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.

Terahertz Response of Excitons in Nanorod Heterostructures

Quantum-confined systems are one of the most promising ways to enable us to control a material's interactions with light. Nanorods in particular offer the right dimensions for exploring and manipulating the terahertz region of the spectrum. In this thesis, we model excitons confined inside a nanorod using the envelope function approximation. A region-matching transfer matrix method allows us to simulate excitonic states inside arbitrary heterostructures grown along the length of the rod. We apply the method to colloidal CdSe rods 70 nm in length and under 10 nm in diameter, capped with ligands of DDPA and pyridine. We extend past studies on these types of rods by taking into account their dielectric permittivity mismatch. Compared to previous calculations and experimentally measured terahertz absorption, we predict a higher energy main 1S$z$ to 2P$z$ transition peak. This indicates that the rods are likely larger in diameter than previously thought. We also investigate a nanorod with GaAs/Al$_{0.3}$Ga$_{0.7}$As coupled double dots. The excitonic transitions were found to be manipulable by varying the strength of an applied electric field. We employ quasi-static state population distributions to simulate the effects of exciton relaxation from optically active states to dim ground states. A critical value of the applied field, corresponding to the exciton binding energy of ~18 meV, was found to dramatically alter the terahertz absorption due to state mixing. Above this critical field, more nuanced shifts in transition energies were observed, and gain from radiative relaxation to the ground state is predicted.

Magnetoexcitonic optical absorption in semiconductors under strong magnetic fields and intense terahertz radiation in the Voigt configuration

The magnetoexcitonic optical absorption of a GaAs bulk semiconductor driven by a terahertz (THz) field is investigated numerically. The method of the solution of the initial-value problem, in combination with the perfect matched layer technique, is used to calculate the optical susceptibility, with Coulomb interaction, Landau quantization, and THz fields involved nonperturbatively. It shows that there appear replicas and sidebands of magnetoexciton of different Landau levels, which greatly enrich the magneto-optical spectrum in the presence of a driving THz field. Copyright (C) EPLA, 2008.

Excitonic optical absorption in semiconductors under intense terahertz radiation

The excitonic optical absorption of GaAs bulk semiconductors under intense terahertz (THz) radiation is investigated numerically. The method of solving initial-value problems, combined with the perfect matched layer technique, is used to calculate the optical susceptibility. In the presence of a driving THz field, in addition to the usual exciton peaks, 2p replica of the dark 2p exciton and even-THz-photon-sidebands of the main exciton resonance emerge in the continuum above the band edge and below the main exciton resonance. Moreover, to understand the shift of the position of the main exciton peak under intense THz radiation, it is necessary to take into consideration both the dynamical Franz-Keldysh effect and ac Stark effect simultaneously. For moderate frequency fields, the main exciton peak decreases and broadens due to the field-induced ionization of the excitons with THz field increasing. However, for high frequency THz fields, the characteristics of the exciton recur even under very strong THz fields, which accords with the recent experimental results qualitatively.

Intersubband optical absorption in a step asymmetric semiconductor quantum well driven by a terahertz field

The nonlinear optical absorption in a three-subband step asymmetric semiconductor quantum well driven by a strong terahertz (THz) field is investigated theoretically by employing the intersubband semiconductor-Bloch equations. We show that the optical absorption spectrum strongly depends on the intensity, frequency, and phase of the pump THz wave. The strong THz field induces THz sidebands and Autler-Townes splitting in the probe absorption spectrum. Varying the pump frequency can bring not only the new absorption peaks but also the changing of the energy separation of the two higher-energy levels. The dependence of the absorption spectrum on the phase of the pump THz wave is also very remarkable.

