Browsing by Author "Dana, Aykutlu"

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Open Access
All-chalcogenide variable infrared filter
(SPIE, 2009) Kondakcı, H. Esat; Köyle, Özlem; Yaman, Mecit; Dana, Aykutlu; Bayındır, Mehmet
We present the design, fabrication, characterization of spatially variable infrared filter and a demonstration of the filter as a simple infrared spectrometer. A varying photonic band gap filter which consists of thermally evaporated, high refractive index contrast amorphous chalcogenide glass multilayers, makes the structure suitable to be used as spectrometer. Due to graded thickness structure, the filter exhibits a position dependent stop band and a cavity mode ranging from 2 to 8 μm wavelengths. It is demonstrated that the filter can be used to detect absorption peaks of common gases in the cavity mode range of the filter. © 2009 SPIE.
Open Access
Biocompatible electroactive tetra (aniline)-conjugated peptide nanofibers for neural differentiation
(American Chemical Society, 2018) Arioz, Idil; Erol, Ozlem; Bakan, Gokhan; Dikecoglu, F. Begum; Topal, Ahmet E.; Urel, Mustafa; Dana, Aykutlu; Tekinay, Ayse B.; Güler, Mustafa O.
Peripheral nerve injuries cause devastating problems for the quality of patients' lives, and regeneration following damage to the peripheral nervous system is limited depending on the degree of the damage. Use of nanobiomaterials can provide therapeutic approaches for the treatment of peripheral nerve injuries. Electroactive biomaterials, in particular, can provide a promising cure for the regeneration of nerve defects. Here, a supramolecular electroactive nanosystem with tetra(aniline) (TA)-containing peptide nanofibers was developed and utilized for nerve regeneration. Self-assembled TA-conjugated peptide nanofibers demonstrated electroactive behavior. The electroactive self-assembled peptide nanofibers formed a well-defined three-dimensional nanofiber network mimicking the extracellular matrix of the neuronal cells. Neurite outgrowth was improved on the electroactive TA nanofiber gels. The neural differentiation of PC-12 cells was more advanced on electroactive peptide nanofiber gels, and these biomaterials are promising for further use in therapeutic neural regeneration applications.
Open Access
Biosensors for early disease diagnosis
(John Wiley & Sons, 2016-03-11) Topal, Ahmet E.; Özkan, Alper Devrim; Dana, Aykutlu; Tekinay, Ayse B.; Güler, Mustafa O.; Güler, Mustafa O.; Tekinay, Ayşe B.
This chapter focuses on biosensor types, their detection limits, analysis times, and the diseases they are suitable for detecting. In addition, as nanomaterials are an effective means of producing small‐scale diagnostic devices, nanostructures have been commonly employed in biosensor design. Consequently, a section is devoted to the types of nanomaterials currently under use in biosensor design. Biosensors can be classified according to their recognition element (e.g., enzymes, antibodies, nucleic acids), output type (e.g., optical, electrical, mechanical), detection principle (e.g., surface plasmon resonance (SPR) based, surface‐enhanced Raman spectroscopy (SERS) based, quartz crystal microbalance (QCM) based), or intended use (in vivo or ex vivo). These factors all play vital roles in determining the sensitivity and selectivity of a biosensor and are considered separately.
Open Access
CDs have fingerprints too
(Springer, Berlin, Heidelberg, 2009) Hammouri G.; Dana, Aykutlu; Sunar, B.
We introduce a new technique for extracting unique fingerprints from identical CDs. The proposed technique takes advantage of manufacturing variability found in the length of the CD lands and pits. Although the variability measured is on the order of 20 nm, the technique does not require the use of microscopes or any advanced equipment. Instead, we show that the electrical signal produced by the photodetector inside the CD reader is sufficient to measure the desired variability. We investigate the new technique by analyzing data collected from 100 identical CDs and show how to extract a unique fingerprint for each CD. Furthermore, we introduce a technique for utilizing fuzzy extractors over the Lee metric without much change to the standard code offset construction. Finally, we identify specific parameters and a code construction to realize the proposed fuzzy extractor and convert the derived fingerprints into 128-bit cryptographic keys. © 2009 Springer.
Open Access
Characterization of multilayer self-organized InAs quantum dot embedded waveguides at 1.3 and 1.5 μm
(IEEE, 2007) Akca, B. Imran; Dana, Aykutlu; Aydınlı, Atilla; Rossetti, M.; Li L.; Fiore, A.; Dagli, N.
