Mühendislik ve Doğa Bilimleri Fakültesi

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"2-pirazolin Yapısındaki Yeni Bir Bileşiğin Sentezi, Moleküler Modellemesi ve Monoaminoksidaz İnhibitörü Etkisinin Araştırılması"
(Türkiye Halk Sağlığı Kurumu, 2018) Aksöz Evranos, Begüm; Uçar, Gülberk; Yelekçi, Kemal
Amaç: Nöromediatörlerin yıkımından sorumlu olan monoamin oksidaz (MAO) enziminin izoformlarının (MAO-A ve -B) birçok hastalık ile yakından ilişkili olduğu; MAO inhibitörlerinin depresyon, Parkinson ve Alzheimer hastalığı gibi hastalıkların tedavisinde kullanıldığı bilinmektedir. Grubumuzca daha etkin, tersinir ve az yan etkili yeni bir MAO inhibitörü (SH2U bileşiği) sentezlenmiş ve bu bileşiğin insan MAO enzimini (hMAO) inhibe etme yeteneği incelenmiştir. Ayrıca bu yeni bileşiğin hMAO ile etkileşimi, moleküler modelleme çalışmaları ile detaylı bir şekilde araştırılmıştır. Sentezlenen yeni bileşiğin hMAO’yu kuvvetli bir şekilde yarışmalı ve tersinir olarak inhibe ettiği bulunmuştur. Söz konusu bileşiğin Parkinson ve Alzheimer hastalıklarının tedavisinde ümit verici bir ilaç etken maddesi olabileceği düşünülmektedir. Yöntem: 3’,5’-Dikloro-2’-hidroksi asetofenon ile p-tolualdehit’in metanol içinde KOH varlığında reaksiyona girmesiyle 1-(3,5-dikloro-2-hidroksifenil)- 3-p-tolil prop-2-en-1-on (3’,5’-Dikloro-2’-hidroksi-4- metil şalkon) bileşiği sentez edilmiştir. Daha sonra elde edilen bu bileşiğin etanol içerisinde geri çeviren soğutucu altında izonikotinik asit hidrazit ile muamele edilmesiyle [3-(3,5-dikloro-2-hidroksifenil)-5-p-tolil-4,5- dihidropirazol-1-il] (piridin-4-il) metanon bileşiği sentez edilmiştir. Yapısı doğrulanan bu bileşiğin hMAO enzimi ile etkileşimi, ticari tayin kiti kullanılarak fluorometrik bir yöntemle incelenmiştir. Ayrıca, söz konusu yeni bileşik ile hMAO arasındaki etkileşimler, moleküler modelleme çalışmaları ile aydınlatılmıştır. Bulgular: Sentezlenen bileşiğin yapısı, IR, Mass, 1H-NMR ve elemental analiz yöntemleri kullanılarak doğrulanmıştır. Yapısı doğrulanan bu bileşiğin etkin, seçici, tersinir, toksik olmayan bir hMAO-B inhibitörü olduğu ve inhibisyonun yarışmalı olduğu görülmüştür. Moleküler yerleştirme programı kullanılarak bileşiğin hMAO-B enziminin aktif bölgesinde hangi amino asit yan zincirleri ile ne tür girişimleri yaptığı belirlenmiştir. Sonuç: Yeni sentezlenen SH2U bileşiği, hMAO-B enzimini kuvvetle, seçici, yarışmalı ve tersinir olarak inhibe etmiştir. Sentezlediğimiz bileşik, bilinen seçici ama tersinmez MAO-B inhibitörü olan selejilin’den daha etkin ve seçici, tersinir olarak hMAO-B enzimini inhibe etmiştir ve Parkinson ile Alzheimer hastalığı tedavisinde kullanılabilecek bir ilaç etken maddesi olarak ümit vadetmektedir.
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.
Advanced Signal Processing Algorithms for Wireless Communications
(Springer-Verlag Berlin, 2006) Panayırcı, Erdal; Çırpan, Hakan Ali
Traditional wireless technologies are not well suited to meet the extremely demanding requirements of providing the very high data rates with the ubiquity mobility and portability characteristic of cellular systems. Some fundamental barriers related to the nature of the radio channel as well as the limited bandwidth availability at the frequencies of interest stand in the way. Unique sets of efficient advanced signal processing algorithms and techniques is the one of the primary enablers that will allow lifting these limits primarily due to the impressive advent of low cost and low power digital signal processors. As an application of advanced signal processing techniques we will consider the solution of blind phase noise estimation and data detection problem via a computationally efficient sequential Monte Carlo (SMC) methodology in this paper.
