Browsing by Author "Lear, Kevin L., advisor"
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Item Open Access A CMOS compatible optical biosensing system based on local evanescent field shift mechanism(Colorado State University. Libraries, 2011) Yan, Rongjin, author; Lear, Kevin L., advisor; Dandy, David S., committee member; Chandrasekar, V., committee member; Notaros, Branislav, committee memberThe need for label-free integrated optical biosensors has dramatically increased in recent years. Integrated optical biosensors have many advantages, including low-cost, and portability. They can be applied to many fields, including clinical diagnostics, food safety, environmental monitoring, and biosecurity applications. One of the most important applications is point-of-care diagnosis, which means the disease could be tested at or near the site of patient care rather than in a laboratory. We are exploring the issues of design, modeling and measurement of a novel chip-scale local evanescent array coupled (LEAC) biosensor, which is an ideal platform for point-of-care diagnosis. Until now, three generations of LEAC samples have been designed, fabricated and tested. The 1st generation of LEAC sensor without a buried detector array was characterized using a commercial near field scanning optical microscope (NSOM). The sample was polished and was end-fire light coupled using single mode fiber. The field shift mechanism in this proof-to-concept configuration without buried detector arrays has been validated with inorganic adlayers [1], photoresist [2] and different concentrations of CRP proteins [3]. Mode beating phenomena was predicted by the beam propagation method (BPM) and was observed in the NSOM measurement. A 2nd generation LEAC sensor with a buried detector array was fabricated using 0.35μm CMOS process at the Avogo Technologies Inc., Fort Collins, Colorado. Characterizations with both single layer patternings, including photoresist as well as BSA [4] and immunoassay complexes [5] were done with cooperative efforts from various research groups. The BPM method was used to study the LEAC sensor, and the simulation results demonstrated the sensitivity of the LEAC sensor is 16%/nm, which was proved to match well with the experimental data [6]. Different antigen/antibodies, including mouse IgG and Hspx (a tuberculosis reactive antigen), have been used to test the immunoassay ability of LEAC sensor [7]. Many useful data have been collected by using the 2nd generation LEAC chip. However, during the characterization of the Avago chips, some design problems were revealed, including incompatibility with microfluidic integration, restricted detection region, strong sidewall scattering and uncoupled light interference from the single mode fiber. To address these problems, the 3rd generation LEAC sensor chip with buried detector arrays was designed to allow real-time monitoring and compatibility with microfluidic channel integration. 3rd generation samples have been fabricated in the CSU cleanroom and the mesa detector structure has been replaced with the thin insulator detector structure to solve the problems encountered during the characterizations. PDMS microfluidic channels and a multichannel measurement system consisting of a probe card, a multiplexing/amplification circuit and a LabVIEW program have been implemented into the LEAC system. In recent years, outbreaks of fast spreading viral diseases, such as bird flu and H1N1, have drawn a lot of concern of the point-of-care virus detection techniques. To test the virus detection ability of LEAC sensor, 40nm and 200nm polystyrene nanoparticles were immobilized onto the waveguide, and the increased scattered light was collected. Sensitivities of 1%/particle and 0.04%/particle were observed for 200nm and 40nm particles respectively.Item Open Access A plastic total internal reflection-based photoluminescence device for enzymatic biosensors(Colorado State University. Libraries, 2013) Thakkar, Ishan G., author; Lear, Kevin L., advisor; Reardon, Kenneth, committee member; Collins, George, committee memberGrowing concerns for quality of water, food and beverages in developing and developed countries drive sizeable markets for mass-producible, low cost devices that can measure the concentration of contaminant chemicals in water, food, and beverages rapidly and accurately. Several fiber-optic enzymatic biosensors have been reported for these applications, but they exhibit very strong presence of scattered excitation light in the signal for sensing, requiring expensive thin-film filters, and their non-planar structure makes them challenging to mass-produce. Several other planar optical waveguide-based biosensors prove to be relatively costly and more fragile due to constituent materials and the techniques involved in their fabrication. So, a plastic total internal reflection (TIR)-based low cost, low scatter, field-portable device for