Browsing by Subject "Nanomaterials"

Now showing 1 - 16 of 16

Open Access
Aptamer-based point-of-care devices: Emerging technologies and integration of computational methods
(MDPI, 2023-05-22) Aslan, Yusuf; Atabay, Maryam; Chowdhury, Hussain Kawsar; Göktürk, Ilgım; Saylan, Y.; İnci, Fatih
Recent innovations in point-of-care (POC) diagnostic technologies have paved a critical road for the improved application of biomedicine through the deployment of accurate and affordable programs into resource-scarce settings. The utilization of antibodies as a bio-recognition element in POC devices is currently limited due to obstacles associated with cost and production, impeding its widespread adoption. One promising alternative, on the other hand, is aptamer integration, i.e., short sequences of single-stranded DNA and RNA structures. The advantageous properties of these molecules are as follows: small molecular size, amenability to chemical modification, low- or nonimmunogenic characteristics, and their reproducibility within a short generation time. The utilization of these aforementioned features is critical in developing sensitive and portable POC systems. Furthermore, the deficiencies related to past experimental efforts to improve biosensor schematics, including the design of biorecognition elements, can be tackled with the integration of computational tools. These complementary tools enable the prediction of the reliability and functionality of the molecular structure of aptamers. In this review, we have overviewed the usage of aptamers in the development of novel and portable POC devices, in addition to highlighting the insights that simulations and other computational methods can provide into the use of aptamer modeling for POC integration.
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
Bright White-Light Emitting Manganese and Copper Co-Doped ZnSe Quantum Dots
(Wiley, 2011) Panda, S. K.; Hickey, S. G.; Demir, Hilmi Volkan; Eychmuller, A.
Doubly doped quantum dots with highly efficient (17 %) white-light emission (WLE) have been directly synthesized using a one-pot hot-injection technique (see picture). The generation of WLE was due to the judicious manipulation of the synthesis strategy for the co-doping of the host material-ZnSe quantum dots-with Mn and Cu.
Open Access
Coupled thermally general imperfect and mechanically coherent energetic interfaces subject to in-plane degradation
(Mathematical Sciences Publishers, 2017) Esmaeili, A.; Steinmann, P.; Javili, A.
To date, the effects of interface in-plane damage on the thermomechanical response of a thermally general imperfect (GI) and mechanically coherent energetic interface are not taken into account. A thermally GI interface allows for a discontinuity in temperature as well as in the normal heat flux across the interface. A mechanically coherent energetic interface permits a discontinuity in the normal traction but not in the displacement field across the interface. The temperature of a thermally GI interface is a degree of freedom and is computed using a material parameter known as the sensitivity. The current work is the continuation of the model developed by Esmaeili et al. (2016a) where a degrading highly conductive (HC) and mechanically coherent energetic interface is considered. An HC interface only allows for the jump in normal heat flux and not the jump in temperature across the interface. In this contribution, a thermodynamically consistent theory for thermally GI and mechanically coherent energetic interfaces subject to in-plane degradation is developed. A computational framework to model this class of interfaces using the finite element method is established. In particular, the influence of the interface in-plane degradation on the sensitivity is captured. To this end, the equations governing a fully nonlinear transient problem are given. They are solved using the finite element method. The results are illustrated through a series of three-dimensional numerical examples for various interfacial parameters. In particular, a comparison is made between the results of the intact and the degraded thermally GI interface formulation. © 2017 Mathematical Sciences Publishers.
Open Access
Fabrication of mesoporous metal chalcogenide nanoflake silica thin films and spongy mesoporous CdS and CdSe
(Wiley Online Library, 2012-02-16) Türker, Y.; Karakaya, C.; Dag, Ö.