In this paper, we characterized the electro-optic coefficient and loss of multilayer InAs quantum dot laser structures at 1309 and 1515 nm. Quantum dot waveguides were grown by molecular beam epitaxy, where the active region is formed by three or five layers of self-assembled InAs QDs. Loss characterization were carried out by using a 1.3 μm light from a thermally tunable laser. Transmission through the device was recorded as a function of wavelength. Loss coefficient is found to be wavelength and bias voltage dependent
Open Access
Electric field dependence of modulation in multilayer InAs quantum dot waveguides
(IEEE, 2007) Akça, Imran B.; Dana, Aykutlu; Aydınlı, Atilla; Rossetti, M.; Li, A.; Fiore, A.; Dagli, N.
The low voltage modulation in InAs quantum dot waveguides is observed in this paper. We have measured the electro-optic coefficient in multilayer quantum dot structures far away from resonance and obtained an enhancement compared to bulk GaAs. Electro-absorption measurement results suggest that these waveguides are good candidates for use in electro-absorption modulators such as Mach-Zehnder devices.
Open Access
Electro-optic and electro-absorption characterization of InAs quantum dot waveguides
(Optical Society of America, 2008-03) Akça, İmran B.; Dana, Aykutlu; Aydınlı, Atilla; Rossetti, M.; Li, L.; Fiore, A.; Dağlı, N.
Abstract Optical properties of multilayer InAs quantum dot waveguides, grown by molecular beam epitaxy, have been studied under applied electric field. Fabry-Perot measurements at 1515 nm on InAs/GaAs quantum dot structures yield a significantly enhanced linear electro-optic efficiency compared to bulk GaAs. Electro-absorption measurements at 1300 nm showed increased absorption with applied field accompanied with red shift of the spectra. Spectral shifts of up to 21% under 18 Volt bias was observed at 1320 nm. (C) 2008 Optical Society of America.
Open Access
Hyperspectral stochastic optical reconstruction Raman microscopy for label-free super-resolution imaging using surface enhanced Raman spectroscopy
(Springer, 2015) Dana, Aykutlu; Camesano, Terri A.
Super-resolution imaging is an emerging field that has attracted attention in the recent years due to far the reaching impact in biology. All super-resolution techniques use fluorescent labels to image nanoscale biomolecular structures. In contrast, label-free nanoscopic imaging of the chemical environment of biological specimens would readily bridge the supramolecular and the cellular scales, if a chemical fingerprint technique such as Raman scattering can be coupled with superresolution imaging, overcoming the diffraction limit. In order to achieve this goal, we propose to develop a super-resolved stochastic hyperspectral Raman microscopy technique for imaging of biological architectures. The surface enhanced Raman spectroscopy (SERS) signal contains information about the presence of various Raman bands, allowing for the discrimination of families of biomolecules such as lipids, proteins, DNA. The rich, fluctuating spectral information contained in the single molecule SERS signal possesses a great potential in label-free imaging, using stochastic optical reconstruction microscopy (STORM) methods. In a recently published work, we demonstrated 20 nm spatial resolution using the spectrally integrated Raman signal on highly uniform SERS substrates. A mature version of our method would require development of spectrally resolved nanoscale Raman imaging. Development of stochastic Raman imaging addresses the issue by design and construction of a Raman microscope with hyperspectral imaging capability that will allow imaging of different Raman bands of the SERS signal. Novel computational techniques must also be developed that will enable extraction of hyperspectral STORM images corresponding to different Raman bands, while simultaneously allowing conventional STORM data to be collected using the wellestablished labelling techniques. The resulting technique (Hyperspectral Raman STORM or HyperSTORRM) has the potential to complement the available labeled stochastic imaging methods and enable chemically resolved nanoscopy.
Open Access
Infrared absorption spectroscopy of monolayers with thin film interference coatings
(Optical Society of America, 2017) Ayas, Sencer; Bakan, Gökhan; Ozgur, E.; Celebi, Kemal; Dana, Aykutlu
We report high performance Infrared spectroscopy platforms based on interference coatings on metal using CaF2 dielectric films and Ge2Sb2Te5 (GST) phase-change films. IR vibrational bands of proteins and organic monolayers are also detected.
Open Access
Interference coatings for infrared spectroscopy and colorimetric sensing
(OSA, 2018) Bakan, Gökhan; Ayas, Sencer; Özgür, Erol; Çelebi, Kemal; Dana, Aykutlu
Constructive interference and strong interference surfaces are created to sense ultrathin probe materials such as monolayer protein molecules using enhanced infrared absorption spectroscopy and colorimetric detection, respectively.
