The malachite green aptamer was originally engineered for binding specificity to malachite green (MG). The environment inside the aptamer’s electronegative binding pocket was previously harnessed to catalyze an ester cleavage via the stabilization of positively charged intermediates. In order to further explore and expand the catalytic potential of this molecule we have analyzed the binding and chemical properties of MG derivatives. The catalyzed reaction rate is approximately 2000-fold faster than the non-catalyzed reaction rate. This catalytic activity demonstrates the possible significance of electrostatic forces in RNA enzymes. The ability of RNA to catalyze different reactions depending on the substrate provided would have been beneficial in an early RNA world. We have investigated the interactions between the malachite green aptamer and its ligands. This investigation contributes to a better understanding of RNA aptamer interactions with small molecules which are crucial for drug development and RNA based catalysis. Equilibrium dialysis data suggests that MG binds exclusively within the binding pocket. On the other hand, pyronin Y which lacks the third phenyl ring of MG intercalates non-specifically. This confirms that all three phenyl rings have crucial interactions with RNA bases. Isothermal calorimetry data shows a more negative enthalpy value for the binding of tetramethylrosamine (TMR) to the MG aptamer than binding of MG to the MG aptamer. This agrees with the crystal structure of TMR bound to the MG aptamer that shows more extensive base stacking interactions compared to the MG : MG aptamer complex. TMR differs from MG by the addition of an oxygen between two of its phenyl rings, that gives TMR a more planar structure. MG binding to the MG aptamer shows an entropy value increase compared to TMR binding to the MG aptamer. This agrees with available ab initio calculations which show the development of an asymmetrical charge distribution across MG when bound to the MG aptamer.

Energy harvesting from the surrounding environment has become a hot topic in research as an alternative powering solution. The concept deals with scavenging, as well as, harvesting energy from the surrounding energy sources. Harvesting vibrations, through Micro-Power Generators (MPGs) , has drawn a lot of attention recently due to the reduction in the power requirement of the current sensors and integrated ciruits, and the abundance of ambient vibrations in many environments. Vibration Micro-Power generators (VMPGs) use one of three transduction mechanisms: piezoelectric, electromagnetic or electrostatic. Although electrostatic MPGs are the most compatible mechanism with ICs technology, many challenges face their optimal operation including low efficiency due to power electronics switching losses, the need for pre-charge, and the inability to operate in vibration environments with low frequencies and amplitudes. The objective of this thesis is to develop novel electrostatic micro-power generators using switchless architecture to achieve low cost, small footprint, self-sustained and optimal power generation in different vibration environments including low frequencies and amplitudes. The first electrostatic MPG uses an out-of-plane capacitive transducer. The new generator is sensitive enough to extract output power at very low base excitations. It is designed to use ready-made electret as a charging source and is therefore portable and self-sustained. Moreover, the new MPG can be configured as a wideband MPG in its impact mode of operation. A bandwidth of up to 9 Hz has been realized in this mode of operation. An improved version of the MPG is also presented that produces almost 1mW output power at a base excitation amplitude and frequency of 0.08g (RMS) and 86 Hz. Two nonlinear models developed for the free-flight and impact modes of operation of the MPG are presented to allow future analysis and optimization of the system. The second electrostatic MPG uses a novel interdigitated in-plane parallel plate electrostatic transducer. The new implementation can achieve 78% more output power than the original cited implementation. The MPG is fabricated using MEMS surface micromachining. The MPG introduces a new beam suspension system in which the source voltage is unlimited by the pull-in instability and low MPG center frequency can be realized. The MPG uses charged silicon nitride as a charging source. The MPG produces 65 mV at a base acceleration amplitude and frequency of 2g and 1.1 kHz. The prototype achieves 27% less resonance frequency with only one eight the size of the previous implementation. A third electrostatic MPG architecture is introduced. The new architecture eliminates the need for restoring force elements (springs) in the MPG. The architecture can realize arbitrarily low MPG center frequency. It is suitable for both rectilinear and cylindrical structures and can be used with different vibration energy transduction methods. A prototype is fabricated and tested to demonstrate the feasibility of this architecture. The center frequency of the prototype is found to be 2 Hz demonstrating low frequency operation. The nonlinear behavior of switchless (continuous) electrostatic MPGs is further studied for optimal power operation. A consistent approximate analytical solution is developed to describe the nonlinear behavior of switchless comb-finger electrostatic MPGs. The method of multiple scales is used to develop such model. The model was found to be valid for MPGs operating under tight electromechanical coupling conditions and for moderately-large base excitations.