Mesoporous silica metal oxide (ZnO and CdO) thin films have been used as metal ion precursors to produce the first examples of mesoporous silica metal sulfide (mesoSiO2@ZnS, meso-SiO2@CdS) or silica metal selenide (meso-SiO2@ZnSe, meso-SiO2@CdSe) thin films, in which the pore walls are made up of silica and metal sulfide or metal selenide nanoflakes, respectively. A gentle chemical etching with a dilute HF solution of the meso-SiO2@CdS (or mesoSiO2@CdSe) produces mesoporous cadmium sulfide (meso-CdS) (or cadmium selenide, meso-CdSe). Surface modified meso-CdS displays bright blue photoluminescence upon excitation with a UV light. The mesoporous silica metal oxides are formed as metal oxide nanoislands over the silica walls through a self-assembly process of a mixture of metal nitrate salt-two surfactants-silica source followed by calcination step. The reactions, between the H2S (or H2Se) gas and solid precursors, have been carried out at room temperature and monitored using spectroscopy and microscopy techniques. It has been found that these reactions are: 1) taking place through the diffusion of sulfur or selenium species from the top metal oxide layer to the silica metal oxide interface and 2) slow and can be stopped at any stage to obtain mesoporous silica metal oxide metal sulfide or silica metal oxide metal selenide intermediate thin films.
Open Access
Glucose sensors based on electrospun nanofibers: a review
(Springer Verlag, 2016) Senthamizhan, A.; Balusamy, B.; Uyar, Tamer
The worldwide increase in the number of people suffering from diabetes has been the driving force for the development of glucose sensors. The recent past has devised various approaches to formulate glucose sensors using various nanostructure materials. This review presents a combined survey of these various approaches, with emphasis on the current progress in the use of electrospun nanofibers and their composites. Outstanding characteristics of electrospun nanofibers, including high surface area, porosity, flexibility, cost effectiveness, and portable nature, make them a good choice for sensor applications. Particularly, their nature of possessing a high surface area makes them the right fit for large immobilization sites, resulting in increased interaction with analytes. Thus, these electrospun nanofiber-based glucose sensors present a number of advantages, including increased life time, which is greatly needed for practical applications. Taking all these facts into consideration, we have highlighted the latest significant developments in the field of glucose sensors across diverse approaches.
Open Access
Interaction of CO2 with MnOx/Pd(111) reverse model catalytic interfaces
(Wiley, 2023-07-03) Anıl, Arca; Sadak, Ömer Faruk; Karakurt, Bartu; Koçak, Yusuf; Lyubinetsky, Igor; Özensoy, Emrah
Understanding the activation of CO2 on the surface of the heterogeneous catalysts comprised of metal/metal oxide interfaces is of critical importance since it is not only a prerequisite for converting CO2 to value-added chemicals but also often, a rate-limiting step. In this context, our current work focuses on the interaction of CO2 with heterogeneous bi-component model catalysts consisting of small MnOx clusters supported on the Pd(111) single crystal surface. These metal oxide-on-metal ‘reverse’ model catalyst architectures were investigated via temperature programmed desorption (TPD) and x-ray photoelectron spectroscopy (XPS) techniques under ultra-high vacuum (UHV) conditions. Enhancement of CO2 activation was observed upon decreasing the size of MnOx nanoclusters by lowering the preparation temperature of the catalyst down to 85 K. Neither pristine Pd(111) single crystal surface nor thick (multilayer) MnOx overlayers on Pd(111) were not capable of activating CO2, while CO2 activation was detected at sub-monolayer (∼0.7 ML) MnOx coverages on Pd(111), in correlation with the interfacial character of the active sites, involving both MnOx and adjacent Pd atoms. © 2023 The Authors. ChemPhysChem published by Wiley-VCH GmbH.
Open Access
Nanomaterials for medicine
(John Wiley & Sons, 2016-03-11) Güler, Mustafa O.; Tekinay, Ayşe B.; Güler, Mustafa O.; Tekinay, Ayşe B.