enzymatic biosensors is fabricated and demonstrated. The design concept of the TIR-based photoluminescent enzymatic biosensor device is explained. An analysis of economical materials with appropriate optical and chemical properties is presented. PMMA and PDMS are found to be appropriate due to their high chemical resistance, low cost, high optical transmittance and low auto-fluorescence. The techniques and procedures used for device fabrication are discussed. The device incorporated a PMMA-based optical waveguide core and PDMS-based fluid cell with simple multi-mode fiber-optics using cost-effective fabrication techniques like molding and surface modification. Several techniques of robustly depositing photoluminescent dyes on PMMA core surface are discussed. A pH-sensitive fluorescent dye, fluoresceinamine, and an O2-sensitive phosphorescent dye, Ru(dpp) both are successfully deposited using Si-adhesive gel-based as well as HydroThane-based deposition methods. Two different types of pH-sensors using two different techniques of depositing fluoresceinamine are demonstrated. Also, the effect of concentration of fluoresceinamine-dye molecules on fluorescence intensity and scattered excitation light intensity is investigated. The fluorescence intensity to the scattered excitation light intensity ratio for dye deposition is found to increase with increase in concentration. However, both the absolute fluorescence intensity and absolute scatter intensity are found to decrease in different amounts with an increase in concentration. An enzymatic hydrogen peroxide (H2O2) sensor is made and demonstrated by depositing Ruthenium-based phosphorescent dye (Ru(dpp)3) and catalase-enzyme on the surface of the waveguide core. The O2-sensitive phosphorescence of Ru(dpp)3 is used as a transduction signal and the catalase-enzyme is used as a bio-component for sensing. The H2O2 sensor exhibits a phosphorescence signal to scattered excitation light ratio of 100±18 without filtering. The unfiltered device demonstrates a detection limit of (2.20±0.6) µM with the linear range from 200µM to 20mM. An enzymatic lactose sensor is designed and characterized using Si-adhesive gel based Ru(dpp)3 deposition and oxidase enzyme. The lactose sensor exhibits the linear range of up to 0.8mM, which is too small for its application in industrial process control. So, a flow cell-based sensor device with a fluid reservoir is proposed and fabricated to increase the linear range of the sensor. Also, a multi-channel pH-sensor device with four channels is designed and fabricated for simultaneous sensing of multiple analytes.Item Open Access Action potential initiation mechanisms: analysis and numerical study(Colorado State University. Libraries, 2022) Aldohbeyb, Ahmed A., author; Lear, Kevin L., advisor; Vigh, Jozsef, committee member; Prasad, Ashok, committee member; Venayagamoorthy, Karan, committee memberAction potentials (AP) are the unitary elements of information processing in the nervous system. Understanding AP initiation mechanisms is a fundamental step in determining how neurons encode information. However, variation in neuronal response is a characteristic of mammalian neurons, which further complicate the analysis of neuronal firing dynamics. Several studies have associated the variation in AP onset with the type and densities of voltage-gated ion channels, diversity in synaptic inputs, neuron intrinsic properties, cooperative Na+ gating, or AP backpropagation. But the mechanisms that underlie the response variability remain unclear and subject to debate. Even though all these studies tried to answer the same question, the definition of AP onset and rapidity differs between them, highlighting the need for a more systematic and consistent method to quantify AP onset features, and hence analyzing the variation in AP onset. Two novel methods were developed to quantify AP rapidity. The proposed methods have lower relative variation, higher ability to classify neuron types, and higher sensitivity and specificity to voltage-gated Na+ channels parameters than current methods. AP rapidity was used to analyze different factors impacting the AP activation mechanism. However, the prior rapidity quantification methods are subjectively based on the researcher's judgment, which complicates the comparison between different studies. Thus, we proposed a more systematic and consistent method based on the full-width or half-width at half the rising phase peak of the membrane potential's second-time derivative (Vm). First, using an HH-type model, we showed that the peak width methods are sensitive to changes in the Na+ channel parameters and conductance and minimally impacted by changes in the K+ channel parameters compared to the phase slope, the standard quantification method. Second, we compared the peak width methods to the two prior methods, phase slope and error ratio, using recordings from cortical and hippocampal