Browsing by Subject "Biosensors."

Now showing 1 - 6 of 6

Open Access
Design strategies for chemosensors and their applications in molecular scale logic gates
(2013) Guliyev, Ruslan
Open Access
Deterministic and stochastic error modeling of inertial sensors and magnetometers
(2012) Seçer, Görkem
This thesis focuses on the deterministic and stochastic modeling and model parameter estimation of two commonly employed inertial measurement units. Each unit comprises a tri-axial accelerometer, a tri-axial gyroscope, and a tri-axial magnetometer. In the first part of the thesis, deterministic modeling and calibration of the units are performed, based on real test data acquired from a flight motion simulator. The deterministic modeling and identification of accelerometers is performed based on a traditional model. A novel technique is proposed for the deterministic modeling of the gyroscopes, relaxing the test bed requirement and enabling their in-use calibration. This is followed by the presentation of a new sensor measurement model for magnetometers that improves the calibration error by modeling the orientation-dependent magnetic disturbances in a gimbaled angular position control machine. Model-based Levenberg-Marquardt and modelfree evolutionary optimization algorithms are adopted to estimate the calibration parameters of sensors. In the second part of the thesis, stochastic error modeling of the two inertial sensor units is addressed. Maximum likelihood estimation is employed for estimating the parameters of the different noise components of the sensors, after the dominant noise components are identified. Evolutionary and gradient-based optimization algorithms are implemented to maximize the likelihood function, namely particle swarm optimization and gradient-ascent optimization. The performance of the proposed algorithm is verified through experiments and the results are compared to the classical Allan variance technique. The results obtained with the proposed approach have higher accuracy and require a smaller sample data size, resulting in calibration experiments of shorter duration. Finally, the two sensor units are compared in terms of repeatability, present measurement noise, and unaided navigation performance.
Open Access
EBL fabricated plasmonic nanostructures for sensing applications
(2013) Cinel, Neval A
Plasmonics is a major branch of photonics dealing with light-matter interactions in metallic nanostructures. Plasmonic devices provide extreme confinement of electromagnetic oscillations to very small volumes beyond diffraction limit at optical frequencies. Our aim in this thesis study is to demonstrate the utilization of plasmonics for several applications such as optical localized surface plasmon resonance (LSPR) biosensor design, enhancement of signal intensity in surface enhanced Raman spectroscopy (SERS) and absorption enhancement in photodetectors. Firstly, a sensor structure that detects the changes in the refractive index of the surrounding medium by optical transmission measurements was designed. Periodic silver nano-disk arrays on sapphire substrate written by Electron-Beam Lithography (EBL) were used for this aim. Optical characterization was done through transmission/reflection measurements and supported by finite difference time domain (FDTD) simulations. The sensor was first verified by a biotinavidin bioassay. Real time binding studies showed that the sensor response was saturated within the first 30 minutes of application. Concentration dependency of the sensor structure showed an adequate response at the 1 nM-100 nM range. The refractive index sensitivity of the sensor was determined as 354 nm/RIU. The idea was finally applied to the detection of heat killed E.Coli bacteria. Promising results that indicate the possibility of using the sensor for bacteria detection was obtained. Secondly, tandem truncated nano-cones composed of Au-SiO2-Au layers that exhibit highly tunable double resonance behavior were shown to increase SERS signal intensity, for the first time. Enhancement factor (EF) calculations indicated an enhancement factor of 3.86 x107 . The double resonance design showed a 10 fold better enhancement when compared to its single resonance counterpart. This enhancement is believed to be even more prominent for applications such as NIR-SERS and Surface Enhanced Hyper Raman Scattering (SEHRS). Another SERS substrate containing dual layer, periodic, “coupled” concentric rings, separated by a dielectric spacer provided Raman signal intensity 630 times larger than plain gold film and 8 times larger than an “etched” concentric ring structure. The design provided an enhancement factor of 1.67x107 . Finally, Al nanoparticles with plasmonic resonance at UV wavelengths fabricated in between the Schottky contacts of an MSM detector on semi-insulating GaN was shown to yield 1.5 fold enhancement in absorption and photocurrent collection. Plasmonic enhancement in UV was studied for the first time with this study. Another UV-MSM photodetector on GaN that includes subwavelength apertures surrounded by nano-structured metal gratings was compared to a conventional design without gratings. Results indicated an 8 fold enhancement in the photocurrent at the resonant wavelength.