Open Access
Label-free nanometer-resolution imaging of biological architectures through surface enhanced raman scattering
(Nature Publishing Group, 2013) Ayas, Sencer; Çınar, Göksu; Özkan, Alper Devrim; Soran, Zeliha; Ekiz, Oner; Kocaay, Deniz; Tomak, A.; Toren, Pelin; Kaya, Yasin; Tunc, I.; Zareie, H.; Tekinay, T.; Tekinay, Ayse Begum; Güler, Mustafa O.; Dana, Aykutlu
Label free imaging of the chemical environment of biological specimens would readily bridge the supramolecular and the cellular scales, if a chemical fingerprint technique such as Raman scattering can be coupled with super resolution imaging. We demonstrate the possibility of label-free super-resolution Raman imaging, by applying stochastic reconstruction to temporal fluctuations of the surface enhanced Raman scattering (SERS) signal which originate from biomolecular layers on large-area plasmonic surfaces with a high and uniform hot-spot density (> 10(11)/cm(2), 20 to 35 nm spacing). A resolution of 20 nm is demonstrated in reconstructed images of self-assembled peptide network and fibrilated lamellipodia of cardiomyocytes. Blink rate density is observed to be proportional to the excitation intensity and at high excitation densities (> 10 kW/cm(2)) blinking is accompanied by molecular breakdown. However, at low powers, simultaneous Raman measurements show that SERS can provide sufficient blink rates required for image reconstruction without completely damaging the chemical structure.
Open Access
Linear electro-optic coefficient in multilayer self-organized InAs quantum dot structures
(IEEE, 2007) Akca, B. Imran; Dana, Aykutlu; Aydınlı, Atilla; Rossetti, M.; Li L.; Dagli, N.; Fiore, A.
The electro-optic coefficients of self-organized InAs quantum dot layers in molecular beam epitaxy grown laser structures in reverse bias have been investigated. Enhanced electrooptic coefficients compared to bulk GaAs were observed. © 2003 Optical Society of America.
Open Access
Microscopic characterization of peptide nanostructures
(Elsevier, 2012) Mammadov, Rashad; Tekinay, Ayse B.; Dana, Aykutlu; Güler, Mustafa O.
Peptide-based nanomaterials have been utilized for various applications from regenerative medicine to electronics since they provide several advantages including easy synthesis methods, numerous routes for functionalization and biomimicry of secondary structures of proteins which leads to design of self-assembling peptide molecules to form nanostructures. Microscopic characterization at nanoscale is critical to understand processes directing peptide molecules to self-assemble and identify structure-function relationship of the nanostructures. Here, fundamental studies in microscopic characterization of peptide nanostructures are discussed to provide insights in widely used microscopy tools. In this review, we will encompass characterization studies of peptide nanostructures with modern microscopes, such as TEM, SEM, AFM, and advanced optical microscopy techniques. We will also mention specimen preparation methods and describe interpretation of the images. © 2011 Elsevier Ltd.
Open Access
A modular antigen presenting peptide/oligonucleotide nanostructure platform for inducing potent immune response
(Wiley - VCH Verlag GmbH & Co. KGaA, 2017-05) Tohumeken, Sehmus; Gunduz, Nuray; Demircan, M. Burak; Gunay, Gokhan; Topal, Ahmet E.; Khalily, M. Aref; Tekinay, T.; Dana, Aykutlu; Güler, Mustafa O.; Tekinay, Ayse B.
The design and development of vaccines, which can induce cellular immunity, particularly CD8+ T cells hold great importance since these cells play crucial roles against cancers and viral infections. Covalent conjugation of antigen and adjuvant molecules has been used for successful promotion of immunogenicity in subunit vaccines; however, the stimulation of the CD8+ T‐cell responses by this approach has so far been limited. This study demonstrates a modular system based on noncovalent attachment of biotinylated antigen to a hybrid nanofiber system consisting of biotinylated self‐assembling peptide and CpG oligodeoxynucleotides (ODN) molecules, via biotin–streptavidin interaction. These peptide/oligonucleotide hybrid nanosystems are capable of bypassing prior limitations related with inactivated or live‐attenuated virus vaccines and achieve exceptionally high CD8+ T‐cell responses. The nanostructures are found to trigger strong IgG response and effectively modulate cross‐presentation of their antigen “cargo” through close proximity between the antigen and peptide/ODN adjuvant system. In addition, the biotinylated peptide nanofiber system is able to enhance antigen uptake and induce the maturation of antigen‐presenting cells. Due to its versatility, biocompatibility, and biodegradability with a broad variety of streptavidin‐linked antigens, the nanosystem shown here can be utilized as an efficient strategy for new vaccine development.
Open Access
Modulation in InAs quantum dot waveguides
(Optical Society of America, 2007) Akca, B. Imran; Dana, Aykutlu; Aydınlı, Atilla; Rossetti, M.; Li L.; Fiore, A.; Dagli, N.