pyramidal neurons, hippocampal PVBCs, and FS cortical neurons found in online databases. The results showed that the new methods have the lowest variation between neurons within a specific type while significantly differentiating several neuron types. Together, the two studies showed that the peak width methods provide another sensitive tool to investigate the mechanisms impacting AP onset dynamics and provide a better tool to study Na+ channels kinetics and AP onset features. A conductance-based model that includes dynamics of ion concentration and cooperative Na+ channels was developed to investigate the mechanisms responsible for observed neuronal response variation. Random response variability has previously been observed in spike trains evoked from individual neurons by the same DC stimulus, but we observed systematic variation. The first APs' in a burst had attributes that were comparable regardless of the stimulus strength, while the subsequent APs' attributes monotonically change during bursts, and the magnitude of change increases with stimulus strength. These two spike train features were observed in three different neuron types (n = 51), indicating a shared mechanism is responsible for the spike train pattern. Various existing computational models fail to replicate the monotonic variation in AP attributes. We proposed incorporating ion concentration dynamics and cooperative gating to account for the missing behavior. A model with dynamic reversal potential but without cooperative Na+ channel gating reproduces the AP attribute's variation during bursts, but not the first APs' attributes. The first APs' attributes were reproduced only in the presence of a fraction of cooperative Na+ channels. Cooperative gating also enhanced the magnitude of modeled variation of some AP attributes to better match the electrophysiological recordings. Therefore, we conclude that changes in ion concentration dynamics could be responsible for the monotonic change in some AP's attributes during normal neuronal firing, and cooperative gating can enhance this effect. Thus, the two mechanisms contribute to the observed variability in neuronal response, especially the variation in AP rapidity.Item Open Access Characterization of a photoluminescence-based fiber optic sensor system(Colorado State University. Libraries, 2011) Yi, Zhangjing, author; Lear, Kevin L., advisor; Pezeshki, Ali, committee member; Mueller, Jennifer L., committee memberMeasuring multiple analyte concentrations is essential for a wide range of environmental applications, which are important for the pursuit of public safety and health. Target analytes are often toxic chemical compounds found in groundwater or soil. However, in-situ measurement of such analytes still faces various challenges. Some of these challenges are rapid response for near-real time monitoring, simultaneous measurements of multiple analytes in a complex target environment, and high sensitivity for low analyte concentration without sample pretreatment. This thesis presents a low-cost, robust, multichannel fiber optic photoluminescence (PL)-based sensor system using a time-division multiplexing architecture for multiplex biosensor arrays for in-situ measurements in environmental applications. The system was designed based upon an indirect sensing scheme with a pH or oxygen sensitive dye molecules working as the transducer that is easily adaptable with various enzymes for detecting different analytes. A characterization of the multi-channel fiber optic PL-based sensor system was carried out in this thesis. Experiments were designed with interests in investigating this system's performance with only the transducer thus providing reference figures of merit, such as sensitivity and limit of detection, for further experiments or applications with the addition of various biosensors. A pH sensitive dye, fluoresceinamine (FLA), used as the transducer is immobilized in a poly vinyl alcohol (PVA) matrix for the characterization. The system exhibits a sensitivity of 8.66×10 5 M -1 as the Stern-Volmer constant, K SV , in H + concentration measurement range of 0.002 - 891 μM (pH of 3.05 - 8.69). A mathematical model is introduced to describe the Stern-Volmer equation's non-idealities, which are fluorophore fractional accessibility and the back reflection. Channel-to-channel uniformity is characterized with the modified Stern-Volmer model. Combining the FLA with appropriate enzymatic biosensors, the system is capable of 1,2-dichloroethane (DCA) and ethylene dibromide (EDB) detection. The calculated limit of detection (LOD) of the system can be as low as 0.08 μg/L for DCA and 0.14 μg/L for EDB. The performances of fused fiber coupler and bifurcated fiber assembly were investigated for the application in the fiber optic PL-based sensor systems in this thesis. Complex tradeoffs among back reflection noise, coupling efficiency and split ratio were analyzed