Nanomaterials with controlled physical, chemical, and biological characteristics can be used for the therapy of the specific causes of the diseases. There are several ways to develop new materials in nanometer scale. Mainly, top‐down and bottom‐up approaches are the two major techniques to produce nanomaterials. Depending on the application area, either one or both of these approaches can be used to develop materials that can be used in studying pathophysiology of diseases and their diagnosis and therapy. Especially, bioinspired and biomimetic strategies yield products that can replace or accommodate activities of the natural biomolecules. Nevertheless, for effective diagnosis and therapy of diseases, it is almost crucial to first understand the molecular reasons behind disease development. The nanomaterials can be also used in regenerative medicine applications. Although there have been extensive advances in developing nanomaterials for biomedical purposes, only few of them have been translated into clinics.
Open Access
Nanomaterials for neural regeneration
(John Wiley & Sons, 2016-03-11) Sever, Melike; Mammadov, Büşra; Geçer, Mevhibe; Güler, Mustafa O.; Tekinay, Ayşe B.; Güler, Mustafa O.; Tekinay, Ayşe B.
The central nervous system (CNS) consists of a dense network of cells leaving a smaller volume for the extracellular matrix (ECM) components (10‐20% for the brain unlike most other tissues (Cragg, 1979)). The reaction of the nervous tissue to any injury leading to scar tissue formation acts as a barrier for regeneration in the CNS, while it supports regeneration in the peripheral nervous system (PNS). By mimicking several unique characteristics of the natural environment of cells, synthetic materials for neural regeneration can be improved chemically and biologically. Especially bioactivation of materials can be achieved by addition of small chemical moieties to the scaffold particularly found in specific tissues or addition of biologically active molecules derived from natural ECM. The ECM‐derived short peptides are promising candidates to be presented as functional domains on the scaffold surface for use in neural regeneration.
Open Access
Organically modified silica based nanomaterials for functional surfaces
(2012) Budunoğlu, Hülya
Organically modified silicas (ormosils) are unique materials due to their combined properties achieved from organics and inorganics. Ormosils contain at least one non-hydrolysable organic groups which results in a decrease of rigid Si-O-Si bonds, introducing a flexible character. Therefore, ormosils exhibit both flexibility of organics and atmospheric stability of inorganics. Organic group determines the functionalities of ormosils, thus their properties can be adjusted by choice of appropriate organic modification. Ormosils can be easily prepared in mild conditions of sol-gel technique, and can be applied on different surfaces by low cost and simple techniques. In this thesis, we prepared superhydrophobic-superhydrophilic, antireflectiveantifogging, anticorrosion and antiicing (ice retarding) functional surfaces using organically modified silica and its nano-composites in thin film form. Methyltrimethoxysilane (MTMS) is used in the synthesis of all films due to its intrinsically hydrophobic nature. This monomer is found to enable porous film formation without any modifications at ambient temperature and pressure. Superhydrophobic ormosil aerogel films with water contact angles reaching 179.9 and porosity of 86 % have been prepared using phase separated colloidal suspensions of MTMS, which exhibited flexibility, thermal stability and superhydrophilic transition after annealing at 600 C. Antireflective films with high mechanical stability are prepared from co-condensation of MTMS with tetraethylorthosilicate monomer, which exhibited transmission as high as 99.6 % with flexibility and transition to antifogging after annealing at 600 C. Anticorrosion films for glass surfaces have been prepared by encapsulation of ZnO and ZrO2 nanoparticles to yield nano-composites of porous and nonporous ormosil films, which resulted in four times less corrosion compared to bare glass and acts as a barrier layer for corrosion of glass substrates against alkaline corrosion. In formation of antiicing coatings various combinations of ormosil films mentioned are used and correlation between contact angle, stability of contact angle against cooling, surface roughness and freezing times are investigated. Compared to bare glass, freezing times are increased two order of magnitudes.
Open Access
Self-assembled peptide nanofiber templated ALD growth of TiO2 and ZnO semiconductor nanonetworks
(Wiley - V C H Verlag GmbH & Co. KGaA, 2016) Garifullin, R.; Eren, H.; Ulusoy, T. G.; Okyay, Ali Kemal; Bıyıklı, Necmi; Güler, Mustafa O.