Analysis and Optimization of Matching Networks-I Getting Started With Ads
(Springer-Verlag Berlin, 2008) Şengül, Metin Y.
[Abstract Not Available]
Analysis and Optimization of Matching Networks-Ii Getting Started With Microwave Office
(Springer-Verlag Berlin, 2008) Şengül, Metin Y.
[Abstract Not Available]
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]
Atomic Collisions and Free Lepton Pair Production
(2005) Güçlü, Mehmet Cem; Yılmaz, Melek
In this work we have calculated the total cross sections of electron-positron pair production for the collisions of fully stripped gold ions for various energies. We have also compared our calculation with other methods.
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: 7
Channel Modeling for Visible Light Communications
(Springer-Verlag Berlin, 2016) Miramirkhani, Farshad; Uysal, Murat; Panayırcı, Erdal
In this chapter, we present a novel and realistic channel modeling approach for visible light communications that overcomes the limitations of previous works. In our work, we consider wavelength dependency, effect of realistic light sources as well as different types of reflections such as specular and mixed cases of diffuse and specular. We use nonsequential ray tracing algorithms to calculate the detected power and path lengths from source to detector for each ray. These are then processed to yield the channel impulse responses for various indoor environments. We further present a channel characterization study where channel parameters such as channel DC gain, root mean square delay spread, coherence bandwidth, mean excess delay are calculated for different environments.
Citation - WoS: 1
Citation - Scopus: 1
Collectivity in Heavy Nuclei in the Shell Model Monte Carlo Approach
(EDP Sciences, 2014) Özen, Cem; Alhassid, Yoram; Nakada, Hitoshi
The microscopic description of collectivity in heavy nuclei in the framework of the configuration-interaction shell model has been a major challenge. The size of the model space required for the description of heavy nuclei prohibits the use of conventional diagonalization methods. We have overcome this difficulty by using the shell model Monte Carlo (SMMC) method which can treat model spaces that are many orders of magnitude larger than those that can be treated by conventional methods. We identify a thermal observable that can distinguish between vibrational and rotational collectivity and use it to describe the crossover from vibrational to rotational collectivity in families of even-even rare-earth isotopes. We calculate the state densities in these nuclei and find them to be in close agreement with experimental data. We also calculate the collective enhancement factors of the corresponding level densities and find that their decay with excitation energy is correlated with the pairing and shape phase transitions.
A Comparative Study of Energy Models for Turkish Electricity Market Using Leap
(IEEE Computer Society, 2019) Massaga, Daniel Julius; Kirkil, Gökhan; Çelebi, Emre
Fossil fuel thermal power plants constitute a large part of the Turkish electricity generation capacity. Turkish government has been developing several energy policy documents to evaluate how various renewable energy sources of the country can be utilized optimally in the generation of electricity within the next 30 years. This study considers three scenarios in the transition to renewable energy for Turkey; the business as usual (BAU), energy conservation (EC) and renewable energy (REN) scenarios. EC scenario considers the use of energy-efficient appliances and imposing a carbon tax, whereas REN scenario considers increasing the share of the renewable energy sources as much as possible in the power generation mix. These scenarios were evaluated in terms of cost and environmental impact. The LEAP (Long-range Energy Alternatives Planning Model) was used in the research. The REN scenario has been shown to be the optimal energy policy option for Turkey in terms of cost and environmental impact.
Citation - 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: 3
Citation - Scopus: 3
Critical Exponents of Thermal Phase Transitions of Kappa-Carrageenan in Various Salt Solutions
(Wiley-VCH Verlag GmbH, 2009) Tarı, Özlem; Pekcan, Önder
The steady state fluorescence (SSF) technique was employed to study the phase transitions Of kappa-carrageenan in NaCl and KCl solutions. Pyranine was used as a fluorescence probe for monitoring these transitions. Scattered light I(sc) and fluorescence intensity 1 was monitored against temperature to determine transition temperatures and exponents. It was observed that transition temperatures are strongly correlated with the NaCl and KCl contents. The weight-average degree of polymerization DP(w) and gel fraction G exponents (gamma and beta) were measured and found to be in accord with the classical Flory-Stockmayer model.
