Mühendislik ve Doğa Bilimleri Fakültesi

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Citation Count: 4
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.
Citation Count: 2
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) Yelekçi, Kemal; 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 Count: 1
Bayesian estimation of discrete-time cellular neural network coefficients
(TUBITAK Scientific & Technical Research Council Turkey, 2017) Şenol, Habib; 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 Count: 4
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 Count: 8
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 Count: 0
Docking-based virtual screening for potential activity against bacterial pyruvate kinase
(Springer, 2017) Ergün, Çağla; Akten, Ebru Demet; Doruker, Pemra
[Abstract Not Available]
Citation Count: 2
The Effect of Energy Geopolitics on International Climate Change Initiatives
(Uluslararası İlişkiler Konseyi Derneği, 2017) Ediger, Volkan S.
In this article in general the relationship between international climate change initiatives and energy geopolitics was analyzed and in particular the developments in energy geopolitics were investigated with a historical point of view by dividing the years between 1965 and 2014 into periods of geopolitical intensity and geopolitical stability based on long-term periodic variations in oil prices. More specifically the reasons why international initiatives such as the Kyoto Protocol regarded as an important agreement for imposing commitments in climate change mitigation have not been sufficiently successful were investigated. Regarding the Kyoto Protocol the failure stemmed from three main reasons. The first and the most important reason was the intensification of geopolitical tensions on a global scale. The second reason was the differences among states in terms of their energy needs and possession of indigenous energy sources. The last reason was the ambiguity regarding the role of the state and the market at the implementation level. The author links the general failure in the efforts to tackle climate change to the developments in energy geopolitics and argues that the competition periods in energy geopolitics as observed during the oil crises decrease the chances of success for international initiatives on climate change.
Enerji Jeopolitiğinin Uluslararası İklim Değişikliği Girişimleri Üzerindeki Etkisi
(Uluslararası İlişkiler Konseyi Derneği İktisadi İşletmesi, 2017) Ediger, Volkan S.
Genel olarak iklim değişikliği girişimleri ile enerji jeopolitiği arasındaki ilişkinin analiz edildiği bu makalede, başta petrol fiyatlarındaki artışlar olmak üzere, enerji jeopolitiğindeki gelişmeler, 1965-2014 arasında enerji jeopolitiğinin şiddetlendiği ve durağanlaştığı dönemlere ayrılarak, tarihsel bakış açısıyla incelenmiştir. Özel olarak, Kyoto Protokolü gibi iklim değişikliğinin önlenmesi konusunda yükümlülük getirmesi bakımından önemli bir anlaşma olarak kabul edilen uluslararası girişimlerin neden yeterince başarılı olmadığı araştırılmıştır. Kyoto Protokolü özelinde başarısızlığın üç temel nedeni bulunmaktadır. Bunlardan birincisi ve en önemlisi dünya genelinde enerji jeopolitiğinin şiddetleniyor olmasıdır. İkinci neden ülkelerin farklı enerji ihtiyaçları ve farklı yerli enerji kaynaklarının bulunması, üçüncüsü de uygulamalarda devlet ve özel sektörün rolünün yeterince belirgin olmamasıdır. Yazar, iklim değişikliği konusundaki genel başarısızlığın başlıca nedenini enerji jeopolitiğindeki gelişmelere bağlamakta ve petrol krizleriyle somutlaşan küresel enerji politiğindeki mücadele dönemlerinin, iklim değişikliği gibi konulardaki uluslararası girişimlerin başarı şansını azalttığını savunmaktadır.
Citation Count: 4
Europeanization under Membership Uncertainty: The Cases of Environmental and Energy Policy in Turkey
(Uluslararası İlişkiler Konseyi Derneği, 2013) Yıldırım, Cagri; Baysan, Alper; Ediger, Volkan S.
This article examines modalities of rule adoption from the EU's acquis communautaire under conditions of membership uncertainty Drawing upon the case of Turkey we probe into the viability of a policy-type approach (drawing upon Theodor Lowi). Our main contention is that the substantive design of policies (distributive or redistributive qualities) has consequential implications for the form (conflict-free vs. veto player constellations) and outcome (transposition likelihood) of the subsequent political process. The proposed policy-type approach internalist in its outlook is thus readily compatible with available Europeanization models which are externalist insofar as being premised on the study of domestic politics. In terms of policymaking the EU needs to make more frequent use of policy-based intermediate rewards to encourage rule adoption where membership prospects are uncertain.
