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Article Citation - WoS: 1Citation - Scopus: 13-State Protein Secondary Structure Prediction Based on Scope Classes(Inst Tecnologia Parana, 2021) Atasever, Sema; Azginoglu, Nuh; Erbay, Hasan; Aydin, Zafer; 01. Abdullah Gül University; 02. 04. Bilgisayar Mühendisliği; 02. Mühendislik FakültesiImproving the accuracy of protein secondary structure prediction has been an important task in bioinformatics since it is not only the starting point in obtaining tertiary structure in hierarchical modeling but also enhances sequence analysis and sequence-structure threading to help determine structure and function. Herein we present a model based on DSPRED classifier, a hybrid method composed of dynamic Bayesian networks and a support vector machine to predict 3-state secondary structure information of proteins. We used the SCOPe (Structural Classification of Proteins-extended) database to train and test the model. The results show that DSPRED reached a Q(3) accuracy rate of 82.36% when trained and tested using proteins from all SCOPe classes. We compared our method with the popular PSI PRED on the SCOPe test datasets and found that our method outperformed PSI PRED.Article 3D Sampling of K-Space With Non-Cartesian Trajectories in MR Imaging(Gazi Univ, Fac Engineering Architecture, 2025) Dundar, Mehmet Sait; Gumus, Kazim Z.; Yilmaz, Bulent; 01. Abdullah Gül UniversityThis study presents an innovative approach to 3D k-space sampling in MR imaging using non-Cartesian concentric shell trajectories. The method involves 32 concentric shells of varying radii, allowing for rapid data acquisition through undersampling techniques. Simulations using IDEA software demonstrate that this approach can fill the k-space in less than one second, a significant time reduction compared to traditional FLASH sequences that can take 3-4 minutes. The concentric shell model enhances imaging efficiency by minimizing artifacts and ensuring uniform k-space filling, leading to higher resolution and faster scans. This technique shows promise for clinical applications, particularly in dynamic imaging scenarios such as acute stroke and pediatric radiology, where speed and precision are critical. As illustrated in Figure A, the concentric shell trajectories enable uniform k-space filling, significantly reducing scan times and improving image quality. These results are based on the simulations conducted with IDEA software.Article A Comprehensive Review on the Extraction and Recovery of Lithium from Primary and Secondary Sources: Advances Toward Battery-Grade Materials(Wiley, 2025) Top, Soner; Kursunoglu, Sait; Altiner, Mahmut; 01. Abdullah Gül University; 02.07. Malzeme Bilimi ve Nanoteknoloji Mühendisliği; 02. Mühendislik FakültesiLithium-ion battery (LIB) technologies have become indispensable to modern energy systems, driving global demand for high-purity lithium compounds. This review focuses on lithium recovery and purification strategies for battery-grade lithium carbonate (Li2CO3) and lithium hydroxide (LiOH), addressing both primary sources (brines and minerals) and secondary sources (waste materials). Industrially established processes, such as evaporation-based brine treatment and conventional metallurgical methods, are discussed alongside emerging techniques, including membrane separation, solvent extraction, and CO2-assisted precipitation. Particular attention is given to lithium precipitation mechanisms, the behaviour of co-existing ions during extraction, and the specific quality requirements for cathode material synthesis. By evaluating process scalability, environmental impact, and product purity, this review provides a comprehensive understanding of current practices and future directions. Additionally, it highlights the growing importance of lithium in the context of accelerating electric vehicle (EV) adoption, underscoring the bright and expanding future of the lithium industry.Article Citation - WoS: 6Citation - Scopus: 6Absorption Enhancement by Semi-Cylindrical Structures for an Organic Solar Cell Application(Optical Soc Amer, 2020) Hah, Dooyoung; 01. Abdullah Gül University; 02. Mühendislik Fakültesi; 02.05. Elektrik & Elektronik MühendisliğiOrganic solar cells are attractive for various applications with their flexibility and low-cost manufacturability. In order to increase their attractiveness in practice, it is essential to improve their energy conversion efficiency. In this work, semi-cylindrical-shell-shaped structures are proposed as one of the approaches, aiming at absorption enhancement in an organic solar cell. Poly(3-hexylthiophene-2,5-diyl) blended with indene-C60 bisadduct (P3HT:ICBA) is considered as the active layer. Light coupling to the guided modes and a geometrical