Open Access
Nanogap based label-free impedimetric biosensors
(2012) Hanoğlu, Oğuz
Despite lots of research going on to find a hope, cancer is still a major cause of death in today‘s world. It has been reported that cancer has some biomarkers in human body and detecting these biomarkers timely can pave the way for early detection and successful treatments. Point-of-care biosensors are highly promising for this mission. If these biosensors can achieve sensitivity and reliability with a low-cost and simple platform, they can address a large mass of people who are at the early stages of cancer without any clear symptoms yet. For this purpose, various biosensing mechanisms can be used to convert the signal coming from the recognition elements on the biosensor surface to the digital domain for signal processing. One of these mechanisms, impedimetric (impedance based) sensing is a very appealing electrical biosensing method since this method can offer label-free, low-cost, low-power requirement, miniaturizable, and chip-integrable detection platforms. However, impedimetric sensing in liquid medium is problematic, since during the electrical measurements, ion-based undesired layers (electrical double layers) are formed over the electrodes in the target liquid. Unfortunately, these layers act like a shield against the applied electric field to the liquid and can prevent the detection of the target biomarkers. In this thesis, a nanogap based label-free biosensor structure is designed and using this design impedimetric sensing in liquid medium is demonstrated at low frequencies (1 kHz – 100 kHz). Low frequency platforms are quite amenable to low-cost applications like point-of-care biosensing. The designed structure utilizes nanometer scale electrode separation (nanogap). Theoretical calculations show that nanogap reduces the undesired effect of electrical double layer. Moreover, nanogap also helps in minimizing the volume of the required liquid for the measurement. Design, fabrication, surface functionalization and biotinylation stages of the biosensor are realized in a cleanroom environment and biomimetic materials laboratory. The fabricated biosensor is tested by introducing the target molecules (streptavidin) in a phosphate-buffered saline solution. A parameter analyzer with a capacitance-voltage unit and a probe station are used for the impedance measurements. With these biosensors, label-free detection of streptavidin is observed for 100 µg/mL, 10 µg/mL, 1 µg/mL, 100 ng/mL and 10 ng/mL concentrations. This is, to the best of our knowledge, the first demonstration of streptavidin detection in nanogap based label-free impedimetric biosensors. The above-mentioned concentrations show that these biosensors are promising for commercial applications. Sensitivity to the dielectric constant of the target medium is measured to be 132 pF per unit change in the dielectric constant at 10 kHz measurement frequency. Reliability tests are performed: stable and repeatable operation of the sensors are checked and verified. In conclusion, this proof-of-concept study shows that nanogap based biosensors would be a suitable and appealing choice for sensitive, reliable, simple, low-power and low-cost point-of care biosensing applications. Next step would be utilizing the platform presented in this work in detecting specific cancer biomarkers like PSA or CA125. Thereby, developed further and commercialized, nanogap based label-free impedimetric biosensors can act in the battle of human being against cancer in the future.
