Browsing by Author "Mutlu, M."

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Open Access
Asymmetric chiral metamaterial circular polarizer based on four U-shaped split ring resonators
(Optical Society of America, 2011-04-28) Mutlu, M.; Akosman, A. E.; Serebryannikov, A. E.; Özbay, Ekmel
An asymmetric chiral metamaterial structure is constructed by using four double-layered U-shaped split ring resonators, which are each rotated by 90° with respect to their neighbors. The peculiarity of the suggested design is that the sizes of the electrically and magnetically excited rings are different, which allows for equalizing the orthogonal components of the electric field at the output interface with a 90° phase difference when the periodic structure is illuminated by an x-polarized wave. As a result, left-hand circular polarization and right-hand circular polarization are obtained in transmission at 5:1 GHz and 6:4 GHz, respectively. The experiment results are in good agreement with the numerical results.
Open Access
Asymmetric transmission of linearly polarized waves and polarization angle dependent wave rotation using a chiral metamaterial
(Optical Society of America, 2011-07-18) Mutlu, M.; Akosman, A. E.; Serebryannikov, A. E.; Özbay, Ekmel
An electrically thin chiral metamaterial structure composed of four U-shaped split ring resonator pairs is utilized in order to realize polarization rotation that is dependent on the polarization of the incident wave at 6.2 GHz. The structure is optimized such that a plane wave that is linearly polarized at an arbitrary angle is an eigenwave of the system at this frequency. The analytical relation between the incident polarization and the polarization rotation is derived using transmission matrices. Furthermore, the proposed structure exhibits an asymmetric transmission of linearly polarized waves at 6.2 GHz. Plane waves traveling in opposite but perpendicular directions to the material plane are rotated by different angles. On the other hand, four incident polarization angles have been found for the same structure, at which the transmission is symmetric. The experiment results are in good agreement with the numerical results. (C)2011 Optical Society of America
Open Access
Biocatalytic protein membranes fabricated by electrospinning
(Elsevier B.V., 2016) Kabay, G.; Kaleli, G.; Sultanova, Z.; Ölmez, T. T.; Şeker, U. Ö. Ş.; Mutlu, M.
In this study, a protein-based catalytic membrane was produced by electrospinning. Membrane activity was characterised in terms of response current for various glucose concentrations. We focused on the preparation of a scaffold by converting a globular protein to other structural forms using catastrophic solvents. A scaffolding protein, bovine serum albumin, and an enzyme, glucose oxidase (GOD), were selected as a model natural carrier matrix and a biologically active agent, respectively. Beta-mercaptoethanol (β-ME) was used to convert the globular protein to an amyloid-like form. A structural stabilising agent, 2,2,2-triflouroethanol (TFE), was used to maintain the final α-helical structure of the amyloid-like protein. The TFE:PBS (phosphate-buffered saline) ratio and various electrospinning parameters were analysed to minimise activity loss. Using this approach, we applied electrospinning to an active enzyme to obtain biocatalytic nanofibrous membranes. After optimising the protein electrospinning process, the activities of the protein nanofibrous membranes were monitored. GOD remained active in the new membrane structure. The highest enzyme activity was observed for the membranes prepared with a 1.5:1 (v:v) TFE:PBS solvent ratio. In that particular case, the immobilized enzyme created a current of 0.7 μA and the apparent activity was 2547 ± 132 U/m2.
Open Access
Broadband circular polarizer based on high-contrast gratings
(Optical Society of America, 2012-05-30) Mutlu, M.; Akosman, A. E.; Özbay, Ekmel
A circular polarizer, which is composed of periodic and two-dimensional dielectric high-contrast gratings, is designed theoretically such that a unity conversion efficiency is achieved at λ0 = 1.55 μm. The operation is obtained by the achievement of the simultaneous unity transmission of transverse magnetic and transverse electric waves with a phase difference of π/2, meaning that an optimized geometrical anisotropy is accomplished. By the utilization of the rigorous coupled-wave analysis and finite-difference time-domain methods, it is shown that a percent bandwidth of ∼50% can be achieved when the operation bandwidth is defined as the wavelengths for which the conversion efficiency exceeds 0.9.