with theoretical and experimental data. A series of experiments and simulations were carried out to compare the two types of fiber assemblies in the PL-based sensor systems in terms of excess loss, split ratio, back reflection, and coupling efficiency. A noise source analysis of three existing PL-intensity-based fiber optic enzymatic biosensor systems is provided to reveal the power distribution of different noise components. The three systems are a single channel system with a spectrometer as the detection device, a lab-developed multi-channel system, and a commercial prototype multi-channel system both using a photomultiplier tube (PMT) as the detection device. The thesis discusses the design differences of all three systems and some of the circuit design alteration attempts for performance improvements.Item Open Access CMOS-compatible on-chip optical interconnects(Colorado State University. Libraries, 2009) Pownall, Robert Elliott, author; Lear, Kevin L., advisorThe increase in complexity of integrated circuits (ICs) over the past five decades has resulted increasing demands on the interconnect layers. In the past decade, the ability of conventional "electrical signal down a metal wire" interconnect to keep up with the increasing demands placed on interconnect has come more and more into question. To meet the increasing demands on interconnect and to get around the limitation of conventional "metal wire" interconnect, various forms of optical interconnect have been proposed.Item Open Access Design, optimziation and fabrication of an integrated optoelectronic sensing chip with applications in groundwater contaminant detection and biosensing(Colorado State University. Libraries, 2014) Erickson, Timothy, author; Lear, Kevin L., advisor; Roberts, Jacob, committee member; Notaros, Branislav, committee member; Collins, George, committee memberThe LEAC (Local Evanescent Array Coupled) chip is a CMOS-compatible, waveguide-based, label-free, optoelectronic sensor, which can function as a biosensor or environmental sensor. Unique among optoelectronic sensors, the ~1 cm2 LEAC chip features an integrated photodetector array, which increases device portability, enables multi-analyte detection on a single waveguide, and simplifies system instrumentation. At its core, the LEAC chip is simply a precision refractometer, which can sense very small changes in refractive index (~5x10-6) in its multiple upper cladding sensing regions. The chip can be functionalized for detection of biomarkers or groundwater contaminants, which bind or diffuse into the waveguide's upper cladding sensing region, thereby producing a measurable change in refractive index. The research conducted during my doctoral studies has addressed two important goals. The first was to optimize the chip's sensing performance. The second goal was to run proof of concept experiments, in order to demonstrate its utility in practical sensing applications. By incorporating multiple engineering improvements, the sensing performance of the LEAC chip has been improved to the point where it may be competitive with low-end surface plasmon resonance (SPR) systems for bulk refractive index sensing. We have demonstrated the LEAC sensing platform for both environmental and biosensing applications. These include sensing aromatic hydrocarbons such as benzene, toluene and xylenes in groundwater at sub-ppm concentrations and detection of the cardiac infarction biomarker TroponinI. Research results have been communicated in peer-reviewed journals and presented at conferences, as summarized in Appendix J. Additionally, the intellectual property that was developed during the course of research activities has served as the basis for several patent filings. This dissertation provides a comprehensive account of research conducted on the LEAC sensing platform, while working as a graduate student in Dr. Kevin Lear's laboratory. It is structured in the following manner. In Chapter 1, the basic functionality of LEAC chip is introduced, while providing the necessary background to motivate its development. Chapter 2 provides a comprehensive and comparative overview of other label-free biosensors and groundwater aromatic hydrocarbon contaminant sensors. It reviews the requirements of other sensing systems and demonstrates the uniquely portable aspects of LEAC chip technology. It is provided for completeness, in order to summarize the state-of-the-art in the field of portable sensing and highlight some of the unique advantages of the LEAC sensor. In Chapter 3, the engineering aspects of performance optimization over prior art are described in detail. Whereas the 1st generation LEAC chip was fabricated at Avago Technologies, all 2nd generation LEAC chips have been fabricated by myself in the CSU cleanroom or at the Colorado Nanofabrication Lab in Boulder. The development of 2nd generation LEAC chips, including device physics, modeling, and fabrication