Structure-function studies of serine hydrolases: synthesis of a gene for ∝-lytic protease and the purification and characterization of a mutant β-lactamase

The author has constructed a synthetic gene for ∝-lytic protease. Since the DNA sequence of the protein is not known, the gene was designed by using the reverse translation of ∝-lytic protease's amino acid sequence. Unique restriction sites are carefully sought in the degenerate DNA sequence to aid in future mutagenesis studies. The unique restriction sites are designed approximately 50 base pairs apart and their appropriate codons used in the DNA sequence. The codons used to construct the DNA sequence of ∝-lytic protease are preferred codons in E-coli or used in the production of β-lactamase. Codon usage is also distributed evenly to ensure that one particular codon is not heavily used. The gene is essentially constructed from the outside in. The gene is built in a stepwise fashion using plasmids as the vehicles for the ∝-lytic oligomers. The use of plasmids allows the replication and isolation of large quantities of the intermediates during gene synthesis. The ∝-lytic DNA is a double-stranded oligomer that has sufficient overhang and sticky ends to anneal correctly in the vector. After six steps of incorporating ∝-lytic DNA, the gene is completed and sequenced to ensure that the correct DNA sequence is present and that no mutations occurred in the structural gene.

β-lactamase is the other serine hydrolase studied in this thesis. The author used the class A RTEM-1 β- lactamase encoded on the plasmid pBR322 to investigate the roll of the conserved threonine residue at position 71. Cassette mutagenesis was previously used to generate all possible amino acid substitutions at position 71. The work presented here describes the purification and kinetic characterization of a T71H mutant previously constructed by S. Schultz. The mutated gene was transferred into plasmid pJN for expression and induced with IPTG. The enzyme is purified by column chromatography and FPLC to homogeneity. Kinetic studies reveal that the mutant has lower k_(cat) values on benzylpenicillin, cephalothin and 6-aminopenicillanic acid but no changes in k_m except for cephalothin which is approximately 4 times higher. The mutant did not change siginificantly in its pH profile compared to the wild-type enzyme. Also, the mutant is more sensitive to thermal denaturation as compared to the wild-type enzyme. However, experimental evidence indicates that the probable generation of a positive charge at position 71 thermally stabilized the mutant.

Experiments in Neutrino Mass and Mixing: Part I - New Limits on Heavy Neutrino Emission in Nuclear Beta Decay. Part II - Fast Neutron Backgrounds for the San Onofre Neutrino Detector

In Part I of this thesis, a new magnetic spectrometer experiment which measured the β spectrum of ^(35)S is described. New limits on heavy neutrino emission in nuclear β decay were set, for a heavy neutrino mass range between 12 and 22 keV. In particular, this measurement rejects the hypothesis that a 17 keV neutrino is emitted, with sin^2 θ = 0.0085, at the 6δ statistical level. In addition, an auxiliary experiment was performed, in which an artificial kink was induced in the β spectrum by means of an absorber foil which masked a fraction of the source area. In this measurement, the sensitivity of the magnetic spectrometer to the spectral features of heavy neutrino emission was demonstrated.

In Part II, a measurement of the neutron spallation yield and multiplicity by the Cosmic-ray Underground Background Experiment is described. The production of fast neutrons by muons was investigated at an underground depth of 20 meters water equivalent, with a 200 liter detector filled with 0.09% Gd-loaded liquid scintillator. We measured a neutron production yield of (3.4 ± 0.7) x 10^(-5) neutrons per muon-g/cm^2, in agreement with other experiments. A single-to-double neutron multiplicity ratio of 4:1 was observed. In addition, stopped π^+ decays to µ^+ and then e^+ were observed as was the associated production of pions and neutrons, by the muon spallation interaction. It was seen that practically all of the π^+ produced by muons were also accompanied by at least one neutron. These measurements serve as the basis for neutron background estimates for the San Onofre neutrino detector.

