Submitted to the faculty of Indiana University In partial fulfillment of the requirements for the degree Master in Bioinformatics In the School of Informatics, Indiana University, December 2004 / The aggregation rate of B-Lactoglobulin (BLG) was studied using turbidimetry and dynamic light scattering in the range 5.8<pH,3.5 at a fixed ionic strength of 4.5 mM, and in the range 4.5 - 500mM NACl at a fixed pH of 5.0. The initial slope of turbidity vs time curve was used to define an initial rate. The highest initial rates of aggregation were observed in the pH range 4.50 to 4.75 but the increase in aggregation rate when the pH was reduced from 5.0 to 4.69 was large compared to its decrease when the pH was reduced from pH 4.69 to 4.20; i.e. the dependence of initial rate on pH was highly asymmetric. The rate of aggregation at pH 5.0 strongly increased with decrease in ionic strength I from 100 to 4.5 mM and was found to be nearly linear with 1/ I. QELS measurements at pH 5.22 and 5.40 at I = 4.5mM revealed that particle size increased with time. Eventual appearances of bimodal distributions showed fast and slow modes corresponding to the BLG dimer and to hydrodynamic diameter 100-800 nm. Measurements at 4.0 and 4.2 indicated the consumption of dimers in the first few minutes to form higher order aggregates. Electrostatic modeling via Delphi was used to visualize the electrostatic poetnetial around the BLG dimer in order to elucidate the pH and ionic strength dependence of BLG aggregation rates. The aggregation process appears to comprise firstly an initial fast consumption of dimer, whose dependence on pH and I arises from the interaction of the positive and negative domains of interacting dimers; and secondly, the slow formation of much larger aggregates with relatively little sensitivity to pH and I. The open-ended nature of BLG aggregation is thought to arise from the asymmetry of the dimer charge distribution in the range 4.2<pH<5.2. Polyanions appear to inhibit aggregation. However, the role of polyanions in minimizing BLG aggregation was observed immediately after the addition of polyanioin to the protein. / Bioinformatics

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In this thesis we used atomic force microscopy (AFM) to investigate systematically the behaviour of both electrostatically stabilised silica and sterically stabilised polystyrene (PS) colloidal systems on freshly cleaved mica substrates. For the silica colloidal nanoparticles we explored the effect of colloidal suspension concentration, particle size, and different application techniques on both the adsorption behaviour and subsequent structuring of the particles. For the PS colloidal nanoparticles we explored concentration effects and experimented with both dip-coating and droplet application techniques. We showed that silica nanoparticles adsorbed onto mica via irreversible adsorption that possessed lateral mobility due to the weak attraction between the nanoparticles and the substrate, facilitating subsequent capillary structuring of the nanoparticles during drying. We associated the effects of volume fraction with Debye screening, and kinetics effects with particle size and volume fraction. We also successfully imaged a partially dried film and showed the role of convective/capillary forces in the structuring of the nanoparticles. Studies with variations in particle size generated a number of different topography structures; with dewetting phenomena observed for 10 nm nanoparticles and the formation of crystalline structures for 100 nm nanoparticles. Spin coating techniques were used to produce even larger crystalline structures of nanoparticles. Size dependent ordering occurred for low concentration samples due to the polydispersity of the colloidal suspension. We showed that acceleration can affect interparticle spacing. We also studied the role of rotational speed on the crystallinity of the particle configurations and showed how fine tuning of rotational speed can generate large scale monolayer crystalline formations of nanoparticles.

Inelastic collisions between dipolar molecules, assumed to be trapped in a static electric field at cold (> 10−3K) temperatures, are investigated and compared with elastic collisions. For molecules with a Λ-doublet energy-level structure, a dipole moment arises because of the existence of two nearly degenerate states of opposite parity, and the collision of two such dipoles can be solved entirely analytically in the energy range of interest. Cross sections and rate constants are found to satisfy simple, universal formulas. In contrast, for molecules in a Σ electronic ground state, the static electric field induces a dipole moment in one of three rotational sublevels. Collisions between two rotor dipoles are calculated numerically; the results scale simply with molecule mass, rotational constant, dipole moment, and field strength. It might be expected that any particles interacting only under the influence of the dipole-dipole interaction would show similar behavior; however, the most important and general result of this research is that at cold temperatures inelastic rate constants and cross sections for dipoles depend strongly upon the internal structure of the molecules. The most prominent difference between the Λ-doublet and rotor molecules is variation of the inelastic cross section with applied field strength. For Λ-doublet dipoles, cross sections decrease with increasing field strength. For rotor dipoles, cross sections increase proportionally with the square of field strength. Furthermore, the rate constants of the two types of molecules depend very differently on the angular orientations of the dipoles in the electric field.