advantage are attributed to this absorption enhancement. Finite-difference time-domain methods and finite element analysis are used to examine the absorption spectra for two types of devices, i.e., a debossed type and an embossed type. It is shown that absorption enhancement increases as the radius of the cylinder increases, but reaches a saturation at about 4-mu m radius. The average absorption enhancement with an active layer thickness of 200 nm and radius of 4 mu m, and for incidence angles between 0 degrees and 70 degrees, is found as 51%-52% for TE-polarized input and as 30%-33% for TM-polarized input when compared to a flat structure. Another merit of the proposed structures is that the range of incidence angles where the integrated absorption is at the level of the normal incidence is significantly broadened, reaching 70 degrees-80 degrees. This feature can be highly useful especially when organic solar cells are to be placed around a round object. The study results also exhibit that the proposed devices bear broadband absorption characteristics. (C) 2020 Optical Society of AmericaArticle Citation - WoS: 5Citation - Scopus: 5Admissible Invariants of Genus 3 Curves(Springer Heidelberg, 2015) Cinkir, Zubeyir; 01. Abdullah Gül University; 02.02. Endüstri Mühendisliği; 02. Mühendislik FakültesiSeveral invariants of polarized metrized graphs and their applications in Arithmetic Geometry are studied recently. In this paper, we explicitly calculated these admissible invariants for all curves of genus 3. We find the sharp lower bound for the invariants phi, lambda and epsilon for all polarized metrized graphs of genus 3. This improves the lower bound given for Effective Bogomolov Conjecture for such curves.Conference Object Adult Zebrafish Brain as a Demyelination Model and Role of WNF Signaling in Remyelination(Wiley, 2024) Bora, U.; Demirbasoglu, E. S.; Turhanlar-Sahin, E.; Guner, H.; Ozhan, G.; 01. Abdullah Gül University; 04. Yaşam ve Doğa Bilimleri Fakültesi; 04.02. Moleküler Biyoloji ve GenetikArticle Citation - WoS: 34Citation - Scopus: 38Advances in Micelle-Based Drug Delivery: Cross-Linked Systems(Bentham Science Publ Ltd, 2017) Isoglu, Ismail Alper; Ozsoy, Yildiz; Isoglu, Sevil Dincer; 01. Abdullah Gül University; 04. Yaşam ve Doğa Bilimleri Fakültesi; 04.01. BiyomühendislikThere are several barriers that drug molecules encounter in body beginning from kidney filtration and reticulo-endothelial system (RES) clearance to cellular trafficking. Multifunctional nanocarriers have a great potential for the delivery of drugs by enhancing therapeutic activity of existing methodologies. A variety of nanocarriers are constructed by different material types, which have unique physicochemical properties for drug delivery applications. Micelles formed by amphiphilic polymers are one of the most important drug/nanocarrier formulation products, in which the core part is suitable for encapsulation of hydrophobic agent whereas the outer shell can be utilized for targeting the drug to the disease area. Micelles as self-assembled nanostructures may encounter difficulties in biodistribution of encapsulated drugs because they have a tendency to be dissociated in dilution or high ionic strength. Therefore, therapeutic efficiency is decreased and it requires high amount of drug to be administered to achieve more efficient result. To overcome this problem, covalently stabilized structures produced by cross-linking in core or shell part, which can prevent the micelle dissociation and regulate drug release, have been proposed. These systems can be designed as responsive systems in which cross-links are degradable or hydrolysable under specific conditions such as low pH or reductive environment. These are enhancing characteristics in drug delivery because their cleavage allows the release of bioactive agent encapsulated in the carrier at a certain site or time. This review describes the chemical methodologies for the preparation of cross-linked micelles, and reports an update of latest studies in literature.Article Citation - WoS: 4Citation - Scopus: 4All-Polymer Ultrasonic Transducer Design for an Intravascular Ultrasonography Application(Tubitak Scientific & Technological Research Council Turkey, 2019) Hah, Dooyoung; 01. Abdullah Gül University; 02. Mühendislik Fakültesi; 02.05. Elektrik & Elektronik MühendisliğiIntravascular ultrasonography (IVUS), a medical imaging modality, is used to obtain cross-sectional views of blood vessels from inside. In IVUS, transducers are brought to the proximity of the imaging targets so that high-resolution images can be obtained at high frequency without much concern of signal attenuation. To eliminate mechanical rotation rendered in conventional IVUS, it is proposed to manufacture a transducer