A novel electrostatic analyzer (ESA) simulation method that differs significantly from traditional methods is presented in this study, the "reverse-fly" simulation method. The simulation process and its applications are discussed in detail. This method is tested by comparing its results to the published test data of three experimental instruments; The Proton Electrostatic Analyzer-High Geometric Factor (PESA-H) instrument on the Wind mission [Lin, et al. 1995], the 2π-Toroidal Analyzer (2πTA) of Young, et al., [1988], and the Hot Plasma Composition Analyzer (HPCA) to be used in the upcoming Magnetospheric Multi-scale (MMS) mission. The strong agreement between simulation and experimental results verifies the accuracy of this technique. Our results reveal detailed properties of ESA response that are not practical to assess using laboratory data. This simulation method then is used to compare the transmission characteristics of five published ESA geometries to efficiently determine the optimal ESA geometry for use in future space missions. We show that the simulation methods described here are an important contribution to instrument design and development techniques and are critical to efficient and accurate verification of instrument performance.

The malachite green aptamer was originally engineered for binding specificity to malachite green (MG). The environment inside the aptamer’s electronegative binding pocket was previously harnessed to catalyze an ester cleavage via the stabilization of positively charged intermediates. In order to further explore and expand the catalytic potential of this molecule we have analyzed the binding and chemical properties of MG derivatives. The catalyzed reaction rate is approximately 2000-fold faster than the non-catalyzed reaction rate. This catalytic activity demonstrates the possible significance of electrostatic forces in RNA enzymes. The ability of RNA to catalyze different reactions depending on the substrate provided would have been beneficial in an early RNA world. We have investigated the interactions between the malachite green aptamer and its ligands. This investigation contributes to a better understanding of RNA aptamer interactions with small molecules which are crucial for drug development and RNA based catalysis. Equilibrium dialysis data suggests that MG binds exclusively within the binding pocket. On the other hand, pyronin Y which lacks the third phenyl ring of MG intercalates non-specifically. This confirms that all three phenyl rings have crucial interactions with RNA bases. Isothermal calorimetry data shows a more negative enthalpy value for the binding of tetramethylrosamine (TMR) to the MG aptamer than binding of MG to the MG aptamer. This agrees with the crystal structure of TMR bound to the MG aptamer that shows more extensive base stacking interactions compared to the MG : MG aptamer complex. TMR differs from MG by the addition of an oxygen between two of its phenyl rings, that gives TMR a more planar structure. MG binding to the MG aptamer shows an entropy value increase compared to TMR binding to the MG aptamer. This agrees with available ab initio calculations which show the development of an asymmetrical charge distribution across MG when bound to the MG aptamer.

Energy harvesting from the surrounding environment has become a hot topic in research as an alternative powering solution. The concept deals with scavenging, as well as, harvesting energy from the surrounding energy sources. Harvesting vibrations, through Micro-Power Generators (MPGs) , has drawn a lot of attention recently due to the reduction in the power requirement of the current sensors and integrated ciruits, and the abundance of ambient vibrations in many environments. Vibration Micro-Power generators (VMPGs) use one of three transduction mechanisms: piezoelectric, electromagnetic or electrostatic. Although electrostatic MPGs are the most compatible mechanism with ICs technology, many challenges face their optimal operation including low efficiency due to power electronics switching losses, the need for pre-charge, and the inability to operate in vibration environments with low frequencies and amplitudes. The objective of this thesis is to develop novel electrostatic micro-power generators using switchless architecture to achieve low cost, small footprint, self-sustained and optimal power generation in different vibration environments including low frequencies and amplitudes. The first electrostatic MPG uses an out-of-plane capacitive transducer. The new generator is sensitive enough to extract output power at very low base excitations. It is designed to use ready-made electret as a charging source and is therefore portable and self-sustained. Moreover, the new MPG can be configured as a wideband MPG in its impact mode of operation. A bandwidth of up to 9 Hz has been realized in this mode of operation. An improved version of the MPG is also presented that produces almost 1mW output power at a base excitation amplitude and frequency of 0.08g (RMS) and 86 Hz. Two nonlinear models developed for the free-flight and impact modes of operation of the MPG are presented to allow future analysis and optimization of the system. The second electrostatic MPG uses a novel interdigitated in-plane parallel plate electrostatic transducer. The new implementation can achieve 78% more output power than the original cited implementation. The MPG is fabricated using MEMS surface micromachining. The MPG introduces a new beam suspension system in which the source voltage is unlimited by the pull-in instability and low MPG center frequency can be realized. The MPG uses charged silicon nitride as a charging source. The MPG produces 65 mV at a base acceleration amplitude and frequency of 2g and 1.1 kHz. The prototype achieves 27% less resonance frequency with only one eight the size of the previous implementation. A third electrostatic MPG architecture is introduced. The new architecture eliminates the need for restoring force elements (springs) in the MPG. The architecture can realize arbitrarily low MPG center frequency. It is suitable for both rectilinear and cylindrical structures and can be used with different vibration energy transduction methods. A prototype is fabricated and tested to demonstrate the feasibility of this architecture. The center frequency of the prototype is found to be 2 Hz demonstrating low frequency operation. The nonlinear behavior of switchless (continuous) electrostatic MPGs is further studied for optimal power operation. A consistent approximate analytical solution is developed to describe the nonlinear behavior of switchless comb-finger electrostatic MPGs. The method of multiple scales is used to develop such model. The model was found to be valid for MPGs operating under tight electromechanical coupling conditions and for moderately-large base excitations.

