Browsing by Author "Yilmaz, M."

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Open Access
Adopting augmented reality for the purpose of software development process training and improvement: an exploration
(Springer, Cham, 2018) Ohri, İ.; Öge, İ.; Orkun, B.; Yilmaz, M.; Tüzün, Eray; Clarke, P.; O’Connor, R. V.
Augmented reality (AR) is a technological field of study that bridges the physical and digital world together with a view to improving user experience. AR holds great potential to change the delivery of software services or software process improvement by utilizing a specific set of components. The purpose of this exploratory study is to propose an integration framework to support AR for improving the onboarding process, notably in introducing new hires to the development process while performing their daily tasks. In addition, it also aims to enhance the software development workflow process using AR. Similar to a GPS device that can guide you from point A to point B, our goal is to create software artifacts like navigation components where software teams may benefit from digitally enhanced working conditions provided using AR. After conducting a review in the literature, we confirmed that there is lack of studies about the combination of augmented reality with software engineering disciplines for onboarding. In this paper, we formalized our approach based on the benefits of AR. Ultimately; we propose an AR-based preliminary model for improving the software development process.
Open Access
All-silicon ultra-broadband infrared light absorbers
(Nature Publishing Group, 2016) Gorgulu, K.; Gok, A.; Yilmaz, M.; Topalli, K.; Blylkll, N.; Okyay, Ali Kemal
Absorbing infrared radiation efficiently is important for critical applications such as thermal imaging and infrared spectroscopy. Common infrared absorbing materials are not standard in Si VLSI technology. We demonstrate ultra-broadband mid-infrared absorbers based purely on silicon. Broadband absorption is achieved by the combined effects of free carrier absorption, and vibrational and plasmonic absorption resonances. The absorbers, consisting of periodically arranged silicon gratings, can be fabricated using standard optical lithography and deep reactive ion etching techniques, allowing for cost-effective and wafer-scale fabrication of micro-structures. Absorption wavebands in excess of 15 micrometers (5-20 μm) are demonstrated with more than 90% average absorptivity. The structures also exhibit broadband absorption performance even at large angles of incidence (θ = 50°), and independent of polarization.
Open Access
Canonical Wnt signaling is antagonized by noncanonical Wnt5a in hepatocellular carcinoma cells
(BioMed Central, 2009) Yuzugullu, H.; Benhaj, K.; Ozturk, N.; Senturk, S.; Celik, E.; Toylu, A.; Tasdemir, N.; Yilmaz, M.; Erdal, E.; Akcali, K. C.; Atabey, N.; Ozturk, M.
Background: β-catenin mutations that constitutively activate the canonical Wnt signaling have been observed in a subset of hepatocellular carcinomas (HCCs). These mutations are associated with chromosomal stability, low histological grade, low tumor invasion and better patient survival. We hypothesized that canonical Wnt signaling is selectively activated in well-differentiated, but repressed in poorly differentiated HCCs. To this aim, we characterized differentiation status of HCC cell lines and compared their expression status of Wnt pathway genes, and explored their activity of canonical Wnt signaling. Results: We classified human HCC cell lines into "well-differentiated" and "poorly differentiated" subtypes, based on the expression of hepatocyte lineage, epithelial and mesenchymal markers. Poorly differentiated cell lines lost epithelial and hepatocyte lineage markers, and overexpressed mesenchymal markers. Also, they were highly motile and invasive. We compared the expression of 45 Wnt pathway genes between two subtypes. TCF1 and TCF4 factors, and LRP5 and LRP6 co-receptors were ubiquitously expressed. Likewise, six Frizzled receptors, and canonical Wnt3 ligand were expressed in both subtypes. In contrast, canonical ligand Wnt8b and noncanonical ligands Wnt4, Wnt5a, Wnt5b and Wnt7b were expressed selectively in well- and poorly differentiated cell lines, respectively. Canonical Wnt signaling activity, as tested by a TCF reporter assay was detected in 80% of well-differentiated, contrary to 14% of poorly differentiated cell lines. TCF activity generated by ectopic mutant β-catenin was weak in poorly differentiated SNU449 cell line, suggesting a repressive mechanism. We tested Wnt5a as a candidate antagonist. It strongly inhibited canonical Wnt signaling that is activated by mutant β-catenin in HCC cell lines. Conclusion: Differential expression of Wnt ligands in HCC cells is associated with selective activation of canonical Wnt signaling in well-differentiated, and its repression in poorly differentiated cell lines. One potential mechanism of repression involved Wnt5a, acting as an antagonist of canonical Wnt signaling. Our observations support the hypothesis that Wnt pathway is selectively activated or repressed depending on differentiation status of HCC cells. We propose that canonical and noncanonical Wnt pathways have complementary roles in HCC, where the canonical signaling contributes to tumor initiation, and noncanonical signaling to tumor progression. © 2009 Yuzugullu et al; licensee BioMed Central Ltd.
