Studies of Protein-Protein and Protein-Water Interactions by Small Angle X-Ray Scattering, Terahertz Spectroscopy, ASMOS, And Computer Simulation

The protein folding problem has been one of the most challenging subjects in biological physics due to its complexity. Energy landscape theory based on statistical mechanics provides a thermodynamic interpretation of the protein folding process. We have been working to answer fundamental questions about protein-protein and protein-water interactions, which are very important for describing the energy landscape surface of proteins correctly. At first, we present a new method for computing protein-protein interaction potentials of solvated proteins directly from SAXS data. An ensemble of proteins was modeled by Metropolis Monte Carlo and Molecular Dynamics simulations, and the global X-ray scattering of the whole model ensemble was computed at each snapshot of the simulation. The interaction potential model was optimized and iterated by a Levenberg-Marquardt algorithm. Secondly, we report that terahertz spectroscopy directly probes hydration dynamics around proteins and determines the size of the dynamical hydration shell. We also present the sequence and pH-dependence of the hydration shell and the effect of the hydrophobicity. On the other hand, kinetic terahertz absorption (KITA) spectroscopy is introduced to study the refolding kinetics of ubiquitin and its mutants. KITA results are compared to small angle X-ray scattering, tryptophan fluorescence, and circular dichroism results. We propose that KITA monitors the rearrangement of hydrogen bonding during secondary structure formation. Finally, we present development of the automated single molecule operating system (ASMOS) for a high throughput single molecule detector, which levitates a single protein molecule in a 10 µm diameter droplet by the laser guidance. I also have performed supporting calculations and simulations with my own program codes.

Material characterization and process development for indium-arsenide / indium-gallium-antimonide channel, high electron mobility transistors for low power, high speed applications

Efforts to push the performance of transistors for millimeter-wave and microwave applications have borne fruit through device size scaling and the use of novel material systems. III-V semiconductors and their alloys hold a distinct advantage over silicon because they have much higher electron mobility which is a prerequisite for high frequency operation. InGaAs/InP pseudomorphic heterojunction bipolar transistors (HBTs) have demonstrated fT of 765 GHz at room temperature and InP based high electron mobility transistors (HEMTs) have demonstrated fMax of 1.2 THz. The 6.1 A lattice family of InAs, GaSb, AlSb covers a wide variety of band gaps and is an attractive future material system for high speed device development. Extremely high electron mobilities ~ 30,000 cm^2 V^-1s^-1 have been achieved in modulation doped InAs-AlSb structures. The work described in this thesis involves material characterization and process development for HEMT fabrication on this material system.