Biological membranes are quasi two-dimensional self-assembled structure, primarily serving as a barrier to the leakage of cell’s contents. The main constituents of biological membrane are various amphiphilic lipids that form bilayers in an aqueous environment. These lipids carry acidic and/or basic functional groups that ionize in water, giving some of them a net electrical charge. Such a lipid molecule, when integrated into the membrane, experiences electrostatic forces from all other charged objects around it, including ions, surrounding lipids, and other molecules such as cationic peptides. The electrostatic interaction can profoundly influence the membrane, to which many phenomena with physiological significance as well as biophysical interest can be ascribed. In this thesis, we concentrate on investigating the electrostatic properties of lipid membranes. First, we study how the electrostatic interaction affects their preferred structure. To this end, we adopt a coarse-grain model that preserves the dominant characteristics of the lipids, in which the electrostatic interaction is treated within the “renormalized” Debye-H¨uckel theory. In particular, we calculate the spontaneous curvature of a phospholipid monolayer, along with other associated quantities. Our results suggest that such divalent ions as Mg2+ can stabilize HII phases of lipids (inverted hexagonal phases), which would otherwise form lamellar phases. Second,we investigate the competitive binding of ions and cationic peptides onto a monolayer of lipopolysaccharide (LPS) molecules, a class of highly charged bio-molecules found in the outer leaflet of the outer membranes of gram-negative (G-) bacteria. Cationic anti-microbial peptides (AMPs) can selectively kill bacteria, and it is suggested that they destabilize the LPS layer, easing their permeation across it, a process of great physiological and clinical interest. To this end, we model the LPS layer as a collection of charged “binding sites”, based on which we study the binding of cations (monovalent and divalent) and cationic peptides onto the layer. Our calculations suggest that the peptides can compete with divalent ions on the binding to the layer. It has been empirically known that since the stability of an LPS layer relies greatly on the bridging of divalent ions, the substitution of these ions by the peptides significantly compromises its stability. Our results offer a quantitative basis for this observation, thus providing a possible mechanism of an important step in the action of AMPs against G- bacteria.

In earlier research in our lab, the manipulation of microtubules on gold patterned silicon wafers was achieved by E-beam lithography, Poly (ethylene glycol) self assembled monolayers (PEG-SAMs) and electrophoresis. To develop a technique for delicate single microtubule manipulation, further studies need to be done on PEG-SAMs and electrophoresis. As a foundation of this goal, we examined the electric field in an aqueous solution between two planar electrodes and the compatibility of the antifouling property of PEG-SAMs with the electric field. For this purpose, the distribution of microbeads was analyzed using a Boltzmann distribution. The amount of adsorbed microtubules on a PEG-SAM was examined to test the compatibility of the antifouling property of a PEG-SAM with concomitant exposure to electric field. It is shown that the product of the electric field and the effective charge of the microbead does not have a linear relation with the applied electric potential but an exponentially increasing function with respect to the potential. The antifouling property of the PEG-SAM was not retained after an exposure to the electric field.

