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.

Functional surface chemistry of carbon-based nanostructures

The recently discovered abilities to synthesize single-walled carbon nanotubes and prepare single layer graphene have spurred interest in these sp2-bonded carbon nanostructures. In particular, studies of their potential use in electronic devices are many as silicon integrated circuits are encountering processing limitations, quantum effects, and thermal management issues due to rapid device scaling. Nanotube and graphene implementation in devices does come with significant hurdles itself. Among these issues are the ability to dope these materials and understanding what influences defects have on expected properties. Because these nanostructures are entirely all-surface, with every atom exposed to ambient, introduction of defects and doping by chemical means is expected to be an effective route for addressing these issues. Raman spectroscopy has been a proven characterization method for understanding vibrational and even electronic structure of graphene, nanotubes, and graphite, especially when combined with electrical measurements, due to a wealth of information contained in each spectrum. In Chapter 1, a discussion of the electronic structure of graphene is presented. This outlines the foundation for all sp2-bonded carbon electronic properties and is easily extended to carbon nanotubes. Motivation for why these materials are of interest is readily gained. Chapter 2 presents various synthesis/preparation methods for both nanotubes and graphene, discusses fabrication techniques for making devices, and describes characterization methods such as electrical measurements as well as static and time-resolved Raman spectroscopy. Chapter 3 outlines changes in the Raman spectra of individual metallic single-walled carbon nantoubes (SWNTs) upon sidewall covalent bond formation. It is observed that the initial degree of disorder has a strong influence on covalent sidewall functionalization which has implications on developing electronically selective covalent chemistries and assessing their selectivity in separating metallic and semiconducting SWNTs. Chapter 4 describes how optical phonon population extinction lifetime is affected by covalent functionalization and doping and includes discussions on static Raman linewidths. Increasing defect concentration is shown to decrease G-band phonon population lifetime and increase G-band linewidth. Doping only increases G-band linewidth, leaving non-equilibrium population decay rate unaffected. Phonon mediated electron scattering is especially strong in nanotubes making optical phonon decay of interest for device applications. Optical phonon decay also has implications on device thermal management. Chapter 5 treats doping of graphene showing ambient air can lead to inadvertent Fermi level shifts which exemplifies the sensitivity that sp2-bonded carbon nanostructures have to chemical doping through sidewall adsorption. Removal of this doping allows for an investigation of electron-phonon coupling dependence on temperature, also of interest for devices operating above room temperature. Finally, in Chapter 6, utilizing the information obtained in previous chapters, single carbon nanotube diodes are fabricated and characterized. Electrical performance shows these diodes are nearly ideal and photovoltaic response yields 1.4 nA and 205 mV of short circuit current and open circuit voltage from a single nanotube device. A summary and discussion of future directions in Chapter 7 concludes my work.