Intersubband absorption energy shifts in 3-level system for asymmetric quantum well terahertz emitters

Intersubband absorption energy shifts in 3-level system stemming from depolarization and excitonlike effects are investigated. Analytically, the expressions we derive present good explanations to the conventional 2-level results and bare potential transition energy results; and numerical results show that they are more exact than the previous studies to describe the 3-level system depolarization and excitonlike shift (DES) character especially for higher carrier density (more than 8 x 10(11) cm(-2)). One interesting detail we find is that the "large blue" DES becomes "slight redshift" in the low doping limit (less than 1.9 x 10(11) cm(-2)), which may be neglected by the previous studies of intersubband transitions. Temperature character of DES in the step well structure is also numerically studied. Finally the above are applied to calculate asymmetric step quantum well structures. The two main functional aspects of terahertz (THz) emitters are discussed and several basic optimizing conditions are considered. By adjusting the well geometry parameters and material composition systematically, some optimized structures which satisfy all of the six conditions are recommended in tables. These optimizations may provide useful references to the design of 3-level-based optically pumping THz emitters.

Bioavailability of plant pigment phytochemicals in Angelica keiskei in older adults: A pilot absorption kinetic study

BACKGROUND/OBJECTIVES: Angelica keiskei is a green leafy vegetable rich in plant pigment phytochemicals such as flavonoids and carotenoids. This study examined bioavailability of flavonoids and carotenoids in Angelica keiskei and the alteration of the antioxidant performance in vivo.SUBJECTS AND MATERIALS: Absorption kinetics of phytochemicals in Angelica keiskei were determined in healthy older adults (>60 y, n = 5) and subjects with metabolic syndrome (n = 5). Subjects consumed 5 g dry Angelica keiskei powder encapsulated in gelatin capsules with a low flavonoid and carotenoid liquid meal. Plasma samples were collected at baseline, 0.5, 1, 2, 3, 4, 5, 6, 7, and 8 h. Samples were analyzed for flavonoids and carotenoids using HPLC systems with electrochemical and UV detection, respectively, and for total antioxidant performance by fluorometry.RESULTS: After ingestion of Angelica keiskei increases in plasma quercetin concentrations were observed at 1-3 and 6-8 hr in the healthy group and at all time points in the metabolic syndrome group compared to baseline (P < 0.05). Plasma lutein concentrations were significantly elevated in both the healthy and metabolic syndrome groups at 8 hr (P < 0.05). Significant increases in total antioxidant performance were also observed in both the healthy and the metabolic syndrome groups compared to baseline (P < 0.05).CONCLUSIONS: Findings of this study clearly demonstrate the bioavailability of phytonutrients of Angelica keiskei and their ability to increase antioxidant status in humans.

Impact and energy absorption of empty and foam-filled conical tubes

Foam-filled conical tubes have recently emerged as efficient energy absorbing devices to mitigate the adverse effects of impacts. The primary aim of this thesis was to generate research and design information on the impact and energy absorption response of empty and foam-filled conical tubes, and to facilitate their application in energy absorbing systems under axial and oblique loading conditions representative of those typically encountered in crashworthiness and impact applications. Finite element techniques supported by experiments and existing results were used in the investigation. Major findings show that the energy absorption response can be effectively controlled by varying geometry and material parameters. A useful empirical formula was developed for providing engineering designers with an initial estimate of the load ratio and hence energy absorption performances of these devices. It was evident that foam-filled conical tubes enhance the energy absorption capacity and stabilise the crush response for both axial and oblique impact loading without a significant increase in the initial peak load. This is practically beneficial when higher kinetic energy needs to be absorbed, thus reducing the impact force transmitted to the protected structure and occupants. Such tubes also increase and maintain the energy absorption capacity under global bending as well as minimise the reduction of energy absorption capacity with increasing load angle. Furthermore, the results also highlight the feasibility of adding a foam-filled conical tube as a supplementary device in energy absorbing systems, since the overall energy absorption performance of such systems can be favourably enhanced by only including a relatively small energy absorbing device. Above all, the results demonstrate the superior performance of foam-filled conical tube for mitigating impact energy in impact and crashworthiness applications.

Absorption of intense electromagnetic beams in a magnetoplasma

The multiphoton inverse bremsstrahlung absorption of two intense electromagnetic beams passing through a magnetized plasma is studied. The rate of absorption of electromagnetic energy by the electrons is calculated by deriving a kinetic equation for the electrons. It is found that the absorption enhances when the frequency of one electromagnetic beam is more, and that of the other electromagnetic beam is less, than the electron-cyclotron frequency. A possible application to extragalactic radio sources is discussed.