Here peptide amphiphile (PA) nanofiber network is exploited as a three‐dimensional soft template to construct anatase TiO2 and wurtzite ZnO nanonetworks. Atomic layer deposition (ALD) technique is used to coat the organic nanonetwork template with TiO2and ZnO. ALD method enables uniform and conformal coatings with precisely controlled TiO2 and ZnO thickness. The resulting semiconducting metal oxide nanonetworks are utilized as anodic materials in dye‐sensitized solar cells. Effect of metal oxide layer thickness on device performance is studied. The devices based on thin TiO2 coatings (<10 nm) demonstrate considerable dependence on material thickness, whereas thicker (>17 nm) ZnO‐based devices do not show an explicit correlation.
Open Access
Self-assembled peptide nanostructures for functional materials
(Institute of Physics Publishing, 2016) Ekiz, M. S.; Cinar, G.; Khalily, M. A.; Güler, Mustafa O.
Nature is an important inspirational source for scientists, and presents complex and elegant examples of adaptive and intelligent systems created by self-assembly. Significant effort has been devoted to understanding these sophisticated systems. The self-assembly process enables us to create supramolecular nanostructures with high order and complexity, and peptide-based self-assembling building blocks can serve as suitable platforms to construct nanostructures showing diverse features and applications. In this review, peptide-based supramolecular assemblies will be discussed in terms of their synthesis, design, characterization and application. Peptide nanostructures are categorized based on their chemical and physical properties and will be examined by rationalizing the influence of peptide design on the resulting morphology and the methods employed to characterize these high order complex systems. Moreover, the application of self-assembled peptide nanomaterials as functional materials in information technologies and environmental sciences will be reviewed by providing examples from recently published high-impact studies.
Open Access
Self-assembled peptide template directed synthesis of one-dimensional inorganic nanostructures and their applications
(2012) Acar, Handan
Engineering at the nano scale has been an active area of science and technology over the last decade. Inspired by nature, synthesis of functional inorganic materials using synthetic organic templates constitutes the theme of this thesis. Developing organic template directed synthesis approach for inorganic nanomaterial synthesis was aimed. For this purpose, an amyloid like peptide sequence which is capable of self-assembling into nanofibers in convenient conditions was designed and decorated with functional groups showing relatively high affinity to special inorganic ions, which are presented at the periphery of the one-dimensional peptide nanofiber. These chemical groups facilitated the deposition of targeted inorganic monomers onto the nanofibers yielding one-dimensional organic-inorganic core-shell nanostructures. The physical and chemical properties of the synthesized peptide nanofibers and inorganic nanostructures were characterized using both qualitative and quantitative methods. First, silica nanotubes were obtained by silica mineralization around these peptide nanofiber templates for the construction of sensors for explosives. The fluorescence dye was used to coat the silica nanotubes to detect explosive vapor. The surface of the silica nanotubes were porous enough to adsorb more dye compared to the silica nanoparticles and silica film, and causes faster fluorescence quenching in the presence of explosives like trinitrotoluene and dinitrotoluene. The silica nanotubes which synthesized with this peptide nanofiber templates can be used in catalysis and sensors in which high surface area is advantageous. In the second part of the thesis, titanium dioxide nanotubes were obtained from titania mineralization. They are wellknown with their fascinating properties as a result of the one-dimensional nanostructure, such as more efficient electron transfer and less electron-hole recombination. The sufficient photoactivity of titanium dioxide makes them suitable materials for Dye-Sensitized Solar-Cell construction. It is demonstrated that the peptide nanofiber templated titanium dioxide nanotubes have more than two times more efficiency compared to template-free synthesized titanium dioxide particles. Finally, designed peptide sequence was conducted to a multi-step seeding mediated growth method for gold mineralization around peptide nanofibers. The gold-peptide hybrid nanostructures with different packing characteristics and sizes were synthesized and fully characterized. Further, it was demonstrated that the dry film of these nanostructures showed a resistive switching dominant conductivity, due to the nanogaps in between gold nanoparticles as a result of particle alignment driven by the peptide nanofiber. The results obtained in this thesis encourage use of a new “bottom-up” synthesis approach. Specially designed peptides with desired properties and functional groups were synthesized and peptide nanofibers formed were further used as templates for inorganic mineralization. Not only it is possible to synthesis high amount of nanostructure with this approach, but also formed one-dimensional nanostructures show advance functionalities used in several applications as a part of the thesis scope. This methodology is suitable for many metals and metal oxide based applications.