array on a flexible substrate and wrap it around a cylindrical frame. The transducer of consideration is a capacitive micromachined ultrasonic transducer (CMUT). The whole device needs to be made out of polymers to be able to endure a high degree of bending (radius: 1 mm) Bending of the devices leads to considerable changes in the device characteristics, including resonant frequency and pull-in voltage due to geometrical dimension changes and stress induced. The main purpose of this work is to understand the effect of bending on the device characteristics by means of finite element analysis. Another objective of the work is to understand the relationships between such an effect and the device geometries. It is learned that the bending-induced stress depends strongly on anchor width, membrane thickness, and substrate thickness. It is also learned that resonant frequency and pull-in voltage become lower in most cases because of using a flexible substrate in comparison to those of the device on a rigid substrate. Bending-induced stress increases the spring constant and hence increases resonant frequency and pull-in voltage, although this effect is relatively weaker. For most of the device geometries, pull-in voltage is too high for the polymer material to endure. This is the main drawback of the all-polymer CMUT. In order to meet the design goal of 20 MHz resonant frequency, the membrane radius has to be smaller than 7.7 mu m for a thickness of 3 mu m.Article Citation - WoS: 7Citation - Scopus: 7Amorphous Boron Nitride at High Pressure(Taylor & Francis Ltd, 2016) Durandurdu, Murat; 01. Abdullah Gül University; 02.07. Malzeme Bilimi ve Nanoteknoloji Mühendisliği; 02. Mühendislik FakültesiThe pressure-induced phase transformation in hexagonal boron nitrite and amorphous boron nitrite is studied using ab initio molecular dynamics simulations. The hexagonal-to-wurtzite phase transformation is successfully reproduced in the simulation with a transformation mechanism similar to one suggested in experiment. Amorphous boron nitrite, on the other hand, gradually transforms to a high-density amorphous phase with the application of pressure. This phase transformation is irreversible because a densified amorphous state having both sp(3) and sp(2) bonds is recovered upon pressure release. The high-density amorphous state mainly consists of sp(3) bonds and its local structure is quite similar to recently proposed intermediate boron nitrite phases, in particular tetragonal structure (P4(2)/mnm), rather than the known the wurtzite or cubic boron nitrite due to the existence of four membered rings and edge sharing connectivity. On the basis of this finding we propose that amorphous boron nitrite might be best candidate as a starting structure to synthesize the intermediate phase(s) at high pressure and temperature (probably below 800 degrees C) conditions.Article Citation - WoS: 5Citation - Scopus: 5Amorphous Silicon Hexaboride at High Pressure(Taylor & Francis Ltd, 2020) Durandurdu, Murat; 01. Abdullah Gül University; 02.07. Malzeme Bilimi ve Nanoteknoloji Mühendisliği; 02. Mühendislik FakültesiWe investigate the pressure-induced structural phase transformation of amorphous silicon hexaboride (a-SiB6) using a constant pressure first principles approach. a-SiB6 is found to undergo a gradual phase transformation to a high-density amorphous phase (HDA) in which the average coordination number of both B and Si atoms is about 6. The HDA phase consists of differently coordinated motifs ranging from 4 to 8. B-12 icosahedra are found to persist during compression of a-SiB6 and the structural modifications primarily occur around Si atoms and in the regions linking pentagonal pyramid-like configurations to each other. Upon pressure release, an amorphous structure, similar to the uncompressed one, is recovered, indicating a reversible amorphous-to-amorphous phase change in a-SiB6. When the electronic structure is considered, the HDA phase is perceived to have a wider forbidden band gap than the uncompressed one.Article Citation - WoS: 3Citation - Scopus: 3Amorphous Silicon Hexaboride: A First-Principles Study(Taylor & Francis Ltd, 2018) Durandurdu, Murat; 01. Abdullah Gül University; 02.07. Malzeme Bilimi ve Nanoteknoloji Mühendisliği; 02. Mühendislik FakültesiWe report for the first time the atomic structure, electronic structure and mechanical properties of amorphous silicon hexaboride (a-SiB6) based on first-principles molecular dynamics simulation. The a-SiB6 model is generated from the melt and predominantly consists of pentagonal pyramid-like configurations and B-12 icosahedral molecules, similar to what has been observed in most boron-rich materials. The mean coordination number of B and Si atoms are 5.47 and 4.55, respectively. The