is rigorously described. In Chapter 4, the bulk refractive index sensing capabilities of the chip are demonstrated as well as the chip's capacity to perform multi-analyte dry sensing assays . Through design improvements, it is quantitatively shown that the 2nd generation chip is over two orders of magnitude more sensitive than the 1st generation chip. In Chapter 5, the environmental sensing capabilities of the LEAC chip are presented. Teflon AF is first characterized as a unique film for sensing BTX (benzene, toluene, and xylene) contaminants in water using near-IR surface plasmon resonance. Then LEAC chips functionalized with Teflon AF are demonstrated for BTX sensing in water at sub-ppm concentrations. Interference from potential matrix interfering contaminants is evaluated. In Chapter 6, the biosensing capabilities of the LEAC chip are discussed. The LEAC chip is validated for detection of Troponin I. In Chapter 7, areas for future improvements to the LEAC sensing platform are briefly touched upon along with concluding remarks. A number of appendices related to very specific technical aspects of my work have been included as helpful documentation. These appendices include fabrication process flows, the data acquisition system, transimpedance amplifier design, grating coupler designs, mask designs (including testing structures), and other protocols. A list of publications and conferences is provided at the end of this report in Appendix I.Item Open Access Impact of thermal management on vertical-cavity surface-emitting laser (VCSEL) power and speed(Colorado State University. Libraries, 2011) Safaisini, Rashid, author; Lear, Kevin L., advisor; Marconi, Mario C., committee member; Reising, Steven C., committee member; Sites, James R., committee memberIncreasing the modulation bandwidth and output power of vertical-cavity surface-emitting lasers (VCSELs) are of great importance in a variety of applications such as data communication systems. The high temperature generated in the active region of VCSELs is one of the main limiting factors in achieving high power and high speed operation. This work is focused on investigating the effects of thermal management on improving AC and DC properties of VCSELs and achieving higher thermal performance devices. Thermal heatsinking is obtained by surrounding the VCSEL mesas with high thermal conductivity materials such as copper and also using passive heatsinking by flip-chip bonding the laser dies on a GaAs heat spreader. The research includes fabricating and characterizing 980 nm bottom-emitting and 670 nm top-emitting oxide-confined VCSELs. This dissertation is divided into three main parts: high-power, high-speed 980 nm VCSEL arrays, low thermal resistance 670 nm VCSELs, and temperature dependent dynamics of 980 nm VCSELs. Experimental work performed on fabricating and characterizing 980 nm, bottom-emitting, oxide-confined VCSEL arrays and single elements is presented first. The result of DC and AC characterization confirms the effectiveness of Cu electroplating of mesas and flip-chip bonding in reducing VCSELs' thermal resistance to obtain lower operating temperatures. Uniformity of frequency response and operating wavelength across the arrays also motivates managing thermal issues and is an indication of uniform distribution of current and heat flux on the array. This research resulted in record VCSEL arrays with frequency response of approximately 8 GHz and operating CW power of 200 mW. These 28-element, 18µm aperture diameter arrays represent the highest power reported for a VCSEL or VCSEL array with greater than 1 GHz modulation bandwidth. The second part of this dissertation details the fabrication steps and DC characterization of visible, 670 nm, top-emitting, oxide-confined VCSELs. Since achieving high operating temperatures is one of the main challenges in realizing improved red VCSELs, the effect of mesa heatsinking on improving their DC behavior using copper electroplating of mesas is studied. Thermal modeling of the copper plated VCSELs also facilitates better understanding and analysis of the experimental results. A photomask and process flow were designed to fabricate VCSELs with a variety of mesa diameters and inner and outer plating sizes to investigate the major direction of heat flow in the VCSELs and decrease VCSEL thermal resistance and thus increase the output power. Although copper plating significantly reduces thermal resistance, it did not substantially increase maximum operating temperature of the red devices and also put the mesas under stress that might not be desired. This study led us to analyzing the effects of stress on the VCSEL mesas which is induced by the copper films. Finally, the temperature dependence of 980 nm VCSEL dynamics is investigated using noise spectra measurement. This analysis provides some useful insights in understanding how temperature alters VCSEL properties and how these