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].
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 - Scopus: 5
Design and Implementation of a Negative Feedback Oscillator Circuit Based on a Cellular Neural Network With an Opposite Sign Template
(2010) Tander, Baran; Özmen, Atilla; Özçelep, Yasin
In this paper explicit amplitude and frequency expressions for a Cellular Neural Network with an Opposite-Sign Template (CNN-OST) under oscillation condition are derived and a novel inductorless oscillator circuit with negative feedbacks based on this simple structure is designed and implemented. The system is capable of generating quasi-sine signals with tuneable amplitude and frequency which can't be provided at the same time in the classical oscillator circuits.
Citation - Scopus: 1
Effect of Temperature and Graphene Oxide on the Swelling of Paam-Go Composite Gels
(Avestia Publishing, 2019) Osma, Büşra; Akın Evingür, Gülşen; Pekcan, Önder
Graphene oxide (GO) is a two dimensional carbon material with similar one-atom thickness, and is a light material having extremely high strength and thermal stability [1]. Thus, GO is an efficient filler for the enhancement of the electrical, mechanical and thermal properties of composite materials [2]. We focused on GO as a nanofiller in polyacrylamide hydrogels and PAAm-GO composites to investigate the effect of temperature and graphene oxide on the swelling. Polyacrylamide (PAAm) hydrogels have been proposed for use as promising biomaterials in biomedical and tissue engineering. The composite gels were prepared by free radical crosslinking copolymerization with GO content varying in the range between 8 and 50 μl of GO. The effects of temperature and graphene oxide on the swelling of the composites were studied. The swelling experiment was performed in the distilled water. Decreasing in pyranine (Py) as a fluorescence probe and emission light intensity (Iem) were monitored by steady state fluorescence spectroscopy. Since the increase in Isc corresponds to the increase in turbidity of the swelling composite gel, the corrected fluorescence intensity, I was introduced to analyze the swelling processes. The Stern-Volmer equation combined with Li-Tanaka models was used to explain the behaviour of I during swelling processes. The cooperative diffusion coefficients and time constants were calculated as a function of temperature and GO, respectively.
Citation - 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.
Electricity Market Equilibrium Models With Dynamic Demand Functions
(2013) Çelebi, Emre
Many electricity market models have either mostly ignored the demand response to changing prices (e.g. day-ahead models with mostly fixed demand) or at the other extreme they assumed that the full demand response occurred within one hour. Moreover the capital stock adjustment and the forward-looking nature of consumers are usually omitted. In this paper we propose variational inequality models for electricity markets with dynamic demand models where the intertemporal nature of consumption (i.e. the current consumption decision affects capital stock/habits and thus the future preferences and demand) is recognized. It is intended that the proposed models would develop a framework for electricity market equilibrium models that incorporate the dynamics of the demand side. © 2013 IEEE.
Citation - WoS: 3
Citation - Scopus: 3
An Equivalence Class Decomposition of Finite Metric Spaces Via Gromov Products
(Elsevier Science Bv, 2017) Bilge, Ayşe Hümeyra; Çelik, Derya; Koçak, Şahin
Let (X, d) be a finite metric space with elements P-i, i = 1,..., n and with the distance functions d(ij) The Gromov Product of the "triangle" (P-i, P-j, P-k) with vertices P-t, P-j and P-k at the vertex Pi is defined by Delta(ijk) = 1/2(d(ij) + d(ik) - d(jk)). We show that the collection of Gromov products determines the metric. We call a metric space Delta-generic, if the set of all Gromov products at a fixed vertex P-i has a unique smallest element (for i = 1,., n). We consider the function assigning to each vertex P-i the edge {P-i, P-k} of the triangle (P-i, P-j, P-k) realizing the minimal Gromov product at P-i and we call this function the Gromov product structure of the metric space (X, d). We say two Delta-generic metric spaces (X, d) and (X, d') to be Gromov product equivalent, if the corresponding Gromov product structures are the same up to a permutation of X. For n = 3, 4 there is one (Delta-generic) Gromov equivalence class and for n = 5 there are three (Delta-generic) Gromov equivalence classes. For n = 6 we show by computer that there are 26 distinct (Delta-generic) Gromov equivalence classes. (C) 2017 Elsevier B.V. All rights reserved.

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