Open Access
Self-assembly of bacterial amyloid protein nanomaterials on solid surfaces
(Academic Press, 2018) Onur, Tuğçe; Yuca, Esra; Ölmez, Tolga Tarkan; Şeker, Urartu Özgür Şafak
Hypothesis: Amyloid-forming biofilm proteins of Escherichia coli, namely CsgA and CsgB, can form self-assembled nanofibers on solid surfaces. These proteins can be programmed to form bio-nanomaterials for functional applications. Experiments: In this study, the assembly of the CsgA and CsgB protein on solid surfaces was investigated in real time using a quartz crystal microbalance instrument with dissipation monitoring. The assembly kinetics of the CsgA and CsgB proteins in various settings on solid surfaces were investigated. Protein nanowires were investigated using electron microscopy. Findings: CsgA protein polymers and CsgB-added CsgA polymers form densely packed biofilm on gold surfaces, whereas CsgB polymers and CsgA-added CsgB polymers form biofilms with high water-holding capacity according to the dissipation data. Electron microscopy images of nanofibers grown on gold surfaces showed that CsgA and CsgB polymers include thicker nanofibers compared to the nanofibers formed by CsgA-CsgB protein combinations. The resulting nano/microstructures were found to have strong fluorescence signals in aqueous environments and in chloroform while conserving the protein nanowire network.
Open Access
Synthetic genetic circuits for self-actuated cellular nanomaterial fabrication devices
(American Chemical Society, 2019) Ölmez, Tolga Tarkan; Şahin-Kehribar, Ebru; Işılak, Musa Efe; Lu, T. K.; Şeker, Urartu Özgür Şafak
Genetically controlled synthetic biosystems are being developed to create nanoscale materials. These biosystems are modeled on the natural ability of living cells to synthesize materials: many organisms have dedicated proteins that synthesize a wide range of hard tissues and solid materials, such as nanomagnets and biosilica. We designed an autonomous living material synthesizing system consisting of engineered cells with genetic circuits that synthesize nanomaterials. The circuits encode a nanomaterial precursor-sensing module (sensor) coupled with a materials synthesis module. The sensor detects the presence of cadmium, gold, or iron ions, and this detection triggers the synthesis of the related nanomaterial-nucleating extracellular matrix. We demonstrate that when engineered cells sense the availability of a precursor ion, they express the corresponding extracellular matrix to form the nanomaterials. This proof-of-concept study shows that endowing cells with synthetic genetic circuits enables nanomaterial synthesis and has the potential to be extended to the synthesis of a variety of nanomaterials and biomaterials using a green approach.