properties can be improved. A VCSEL with 7 µm aperture diameter was fabricated from the same epitaxial material and followed the same processing steps as the VCSEL arrays. Relaxation oscillation frequencies and damping factors as functions of bias current and stage temperature were extracted. These results along with the VCSEL DC measurement were used to estimate the laser differential gain as a function of temperature. The differential gain was shown to be relatively temperature independent over a temperature range of 10 °C to 70 °C with an average value of approximately 12×10-16 cm2. This research led us to the conclusion that improving the output power at elevated temperatures should yield better frequency response in this case. The VCSEL output power reduction was observed to be the major cause of bandwidth reduction at elevated temperatures for the device under test. This work is the first report on the measurement of temperature dependence of VCSEL dynamics.Item Open Access Modeling of optical waveguides with porous silica claddings and their use in LEAC sensors(Colorado State University. Libraries, 2014) Obeidat, Yusra Mahmoud, author; Lear, Kevin L., advisor; Pasricha, Sudeep, committee member; Pinaud, Olivier, committee memberIntegrated optical biosensors have many advantages such as low-cost, portability and the ability to detect multiple analytes on a single waveguide. They can be used in many important applications including biosensing applications. Previous research work focused on the issues of design, modeling and measurement of the local evanescent array coupled (LEAC) biosensor. The sensors were made using conventional dielectrics such as SiO2 and SiNx. The large increase in the complexity of the integrated circuits has increased the need for developing low-k dielectrics as new materials to cope with the integration challenges and improve operating speed. Furthermore, optical interconnects are required to be used to replace electrical interconnects in ICs to meet future goals. This increases the need for simultaneous manufacturing of electronics and optics on the same chip using a CMOS process. The research conducted during my Master of Science studies has addressed two important goals. The first was to use models to calculate surface and volume scattering losses in optical waveguides, especially, ones with porous silica claddings. The second goal was to use the simulation results to demonstrate the possibility of using porous silica in designing optical waveguides and LEAC sensors. By applying these models to porous silica optical waveguides described in previous publications, the agreement between their experimental results and the models results have been proved. Thus, these models can be used in the future to calculate the scattering losses in optical waveguides including ones with porous silica cladding. The main methods that are used to prepare porous silica and the models that are used to determine the effective index of porous silica have been discussed. A Matlab modesolver was used to simulate porous silica waveguides. Predictions for sensor sensitivity and waveguide loss as a function of waveguide dimension have been made using modesolver simulation results. The results demonstrate the ability to use porous silica in LEAC sensors in the future.Item Open Access Optical detection methods for microfluidic devices(Colorado State University. Libraries, 2020) Koepke, Marina M., author; Lear, Kevin L., advisor; Wilson, Jesse, committee member; Gustafson, Daniel, committee memberOptical technology is a common tool integrated onto microfluidic devices to aid in data collection and counting for biological and chemical research. In this study, a simple optical technique was investigated as a detection method for microfluidic impedance cytometry (MIC) devices. The MIC devices were designed to characterize size and structure of parasite eggs through electrical impedance measurements. This data could directly benefit the medical and veterinary communities by providing information to aid in addressing helminth infections in humans and animals. The current MIC device and instrumentation does not provide a robust way to validate which impedance changes correlate to parasite eggs passing through the electrodes. To address this, an optical detection method was designed, implemented and tested on two different types of microfluidic devices: a glass device and printed circuit board (PCB) device. The optical hardware was accompanied by a trigger circuit that was used to process and manipulate the detected light signal. The circuit was designed with a sensitivity that would detect small changes in light from strongyle-type eggs flowing through the microfluidic channel. The trigger circuit was composed of multiple stages of signal amplification and oscillation suppression techniques so the changes in light could clearly be detected by the electronics. This