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.

Improving the freshman electrical and computer engineering lab

This thesis covers the challenges of creating and maintaining an introductory engineering laboratory. The history of the University of Illinois Electrical and Computer Engineering department’s introductory course, ECE 110, is recounted. The current state of the course, as of Fall 2008, is discussed along with current challenges arising from the use of a hand-wired prototyping board with logic gates. A plan for overcoming these issues using a new microcontroller-based board with a pseudo hardware description language is discussed. The new microcontroller based system implementation is extensively detailed along with its new accompanying description language. This new system was tried in several sections of the Fall 2008 semester alongside the old system; the students’ final performances with the two different approaches are compared in terms of design, performance, complexity, and enjoyment. The system in its first run shows great promise, increasing the students’ enjoyment, and improving the performance of their designs.