model shows a semiconducting behaviour with a theoretical bandgap energy of 0.3eV. The conduction tail states are found to be highly localised and hence the n-type doping is suggested to be more difficult than the p-type doping for a-SiB6. The bulk modulus and Vickers hardness of a-SiB6 are estimated to be about 118 and 13-17GPa, respectively.Article Citation - WoS: 1Amorphous to Amorphous Phase Transformation in Boron-Rich Amorphous Silicon Borides: An Ab Initio Study(Taylor & Francis Ltd, 2024) Karacaoglan, Aysegul Ozlem Cetin; Durandurdu, Murat; 01. Abdullah Gül University; 02.07. Malzeme Bilimi ve Nanoteknoloji Mühendisliği; 02. Mühendislik FakültesiThis study employs a constant-pressure ab initio approach to investigate the high-pressure behavior of five distinct boron-rich amorphous silicon borides. A unique amorphous-to-amorphous phase transition is exposed, providing insights into the structural resilience of these materials under extreme conditions. Our results reveal a gradual increase in the coordination number of both B and Si atoms under pressure, with subsequent densification upon pressure release. Yet the recovered amorphous phases closely resemble the uncompressed states, highlighting the reversibility of these phase changes. Significant structural modifications around Si atoms are observed, emphasizing their pivotal role in the observed phase transitions. Additionally, pressure-induced metallization is witnessed in these materials, indicating their distinctive electronic behavior under high pressure. This work significantly contributes to a deeper understanding of the high-pressure behavior of boron-rich amorphous silicon borides and opens avenues for exploring their potential applications in fields requiring exceptional structural stability and unique pressure-dependent properties.Article Citation - WoS: 8Citation - Scopus: 9Amorphous Zirconia: Ab Initio Molecular Dynamics Simulations(Taylor & Francis Ltd, 2017) Durandurdu, Murat; 01. Abdullah Gül University; 02.07. Malzeme Bilimi ve Nanoteknoloji Mühendisliği; 02. Mühendislik FakültesiWe investigate the short-range order of the liquid and amorphous zirconia using an ab initio molecular dynamics technique. Both forms of zirconia are projected to be structurally close to each other. The amorphous network has predominantly seven-fold coordinated Zr atoms (similar to% 65), and three-fold and four-fold coordinated O atoms (similar to 46%), and hence it resembles locally the monoclinic zirconia phase. Within the known limitations of the DFT-GGA calculation, the liquid state is predicted to be semi-metal, whereas the amorphous form is projected to be semiconductor having a band gap energy of similar to 3.5 eV. We find an asymmetry in localisation of the band tail states. On the basis of this finding, we discuss possible distinctions in n-type and p-type doping in amorphous zirconia.Article An Extension of Lucas's Theorem(indian Nat Sci Acad, 2025) Cinkir, Zubeyir; Ozturkalan, Aysegul; 01. Abdullah Gül University; 02.02. Endüstri Mühendisliği; 02. Mühendislik FakültesiWe give elementary proofs of some congruence criteria to compute binomial coefficients modulo a prime number. These criteria are analogues to the symmetry property of binomial coefficients. We give extended version of Lucas's Theorem by using those criteria. We give applications of these criteria by describing a method to derive identities and congruences involving sums of binomial coefficients.Article Citation - WoS: 5Citation - Scopus: 5Analysis of Electret-Based Vibration Energy Harvesting Devices With Curved-Beam Hinges(Sage Publications Ltd, 2023) Hah, Dooyoung; 01. Abdullah Gül University; 02. Mühendislik Fakültesi; 02.05. Elektrik & Elektronik MühendisliğiRecently, vibration energy harvesting devices have gained growing interests. One of the main requirements for them is a broad bandwidth owing to stochastic spectral characteristics of the general vibration sources. Among various approaches for wide bandwidth, curved-beam hinges are quite attractive due to their simple structures. Although there have been several reports on curved beams, a more detailed study is needed. The device under study is an electret-based one with balanced comb-drive configuration. The whole system is modeled by using nonlinear stochastic differential equations. The numerical analysis results show that there is an optimum curve height for maximum power output, which depends on various conditions, such as external vibration strength, comb-drive dimensions, and initial electret charges. At the external acceleration magnitude of 0.02g and 0.05g, the device with curved beams can produce up to 2.9 times and 4.8 times higher power output, respectively, than one with straight beams for given device geometries. To