Abstract The research compares the efficiency of particle removal from exhaust of ritual money burning by an electrostatic precipitator (ESP) and a bag-house filter (BH), both have a capacity of around 30-35 Am3/min. A stainless steel chamber of 0.6 m in diameter and 1.0 m in height was used for the ritual money burning. Combustion gas from the chamber was cooled to 300-400oC by mixing with a certain proportion of ambient air and further cooled to around 100-130oC by a fin tube gas cooler before entering either to the ESP or the BH. Results indicate that TSP in the influent gas could be reduced from 6-392 (average 83) to 1-143 (average 22) mg/Nm3 by the ESP with gas velocities of 5-10 cm/s at 100-120 oC through the spacing between collecting plates. TSP emission factors of 0.0295-9.94 (average ¡Ó standard deviation = 1.81¡Ó2.25) and 0.031-3.36 (average ¡Ó standard deviation = 0.27¡Ó0.26) g/(kg combusted ritual money), respectively, were obtained before and after the ESP filtration. Although the ESP had an initial TSP removal of 80-99%, the performance dropped in a few operation hours because of a fouling of the plate surfaces by the collected fume dusts. Cleaning of the plate surfaces helped in the recovery of the performance, however, it dropped after a few cycles of collection and cleaning. Results from BH tests indicate that TSP in the influent gas to it could be reduced from 9-182 (average 72) to 0-12 (average 2.0) mg/Nm3 with the gas flow through the filter cloth with a velocity of 3.3 cm/s at 120-130 oC which resulted in an initial pressure drop of around 100 mmAq. It was observed that some fine dusts would escape from the cloth fiber spaces when the backwash pulse was operated. It is recommended that the backwash cycle should be minimized and trigged after the gas pressure drop over the cloth reaches up to 300 mmAq. TSP emission factors of 0.0176-1.64 (average ¡Ó standard deviation = 0.52¡Ó0.33) and 0-0.491 (average ¡Ó standard deviation = 0.02¡Ó0.05) g/(kg combusted ritual money), respectively, were obtained before and after the BH filtration. BH filtration is recommended for the TSP control in the ritual money buring. XRD(X-Ray Diffraction) examination of a bottom ash sample indicates that the ash has an elemental composition of O, Na, Al, and Si of 49.9, 11.8, 23.8, and 15.1%, respectively. SEM(Scanning Electron Microscope) analysis indicates that the collected fly ash and the bottom ash have particle sizes of 20-110 (mostly 45-60 nm) and 50-300 (average 250) nm, respectively.

This paper proposed a low-cost and high-throughput method to fabricate lensed optical fibers. SU-8 Photoresist is used as the material for fabricating the proposed lens structure and is directly applied on two kinds of optical fiber tip, single mode glass fibers (O.D.=125 £gm) and plastic graded-index plastic fiber (O.D.=500 £gm), utilizing surface tension force to form a hemi-circular shape lens structure. The hemi-circular shape SU-8 lens is then electrostatically pulled to form non-spherical shape in an uniform electric field at a temperature higher than the glass temperature (Tg) of SU-8. Microlens with various radius of curvature can be easily produced by tuning the applied electric fields during the electrostatic pulling process. In addition, this study also measures the UV-Vis-NIR spectrum SU-8 photoresist to confirm the optical property of SU-8. Results indicate the SU-8 has high optical transmittance from the wavelength range of 380-1600 nm. SEM observation also indicates the fabricated SU-8 microlens has excellent surface smoothness which is essential for optical applications. A commercial optical simulation software of ZEMAX® is used to predict the light path of the fabricated lensed fiber. The numerical results show good agreement with the experimental test obtained by projecting laser light into a diluted fluorescence solution. Furthermore, a Fabry-Perot laser chip with the wavelength of 1310 nm is used for light coupling test for the fabricated lensed fibers. Results show the coupling efficiency is up to 78% at working distance of 90 £gm while using the plastic lensed fiber (R =48 £gm), which is around 2 fold higher than that of a flat-end fiber. The coupling efficiency of glass lensed fiber (R =23 £gm) is up to 72% at working distance of 24 £gm, which is around 2.3 fold higher than that of a flat-end fiber. The proposed method is feasible of producing high-quality lensed optical fiber in a high throughput and low-cost way. The method proposed in the current study may give substantial impacts on fabricating lensed fiber in the future.

The Laser Ablation of Microparticle Aerosols (LAMA) process produces nanoparticles by ablating microparticles that are entrained in an aerosol. Two of the main advantages of this process are that the particles produced are charged (preventing agglomeration) and bare (without a capping layer). Two different techniques are possible to collect the nanoparticles. In this work, the charged state of the particles formed was utilized to collect them electrostatically. This approach has the additional advantage that particles can be selected according to their size. The focus here was a particular application for gas separation. The nanoparticles produced were directly collected in a polymeric liquid, which was then irradiated with ultraviolet light to form a rubbery film. These membranes were tested for olefin/paraffin gas separation, a challenge that finds many applications, notably in the petroleum industry. / text