This thesis reports design and implementation of a MEMS based resonant mass sensor for cell detection applications. The main objective of the thesis is the real-time detection of captured cells inside liquid medium and obtaining the detection results by electronic means, without the aid of any external optical instruments. A new resonant mass sensor architecture is presented that has various advantages over its conventional counterparts. The device oscillates in the lateral direction, eliminating squeeze film damping. A thin parylene layer coated on the device prevents liquids from entering the narrow gaps of the device, further improving the quality factor. The resonator is embedded on the floor of a microchannel. A gold film on the proof mass facilitates antibody based cell capture on the device. Theoretical background regarding resonator operation is investigated. Various resonator designs are presented, taking into account design trade-offs, application v considerations, and fabrication limitations. The design procedure is verified with MATLAB Simulink modeling results and finite element simulations. A new process flow has been developed for resonator fabrication, combining SOI, glass, and polymer micromachining. Modifications have been done on the flow for the solution of problems encountered during device fabrication. Each device has a foot print area of 1.5 x 0.5 cm2. The majority of this area is occupied by fluidic connections and reservoirs. Resonance characterization results in air and water have shown that there is significant quality factor enhancement with the parylene coating method. The quality factor decreases to only 170 in water from 610 in air, when the resonator is coated with a thin layer of parylene. Uniformity and linearity tests revealed that the devices have a standard deviation of only 1.9% for different analyte capture sites and an R2 of 0.997 for mass loads as high as 2.7 ng. Detection of Saccharomyces cerevisiae type yeast cells has been done using the resonators. Mass measurement of single yeast cell (13 pg) and yeast clusters (102 pg) have been performed. Antibody and thiol-gold chemistry based Candida Albicans type bacteria capture and detection has also been made in both air and water environments. The mass of several captured bacterial cells in air has been measured as 95pg. Two bacterial cells have been captured on one device inside water and their mass has been measured as 85 pg. It is worthy to note that all mass measurements are consistent with theoretical expectations.

In this thesis, conventional and unconventional technologies have been studied and combined in order to make heterogeneous microfluidics with potential advantages, especially in biological applications. Many conventional materials, like silicon, glass, thermoplastic polymers, polyimide and polydimethylsiloxane (PDMS) have been combined in building heterogeneous microfluidic devices or demonstrators. Aside from these materials, unconventional materials for microfluidics such as stainless steel and the fluoroelastomer Viton have been explored. The advantages of the heterogeneous technologies presented were demonstrated in several examples: (1) For instance, in cell biology, surface properties play an important role. Different functions were achieved by combining microengineering and surface modification. Two examples were made by depositing a Teflon-like film: a) a non-textured surface was made hydrophobic to allow higher pressures for cell migration studies and b) a surface textured by ion track technology was even made super-hydrophobic. (2) In microfluidics, microactuators used for fluid handling are important, e.g. in valves and pumps. Here, microactuators that can handle high-pressures were presented, which may allow miniaturization of high performance bioanalyses that until now have been restricted to larger instruments. (3) In some applications the elastomer PDMS cannot be used due to its high permeability and poor solvent resistivity. Viton can be a good replacement when elasticity is needed, like in the demonstrated paraffin actuated membrane.(4) Sensing of bio-molecules in aquatic solutions has potential in diagnostics on-site. A proof-of-principle demonstration of a potentially highly sensitive biosensor was made by integrating a robust solidly mounted resonator in a PDMS based microfluidic system. It is concluded that heterogeneous technologies are important for microfluidic systems like micro total analysis systems (µTAS) and lab-on-chip (LOC) devices.

A computer model based on minimization of the free energy, capable to predict contact angles and spreading transitions between Wenzel and Cassie mode for drops placed on surfaces with different topography were implemented in matlab. Simulations were compared with experiments documented in the literature. These showed that reported transitions between Cassie and Wenzel mode can be explained by minimization of the free energy. In this report, a study on the possibility of constructing water repellent paper surfaces with a combination of treatment with octadecyltrichlorosilane and topography changes, is included.

