAm)-kappa carrageenan (kappa C) composite gels were prepared via free radical crosslinking copolymerization with various (w/v) percentages of kappa C in the range between 0.5 and 3 (w/v)% of kappa C . Elasticity properties such as stress strain and compressive elastic modulus S of these composite gels were studied in various kappa C content and at several temperatures. The content and temperature dependence of the compressive elastic modulus S of the swollen PAAm-kappa C composite gels due to volume phase transition were produced by using tensile testing technique. It is understood that the compressive elastic modulus was found to decrease up to 1 (w/v)% of kappa C and then increase by increasing kappa C contents at constant temperatures. The composite preserves the ability to undergo the volume phase transition and its compressive elastic modulus is found to be strongly dependent on the kappa C content and temperature. It is observed that the compressive elastic modulus increased when temperature is increased up to 40 degrees C and then decreases below this temperature for all composite gels. However PAAm-kappa C composite gel presented lower values for the compressive elastic modulus showing a minima at 40 degrees C for 1 (w/v)% of kappa C content gel.

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