method proved to be successful in detecting voltage changes ranging from 1.7 mV to 6.8 mV which resulted from strongyle egg sized particles (63-75 μm in diameter) flowing through the microfluidic channel. Adaptations for the optics, bench set-up and microfluidic device design were investigated to transfer this method to different laboratory settings. This study outlines the process of utilizing basic lab tools and components to create an easy to implement optical detection method for a variety of chip designs and laboratory set-ups.Item Open Access Optofluidic intracavity spectroscopy for spatially, temperature, and wavelength dependent refractometry(Colorado State University. Libraries, 2012) Kindt, Joel D., author; Lear, Kevin L., advisor; Buchanan, Kristen, committee member; Notaros, Branislav, committee memberA microfluidic refractometer was designed based on previous optofluidic intracavity spectroscopy (OFIS) chips utilized to distinguish healthy and cancerous cells. The optofluidic cavity is realized by adding high reflectivity dielectric mirrors to the top and bottom of a microfluidic channel. This creates a plane-plane Fabry-Perot optical cavity in which the resonant wavelengths are highly dependent on the optical path length inside the cavity. Refractometry is a useful method to determine the nature of fluids, including the concentration of a solute in a solvent as well as the temperature of the fluid. Advantages of microfluidic systems are the easy integration with lab-on-chip devices and the need for only small volumes of fluid. The unique abilities of the microfluidic refractometer in this thesis include its spatial, temperature, and wavelength dependence. Spatial dependence of the transmission spectrum is inherent through a spatial filtering process implemented with an optical fiber and microscope objective. A sequence of experimental observations guided the change from using the OFIS chip as a cell discrimination device to a complimentary refractometer. First, it was noted the electrode structure within the microfluidic channel, designed to trap and manipulate biological cells with dielectrophoretic (DEP) forces, caused the resonant wavelengths to blue-shift when the electrodes were energized. This phenomenon is consistent with the negative dn/dT property of water and water-based solutions. Next, it was necessary to develop a method to separate the optical path length into physical path length and refractive index. Air holes were placed near the microfluidic channel to exclusively measure the cavity length with the known refractive index of air. The cavity length was then interpolated across the microfluidic channel, allowing any mechanical changes to be taken into account. After the separation of physical path length and refractive index, it was of interest to characterize the temperature dependent refractive index relationship, n(T), for phosphate buffered saline. Phosphate buffered saline(PBS) is a water-based solution used with our biological cells because it maintains an ion concentration similar to that found in body fluids. The n(T) characterization was performed using a custom-built isothermal apparatus in which the temperature could be controlled. To check for the accuracy of the PBS refractive index measurements, water was also measured and compared with known values in the literature. The literature source of choice has affiliations to NIST and a formulation of refractive index involving temperature and wavelength dependence, two parameters which are necessary for our specialized infrared wavelength range. From the NIST formula, linear approximations were found to be dn/dT = -1.4×10-4 RIU °C-1 and dn/dλ = -1.5×10-5 RIU nm-1 for water. A comparison with the formulated refractive indices of water indicated the measured values were off. This was attributed to the fact that light penetration into the HfO2/SiO2 dielectric mirrors had not been considered. Once accounted for, the refractive indices of water were consistent with the literature, and the values for PBS are believed to be accurate. A further discovery was the refractive index values at the discrete resonant wavelengths were monotonically decreasing, such that the dn/dλ slope for water was considerably close to the NIST formula. Thus, n(T,λ) was characterized for both water and PBS. A refractive index relationship for PBS with spatial, temperature, and wavelength dependence is particularly useful for non-uniform temperature distributions caused by DEP electrodes. First, a maximum temperature can be inferred, which is the desired measurement for cell viability concerns. In addition, a lateral refractive index distribution can be measured to help quantify the gradient index lenses that are formed by the energized electrodes. The non-uniform temperature distribution was also simulated with a finite element analysis software package. This simulated temperature distribution was converted to a