Open Access
Broadband quarter-wave plates at near-infrared using high-contrast gratings
(2013) Mutlu, M.; Akosman, A.E.; Kurt G.; Gokkavas, M.; Özbay, Ekmel
In this paper, we report the theoretical and experimental possibility of achieving a quarter-wave plate regime by using high-contrast gratings, which are binary, vertical, periodic, near-wavelength, and two-dimensional high refractive index gratings. Here, we investigate the characteristics of two distinct designs, the first one being composed of silicon-dioxide and silicon, and the second one being composed of silicon and sapphire. The suggested quarter-wave plate regime is achieved by the simultaneous optimization of the transverse electric and transverse magnetic transmission coefficients, TTE and TTM, respectively, and the phase difference between these transmission coefficients, such that |TTM| ≅ |TTE| and \TTM - \TTE ≅ -/2. As a result, a unity circular polarization conversion efficiency is achieved atλ0 = 1.55 μm for both designs. For the first design, we show the obtaining of unity conversion efficiency by using a theoretical approach, which is inspired by the periodic waveguide interpretation, and rigorous coupled-wave analysis (RCWA). For the second design, we demonstrate the unity conversion efficiency by using the results of finite-difference time-domain (FDTD) simulations. Furthermore, the FDTD simulations, where material dispersion is taken into account, suggest that an operation percent bandwidth of 51% can be achieved for the first design, where the experimental results for the second design yield a bandwidth of 33%. In this context, we define the operation regime as the wavelength band for which the circular conversion efficiency is larger than 0.9. © 2013 SPIE.
Open Access
Chiral metamaterials: from optical activity and negative refractive index to asymmetric transmission
(IOP Publishing, 2013-01-30) Li, Z.; Mutlu, M.; Özbay, Ekmel
We summarize the progress in the development and application of chiral metamaterials. After a brief review of the salient features of chiral metamaterials, such as giant optical activity, circular dichroism, and negative refractive index, the common method for the retrieval of effective parameters for chiral metamaterials is surveyed. Then, we introduce some typical chiral structures, e.g., chiral metamaterial consisting of split ring resonators, complementary chiral metamaterial, and composite chiral metamaterial, on the basis of the studies of the authors’ group. The coupling effect during the construction of bulk chiral metamaterials is mentioned and discussed. We introduce the application of bianisotropic chiral structures in the field of asymmetric transmission. Finally, we mention a few directions for future research on chiral metamaterials.
Open Access
Compact wavelength de-multiplexer design using slow light regime of photonic crystal waveguides
(Optical Society of American (OSA), 2011) Akosman, A.E.; Mutlu, M.; Kurt H.; Özbay, Ekmel
We demonstrate the operation of a compact wavelength demultiplexer using cascaded single-mode photonic crystal waveguides utilizing the slow light regime. By altering the dielectric filling factors of each waveguide segment, we numerically and experimentally show that different frequencies are separated at different locations along the waveguide. In other words, the beams of different wavelengths are spatially dropped along the transverse to the propagation direction. We numerically verified the spatial shifts of certain wavelengths by using the two-dimensional finite-difference time-domain method. The presented design can be extended to de-multiplex more wavelengths by concatenating additional photonic crystal waveguides with different filling factors. © 2011 Optical Society of America.
Open Access
Developing a transducer based on localized surface plasmon resonance (LSPR) of gold nanostructures for nanobiosensor applications
(Trans Tech Publications, 2013) Turhan, Adil Burak; Ataman, D.; Çakmakyapan, S.; Mutlu, M.; Özbay, Ekmel; Vlachos, D. S.; Hristoforou, E.
In this work, we report the nanofabrication, optical characterization, and electromagnetic modeling of various nanostructure arrays for localized surface plasmon resonance (LSPR) based biosensing studies. Comparison of the experimental results and simulation outputs of various nanostructure arrays was made and a good correspondence was achieved.
