It is very important to find the best conditions for some enzymes to do the best catalysis in current pharmaceutical industries. Based on the results above, we could say that this set-up could be widely used in finding the optimal condition for best enzyme activity of a certain enzyme. Instead of looking for the best condition for enzyme activity by doing many similar reactions repeatedly, we can complete this assignment with just one run if we could apply enough conditions.

We investigated the surface bonding of various adsorbates (0, S, C{sub 2}H{sub 3} and NO) along with the resulting relaxation of the Pt(111) surface using low energy electron diffiraction (LEED). LEED experiments have been performed on these ordered overlayers along with theoretical structural analysis using automated tensor LEED (ATLEED). The resulting surface structures of these ordered overlayers exhibit similar adsorbate-induced relaxations. In all cases the adsorbate occupies the fcc hollow site and induces an approximately 0.1 A buckling of the metal surface. The three metal atoms directly bonded to the adsorbate are ``pulled`` out of the surface and the metal atom that is not bound to the adsorbate is `pushed`` inward. In order to understand the reliability of such details, we have carried out a comprehensive study of various non-structural parameters used in a LEED computation. We also studied the adsorption of water on the Pt(lll) surface. We ordered an ultra thin ice film on this surface. The film`s surface is found to be the (0001) face of hexagonal ice. This surface is apparently terminated by a full-bilayer, in which the uppermost water molecules have large vibrational amplitudes even at temperatures as low as 90 K. We examined two other …

The author has applied the Terahertz Time Domain Interferometric (THz-TDI) technique to probe the ultrafast dynamic response of a Superconducting-Insulating-Superconducting (SIS) tunnel junction and a Quantum Point Contact (QPC). The THz-TDI technique involves monitoring changes in the dc current induced by interfering two picosecond electrical pulses on the junction as a function of time delay between them. Measurements of the response of the Nb/AlO{sub x}/Nb SIS tunnel junction from 75--200 GHz are in full agreement with the linear theory for photon-assisted tunneling. Likewise, measurements of the induced current in a QPC as a function of source-drain voltage, gate voltage, frequency, and magnetic field also show strong evidence for photon-assisted transport. These experiments together demonstrate the general applicability of the THz-TDI technique to the characterization of the dynamic response of any micron or nanometer scale device that exhibits a non-linear I-V characteristic. 133 refs., 49 figs.

A lattice gas automaton was implemented on a massively parallel machine (the BBN TC2000) and a vector supercomputer (the CRAY C90). The automaton models Burgers equation {rho}t + {rho}{rho}{sub x} = {nu}{rho}{sub xx} in 1 dimension. The lattice gas evolves by advecting and colliding pseudo-particles on a 1-dimensional, periodic grid. The specific rules for colliding particles are stochastic in nature and require the generation of many billions of random numbers to create the random bits necessary for the lattice gas. The goal of the thesis was to speed up the process of generating the random bits and thereby lessen the computational bottleneck of the automaton.

Atmospheric chemical-radiative-transport (CRT) models are vital in performing research on atmospheric chemical change. Even with the enormous computing capability delivered by massively parallel systems, extended three dimensional CRT simulations are still not computationally feasible. The major obstacle in a CRT model is the nonlinear ODE system describing the chemical kinetics in the model. These ODE systems are usually very stiff and account for anywhere from 75% to 90% of the CPU time required to run a CRT model. In this study, a simple explicit class of time stepping method is developed and demonstrated to be useful in treating chemical ODE systems without the use of a Jacobian matrix. These methods, called preconditioned time differencing methods, are tested on small mathematically idealized problems, box model problems, and full 2-D and 3-D CRT models. The methods are found to be both fast and memory efficient. Studies are performed on both vector and parallel systems. The preconditioned time differencing methods are established as a viable alternative to the more common backward differentiation formulas in terms of CPU speed across architectural platforms.