Thermodynamic and kinetic analysis of carbohydrate binding to the basic lectin from winged bean (Psophocarpus tetragonolobus)

A basic lectin (pI approximately 10.0) was purified to homogeneity from the seeds of winged bean (Psophocarpus tetragonolobus) by affinity chromatography on Sepharose 6-aminocaproyl-D-galactosamine. The lectin agglutinated trypsinized rabbit erythrocytes and had a relative molecular mass of 58,000 consisting of two subunits of Mr 29,000. The lectin binds to N-dansylgalactosamine, leading to a 15-fold increase in dansyl fluorescence with a concomitant 25-nm blue shift in the emission maximum. The lectin has two binding sites/dimer for this sugar and an association constant of 4.17 X 10(5) M-1 at 25 degrees C. The strong binding to N-dansylgalactosamine is due to a relatively positive entropic contribution as revealed by the thermodynamic parameters: delta H = -33.62 kJ mol-1 and delta S0 = -5.24 J mol-1 K-1. Binding of this sugar to the lectin shows that it can accommodate a large hydrophobic substituent on the C-2 carbon of D-galactose. Studies with other sugars indicate that a hydrophobic substituent in alpha- conformation at the anomeric position increases the affinity of binding. The C-4 and C-6 hydroxyl groups are critical for sugar binding to this lectin. Lectin difference absorption spectra in the presence of N-acetylgalactosamine indicate perturbation of tryptophan residues on sugar binding. The results of stopped flow kinetics with N- dansylgalactosamine and the lectin are consistent with a simple one- step mechanism for which k+1 = 1.33 X 10(4) M-1 s-1 and k-1 = 3.2 X 10(- 2) s-1 at 25 degrees C. This k-1 is slower than any reported for a lectin-monosaccharide complex so far. The activation parameters indicate an enthalpically controlled association process.

Probing the aging effect in metallic polypyrrole by terahertz time-domain spectroscopy

Terahertz time-domain spectroscopy has been carried out on a metallic film of polypyrrole (PPy doped by PF6). The sample was exposed to air to investigate how the conductivity of the film varies as a function of time. The absorption and dispersion of the film decrease during initial days, and then tend to saturate. The conductivity of unaged sample follows the Drude model, and upon aging the data fit to the localization-modified Drude model. The fitting parameters show that the number of charge carriers decreases during the aging process. The initial rapid decrease in conductivity suggests that some of the delocalized carriers are localized due to aging. (C) 2007 American Institute of Physics.

Absorption of Electromagnetic Waves in Astrophysical Plasmas

We study parametric Decay Instabilities (PDI) using the kinetic description, in the homogeneous and unmagnetic plasmas. These instabilities cause anomalous absorption of the incident electromagnetic (e.m) radiations. The maximum plasma temperatures reached are functionas of luminocity of the non-thermal radio radiation and the plasma parameters.

Kinetic evolution studies of silver nanoparticles in a bio-based green synthesis process

Silver nanoparticles are being extensively studied due to their widespread applications and unique properties. In the present study, the growth kinetics of silver nanoparticles as synthesized on reduction of silver nitrate solution by aqueous extract of Azadirachta indica leaves was investigated. The formation of silver nanoparticles was preliminarily monitored by measuring the absorption maxima at different time intervals after adding the reducing agent to the silver salt solution (0.5, 1, 1.5, 2, 2.5, 3, 3.5 and 4 h). At different time points characterization studies were conducted using X-ray diffraction studies, FT-IR techniques, zeta potential studies and transmission electron microscopy. The total available silver in the reaction medium was determined at different durations using ICP-OES. The changes in reduction potential in the medium were also monitored using potentiometric analysis. The results confirm a definite change in the medium pertaining to formation of the stable nanoparticles after 2 h, and a significant increase in the agglomeration tendency after 4 h of interaction. The growth kinetic data of the nanoparticles till 3.5 h was found to fit the LSW model confirming diffusion limited growth. (C) 2011 Elsevier B.V. All rights reserved.