Selected nucleic acid binding species (aptamers) have been shown to undergo conformational changes in the presence of ligands, and have been adapted to function as biosensors. We were interested in whether the secondary structures of aptamers could be rationally engineered to undergo ligand dependent conformational changes. To this end, we used rational and computational design methods to generate a number of aptamer biosensors. First, we built upon previous work that showed that antisense oligonucleotides bearing reporter moieties could be used to denature aptamers. Upon addition of ligands, the conformational equilibrium is shifted towards release of the antisense oligonucleotide and a concomitant increase in fluorescence. We attempted to adapt this format to the potential detection of ricin, but were unsuccessful. In order to better evaluate rational designs, we attempted to use computational modeling methods. Again, aptamer biosensors have previously been engineered based on ligand-induced reorganization of secondary structure (as opposed to oligonucleotide displacement), a so-called 'slip-structure' model. We developed an algorithm to evaluate different lisp structures, predicted both aptamers and aptazymes that should have undergone ligand-dependent changes in conformation, and experimentally evaluated the computationally predicted sequences. A number of robust biosensors that could respond to the cytokine VegF and the small molecule flavin were discovered. The computational model was further adapted to an aptamer biosensor that underwent a larger conformational change upon ligand-binding, an antiswitch. In this model, binding of the ligand stabilizes one hairpin structure at the expense of a competing structure (as opposed to merely changing the register of the hairpin as in the previously described slip structure model). Again, we were able to computationally identify a number of antiswitches that upon synthesis were responsive to the ligand theophylline. Finally we again attempted to use rational design methods to optimize not just the degree of signal but also the kinetic performance of aptamer biosensors. To this end, we developed biosensors that signaled within seconds the presence of the coagulation protein thrombin. / text

published_or_final_version / Mechanical Engineering / Doctoral / Doctor of Philosophy

No description available.

A hydrological modelling effort using MODFLOW was undertaken in order to determine the relative importance of some of the factors influencing hydraulic gradient reversals in peatlands. Model domains were of two types, large raised bog type (LRBT) and kettle bog type (KBT), and were made to undergo various levels of meteorological forcing (water deficit). Substrate, too, was varied in order to determine its importance on reversals. Domain-wide reversals were successfully simulated in LRBT systems, but not in KBT systems. Although simulated flow patterns matched field-observed patterns, both pre- and post-drought, simulated reversals occurred more quickly than in the field. This may be due to insufficiently distributed parameters, such as hydraulic conductivity. Reversals were easily terminated by simulating non-drought conditions. In the LRBT system, reversal duration decreased, and time-to-reversal increased, with a decrease in drought severity. Increasing drought severity in KBT systems had the opposite effect on the duration of semi-reversed flow patterns, suggesting a possibly different/additional mechanism for flow reversals in KBT systems. Hydraulic conductivity had an appreciable effect on flow reversal evolution, though neither changing porosity, nor differences in catotelm layering had a great effect.

No description available.

No description available.

Natural ecosystems are dynamic and complex, with many being threatened by human activity. However, humans can also be at the root of a solution to this problem by developing ecosystem engineering which can be used to design, construct, modify, upgrade, repair, remediate, and maintain ecosystems. The aim of this project was to improve virtual ecosystems that can be used to increase the knowledge base for ecological engineering by studying adaptability as a factor for the success of species. This was done by analysing adaptive species in a virtual ecosystem, a computer application with which various configurations can be designed and studied in a closed environment. The virtual ecosystems used in this project represent ecosystems in general rather than any specific ecosystem, and allow for repeatable test cases to be run so that ecosystem dynamics can be studied. Adaptability was defined as the ability of an individual to adjust to a short term environmental pressure according to two factors: the adaptation speed, which is how fast an individual can respond to a change in environment, and the adaptive capacity, which is a quantitative indicator of how much the individual is able to adapt. In this project, experiments were performed to determine the effects of adaptability when applied to one aspect of individuals in an ecosystem. From the results of the experiments it was seen that the adaptation speed value could affect the success of a producer species in an ecosystem both positively and negatively. It was also found that ecosystems with both a consumer and producer species could persist longer when adaptability was incorporated into the individuals of the consumer species.

No description available.

No description available.

This research explores the complexities of database security, encompassing both the computer hardware and software. Also important is its nature as a people oriented issue. A risk analysis of a database system's security can be examined by creating a simulation model. Though, in order for it to be truly meaningful and accurate, all aspects of design, performance and procedure must be thoroughly and carefully scrutinized.Computer or data security is a major problem in today's world of data processing. This thesis outlines the security problem' and presents trends and issues. It also addresses current trends in computer security environments, database risk analysis, and simulations.Risk analysis is a technique used to quantitatively assess the relative value of protective measures. It is useful when appropriately applied and is in some cases required by regulatory agencies.The goal of security environments is to outline the framework which is valuable in assessing security issues and in establishing partitions in the overall environment within which this and other approaches to security can be examined.A simulation prototype is given which demonstrates the concepts of risk analysis for a database system. / Department of Computer Science