Open Access
Novel wireless RF-bioMEMS implant sensors of metamaterials
(2010) Melik, Rohat
Today approximately one out of ten patients with a major bone fracture does not heal properly because of the inability to monitor fracture healing. Standard radiography is not capable of discriminating whether bone healing is occurring normally or aberrantly. To solve this problem, we proposed and developed a new enabling technology of implantable wireless sensors that monitor mechanical strain on implanted hardware telemetrically in real time outside the body. This is intended to provide clinicians with a powerful capability to asses fracture healing following the surgical treatment. Here we present the proof-of-concept in vitro and ex vivo demonstrations of bio-compatible radio-frequency (RF) micro-electro-mechanical system (MEMS) strain sensors for wireless strain sensing to monitor healing process. The operating frequency of these sensors shifts under mechanical loading; this shift is related to the surface strain of the implantable test material. In this thesis, for the first time, we developed and demonstrated a new class of bio-implant metamaterial-based wireless strain sensors that make use of their unique structural advantages in sensing, opening up important directions for the applications of metamaterials. These custom-design metamaterials exhibit better performance in remote sensing than traditional RF structures (e.g., spiral coils). Despite their small size, these meta-sensors feature a low enough operating frequency to avoid otherwise strong background absorption of soft tissue and yet yield higher Q-factors (because of their splits with high electric field density) compared to the spiral structures. We also designed and fabricated flexible metamaterial sensors to exhibit a high level of linearity, which can also conveniently be used on non-flat surfaces. Innovating on the idea of integrating metamaterials, we proposed and implemented a novel architecture of ‘nested metamaterials’ that incorporate multiple split ring resonators integrated into a compact nested structure to measure strain telemetrically over a thick body of soft tissue. We experimentally verified that this nested metamaterial architecture outperforms classical metamaterial structures in telemetric strain sensing. As a scientific breakthrough, by employing our nested metamaterial design, we succeeded in reducing the electrical length of the sensor chip down to λo/400 and achieved telemetric operation across thick soft tissue with a tissue thickness up to 20 cm, while using only sub-cm implantable chip size (compatible with typical orthopaedic trauma implants and instruments). As a result, with nested metamaterials, we successfully demonstrated wireless strain sensing on sheep’s fractured metatarsal and femur using our sensors integrated on stainless steel fixation plates and on sheep’s spine using directly attached sensors in animal models. This depth of wireless sensing has proved to suffice for a vast portfolio of bone fracture (including spine) and trauma care applications in body, as also supported by ongoing in vivo experiments in live animal models in collaboration with biomechanical and medical doctors. Herein, for all generations of our RF-bioMEMS implant sensors, this dissertation presents a thorough documentation of the device conception, design, modeling, fabrication, device characterization, and system testing and analyses. This thesis work paves the way for “smart” orthopaedic trauma implants, and enables further possible innovations for future healthcare.
Open Access
Selective fluorescence sensing of biological thiols using a bodipy based bifunctional probe and the catalytic activity of short peptide amphiphile nanostructures : implications on the oring of life
(2013) Altay, Yiğit
Chemosensor development is an attractive field of modern chemistry and there exist large amount of contribution from all over the world. The biological importance of thiols triggered the development of sensors to differentiate especially cysteine (Cys), homocysteine (Hcy) and glutathione (GSH) which play key roles in biological systems. Concentration of those thiols results in number of diseases and their structural similarity complicates the differentiation. Optical probes especially fluorescent ones are widely employed for that purpose since it offers simplicity, sensitivity and low detection limits as well as real time analysis. BODIPY core is decorated with a Michael acceptor nitro-styrene group to covalent incorporation of thiols and with an aza-crown moiety to recognition of N-terminus of them. The work in this thesis is the first example in which one of them is separated from others or three of them separated from each other’s by chain length difference using fluorescence spectrometry. Formation of short peptides (2-4 aa residues) is considered to be likely under primordial conditions, following a number of scenarios. In this work, it is constructed a short peptide library limiting our choice of amino acids to those believed to be available at larger concentrations such as Gly, Ala, Asp and Cys. It is demonstrated that when acylated at the N-terminus, nanostructures of varying size and shapes were formed. Investigations on the catalytic activity of these nanostructures under different conditions are presented. The findings on the correlation of peptide structure and nanostructure formation and/or catalytic activity are presented.