Open Access
Dielectric inspired scaling of polarization conversion subwavelength resonances in open ultrathin chiral structures
(A I P Publishing LLC, 2015) Serebryannikov, A. E.; Mutlu, M.; Özbay, Ekmel
It is shown that the scaling of subwavelength resonances in open ultrathin chiral structures can be obtained by varying only the permittivity of dielectric spacers, while multiband one-way polarization conversion and related asymmetric transmission remain possible. These features are quite general and obtainable in a wide range of parameter variation. Surprisingly, the difference in the power of ε for the classical ε-1/2 scaling rule and the empirical rules obtained in the present letter does not exceed 22%, giving an important entry point for future theoretical studies and design strategies. Both spectral scaling and conservation of the polarization characteristics can be achieved by using either tunneling or real-index impedance matching. The scaled structures with strong polarization and directional selectivity may have thickness of λ/100 and smaller. © 2015 AIP Publishing LLC.
Open Access
Diodelike asymmetric transmission of linearly polarized waves using magnetoelectric coupling and electromagnetic wave tunneling
(American Physical Society, 2012-05-24) Mutlu, M.; Akosman, A. E.; Serebryannikov, A. E.; Özbay, Ekmel
An asymmetric, reciprocal, diffraction-free transmission of linearly polarized waves in a new diodelike, three-layer, ultrathin, chiral structure is studied theoretically and experimentally. The exploited physical mechanism is based on the maximization of the cross-polarized transmission in one direction due to the polarization selectivity dictated by the peculiar eigenstate combination, which is efficiently controlled by the electromagnetic tunneling through the metallic subwavelength mesh sandwiched between these layers. Simulation and microwave experiment results demonstrate a nearly total intensity transmission at normal incidence in one direction and a small intensity transmission in the opposite direction.
Open Access
Experimental realization of a high-contrast grating based broadband quarter-wave plate
(Optical Society of America, 2012-12-03) Mutlu, M.; Akosman, A. E.; Kurt, G.; Gokkavas, M.; Özbay, Ekmel
Fabrication and experimental characterization of a broadband quarter-wave plate, which is based on two-dimensional and binary silicon high-contrast gratings, are reported. The quarter-wave plate feature is achieved by the utilization of a regime, in which the proposed grating structure exhibits nearly total and approximately equal transmission of transverse electric and transverse magnetic waves with a phase difference of approximately pi/2. The numerical and experimental results suggest a percent bandwidth of 42% and 33%, respectively, if the operation regime is defined as the range for which the conversion efficiency is higher than 0.9. A compact circular polarizer can be implemented by combining the grating with a linear polarizer. (C) 2012 Optical Society of America
Open Access
Highly asymmetric transmission of linearly polarized waves realized with a multilayered structure including chiral metamaterials
(IOP Publishing, 2014) Li, Z.; Mutlu, M.; Özbay, Ekmel
We numerically and experimentally demonstrate highly asymmetric transmission of linearly polarized waves with a multilayered metallic structure. The whole structure has a subwavelength thickness and consists of a thin slab of chiral metamaterial sandwiched between two 90° twisted linear polarizers. The chiral metamaterial is made of two sets of twisting cross wires that can rotate the polarization by 90° at resonance, and the two linear polarizers are simple metallic grating polarizers. The operation principle of the whole structure can be well interpreted by using the Jones matrix method. Our experimental results also verify that chiral metamaterials can be safely integrated into complex structures and treated as an effective medium as long as their resonant modes are not affected by the environment.
Open Access
miR-200c: a versatile watchdog in cancer progression, EMT, and drug resistance
(Springer Verlag, 2016-06) Mutlu, M.; Raza, U.; Saatci, Ö.; Eyüpoğlu, E.; Yurdusev, E.; Şahin, Ö.