Open Access
High-conductivity silicon based spectrally selective plasmonic surfaces for sensing in the infrared region
(Institute of Physics Publishing, 2017) Gorgulu, K.; Gok, A.; Yilmaz, M.; Topalli K.; Okyay, Ali Kemal
Plasmonic perfect absorbers have found a wide range of applications in imaging, sensing, and light harvesting and emitting devices. Traditionally, metals are used to implement plasmonic structures. For sensing applications, it is desirable to integrate nanophotonic active surfaces with biasing and amplification circuitry to achieve monolithic low cost solutions. Commonly used plasmonic metals such as Au and Ag are not compatible with standard silicon complementary metal-oxide-semiconductor (CMOS) technology. Here we demonstrate plasmonic perfect absorbers based on high conductivity silicon. Standard optical lithography and reactive ion etching techniques were used for the patterning of the samples. We present computational and experimental results of surface plasmon resonances excited on a silicon surface at normal and oblique incidences. We experimentally demonstrate our absorbers as ultra-low cost, CMOS-compatible and efficient refractive index sensing surfaces. The experimental results reveal that the structure exhibits a sensitivity of around 11 000 nm/RIU and a figure of merit of up to 2.5. We also show that the sensing performance of the structure can be improved by increasing doping density.
Open Access
Immobilization of laccase on itaconic acid grafted and Cu ( II ) ion chelated chitosan membrane for bioremediation of hazardous materials
(Wiley, 2012) Bayramoglu, G.; Gursel, I.; Yilmaz, M.; Arica, M. Y.
Background: Chitosan membranes were formed through a phase inversion technique and then cross-linked with epichlorohydrin (CHX). Heterogeneous graft copolymerization of itaconic acid (IA) onto membrane was carried out with different monomer concentrations (CHX-g-p(IA)). The membrane properties such as equilibrium swelling ratio, porosity, and contact angle were measured, together with analysis by scanning electron microscopy (SEM), energy dispersive analysis of X-rays (EDAX), atomic force microscopy (AFM), and Fourier transform infrared (FTIR) spectroscopy. Results: The Cu(II) ion incorporated membranes (i.e. CHX-g-p(IA)-Cu(II)) were used for reversible immobilization of laccase using CHX-g-p(IA) membrane as a control system. Maximum laccase adsorption capacities of the CHX-g-p(IA) and CHX-g-p(IA)-Cu(II) membranes (with 9.7% grafting yield) were found to be 6.3 and 17.6 mg mL -1 membrane at pH 4.0 and 6.0, respectively. The K m value for immobilized laccase on CHX-g-p(IA)-Cu(II) (4.16 × 10 -2 mmol L -1) was 2.11-fold higher than that of free enzyme (1.97 × 10 -2 mmol L -1). Finally, the immobilized laccase was used in a batch system for degradation of three different dyes (Reactive Black 5, RB5; Cibacron Blue F3GA, CB; and Methyl Orange, MO). The immobilized laccase on CHX-g-p(IA)-Cu(II) membrane was more effective for removal of MO dye than removal of CB and RB5 dyes. CONCLUSION: Flexibility of the enzyme immobilized grafted polymer chains is expected to provide easy reaction conditions without diffusion limitation for substrate dye molecules and their products. The support described, prepared from green chemicals, can be used for the immobilization of industrially important enzymes. © 2012 Society of Chemical Industry.