refractive index distribution, and focal lengths were calculated for positive and negative gradient index lenses to a smallest possible length of about 10mm.Item Open Access Uncovering details of the electrical properties of cells(Colorado State University. Libraries, 2022) Nejad, Jasmine E., author; Lear, Kevin L., advisor; Tobet, Stuart, committee member; McGrew, Ashley K., committee member; Simske, Steve, committee memberThe electrical properties of cells have long been studied by scientists across many fields, yet there are still major gaps in our understanding of the intrinsic properties of many types of cells, such as parasite eggs, as well as the detailed electrical behavior of excitable cells, such as neurons. This work aims to provide insights into how these properties can be measured and how machine learning can be used to advance our understanding of these phenomena. The first part of this work discusses the development of a microfluidic impedance cytometer for the enumeration and classification of parasite eggs isolated from fecal samples. Current diagnostics in parasitology rely on the manual counting of eggs, cysts, and oocysts on microscope slides that have been isolated from fecal samples. These methods depend on trained technicians with expertise in the preparation of samples and detection of parasites on these slides, which increases cost and turnaround times for diagnosis. This leads many farmers and ranchers to opt to pool fecal samples from multiple animals to save time and labor. In cattle herds, resistance is often due to underdosing, which can be caused by treating all animals to an average weight or treating by the calendar instead of targeted deworming. This blanket use of anthelmintics, or anti-parasitic medication, is leading to concerns about anthelmintic resistance, which would cause major issues in the livestock industry, as well create unforeseen ecological imbalances. The developed microfluidic system provides a proof-of-concept for a microfluidic impedance cytometer capable of measuring the impedance of parasite eggs at multiple frequencies, simultaneously, as each of the eggs passes through a microfluidic channel past a sensing region. This region consists of parallel electrodes on the top and bottom of the channel, allowing for measurement of the voltage across the channel. When an egg passes through, the signal is interrupted, leaving a distinct profile of the electrical properties at each frequency over time. This system shows proof-of-concept of the impedance measurements at 500kHz and 10MHz and provides insights for further exploration of these properties, with the eventual use of machine learning algorithms for discrimination of parasite eggs from debris, and differentiation of parasite genera. The second part of this work discusses machine learning classification of neuronal subtypes based on features extracted from patch-clamp recordings from adult mice, using data acquired from publicly available databases. Classification of neuronal subtypes has been a continuously progressing area of neuroscience, building on advancements in our understanding of the morphology, physiology, and biochemistry of different neurons, and contributing to the accuracy and repeatability of action potential and neuronal circuit models. This work explores the use of k-nearest neighbors, support vector machine, decision tree, logistic regression, and naïve Bayes algorithms for classification of fast-spiking or regular-spiking neurons from the hippocampus or the primary somatosensory cortex. K-nearest neighbors shows the most accurate classification of these groups, using action potential width, amplitude, and onset potential as features (inputs into the algorithm), with the addition of a measure of rapidity (acceleration near action potential onset) showing major increases in classification accuracy. Of the three methods for measuring rapidity, inverse of the full width at half of the maximum of the second derivative of the membrane potential (V̈m) (IFWd2), inverse of the half width at half of the maximum of V̈m (IHWd2), and the slope of the phase plot (V̇m vs. Vm) near AP onset (phase slope), including the phase slope measure of rapidity increased the accuracy to nearly perfect (weighted f1-score > 0.9999). In addition, the use of phase slope and action potential width as the only features for classification produces measures of accuracy, weighted f1-scores, of >0.9996. The results show the value of rapidity in action potential dynamics, the distinct difference between rapidity in APs generated by hippocampal neurons relative to cortical neurons, and low standard deviations for rapidity values in cortical neurons (fast- and regular-spiking). These findings have potential implications for understanding the ion channel dynamics in action potential initiation and propagation, which can improve the modeling of action potentials and neuronal circuits.