The resonance frequency of electrostatically actuated micromachined beams can be tuned substantially by applying a DC voltage bias, first by decreasing the frequency until the onset of pull-in and then by increasing it by the virtue of contact. With the objective of modeling and designing the micromechanical structures after pull-in, a semi-analytical method was developed to determine the length of the contact between the beam and the substrate. The semi-analytical method which is validated on the straight beams is extended for the folded beam structures. This method provides a tool to the microsystem designer to quickly evaluate the deformed configuration of the folded beams after pull-in without the time-intensive contact analysis. This tool is used to design the micro‐speaker elements suitable for emitting low frequency sounds. Multiple instabilities after the pull-in were numerically observed and it was shown that the resonant frequency of an L-shaped beam can be varied in different frequency bands. The speaker element can emit any frequency in a given range, as the resonant frequency of the beam structures can be tuned both before and after pull-in. Operating the speaker element at resonance maximizes the efficiency of the speaker design because the amplitude of vibration is maximum at the resonance frequency. Furthermore, the interplay between the torsional and bending loads is used to minimize the out-of-plane deflection under self weight. A selection criterion is employed to choose a beam structure with optimum stiffness and natural frequency. Beam-based micro-speaker element designs with single and multi-layered suspended structures are proposed. Practical considerations such as volume displacement, mode shapes and dynamic coupling are discussed, on the basis of which design guidelines for a speaker element are proposed. Squeeze film effects and nonlinearity due to the midplane stretching is integrated into the transient analysis model to analyze the effect on the stroke of beam operating at resonance. A comparison between various speaker elements is presented.

Recent developments in the area of microfabrication technologies, has enabled the fabrication of many radio frequency/microwave components with better performance and lower cost than possible with semiconductor based fabrication technology. Many of these microfabricated RF components such as switches and phase shifters, popularly known as RF MEMS, are aimed at reducing the insertion loss and improving other performance parameters such as linearity. For these devices size miniaturization is not necessarily important, as in practical subsystems, these components are integrated with RF front-ends on a laminate. This thesis deals with concepts of a low cost passive phase shifter fabricated in-situ on a microwave laminate. The operation of this Mesoscale Electrostatically actuated Phase shifter on microwave Laminate (MEPL) is similar to that of a micromachined distributed MEMS transmission line (DMTL) phase shifter. In spite of advantages of low losses, wide bandwidth, low DC power consumption and high linearity over semiconductor/MMIC technology, microfabricated phase shifters are often not used in field because of issues related to fabrication reliability, packaging and integration. On the other hand, the proposed MEPL will have all the advantages of conventional MEMS phase shifters with additional benefit of lower cost. Furthermore, these are integrable to form a monolithic phased array. A MEPL phase shifter of 50-bridges periodically distributed on the co-planar waveguide (CPW) transmission line is demonstrated in this thesis. MEMS air bridges are electrostatically actuated to vary the capacitance of the transmission line, which changes the phase velocity of the propagation RF signal, consequently phase at the output port. The realized MEPL is characterized for electromagnetic as well as electromechanical performance. The electromechanical characterization of this device is performed using a Laser Doppler Vibrometer (LDV). The measured data showed good agreement with the analytical data.. Major application of a phase shifter is in a phased array antenna system. MEPL is particularly suited for a monolithic phase array antenna. The proposed monolithic phased array antenna system fabrication approach utilizes extremely simple and economical modern printed circuit board technology to pattern the conventional microwave laminate and copper foil. A complete monolithic phased array antenna system is fabricated on a microwave laminate using an embedded phase shifter operating with electrostatic principles. Other components such as DC block and bias tee are integrated into the CPW-microstrip transitions to optimize the space and performance. Integrated phased array antenna is fabricated and tested to demonstrate the beam steering capability. Measured S11 is better than -15dB at the operating frequency of 9.8GHz. The beam steering capability is shown as proof of concept by showing the beam scan angle of 10deg with bias voltage of 125V. The mesoscale phase shifter demonstrated in this thesis has several advantages compared to micromachined phase shifters. The proposed fabrication approach does not use metal deposition/patterning process, which removes the need of high cost clean room and sophisticated films deposition equipments. Secondly, as there are no thin films used, stiction is not expected on phase shifters fabricated with this approach. Since this approach uses thicker metal films, the power handling capability is expected to be significantly higher than micromachined phase shifters. Since conventional phased array antenna system components are fabricated on a microwave laminate, micro machined phase shifters realized on semiconductor substrates are required to be packaged separately before integrating with such phased array circuits. Packaging of the micro-machined RF-MEMS/MEMS devices is still a major issue and contributes to a substantial part of the total cost. Unlike micromachined phase shifters which are required to be packaged and then embedded in phased array applications, device presented in this thesis is packaged in-situ. Compared to similar monolithic phased array antenna reported on silicon substrate which are limited by wafer size, these arrays can be easily extended for larger arrays on microwave laminate as these are available in large size. To summarize, the proposed fabrication approach for phase shifters overcomes many limitations of micromachined components for microwave applications while retaining most of their advantages compared to other existing approaches based on ferrites or semiconductor technologies.