MicroRNAs (miRNAs) are 20–22-nucleotide small endogenous non-coding RNAs which regulate gene expression at post-transcriptional level. In the last two decades, identification of almost 2600 miRNAs in human and their potential to be modulated opened a new avenue to target almost all hallmarks of cancer. miRNAs have been classified as tumor suppressors or oncogenes depending on the phenotype they induce, the targets they modulate, and the tissue where they function. miR-200c, an illustrious tumor suppressor, is one of the highly studied miRNAs in terms of development, stemness, proliferation, epithelial-mesenchymal transition (EMT), therapy resistance, and metastasis. In this review, we first focus on the regulation of miR-200c expression and its role in regulating EMT in a ZEB1/E-cadherin axis-dependent and ZEB1/E-cadherin axis-independent manner. We then describe the role of miR-200c in therapy resistance in terms of multidrug resistance, chemoresistance, targeted therapy resistance, and radiotherapy resistance in various cancer types. We highlight the importance of miR-200c at the intersection of EMT and chemoresistance. Furthermore, we show how miR-200c coordinates several important signaling cascades such as TGF-β signaling, PI3K/Akt signaling, Notch signaling, VEGF signaling, and NF-κB signaling. Finally, we discuss miR-200c as a potential prognostic/diagnostic biomarker in several diseases, but mainly focusing on cancer and its potential application in future therapeutics.
Open Access
MiR-564 acts as a dual inhibitor of PI3K and MAPK signaling networks and inhibits proliferation and invasion in breast cancer
(Nature Publishing Group, 2016) Mutlu, M.; Saatci, Ö.; Ansari, S. A.; Yurdusev, E.; Shehwana, H.; Konu, Ö.; Raza, U.; Şahin, Ö.
Dysregulation of PI3K and MAPK pathways promotes uncontrolled cell proliferation, apoptotic inhibition and metastasis. Individual targeting of these pathways using kinase inhibitors has largely been insufficient due to the existence of cross-talks between these parallel cascades. MicroRNAs are small non-coding RNAs targeting several genes simultaneously and controlling cancer-related processes. To identify miRNAs repressing both PI3K and MAPK pathways in breast cancer, we re-analyzed our previous miRNA mimic screen data with reverse phase protein array (RPPA) output, and identified miR-564 inhibiting both PI3K and MAPK pathways causing markedly decreased cell proliferation through G1 arrest. Moreover, ectopic expression of miR-564 blocks epithelial-mesenchymal transition (EMT) and reduces migration and invasion of aggressive breast cancer cells. Mechanistically, miR-564 directly targets a network of genes comprising AKT2, GNA12, GYS1 and SRF, thereby facilitating simultaneous repression of PI3K and MAPK pathways. Notably, combinatorial knockdown of these target genes using a cocktail of siRNAs mimics the phenotypes exerted upon miR-564 expression. Importantly, high miR-564 expression or low expression of target genes in combination is significantly correlated with better distant relapse-free survival of patients. Overall, miR-564 is a potential dual inhibitor of PI3K and MAPK pathways, and may be an attractive target and prognostic marker for breast cancer. © The Author(s) 2016.
Open Access
The miR-644a/CTBP1/p53 axis suppresses drug resistance by simultaneous inhibition of cell survival and epithelialmesenchymal transition in breast cancer
(Impact Journals LLC, 2016) Raza, U.; Saatci, O.; Uhlmann, S.; Ansari, S. A.; Eyüpoglu, E.; Yurdusev, E.; Mutlu, M.; Ersan, P. G.; Altundağ, M. K.; Zhang, J. D.; Dogan, H. T.; Güler, G.; Şahin, Ö.