Future of earthquake early warning : quantifying uncertainty and making fast automated decisions for applications

Earthquake early warning (EEW) systems have been rapidly developing over the past decade. Japan Meteorological Agency (JMA) has an EEW system that was operating during the 2011 M9 Tohoku earthquake in Japan, and this increased the awareness of EEW systems around the world. While longer-time earthquake prediction still faces many challenges to be practical, the availability of shorter-time EEW opens up a new door for earthquake loss mitigation. After an earthquake fault begins rupturing, an EEW system utilizes the first few seconds of recorded seismic waveform data to quickly predict the hypocenter location, magnitude, origin time and the expected shaking intensity level around the region. This early warning information is broadcast to different sites before the strong shaking arrives. The warning lead time of such a system is short, typically a few seconds to a minute or so, and the information is uncertain. These factors limit human intervention to activate mitigation actions and this must be addressed for engineering applications of EEW. This study applies a Bayesian probabilistic approach along with machine learning techniques and decision theories from economics to improve different aspects of EEW operation, including extending it to engineering applications.

Existing EEW systems are often based on a deterministic approach. Often, they assume that only a single event occurs within a short period of time, which led to many false alarms after the Tohoku earthquake in Japan. This study develops a probability-based EEW algorithm based on an existing deterministic model to extend the EEW system to the case of concurrent events, which are often observed during the aftershock sequence after a large earthquake.

To overcome the challenge of uncertain information and short lead time of EEW, this study also develops an earthquake probability-based automated decision-making (ePAD) framework to make robust decision for EEW mitigation applications. A cost-benefit model that can capture the uncertainties in EEW information and the decision process is used. This approach is called the Performance-Based Earthquake Early Warning, which is based on the PEER Performance-Based Earthquake Engineering method. Use of surrogate models is suggested to improve computational efficiency. Also, new models are proposed to add the influence of lead time into the cost-benefit analysis. For example, a value of information model is used to quantify the potential value of delaying the activation of a mitigation action for a possible reduction of the uncertainty of EEW information in the next update. Two practical examples, evacuation alert and elevator control, are studied to illustrate the ePAD framework. Potential advanced EEW applications, such as the case of multiple-action decisions and the synergy of EEW and structural health monitoring systems, are also discussed.

Propagation of the fast magnetosonic wave in a tokamak plasma

The propagation of the fast magnetosonic wave in a tokamak plasma has been investigated at low power, between 10 and 300 watts, as a prelude to future heating experiments.

The attention of the experiments has been focused on the understanding of the coupling between a loop antenna and a plasma-filled cavity. Special emphasis has been given to the measurement of the complex loading impedance of the plasma. The importance of this measurement is that once the complex loading impedance of the plasma is known, a matching network can be designed so that the r.f. generator impedance can be matched to one of the cavity modes, thus delivering maximum power to the plasma. For future heating experiments it will be essential to be able to match the generator impedance to a cavity mode in order to couple the r.f. energy efficiently to the plasma.

As a consequence of the complex impedance measurements, it was discovered that the designs of the transmitting antenna and the impedance matching network are both crucial. The losses in the antenna and the matching network must be kept below the plasma loading in order to be able to detect the complex plasma loading impedance. This is even more important in future heating experiments, because the fundamental basis for efficient heating before any other consideration is to deliver more energy into the plasma than is dissipated in the antenna system.

The characteristics of the magnetosonic cavity modes are confirmed by three different methods. First, the cavity modes are observed as voltage maxima at the output of a six-turn receiving probe. Second, they also appear as maxima in the input resistance of the transmitting antenna. Finally, when the real and imaginary parts of the measured complex input impedance of the antenna are plotted in the complex impedance plane, the resulting curves are approximately circles, indicating a resonance phenomenon.

The observed plasma loading resistances at the various cavity modes are as high as 3 to 4 times the basic antenna resistance (~ .4 Ω). The estimated cavity Q’s were between 400 and 700. This means that efficient energy coupling into the tokamak and low losses in the antenna system are possible.

Space-charge-limited current in fast neutron irradiated silicon

DC and transient measurements of space-charge-limited currents through alloyed and symmetrical n^+ν n^+ structures made of nominally 75 kΩcm ν-type silicon are studied before and after the introduction of defects by 14 MeV neutron radiation. In the transient measurements, the current response to a large turn-on voltage step is analyzed. Right after the voltage step is applied, the current transient reaches a value which we shall call "initial current" value. At longer times, the transient current decays from the initial current value if traps are present.