Open Access
Nanoscale selective area atomic layer deposition of TiO2 using e-beam patterned polymers
(Royal Society of Chemistry, 2016) Haider A.; Yilmaz, M.; Deminskyi, P.; Eren, H.; Bıyıklı, Necmi
Here, we report nano-patterning of TiO2via area selective atomic layer deposition (AS-ALD) using an e-beam patterned growth inhibition polymer. Poly(methylmethacrylate) (PMMA), polyvinylpyrrolidone (PVP), and octafluorocyclobutane (C4F8) were the polymeric materials studied where PMMA and PVP were deposited using spin coating and C4F8 was grown using inductively coupled plasma (ICP) polymerization. TiO2 was grown at 150 °C using tetrakis(dimethylamido) titanium (TDMAT) and H2O as titanium and oxygen precursors, respectively. Contact angle, scanning electron microscopy (SEM), spectroscopic ellipsometry, and X-ray photoelectron spectroscopy (XPS) measurements were performed to investigate the blocking/inhibition effectiveness of polymer layers for AS-ALD of TiO2. TiO2 was grown with different numbers of growth cycles (maximum = 1200 cycles) on PMMA, PVP, and C4F8 coated substrates, where PMMA revealed complete growth inhibition up to the maximum number of growth cycles. On the other hand, PVP was able to block TiO2 growth up to 300 growth cycles only, whereas C4F8 showed no TiO2-growth blocking capability. Finally, mm-, μm-, and nm-scale patterned selective deposition of TiO2 was demonstrated exploiting a PMMA masking layer that has been patterned using e-beam lithography. SEM, energy-dispersive X-ray spectroscopy (EDX) line scan, EDX elemental mapping, and XPS line scan measurements cumulatively confirmed the self-aligned deposition of TiO2 features. The results presented for the first time demonstrate the feasibility of achieving self-aligned TiO2 deposition via TDMAT/H2O precursor combination and e-beam patterned PMMA blocking layers with a complete inhibition for >50 nm-thick films.
Open Access
Practical multi-featured perfect absorber utilizing high conductivity silicon
(Institute of Physics Publishing, 2016) Gok, A.; Yilmaz, M.; Bıyıklı, N.; Topallı, K.; Okyay, Ali Kemal
We designed all-silicon, multi-featured band-selective perfect absorbing surfaces based on CMOS compatible processes. The center wavelength of the band-selective absorber can be varied between 2 and 22 μm while a bandwidth as high as 2.5 μm is demonstrated. We used a silicon-on-insulator (SOI) wafer which consists of n-type silicon (Si) device layer, silicon dioxide (SiO2) as buried oxide layer, and n-type Si handle layer. The center wavelength and bandwidth can be tuned by adjusting the conductivity of the Si device and handle layers as well as the thicknesses of the device and buried oxide layers. We demonstrate proof-of-concept absorber surfaces experimentally. Such absorber surfaces are easy to microfabricate because the absorbers do not require elaborate microfabrication steps such as patterning. Due to the structural simplicity, low-cost fabrication, wide spectrum range of operation, and band properties of the perfect absorber, the proposed multi-featured perfect absorber surfaces are promising for many applications. These include sensing devices, surface enhanced infrared absorption applications, solar cells, meta-materials, frequency selective sensors and modulators. © 2016 IOP Publishing Ltd.
Open Access
Serious game plug-in experience for devops
(Rheinisch-Westfaelische Technische Hochschule Aachen, 2018) Üsfekes, Ç.; Macit, Y.; Yilmaz, M.; Tüzün, Eray
In terms of DevOps, efficiency and speed are important dimensions that define customer satisfaction. With serious game applications, it is aimed to make the everyday industrial software efforts more efficient and faster in a competitive environment. DevOps activities potentially could be gamified to provide a competitive environment where the participants are awarded to increase productivity in a software development environment. Defect management is one of the most important components in DevOps activities in terms of customer satisfaction. In order to solve the detected bug in a shorter amount of time, the engineers participate in a competitive environment, commit to a bid to resolve bug faster, where the results are observable by other engineers in a game environment. In this study, the development and game flow of an auction-based serious game application for effective defect management is described.