A novel method based on pulse current electrodeposition (PCE) employing four different waveforms was developed and utilized for fabricating membrane-electrode assemblies (MEAs) with low platinum loading for use in low-temperature proton exchange membrane fuel cells. It was found that both peak deposition current density and duty cycle control the nucleation rate and the growth of platinum crystallites. Based on the combination of parameters used in this study, the optimum conditions for PCE were found to be a peak deposition current density of 400 mA cm-2, a duty cycle of 4%, and a pulse generated and delivered in the microsecond range utilizing a ramp-down waveform. MEAs prepared by PCE using the ramp-down waveform show performance comparable with commercial MEAs that employ ten times the loading of platinum catalyst. The thickness of the pulse electrodeposited catalyst layer is about 5-7 µm, which is ten times thinner than that of commercial state-of-the-art electrodes. MEAs prepared by PCE outperformed commercial MEAs when subjected to a series of steady-state and transient lifetime tests. In steady-state lifetime tests, the average cell voltage over a 3000-h period at a constant current density of 619 mA cm-2 for the in-house and the state-of-the-art MEAs were 564 mV and 505 mV, respectively. In addition, the influence of substrate and carbon powder type, hydrophobic polymer content in the gas diffusion layer, microporous layer loading, and the through-plane gas permeability of different gas diffusion layers on fuel cell performance were investigated and optimized. Finally, two mathematical models based on the microhardness model developed by Molina et al. [J. Molina, B. A. Hoyos, Electrochim. Acta, 54 (2009) 1784-1790] and Milchev [A. Milchev, “Electrocrystallization: Fundamentals of Nucleation And Growth” 2002, Kluwer Academic Publishers, 189-215] were refined and further developed, one based on pure diffusion control and another based on joint diffusion, ohmic and charge transfer control developed by Milchev [A. Milchev, J. Electroanal. Chem., 312 (1991) 267-275 & A. Milchev, Electrochim. Acta, 37 (12) (1992) 2229-2232]. Experimental results validated the above models and a strong correlation between the microhardness and the particle size of the deposited layer was established.

A novel method based on pulse current electrodeposition (PCE) employing four different waveforms was developed and utilized for fabricating membrane-electrode assemblies (MEAs) with low platinum loading for use in low-temperature proton exchange membrane fuel cells. It was found that both peak deposition current density and duty cycle control the nucleation rate and the growth of platinum crystallites. Based on the combination of parameters used in this study, the optimum conditions for PCE were found to be a peak deposition current density of 400 mA cm-2, a duty cycle of 4%, and a pulse generated and delivered in the microsecond range utilizing a ramp-down waveform. MEAs prepared by PCE using the ramp-down waveform show performance comparable with commercial MEAs that employ ten times the loading of platinum catalyst. The thickness of the pulse electrodeposited catalyst layer is about 5-7 µm, which is ten times thinner than that of commercial state-of-the-art electrodes. MEAs prepared by PCE outperformed commercial MEAs when subjected to a series of steady-state and transient lifetime tests. In steady-state lifetime tests, the average cell voltage over a 3000-h period at a constant current density of 619 mA cm-2 for the in-house and the state-of-the-art MEAs were 564 mV and 505 mV, respectively. In addition, the influence of substrate and carbon powder type, hydrophobic polymer content in the gas diffusion layer, microporous layer loading, and the through-plane gas permeability of different gas diffusion layers on fuel cell performance were investigated and optimized. Finally, two mathematical models based on the microhardness model developed by Molina et al. [J. Molina, B. A. Hoyos, Electrochim. Acta, 54 (2009) 1784-1790] and Milchev [A. Milchev, “Electrocrystallization: Fundamentals of Nucleation And Growth” 2002, Kluwer Academic Publishers, 189-215] were refined and further developed, one based on pure diffusion control and another based on joint diffusion, ohmic and charge transfer control developed by Milchev [A. Milchev, J. Electroanal. Chem., 312 (1991) 267-275 & A. Milchev, Electrochim. Acta, 37 (12) (1992) 2229-2232]. Experimental results validated the above models and a strong correlation between the microhardness and the particle size of the deposited layer was established.

A refinement of a minimal model for protein folding originally proposed by Imamura is presented. The representation of the alpha-helix has been improved by adding in explicit modelling of the entire peptide unit. A four-helix bundle consisting of four alpha-helices and three loop regions is generated with the parallel tempering Monte Carlo scheme. Six native states are found for the given sequence, four U-bundle and two Z-bundle states. All six states have energies of E approx -218ε and all appear equally likely to occur in simulation. The highest probability of folding a native state is found to be at a hydrophobic strength of Ch = 0.8 which agrees with the value of Ch = 0.7 used by Imamura in his studies of alpha to beta structural conversions. Two folding stages are observed in the temperature spectrum dependent on the magnitude of the hydrophobic strength parameter. The two stages observed as temperature decreases are 1) the hydrophobic energy causes the random coil to collapse into a compact globule 2) the secondary structure starts forming below a temperature of about T = 0.52ε/kB. The temperature of the first stage, which corresponds to the characteristic collapse temperature Tθ, is highly dependent on the hydrophobic strength. The temperature of the second stage is constant with respect to hydrophobic strength. Attempts to measure the characteristic folding temperature, Tf , from the structural overlap function proved to be difficult due mostly to the presence of six minima and the complications that arose in the parallel tempering Monte Carlo scheme. However, a rough estimate of Tf is obtained at each hydrophobic strength from a native state density analysis. Tf is found to be significantly lower than Tθ.