We describe a spectral approach to the investigation of fluid instability, generalized turbulence, and the interpenetration of fluids across an interface. The Technique also applies to a single fluid with large variations in density. Departures of fluctuating velocity components from the local mean are far subsonic, but the mean Mach number can be large. Validity of the description is demonstrated by comparisons with experiments on turbulent mixing due to the late stages of Rayleigh-Taylor instability, when the dynamics become approximately self-similar in response to a constant body force. Generic forms for anisotropic spectral structure are described and used as a basis for deriving spectrally integrated moment equations that can be incorporated into computer codes for scientific and engineering analyses.

Nuclear magnetic resonance techniques are traditionally used to study molecular level structure and dynamics with a noted exception in medically applied NMR imaging (MRI). In this work, new experimental methods and theory are presented relevant to the study of macroscopic morphology and dynamics using NMR field gradient techniques and solid state two-dimensional exchange NMR. The goal in this work is not to take some particular system and study it in great detail, rather it is to show the utility of a number of new and novel techniques using ideal systems primarily as a proof of principle. By taking advantage of the analogy between NMR imaging and diffraction, one may simplify the experiments necessary for characterizing the statistical properties of the sample morphology. For a sample composed of many small features, e.g. a porous medium, the NMR diffraction techniques take advantage of both the narrow spatial range and spatial isotropy of the sample`s density autocorrelation function to obtain high resolution structural information in considerably less time than that required by conventional NMR imaging approaches. The time savings of the technique indicates that NMR diffraction is capable of finer spatial resolution than conventional NMR imaging techniques. Radio frequency NMR imaging with a …

Radioactive metal waste makes up a significant portion of the waste currently being sent for disposal. Recovery of this metal as a valuable resource is possible through the use of decontamination technologies. Through the development and use of expert systems a comparison can be made of laser decontamination, a technology currently under development at Ames Laboratory, with currently available decontamination technologies for applicability to the types of metal waste being generated and the effectiveness of these versus simply disposing of the waste. These technologies can be technically and economically evaluated by the use of expert systems techniques to provide a waste management decision making tool that generates, given an identified metal waste, waste management recommendations. The user enters waste characteristic information as input and the system then recommends decontamination technologies, determines residual contamination levels and possible waste management strategies, carries out a cost analysis and then ranks, according to cost, the possibilities for management of the waste. The expert system was developed using information from literature and personnel experienced in the use of decontamination technologies and requires validation by human experts and assignment of confidence factors to the knowledge represented within.

The ability of organisms to evolve and adapt to the environment has provided mother nature with a rich and diverse set of species. Only organisms well adapted to their environment can survive from one generation to the next, transferring on the traits, that made them successful, to their offspring. Competition for resources and the ever changing environment drives some species to extinction and at the same time others evolve to maintain the delicate balance in nature. In this disertation we present the multi-niche crowding genetic algorithm, a computational metaphor to the survival of species in ecological niches in the face of competition. The multi-niche crowding genetic algorithm maintains stable subpopulations of solutions in multiple niches in multimodal landscapes. The algorithm introduces the concept of crowding selection to promote mating among members with qirnilar traits while allowing many members of the population to participate in mating. The algorithm uses worst among most similar replacement policy to promote competition among members with similar traits while allowing competition among members of different niches as well. We present empirical and theoretical results for the success of the multiniche crowding genetic algorithm for multimodal function optimization. The properties of the algorithm using different parameters are …

Interest in solid state physics naturally gravitates towards novel systems such as the copper oxide superconductors or the alkali-doped fullerenes. This paper tackles high temperature superconductivity by extension of the BCS theory for ordinary superconductors, in particular, incorporation of anharmonicity in phonon dynamics and anisotropy in electron-phonon coupling. These refinements can account for many anomalous properties of the cuprates. Phonon anharmonicity is consistent with a small isotope effect at optimal doping and a larger isotope effect in suboptimal systems. Anisotropy in the interaction, a plausible consequence of certain anharmonic models, can circumvent objections to electron-phonon coupling based on transport measurements. Such anisotropy is consistent with gap anisotropy and strong temperature dependence of Hall coefficient. In contrast to cuprates, the doped fullerenes appear understandable within the standard model of single electron band theory and BCS theory. Microscopic parameters derivable from transport and critical field measurements yield a self-consistent picture of a disordered Type-2 BCS superconductor. Isotope effects imply that superconductivity is mediated by carbon phonons opposed to alkali atom vibrations. The novel properties of the fullerenes are generally traceable to their microscopic heterogeneity, being a collection of tightly bound but weakly overlapping molecules. Separation of electronic regimes into weak intermolecular overlap …