Open Access
Synthetic genetic circuits to monitor nanomaterial triggered toxicity
(2020-07) Saltepe, Behide
In the past decades, nanomaterial (NM) usage in various fields has been of great interest because of their unique properties that show tuneable optical and physical properties depending on their size. Yet, safety concerns of NMs on human or environment arise with increased NM usage. Thanks to their small size, NMs can easily penetrate through cellular barriers and their high surface-to-volume ratio makes them catalytically active creating stress on cells such as protein unfolding, DNA damage, ROS generation etc. Hence, biocompatibility assessment of NMs has been analyzed before their field application such as drug delivery and imaging which requiring human exposure. Yet, conventional biocompatibility tests fall short of providing a fast toxicity report. One aspect of the present thesis is to develop a living biosensor to report biocompatibility of NMs with the aim of providing fast feedback to engineer them with lower toxicity levels before applying on humans. For this purpose, heat shock response (HSR), which is the general stress indicator, was engineered utilizing synthetic biology approaches. Firstly, four highly expressed heat shock protein (HSP) promoters were selected among HSPs. In each construct, a reporter gene was placed under the control of these HSP promoters to track signal change upon stress (i.e., heat or NMs) exposure. However, initial results indicated that native HSPs are already active in cells to maintain cellular homeostasis. Moreover, they need to be engineered to create a proper stress sensor. Thus, these native HSP promoters were engineered with riboregulators and results indicated that these new designs eliminated unwanted background signals almost entirely. Yet, this approach also led to a decrease in expected sensor signal upon stress treatment. To increase the sensor signal, a positive feedback loop using bacterial communication, quorum sensing, method was constructed. HSR was integrated with QS circuit showed that signal level increased drastically. Yet, background signal also increased. Moreover, instead of using activation based HSR system as in Escherichia coli, repression based system was hypothesized to solve the problem. Thus, a repression based genetic circuit, inspired by the HSR mechanism of Mycobacterium tuberculosis, was constructed. These circuits could report the toxicity of quantum dots (QDs) in 1 hour. As a result, these NM toxicity sensors can provide quick reports, which can lower the demand for additional experiments with more complex organisms. As part of this study, a source detection circuit coupling HSR mechanism with metal induced transcription factors (TFs) has been constructed to report the source of the toxic compound. For this purpose, gold and cadmium were selected as model ions. In the engineered circuits, stress caused by metal ions activates expression of regulatory elements such as TFs of specific ions (GolS for gold and CadR and MerR(mut) for cadmium) and a site-specific recombinase. In the system, the recombinase inverts the promoter induced by TF-metal ion complex, and a reporter has been expressed based on the inducer showing the source of the stress as either gold or cadmium. Finally, a mammalian cellular toxicity sensor has been developed using similar approaches used in bacterial sensors. To begin with, two HSP families have been selected: HSP70 and α-Bcrystallin. Initial circuits were designed using promoter regions of both protein families to control the expression of a reporter, gfp. Both circuits were tested with heat and cadmium ions with varying concentrations and results showed that HSP70-based sensor had high background signal because of its active role in cellular homeostasis and protein folding in cells. Additionally, a slight increase was observed after heat treatment. Similar results were observed for α-Bcrystallin-based sensor; yet, these outcomes were not suitable for a desirable sensor requiring tight control. Thus, we decided to transfer the bacterial repression based toxicity sensor into mammalian cells. At the beginning, expression of the repressor, HspR, from M. tuberculosis was checked in HEK293T cell line and modified with nuclear localization signal (NLS) to localize the repressor in the nucleus. Further, a minimal promoter (SV40) controlling the expression of a reporter was engineered with single and double inverted repeats (IRs) for HspR binding. Then, HspR and engineered reporter circuits were co-trasfected to track signals at normal growth conditions and upon stress. Each circuit was tested with heat and cadmium treatment and results were showed repression of GFP expression by HspR at normal conditions, but no significant signal increase was observed upon stress. Hence, constructed mammalian circuits require more optimization to find optimum working conditions of sensors. To sum up, in this study, a powerful candidate to manufacture ordered gene circuits to detect nanomaterial-triggered toxicity has been demonstrated. Unlike previous studies utilizing HSR mechanism as stress biosensors, we re-purposed the HSR mechanism of both bacteria and mammalian cells with different engineering approaches (i.e., riboregulators, quorum sensing mechanism, promoter engineering). As a result, an easy-to-use, cheap and fast acting nanomaterial-triggered toxicity assessment tool has been developed. Also, initial principles of mammalian whole cell biosensor design for the same purpose have been indicated to expand the limited toxicity detection strategies utilizing mammalian cells. This study contributed for the detection of toxic NMs providing a feedback about the fate of these NMs so that one can engineer them to make biocompatible before field application.