Tumor cells develop drug resistance which leads to recurrence and distant metastasis. MicroRNAs are key regulators of tumor pathogenesis; however, little is known whether they can sensitize cells and block metastasis simultaneously. Here, we report miR-644a as a novel inhibitor of both cell survival and EMT whereby acting as pleiotropic therapy-sensitizer in breast cancer. We showed that both miR-644a expression and its gene signature are associated with tumor progression and distant metastasis-free survival. Mechanistically, miR-644a directly targets the transcriptional co-repressor C-Terminal Binding Protein 1 (CTBP1) whose knock-outs by the CRISPRCas9 system inhibit tumor growth, metastasis, and drug resistance, mimicking the phenotypes induced by miR-644a. Furthermore, downregulation of CTBP1 by miR-644a upregulates wild type- or mutant-p53 which acts as a 'molecular switch' between G1-arrest and apoptosis by inducing cyclin-dependent kinase inhibitor 1 (p21, CDKN1A, CIP1) or pro-apoptotic phorbol-12-myristate-13-acetate-induced protein 1 (Noxa, PMAIP1), respectively. Interestingly, an increase in mutant-p53 by either overexpression of miR-644a or downregulation of CTBP1 was enough to shift this balance in favor of apoptosis through upregulation of Noxa. Notably, p53- mutant patients, but not p53-wild type ones, with high CTBP1 have a shorter survival suggesting that CTBP1 could be a potential prognostic factor for breast cancer patients with p53 mutations. Overall, re-activation of the miR-644a/CTBP1/p53 axis may represent a new strategy for overcoming both therapy resistance and metastasis.
Open Access
Multiband one-way polarization conversion in complementary split-ring resonator based structures by combining chirality and tunneling
(OSA - The Optical Society, 2015) Serebryannikov, A. E.; Beruete, M.; Mutlu, M.; Özbay, Ekmel
Multiband one-way polarization conversion and strong asymmetry in transmission inspired by it are demonstrated in ultrathin sandwiched structures that comprise two twisted aperture-type arrays of complementary split-ring resonators (CSRRs), metallic mesh, and dielectric layers. The basic features of the resulting mechanism originate from the common effect of chirality and tunneling. The emphasis is put on the (nearly) perfect polarization conversion of linear incident polarization into the orthogonal one and related diodelike asymmetric transmission within multiple narrow bands. Desired polarization conversion can be obtained at several resonances for one of the two opposite incidence directions, whereas transmission is fully blocked for the other one. The resonances, at which the (nearly) perfect conversion takes place, are expected to be inherited from similar structures with parallel, i.e., not rotated CSRR arrays that do not enable chirality and, thus, polarization conversion. It is found that the basic transmission and polarization conversion features and, thus, the dominant physics are rather general, enabling efficient engineering of such structures. The lowest-frequency resonance can be obtained in structures made of conventional materials with total thickness less than λ?/ 50 and up to ten such resonances can correspond to thickness less than λ ?/ 20 . ©2015 Optical Society of America.
Open Access
Nanofabrication and plasma polymerization assisted surface modification of a transducer based on localized surface plasmon resonance of gold nanostructure arrays for biosensor applications
(S P I E - International Society for Optical Engineering, 2012-07-31) Turhan, A. B.; Ataman, D.; Sen, Y.; Mutlu, M.; Özbay, Ekmel
The nanofabrication and surface modification of a transducer based on localized surface plasmon resonance (LSPR) of gold nanostructure arrays for biosensing was studied. We used electron beam lithography for the nanopatterning technique, which let us choose LSPR sensor properties by providing immense control over nanostructural geometry. A critical step in the utilization of this transducer is to form a selective biolayer over the gold nanostructures. We applied plasma polymerization and wet chemistry techniques for ethylenediamine (EDA) modification and glutaraldehyde immobilization as intermediate layers, respectively. The gold nanostructure arrays were primarily modified using EDA in order to activate the surface with amine groups that are cross-linked with later added avidin molecules by the help of glutaraldhyde layer residing in between. The success of plasma polymerization was validated with x-ray photoelectron spectroscopy measurements. As a last step, we introduced biotin to the surface (biotin has a high affinity for avidin). We were able to detect the LSPR resonance wavelength shift in the transmission spectra at each step of modification, including the avidin-biotin interaction, which acts as a model for specific molecule detection using LSPR. (C) 2012 Society of Photo-Optical Instrumentation Engineers (SPIE).