Modulation in molecular beam epitaxy grown self-assembled InAs quantum dot waveguides have been studied at 1500 nm as a function of wavelength and voltage. Enhanced electro-optic coefficients compared to bulk GaAs were observed. © 2007 Optical Society of America.
Open Access
Modulation of multilayer InAs quantum dot waveguides under applied electric field
(Optical Society of America, 2007) Akça, Imran B.; Dana, Aykutlu; Aydınlı, Atilla; Rossetti, M.; Li L.; Fiore, A.; Dagli, N.
Electric field dependence of optical modulation in self assembled InAs quantum dot waveguides have been studied at 1300 and 1500 nm. Electro-absorption and electro-optic coefficients of these waveguides have been obtained at both wavelengths. © 2007 Optical Society of America.
Open Access
Multispectral plasmonic structures using native aluminum oxide and aluminum
(OSA, 2017) Ayaş, Sencer; Bakan, Gökan; Dana, Aykutlu
We report the use of native aluminum oxide to fabricate periodic metal-insulator-metal resonators with simultaneous resonances in the visible and IR wavelengths. The cavity size is in the order of λ3/25000 in the NIR.
Open Access
Mussel inspired dynamic cross-linking of self-healing peptide nanofiber network
(Wiley, 2013) Ceylan, Hakan; Urel, Mustafa; Erkal, Turan S.; Tekinay, Ayse B.; Dana, Aykutlu; Güler, Mustafa O.
A general drawback of supramolecular peptide networks is their weak mechanical properties. In order to overcome a similar challenge, mussels have adapted to a pH-dependent iron complexation strategy for adhesion and curing. This strategy also provides successful stiffening and self-healing properties. The present study is inspired by the mussel curing strategy to establish iron cross-link points in self-assembled peptide networks. The impact of peptide-iron complexation on the morphology and secondary structure of the supramolecular nanofibers is characterized by scanning electron microscopy, circular dichroism and Fourier transform infrared spectroscopy. Mechanical properties of the cross-linked network are probed by small angle oscillatory rheology and nanoindentation by atomic force microscopy. It is shown that iron complexation has no influence on self-assembly and β-sheet-driven elongation of the nanofibers. On the other hand, the organic-inorganic hybrid network of iron cross-linked nanofibers demonstrates strong mechanical properties comparable to that of covalently cross-linked network. Strikingly, iron cross-linking does not inhibit intrinsic reversibility of supramolecular peptide polymers into disassembled building blocks and the self-healing ability upon high shear load. The strategy described here could be extended to improve mechanical properties of a wide range of supramolecular polymer networks. A simple and versatile method for improving mechanical performance of supramolecular polymers is described. Inspired by a mussel curing mechanism, reversible iron cross-linking into a self-assembled peptide network significantly enhances the mechanical properties while having no impact on the β-sheet-driven self-assembly. The network retains its pH-dependent reversibility and self-healing properties. Copyright © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.
Open Access
Permanent tuning of optical resonant modes of chalcogenide-coated microresonators
(OSA - The Optical Society, 2020) Hüseyinoğlu, Ersin; Özgür, Erol; Bakan, G.; Ortaç, Bülend; Dana, Aykutlu
Chalcogenide materials are promising for optical resonant mode tuning of whispering gallery mode (WGM) microresonators due to their high nonlinearity. In this study, this phenomenon was demonstrated for Ge2Sb2Te5- coated toroidal microresonators using an optical postprocess, which utilizes the intrinsically photosensitive property of the Ge2Sb2Te5 coating. A signal laser was used to illuminate the resonator for permanent tuning of the WGMs in a sensitive manner. 0.01 nm and 0.02 nm permanent tuning of the WGMs was recorded for 5 nm and 10 nm coated resonators, respectively. This technique enables resonance matching of coupled optical resonators, which could pave the way for optoelectronic circuitries employing multiple optical microresonators.
Open Access
Plasmonic absorbers for multispectral and broadband absorption
(SPIE, 2012) Ayaş, Sencer; Güner, Hasan; Türker, Burak; Ekiz, Öner; Dana, Aykutlu
We present polarization dependent multispectral and broadband plasmonic absorbers in the visible spectrum. The spectral characteristics of these structures are tunable over a broad spectrum. Experimental results are verified with the FDTD and RCWA analysis methods. These structures are used as surface enhanced raman spectroscopy(SERS) substrates. Designed structures have resonances that span the Raman Stokes and excitation wavelength. Such structures can be used for energy, LED and other spectroscopy applications. © 2012 Copyright Society of Photo-Optical Instrumentation Engineers (SPIE).