the contrary, at lower and higher vibration magnitudes, straight-beam devices harvest more energy than curved-beam ones. Therefore, it can be concluded that the curved beam height needs to be carefully determined based on the conditions of the application, especially on the characteristics of the external vibration sources.Article Citation - WoS: 2Citation - Scopus: 2Analysis of Optical Gyroscopes With Vertically Stacked Ring Resonators(Tubitak Scientific & Technological Research Council Turkey, 2021) Hah, Dooyoung; 01. Abdullah Gül University; 02. Mühendislik Fakültesi; 02.05. Elektrik & Elektronik MühendisliğiWithout any moving part, optical gyroscopes exhibit superior reliability and accuracy in comparison to mechanical sensors. Microring-resonator-based optical gyroscopes emerged as alternatives for bulky conventional Sagnac interferometer sensors, especially attractive for applications with limited footprints. Previously, it has been reported that planar incorporation of multiple resonators does not bring about improvement in sensitivity for a given area because the increase in Sagnac phase accumulation does not outrun the increase of area. Therefore, it was naturally suggested to consider vertical stacking of ring resonators because then, the resonators can share the same footprint. In this work, sensitivity performances of such configurations with vertically stacked microring resonators are analyzed and compared to that of a basic (single-resonator) configuration. Through comprehensive study, it is learned that the sensitivity performance of the devices with vertically-stacked resonators (either with a single bus waveguide or with two bus waveguides) does not exceed that of the basic sensor device (single resonator with one bus waveguide), i.e. the basic structure is yet to be remained as the most efficient configuration.Conference Object Citation - WoS: 3Citation - Scopus: 3Analytical Design of MEMS Variable Capacitors Based on Shaped-Finger Comb-Drives(Springer Heidelberg, 2022) Hah, Dooyoung; 01. Abdullah Gül University; 02. Mühendislik Fakültesi; 02.05. Elektrik & Elektronik MühendisliğiA variable capacitor is one of the widely used components in radio frequency (RF) circuits. Variable capacitors can benefit from the microelectromechanical systems (MEMS) technology, to be equipped with attractive characteristics such as high quality factor and wide tuning range. One of the design goals for MEMS varactors has been to realize linear capacitance-voltage (C-V) characteristics, for which a design method is proposed in this paper, based on shaped-finger comb-drive actuators. The shaped-finger design method, originally developed for a tunable optical filter application by the author, is redeveloped in this work for a linear C-V varactor. Moreover, the conformal mapping method is employed in calculation of capacitances, making the whole design process more time-efficient, being almost all-analytical with the minimum usage of numerical analysis methods. Effects of sense capacitor finger shapes to the optimized drive capacitor finger shapes and the corresponding C-V characteristics are investigated as well. Variable capacitors with the shaped-finger design show linearity factor (LF)-defined as the maximum deviation from the perfect linear relationship-as good as 0.4%, enormously improved from that of the conventional constant-finger-gap devices (LF: 49.9%). Further probed by 3-D numerical analysis, the C-V characteristics of the designed variable capacitor show LF better than 2.62% in the case of constant-gap sense capacitors, and as good as 0.77% in the case of shaped-finger sense capacitors. Versatility of the design method is further demonstrated by presenting a varactor for linear resonant frequency-voltage (f-V) characteristics in voltage-controlled oscillator (VCO) applications. Finally, effects of etch bias, one of common fabrication imperfections, to the linearity of C-V characteristics are studied. The developed analytical design method with shaped fingers can find a wide range of applications where comb-drive actuators are used.Article Citation - WoS: 15Citation - Scopus: 17Analyzing Lifetime of Energy Harvesting Underwater Wireless Sensor Nodes(Wiley, 2020) Erdem, H. Emre; Gungor, V. Cagri; 01. Abdullah Gül UniversityUnderwater Wireless Sensor Networks (UWSNs) are utilized to monitor underwater environments that pose many challenges to researchers. One of the key complications of UWSNs is the difficulty of changing node batteries after their energy is depleted. This study aims to diminish the issues related to battery replacement by improving node lifetime. For this goal, three energy harvesting devices (turbine harvester, piezoelectric harvester, and hydrophone harvester) are analyzed to