Citation Count: 1
Exploring distinct binding site regions of beta(2)-adrenergic receptor via coarse-grained molecular dynamics simulations
(Scientific Technical Research Council Turkey-Tubitak, 2013) Akdoğan, Ebru Demet; Akdoğan, Ebru Demet
beta(2)-Adrenergic receptor (beta(2)AR) is a G protein-coupled receptor that is highly flexible and able to recognize a wide range of ligands through its conformational variations. Active and inactive conformations revealed by recent crystallographic experiments do not provide a complete dynamic picture of the receptor especially in the binding site. In this study molecular dynamics (MD) simulation through a residue-based coarse-grained model is used as an alternative and efficient method to explore a wider conformational search space. The system was composed of beta(2)AR embedded into a 1-palmitoyl-2-oleoyl-phosphatidylcholine membrane bilayer with surrounding water. A total of 6 mu s of simulation at constant NPT was performed for a system of 6868 coarse-grained beads. The system reached equilibrium at around 0.1 mu s. The overall 3-dimensional structure was well preserved throughout the simulation. Local residue-based fluctuations were in good agreement with fully atomistic MD simulations. Four distinct snapshots were selected and reverse-mapped to all-atom representations with around 65000 atoms. Each reverse-mapped system was later subjected to 100 ns of MD simulation for equilibration. Root mean square deviation clustering analysis yielded distinct receptor conformers for the binding site regions which were suggested to be alternative representations of the binding pocket and thus were proposed as plausible targets in docking-based virtual screening experiments for the discovery of novel antagonists.
Citation Count: 6
Fault tolerant control with re-configuring sliding-mode schemes
(2005) Kerestecioğlu, Feza; Kerestecioğlu, Feza
In this paper a controller design method for linear MIMO systems is presented which a sliding mode controller is reconfigured in case of system faults. Faults are detected with the residual vector generated from a standard linear observer. Once a fault has been detected the fault distribution matrix can be obtained and used to update the corrective or equivalent control parts of the sliding mode controller. As a result fault tolerant adaptive controllers keep the system performance within acceptable limits or at least avoids the system to wind-up. © TÜBITAK.
Citation Count: 6
Foster impedance data modeling via singly terminated LC ladder networks
(TUBITAK Scientific & Technical Research Council Turkey, 2013) Şengül, Metin Y.
In this work a lossless model is developed for the given Foster impedance data. In the model a 2-port short-or open-terminated LC ladder is used. After applying the proposed algorithm a realizable driving-point reactance function that fits the given data is obtained. Next this function is synthesized resulting in the desired model. In the algorithm there is no need to select a circuit topology for the model. Two examples are given to illustrate the utilization of the proposed modeling algorithm.
Citation Count: 9
Greasing the wheels: the Berlin-Baghdad railway and Ottoman oil, 1888?1907
(Routledge Journals, Taylor & Francis Ltd, 2020) Ediger, Volkan S.; Bowlus, John V.
In the 1880s, Germany cultivated an alliance with the Ottoman Empire that led to a concession to build one of history?s most storied, diplomatically contentious, and financially challenging infrastructure projects: the Berlin-Baghdad Railroad. While Germany had many goals in pursuing the project, oil was the only way to make the railroad economic. Drawing on Ottoman archival sources, this article examines the policies and strategies of Sultan Abd?lhamid II in relation to Germany?s attempt to develop Mesopotamian oil from German Emperor Wilhelm II?s visit to Istanbul in 1889 to the conclusion of Germany?s oil concession in 1906/7. It argues that Hamid pursued a pragmatic policy to develop and protect Ottoman oil from being dominated by the powers, especially the British Empire, and, in the process, seeks to reorient our understanding of great power interest in Middle East oil.
