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.

Ultrasonic wave reflection measurements on self-compacting pastes and concretes

The objective of this study was to extend the use of combined longitudinal (P-wave) and shear (S-wave) ultrasonic wave reflection (UWR) to monitor the setting and stiffening of self-compacting pastes and concretes. An additional objective was to interpret the UWR responses of various modified cement pastes. A polymeric buffer with acoustic impedance close to that of cement paste, high impact polystyrene, was chosen to obtain sensitive results from the early hydration period. Criteria for initial and final set developed by our group in a prior study were used to compute setting times by UWR. UWR results were compared with standard penetration measurements. Stiffening behavior and setting times for normal cement pastes, pastes modified with mineral and chemical admixtures, self-compacting pastes, and concretes were explored using penetration resistance, S-wave and P-wave reflection. All three methods showed that set times of pastes varied linearly with w/c, that superplasticizer and fly ash delayed the set times of pastes, and that differences in w/cm, sp/cm, and fa/cm could be detected. Final set times determined from UWR correlated well with those from penetration resistance. Initial set times from S-wave reflection did not correlate very well with those from penetration resistance. Final set times from P-wave and S-wave reflection were roughly the same. Pastes with different chemical admixtures were tested, and the effects of these admixtures on stiffening were determined using UWR. Self-compacting concretes were studied using UWR, and their response and setting times were largely similar to that of corresponding self-compacting pastes. The P-wave reflection response was explored in detail, and the phenomenon of partial debonding and the factors affecting it were explained. Partial debonding is probably caused by autogenous shrinkage at final set, and was controlled and limited by water. The extent of partial debonding was higher with the transducers placed on the side as opposed to the bottom, and the S-wave transducer seemed to promote debonding in the P-wave reflection, whereas the P-wave transducer seemed to reduce debonding in the S-wave reflection. Simultaneous formwork pressure testing and UWR were performed; however, no clear correlation was seen between the two properties.