Before the irradiation, the initial current density-voltage characteristics J(V) agree quantitatively with the theory of trap-free space-charge-limited current in solids. We obtain for the electron mobility a temperature dependence which indicates that scattering due to impurities is weak. This is expected for the high purity silicon used. The drift velocity-field relationships for electrons at room temperature and 77°K, derived from the initial current density-voltage characteristics, are shown to fit the relationships obtained with other methods by other workers. The transient current response for t > 0 remains practically constant at the initial value, thus indicating negligible trapping.

Measurement of the initial (trap-free) current density-voltage characteristics after the irradiation indicates that the drift velocity-field relationship of electrons in silicon is affected by the radiation only at low temperature in the low field range. The effect is not sufficiently pronounced to be readily analyzed and no formal description of it is offered. In the transient response after irradiation for t > 0, the current decays from its initial value, thus revealing the presence of traps. To study these traps, in addition to transient measurements, the DC current characteristics were measured and shown to follow the theory of trap-dominated space-charge-limited current in solids. This theory was applied to a model consisting of two discrete levels in the forbidden band gap. Calculations and experiments agreed and the capture cross-sections of the trapping levels were obtained. This is the first experimental case known to us through which the flow of space-charge-limited current is so simply representable.

These results demonstrate the sensitivity of space-charge-limited current flow as a tool to detect traps and changes in the drift velocity-field relationship of carriers caused by radiation. They also establish that devices based on the mode of space-charge-limited current flow will be affected considerably by any type of radiation capable of introducing traps. This point has generally been overlooked so far, but is obviously quite significant.

Fast numerical methods for mixed, singular Helmholtz boundary value problems and Laplace eigenvalue problems - with applications to antenna design, sloshing, electromagnetic scattering and spectral geometry

This thesis presents a novel class of algorithms for the solution of scattering and eigenvalue problems on general two-dimensional domains under a variety of boundary conditions, including non-smooth domains and certain "Zaremba" boundary conditions - for which Dirichlet and Neumann conditions are specified on various portions of the domain boundary. The theoretical basis of the methods for the Zaremba problems on smooth domains concern detailed information, which is put forth for the first time in this thesis, about the singularity structure of solutions of the Laplace operator under boundary conditions of Zaremba type. The new methods, which are based on use of Green functions and integral equations, incorporate a number of algorithmic innovations, including a fast and robust eigenvalue-search algorithm, use of the Fourier Continuation method for regularization of all smooth-domain Zaremba singularities, and newly derived quadrature rules which give rise to high-order convergence even around singular points for the Zaremba problem. The resulting algorithms enjoy high-order convergence, and they can tackle a variety of elliptic problems under general boundary conditions, including, for example, eigenvalue problems, scattering problems, and, in particular, eigenfunction expansion for time-domain problems in non-separable physical domains with mixed boundary conditions.

Fast Lattice Green's Function Methods for Viscous Incompressible Flows on Unbounded Domains

In this thesis, a collection of novel numerical techniques culminating in a fast, parallel method for the direct numerical simulation of incompressible viscous flows around surfaces immersed in unbounded fluid domains is presented. At the core of all these techniques is the use of the fundamental solutions, or lattice Green’s functions, of discrete operators to solve inhomogeneous elliptic difference equations arising in the discretization of the three-dimensional incompressible Navier-Stokes equations on unbounded regular grids. In addition to automatically enforcing the natural free-space boundary conditions, these new lattice Green’s function techniques facilitate the implementation of robust staggered-Cartesian-grid flow solvers with efficient nodal distributions and fast multipole methods. The provable conservation and stability properties of the appropriately combined discretization and solution techniques ensure robust numerical solutions. Numerical experiments on thin vortex rings, low-aspect-ratio flat plates, and spheres are used verify the accuracy, physical fidelity, and computational efficiency of the present formulations.