Citation Count: 7
The great game in the Levant: energy geopolitics in the Eastern Mediterranean [Levant’ta büyük oyun: Doğu Akdeniz’in enerji jeopolitiği]
(Uluslararası İlişkiler Konseyi Derneği, 2012) Ediger, Volkan S.; Devlen, Balkan; McDonald, Deniz Bingöl
This study explores the historical evolution of the Levant region from the trade system to hydrocarbon geopolitics by using a longue duree approach one which evaluates the region's present situation in light of developments in oil and natural gas exploration production and export. The concepts of great power politics and balance of power frame the investigation of permanent and changing dimensions of hydrocarbon geopolitics. The first of the two hypotheses tested and verified in this study is that the geopolitics of the Levant maintains its historical importance for the global hegemon and for the international state system even though the central thrust of the Levant's geopolitics has been tranformed from trade to energy. The second hypothesis is that regional and global peace and stability increase when the geopolitics of the Levant is in the control of a hegemon. Instances of conflict increase and opportunities for cooperation decrease when the Levant's geopolitics slips from the grasp of a single hegemon as a result of shifts in the balance of power. Following a discussion of threats and opportunities for conflict and cooperation in the Levant region possible strategies for the regional actors are evaluated. Lastly the threats and opportunities that Turkey faces are situated within emergent trends in the energy geopolitics of the region.
Citation Count: 2
High-pass/low-pass section design for 0 degrees-360 degrees lumped-element phase shifters via the real frequency technique
(TUBITAK Scientific & Technical Research Council Turkey, 2017) Şengül, Metin Y.
In this paper an algorithm based on the real frequency technique (RFT) is proposed to design high-pass and low-pass sections of a 0 degrees-360 degrees wide range lumped-element phase shifter. The switching process however is not considered in this work. In the algorithm it is enough to define the section type (high-pass or low-pass) and the number of elements in the sections there is no need to select the exact circuit topologies for the high-pass and low-pass sections. This is a natural consequence of the proposed approach. Unlike in the methods described in the literature there is also no need to derive element value expressions. Two examples are given to illustrate the utilization of the proposed algorithm. The proposed algorithm and results are verified by simulation.
Citation Count: 1
Hybrid MPI plus UPC parallel programming paradigm on an SMP cluster
(TUBITAK Scientific & Technical Research Council Turkey, 2012) Bozkuş, Zeki
The symmetric multiprocessing (SMP) cluster system which consists of shared memory nodes with several multicore central processing units connected to a high-speed network to form a distributed memory system is the most widely available hardware architecture for the high-performance computing community. Today the Message Passing Interface (MPI) is the most widely used parallel programming paradigm for SMP clusters in which the MPI provides programming both for an SMP node and among nodes simultaneously. However Unified Parallel C (UPC) is an emerging alternative that supports the partitioned global address space model that can be again employed within and across the nodes of a cluster. In this paper we describe a hybrid parallel programming paradigm that was designed to combine MPI and UPC programming models. This paradigm's objective is to mix the MPI's data locality control and scalability strengths with UPC's fine-grain parallelism and ease of programming to achieve multiple-level parallelism at the SMP cluster which itself has multilevel parallel architecture. Utilizing a proposed hybrid model and comparing MPI-only to UPC-only implementations this paper presents a detailed description of Cannon's algorithm benchmark application with performance results of a random-access benchmark and the Barnes-Hut N-Body simulation. Experiments indicate that the hybrid MPI+UPC model can significantly provide performance increases of up to double in comparison with UPC-only implementation and up to 20% increases in comparison to MPI-only implementation. Furthermore an optimization was achieved that improved the hybrid performance by an additional 20%.
Citation Count: 16
In silico design of novel and highly selective lysine-specific histone demethylase inhibitors
(Scientific Technical Research Council Turkey-Tubitak, 2011) Akdoğan, Ebru Demet; Yelekçi, Kemal; Yelekçi, Kemal
Histone lysine-specific demethylase (LSD1) is involved in a wide range of epigenetic processes and plays important roles in gene silencing DNA transcription DNA replication DNA repair and heterochromatin formation. Its active site shows a resemblance to those of 2 homologous enzymes monamine oxidase A and B (MAO-A and MAO-B.) In the present work starting from suitable scaffolds and generating thousands of structures from them 10 potential inhibitors were obtained with structural and physicochemical properties selectively suitable for inhibiting LSD1. iLib Diverse software was used to generate the diverse structures and 3 docking tools CDOCKER GOLD and AutoDock were used to find the most probable potential inhibitor based on its binding affinity. The dispositions of the candidate molecules within the organism were checked by ADMET_PSA_2D (polar surface area) versus ADMET_AlogP98 (the logarithm of the partition coefficient between n-octanol and water) and their suitability is discussed. The LSD1 inhibition activities of the candidates were compared with the properties of trans-2-phenylcyclopropylamine (tranylcypromine) and 2-(4-methoxy-phenyl) cyclopropylamine which are the 2 known inhibitors of LSD1.