quantitate their impacts on node lifetime. In addition, two different power management schemes (schedule-driven and event-driven power management schemes) are combined with energy harvesters for further lifetime improvement. Performance evaluations via simulations show that energy harvesting methods joined by power management schemes can improve node lifetime substantially when actual conditions of Istanbul Bosporus Strait are considered. In this respect, turbine harvester makes the biggest impact and provides lifetime beyond 2000 days for most cases, while piezoelectric harvester can perform the same only for low duty cycle or event arrival values at short transmission ranges.Article Citation - WoS: 6Citation - Scopus: 8Anhedonia in Relation to Reward and Effort Learning in Young People With Depression Symptoms(MDPI, 2023) Frey, Anna-Lena; Kaya, M. Siyabend; Adeniyi, Irina; McCabe, Ciara; 01. Abdullah Gül University; 06. İnsan ve Toplum Bilimleri Fakültesi; 06.02. PsikolojiAnhedonia, a central depression symptom, is associated with impairments in reward processing. However, it is not well understood which sub-components of reward processing (anticipation, motivation, consummation, and learning) are impaired in association with anhedonia in depression. In particular, it is unclear how learning about different rewards and the effort needed to obtain them might be associated with anhedonia and depression symptoms. Therefore, we examined learning in young people (N = 132, mean age 20, range 17-25 yrs.) with a range of depression and anhedonia symptoms using a probabilistic instrumental learning task. The task required participants to learn which options to choose to maximize their reward outcomes across three conditions (chocolate taste, puppy images, or money) and to minimize the physical effort required to obtain the rewards. Additionally, we collected questionnaire measures of anticipatory and consummatory anhedonia, as well as subjective reports of "liking", "wanting" and "willingness to exert effort" for the rewards used in the task. We found that as anticipatory anhedonia increased, subjective liking and wanting of rewards decreased. Moreover, higher anticipatory anhedonia was significantly associated with lower reward learning accuracy, and participants demonstrated significantly higher reward learning than effort learning accuracy. To our knowledge, this is the first study observing an association of anhedonia with reward liking, wanting, and learning when reward and effort learning are measured simultaneously. Our findings suggest an impaired ability to learn from rewarding outcomes could contribute to anhedonia in young people. Future longitudinal research is needed to confirm this and reveal the specific aspects of reward learning that predict anhedonia. These aspects could then be targeted by novel anhedonia interventions.Article Citation - WoS: 7Citation - Scopus: 10An Ant Colony Optimisation Algorithm for Balancing Two-Sided U-Type Assembly Lines With Sequence-Dependent Set-Up Times(Springer India, 2018) Delice, Yilmaz; Aydogan, Emel Kizilkaya; Soylemez, Ismet; Ozcan, Ugur; 01. Abdullah Gül University; 07. Fen Bilimleri Enstitüsü; 07.03. Endüstri Mühendisliği Anabilim DalıSome practical arrangements in assembly lines necessitate set-up times between consecutive tasks. To create more realistic models of operations, set-up times must be considered. In this study, a sequence-dependent set-up times approach for two-sided u-type assembly line (TUAL) structures is proposed for the first time. Previous studies on TUAL have not included set-up times in their analyses. Furthermore, an algorithm based on the Ant Colony Optimization (ACO) algorithm, which is using a heuristic priority rule based procedure has been proposed in order to solve this new approach. In this paper, we look at the sequence-dependent set-up times between consecutive tasks and consecutive cycles, called the "forward set-up time'' and the "backward set-up time'', respectively. Additionally, we examine the "crossover set-up time'', which arises from a new sequence of tasks in a crossover station. In order to model more realistic assembly line configurations, it is necessary to include sequence-dependent set-up times when computing all of the operational times such as task starting times and finishing times as well as the total workstation time. In this study, the proposed approach aims to minimize the number of mated-stations as the primary objective and to minimize the number of total workstations as a secondary objective. In order to evaluate the efficiency of the proposed algorithm, a computational study is performed. As can be seen from the experimental results the proposed approach finds promising results for all literature-test problems.