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Theoretical simulations and ultrafast pump-probe laser spectroscopy experiments were used to study photosynthetic pigment-protein complexes and antennae found in green sulfur bacteria such as Prosthecochloris aestuarii, Chloroflexus aurantiacus, and Chlorobium tepidum. The work focused on understanding structure-function relationships in energy transfer processes in these complexes through experiments and trying to model that data as we tested our theoretical assumptions with calculations. Theoretical exciton calculations on tubular pigment aggregates yield electronic absorption spectra that are superimpositions of linear J-aggregate spectra. The electronic spectroscopy of BChl c/d/e antennae in light harvesting chlorosomes from Chloroflexus aurantiacus differs considerably from J-aggregate spectra. Strong symmetry breaking is needed if we hope to simulate the absorption spectra of the BChl c antenna. The theory for simulating absorption difference spectra in strongly coupled photosynthetic antenna is described, first for a relatively simple heterodimer, then for the general N-pigment system. The theory is applied to the Fenna-Matthews-Olson (FMO) BChl a protein trimers from Prosthecochloris aestuarii and then compared with experimental low-temperature absorption difference spectra of FMO trimers from Chlorobium tepidum. Circular dichroism spectra of the FMO trimer are unusually sensitive to diagonal energy disorder. Substantial differences occur between CD spectra in exciton simulations performed with and without realistic …

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The first five chapters of this thesis focus on studies of band anticrossing (BAC) effects in highly electronegativity- mismatched semiconductor alloys. The concept of bandgap bowing has been used to describe the deviation of the alloy bandgap from a linear interpolation. Bowing parameters as large as 2.5 eV (for ZnSTe) and close to zero (for AlGaAs and ZnSSe) have been observed experimentally. Recent advances in thin film deposition techniques have allowed the growth of semiconductor alloys composed of significantly different constituents with ever- improving crystalline quality (e.g., GaAs{sub 1-x}N{sub x} and GaP{sub 1-x}N{sub x} with x {approx}< 0.05). These alloys exhibit many novel and interesting properties including, in particular, a giant bandgap bowing (bowing parameters > 14 eV). A band anticrossing model has been developed to explain these properties. The model shows that the predominant bowing mechanism in these systems is driven by the anticrossing interaction between the localized level associated with the minority component and the band states of the host. In this thesis I discuss my studies of the BAC effects in these highly mismatched semiconductors. It will be shown that the results of the physically intuitive BAC model can be derived from the Hamiltonian of the many-impurity …

The penetration of ambient air pollutants into the indoor environment is of concern owing to several factors: (1) epidemiological studies have shown a strong association between ambient fine particulate pollution and elevated risk of human mortality; (2) people spend most of their time in indoor environments; and (3) most information about air pollutant concentration is only available from ambient routine monitoring networks. A good understanding of ambient air pollutant transport from source to receptor requires knowledge about pollutant penetration across building envelopes. Therefore, it is essential to gain insight into particle penetration in infiltrating air and the factors that affect it in order to assess human exposure more accurately, and to further prevent adverse human health effects from ambient particulate pollution. In this dissertation, the understanding of air pollutant infiltration across leaks in the building envelope was advanced by performing modeling predictions as well as experimental investigations. The modeling analyses quantified the extent of airborne particle and reactive gas (e.g., ozone) penetration through building cracks and wall cavities using engineering analysis that incorporates existing information on building leakage characteristics, knowledge of pollutant transport processes, as well as pollutant-surface interactions. Particle penetration is primarily governed by particle diameter and by the …

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