An ideal drug delivery system should contain an appropriate therapeutic agent and biocompatible carrier. In this study, we investigated the ability of the all-complementary self-assembling peptide AC8 in stabilizing the anticancer compound and determined the in-vitro therapeutic efficacy of the peptide-mediated anticancer drug delivery. The all-complementary peptide AC8 was designed based on the amino acid pairing principle (AAP), which contains hydrogen bonding, electrostatic, and hydrophobic interaction amino acid pairs. AAP interactions make the peptide capable of self-assembling into β-sheet structure in solution in a concentration dependent manner. Peptide solution concentration is a key parameter in controlling the nanoscale assembling of the peptide. The critical assembly concentration (CAC) of the peptide was found ~ 0.01 mg/ml by several techniques. The all-complementary peptide AC8 was found to be able to stabilize neutral state of hydrophobic anticancer compound ellipticine in aqueous solution. The formation of peptide-ellipticine complex was monitored by fluorescence spectroscopy at different mass ratios of peptide-to-ellipticine. The anticancer activity of the complexes with neutral state of ellipticine was found to show great anticancer activity against two cancer cells lines, A-549 and MCF-7. This peptide-mediated anticancer delivery system showed the induction of apoptosis on cancer cells in vitro by flow Cytometry.

A refinement of a minimal model for protein folding originally proposed by Imamura is presented. The representation of the alpha-helix has been improved by adding in explicit modelling of the entire peptide unit. A four-helix bundle consisting of four alpha-helices and three loop regions is generated with the parallel tempering Monte Carlo scheme. Six native states are found for the given sequence, four U-bundle and two Z-bundle states. All six states have energies of E approx -218ε and all appear equally likely to occur in simulation. The highest probability of folding a native state is found to be at a hydrophobic strength of Ch = 0.8 which agrees with the value of Ch = 0.7 used by Imamura in his studies of alpha to beta structural conversions. Two folding stages are observed in the temperature spectrum dependent on the magnitude of the hydrophobic strength parameter. The two stages observed as temperature decreases are 1) the hydrophobic energy causes the random coil to collapse into a compact globule 2) the secondary structure starts forming below a temperature of about T = 0.52ε/kB. The temperature of the first stage, which corresponds to the characteristic collapse temperature Tθ, is highly dependent on the hydrophobic strength. The temperature of the second stage is constant with respect to hydrophobic strength. Attempts to measure the characteristic folding temperature, Tf , from the structural overlap function proved to be difficult due mostly to the presence of six minima and the complications that arose in the parallel tempering Monte Carlo scheme. However, a rough estimate of Tf is obtained at each hydrophobic strength from a native state density analysis. Tf is found to be significantly lower than Tθ.

An ideal drug delivery system should contain an appropriate therapeutic agent and biocompatible carrier. In this study, we investigated the ability of the all-complementary self-assembling peptide AC8 in stabilizing the anticancer compound and determined the in-vitro therapeutic efficacy of the peptide-mediated anticancer drug delivery. The all-complementary peptide AC8 was designed based on the amino acid pairing principle (AAP), which contains hydrogen bonding, electrostatic, and hydrophobic interaction amino acid pairs. AAP interactions make the peptide capable of self-assembling into β-sheet structure in solution in a concentration dependent manner. Peptide solution concentration is a key parameter in controlling the nanoscale assembling of the peptide. The critical assembly concentration (CAC) of the peptide was found ~ 0.01 mg/ml by several techniques. The all-complementary peptide AC8 was found to be able to stabilize neutral state of hydrophobic anticancer compound ellipticine in aqueous solution. The formation of peptide-ellipticine complex was monitored by fluorescence spectroscopy at different mass ratios of peptide-to-ellipticine. The anticancer activity of the complexes with neutral state of ellipticine was found to show great anticancer activity against two cancer cells lines, A-549 and MCF-7. This peptide-mediated anticancer delivery system showed the induction of apoptosis on cancer cells in vitro by flow Cytometry.

This thesis reports design and implementation of a MEMS based gravimetric resonator for cytometry applications. There are mainly two objectives of this thesis / to enable in-flow analysis and to perform closed loop operation that does not require any additional processing or equipment. A novel MEMS based resonator with in-flow capabilities is proposed for detection of agents inside micro channels. High resolution of mass detection inside micro channels is planned to be succeeded with lateral motion in the micro channel floor. The idea embedding lateral resonators emerges from decreasing squeeze film damping during the motion of the resonator. Lateral motion is supported by hydrophobic parylene coating to decrease the damping. Theory and design of the gravimetric resonators are explained and the fabrication flow is constructed and performed successfully by combining SOI, SOG and polymer micro fabrication techniques. Problems during the fabrication are overcome and optimized flow is presented. The devices have a foot print area of 1.5 x 0.5 cm2 which is mainly composed of reservoirs for fluidic connections. Ten types of devices are designed according to their mass sensitivities and compliances. Trade offs between frequency, injected current, and compliance are analyzed successfully by taking also the performance parameters of the interface electronics in to account. Test results reveal that single latex bead with 3 &micro / m diameter and 14.127 pg mass can be sensed successfully and mass sensitivity is measured to be 5.91 fg/Hz for this type of device.