Citation Count: 0
Investigation of intrinsic dynamics and allosteric coupling in human beta 2-adrenergic receptor
(Springer, 2017) Özcan, Özer; Özgür, Canan; Doruker, Pemra; Akten, Ebru Demet
[Abstract Not Available]
Citation Count: 0
Levant’ta büyük oyun: Doğu Akdeniz’in enerji jeopolitiği
(Uluslararası İlişkiler Konseyi Derneği İktisadi İşletmesi, 2012) Ediger, Volkan S.
Levant Bölgesi’ndeki ticaret sisteminden başlayarak bölgenin hidrokarbon jeopolitiğine geçiş sürecine kadar uzanan tarihsel gelişimin uzun erimli (longue dureé) bakış açısıyla incelendiği bu çalışmada, bölgenin günümüzdeki durumu, petrol ve doğal gazın arama, üretim ve ihracı konusunda özellikle 2000’li yıllardan bu yana yaşanan gelişmelerle değerlendirilmiştir. Bölgenin hidrokarbon jeopolitiğindeki çatışma ve iş birliğinin sabit ve değişen boyutlarına, uluslararası ilişkilerin güç politikaları ve güçler dengesi gibi kavramları çerçevesinde özel bir yer verilmiştir. Bu çalışma sonunda test edilerek doğrulanan iki temel hipotezden bir tanesi, zaman içinde ticaretten enerjiye evrimleşen Levant jeopolitiğinin, küresel başat güç ve uluslararası devletler sistemindeki güç dengeleri için önemini uzun tarihi boyunca koruduğudur. Buna bağlı olarak geliştirilen ikinci hipotez de, Levant jeopolitiğinin kontrolünün başat gücün elinde olduğu zamanlarda bölgesel ve küresel çaptaki barış ve istikrarın arttığıdır. Güç dengelerindeki kaymalardan ötürü Levant’taki jeopolitik kontrol tek bir gücün elinden çıkmaya başladığı zamanlarda çatışmalar artmakta, iş birlikleri azalmaktadır. Doğu Akdeniz’in enerji konusunda günümüzde karşı karşıya kaldığı tehdit ve fırsatların incelenmesinin ardından bölgedeki çatışma ve iş birliği olanakları konusunda çıkarımlar yapılarak, bölgesel aktörlerin temel stratejileri değerlendirilmiştir. Levant’ta öne çıkan yeni enerji jeopolitiğinin bölgenin önemli bir gücü olan Türkiye için oluşturacağı tehdit ve fırsatlar tartışılmıştır.
Citation Count: 4
Managing Fuel Coal Supply Chains With Multiple Objectives and Multimode Transportation
(AMER SOC ENGINEERING MANAGEMENT, 2013) Yücekaya, Ahmet; Yücekaya, Ahmet
Power companies require sophisticated tools to manage fuel-coal supply chains which include multiple suppliers coal contracts and multimode transportation routes. In this article a multi-objective model which is integrated with multi-attribute decision-making for the selection of suppliers transportation routes and coal orders is developed. The model simultaneously optimizes multiple objectives such as minimizing purchase costs transportation costs and ash output and it also presents a decision framework on the selection of suppliers transportation routes and coal products that will achieve these objectives. The network and capacity constraints of suppliers and transportation routes are included in the model. The study utilizes multi-objective linear programming and well-known decision rules such as minimax maximin and compromise programming and Analytic Hierarchy Process is employed to determine preferred solutions. The methodology for the solution is illustrated via a case study and an alternative evaluation process is presented. The study demonstrates that the model can be used by power companies to find desired solutions as it provides an opportunity for the inclusion of the preferences of decision-makers and adjustments of the weights for each objective.

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