Open Access
One-way reciprocal spoof surface plasmons and relevant reversible diodelike beaming
(American Physical Society, 2013-05-15) Mutlu, M.; Cakmakyapan, S.; Serebryannikov, A. E.; Özbay, Ekmel
One - way excitation of spoof surface plasmons (SPs) and strongly pronounced diodelike extraordinary transmission of linearly polarized waves in the beaming regime can be obtained by combining spoof SPs and cross-polarization conversion resonances. The reciprocal composite structure that is suggested to realize this mechanism consists of a symmetric metallic grating with a subwavelength slit and a metamaterial based ultrathin 90 degrees polarization rotator and, therefore, shows the broken spatial inversion symmetry. In contrast to the earlier studies of SP inspired transmission through subwavelength slits, asymmetric (one-way) beaming is demonstrated at normal incidence and for both s- and p-polarized incident waves. Furthermore, as an implication of Lorentz reciprocity, the studied diodelike mechanism is reversible, which manifests itself in that transmission is significant for one of the two opposite illumination directions at s polarization and for the other direction at p polarization. The obtained numerical and experimental results verify the general idea and enable us to select the optimal operation regimes.
Open Access
Parametric power spectral density analysis of noise from instrumentation in MALDI TOF mass spectrometry
(2007) Shin H.; Mutlu, M.; Koomen J.M.; Markey, M.K.
Noise in mass spectrometry can interfere with identification of the biochemical substances in the sample. For example, the electric motors and circuits inside the mass spectrometer or in nearby equipment generate random noise that may distort the true shape of mass spectra. This paper presents a stochastic signal processing approach to analyzing noise from electrical noise sources (i.e., noise from instrumentation) in MALDI TOF mass spectrometry. Noise from instrumentation was hypothesized to be a mixture of thermal noise, 1/f noise, and electric or magnetic interference in the instrument. Parametric power spectral density estimation was conducted to derive the power distribution of noise from instrumentation with respect to frequencies. As expected, the experimental results show that noise from instrumentation contains 1/f noise and prominent periodic components in addition to thermal noise. These periodic components imply that the mass spectrometers used in this study may not be completely shielded from the internal or external electrical noise sources. However, according to a simulation study of human plasma mass spectra, noise from instrumentation does not seem to affect mass spectra significantly. In conclusion, analysis of noise from instrumentation using stochastic signal processing here provides an intuitive perspective on how to quantify noise in mass spectrometry through spectral modeling.
Open Access
The effect of SARS-CoV-2 virus on resting-state functional connectivity during adolescence: Investigating brain correlates of psychotic-like experiences and SARS-CoV-2 related inflammation response
(Elsevier B.V., 2023-12) Yilmaz Kafali, H.; Dasgin, Hacer; Sahin Cevik, Didenur; Sozan, S. S.; Oguz, Kader K.; Mutlu, M.; Ozkaya Parlakay, A.; Toulopoulou, Timothea
We first aimed to investigate resting-state functional connectivity (rs-FC) differences between adolescents exposed to SARS-CoV-2 and healthy controls. Secondly, the moderator effect of PLEs on group differences in rs-FC was examined. Thirdly, brain correlates of inflammation response during acute SARS-CoV-2 infection were investigated. Eighty-two participants aged between 14 and 24 years (SARS-CoV-2 (n = 35), controls (n = 47)) were examined using rs-fMRI. Seed-based rs-FC analysis was performed. The positive subscale of Community Assessment of Psychotic Experiences-42 (CAPE-Pos) was used to measure PLEs. The SARS-CoV-2 group had a lesser rs-FC within sensorimotor network (SMN), central executive network (CEN) and language network (LN), but an increased rs-FC within visual network (VN) compared to controls. No significant differences were detected between the groups regarding CAPE-Pos-score. However, including CAPE-Pos as a covariate, we found increased rs-FC within CEN and SN in SARS-CoV-2 compared to controls. Among the SARS-CoV-2 group, neutrophil/lymphocyte and thrombocyte*neutrophil/lymphocyte ratio was correlated with decreased/increased FC within DMN and SN, and increased FC within CEN. Our results showed rs-FC alterations within the SMN, CEN, LN, and VN among adolescents exposed to SARS-CoV-2. Moreover, changes in rs-FC associated with PLEs existed in these adolescents despite the absence of clinical changes. Furthermore, inflammation response was correlated with alterations in FC within the triple network system.