Computer simulations are gaining recognition as educational tools, but in general there is still a line dividing a simulation from a game. Yet as many recent and successful video games heavily involve simulations (SimCity comes to mind), there is not only the growing question of whether games can be used for educational purposes, but also of how a game might qualify as educational. Endemic: The Agent is a project that tries to bridge the gap between educational simulations and educational games. This paper outlines the creation of the project and the characteristics that make it an educational tool, a simulation, and a game.

Using weather data from the Weather Research and Forecasting model (WRF), we analyze the transport of inertial particles in Hurricane Katrina in order to identify coherent patterns of motion. For our analysis, we choose a Lagrangian approach instead of an Eulerian approach because the Lagrangian approach is objective and frame-independent, and gives results which are better defined. In particular, we locate Lagrangian Coherent Structures (LCS), which are smooth sets of fluid particles which are locally most hyperbolic (either attracting or repelling). We implement a variational method for locating LCS and compare the results to previous computation of LCS using Finite-Time Lyapunov Exponents (FTLE) to identify regions of high stretching in the fluid flow.

Dry and steam NanoBonding™ are conceived and researched to bond Si-based surfaces, via nucleation and growth of a two-dimensional SiOxHy or hydrated SiOxHy interphase connecting surfaces at the nanoscale across macroscopic domains. The motivation is to create strong, long lasting, hermetically bonded sensors with their electronics for the development of an artificial pancreas and to bond solar cells to glass panels for robust photovoltaic technology. The first step in NanoBonding™ is to synthesize smooth surfaces with 20 nm wide atomic terraces via a precursor phase, ß-cSiO2 on Si(100) and oxygen-deficient SiOx on the silica using the Herbots-Atluri process and Entrepix’s spin etching. Smooth precursor phases act as geometric and chemical template to nucleate and grow macroscopic contacting domains where cross bridging occurs via arrays of molecular strands in the hydrated SiOxHy interphase. Steam pressurization is found to catalyze NanoBonding™ consistently, eliminating the need for direct mechanical compression that limits the size and shape of wafers to be bonded in turn, reducing the cost of processing. Total surface energy measurements via 3 Liquids Contact Angle Analysis (3L CAA) enables accurate quantitative analysis of the total surface energy and each of its components. 3L CAA at each step in the process shows that surface energy drops to 42.4 ± 0.6 mJ/m2 from 57.5 ± 1.4 mJ/m2 after the Herbots-Atluri clean of an “As Received” wafer. 3L CAA after steam pressurization Nanobonding™ shows almost complete elimination from 13.8 mJ/m2 ± 1.0 to 0.002 ±- 0.0002 mJ/m2 in the contribution of acceptors to the total free surface energy, and an increase from 0.2 ± .03 to 23.8± 1.6 mJ/m2 in the contribution of donors. This is consistent with an increase in hydroxylation of the ß-cSiO2 surface as a consistent precursor phase for cross-bridging. This research optimizes the use of glycerin, water, and α-bromo-naphtalene in the use of 3L CAA to effectively quantify the components of total free surface energy which helps to better understand the most consistent method for NanoBonding™.

In this project, we introduce a type of microscopy which produces correlated topography and fluorescence lifetime images with nanometer resolution. This technique combines atomic force microscopy (AFM) and time resolved confocal fluorescence microscopy to conduct biological and materials research. This method is used to investigate nanophotonic effects on single fluorophores, including quantum dots and fluorescent molecules. For single fluorescent molecules, we investigate the effects of quenching of fluorescence with the probe of an atomic force microscope which is combined and synchronized with a confocal fluorescence lifetime microscope. For quantum dots, we investigate the correlation between the topographic and fluorescence data. With this method of combining an atomic force microscope with a confocal microscope, it is anticipated that there will be applications in nanomaterial characterization and life sciences; such as the determination of the structure of small molecular systems on surfaces, molecular interactions, as well as the structure and properties of fluorescent nanomaterials.

Journalism, by its very nature, is limited, often adhering to a repetitive format and narration style. Consequently, the depth of journalistic stories will always hit a barrier. Fiction, on the other hand, provides an elegant solution by exploring the world through a myriad point of views including complete omniscience. This thesis explores the link between journalism and fiction by taking real-world scenarios and exploring them without journalism's limitations. It includes three novellas totaling 25,000 words drawn from true-to-life research papers, news stories and manifestos to paint a realistic picture of a technological reality in the near future, a style of writing one might call futurecasting. The thesis also contains an analysis of the techniques used in contemporary fiction and an analysis of their implementation within the novellas. The goal of the novellas is to let researchers to explore the impact of their work before its mass dissemination in order to shape societal, national and international policy responsibly. Similarly, novellas like this and others similar allow society to discover the beauty of science through fiction. These are some of fiction's greatest roles in science and society.

Climate change is one of the biggest challenges facing today's society.Since the late 19th century, the global average temperature has been rising. In order to minimize the temperature increase of the earth, it is necessary to develop alternative energy technologies that do not depend on fossil fuels. Solar fuels are one potential energy source for the future. Solar fuel technologies use catalysts to convert low energy molecules into fuels via artificial photosynthesis. TiO2, or titania, is an important model photocatalyst for studying these reactions. It is also important to use remaining fossil fuel resources efficiently and with the lowest possible greenhouse gas emissions. Fuel cells are electrochemical devices that aim to accomplish this goal and CeO2, or ceria, is an important material used in these devices. One way to observe the atomic structure of a material is with a transmission electron microscope (TEM). A traditional transmission electron microscope employs a beam of fast electrons to form atomic resolution images of a material. While imaging gives information about the positions of the atoms in the material, spectroscopy gives information about the composition and bonding of the material. A type of spectroscopy that can be performed inside the transmission electron microscope is electron energy loss spectroscopy (EELS), which provides a fundamental understanding of the electronic structure of a material. The energy loss spectrum also contains information on the chemical bonding in the material, and theoretical calculations that model the spectra are essential to correctly interpreting this bonding information. FEFF is a software that performs EELS calculations. Calculations of the oxygen K edges of TiO2 and CeO2 were made using FEFF in order to understand the changes that occur in the spectrum when oxygen vacancies are introduced as well as the changes near a grain boundary.

In this experiment, an attempt was made to measure the index of refraction of a thin glass microscope slide, with a known thickness of 1.01 mm. A monochromatic laser with wavelength of 532nm was employed to generate the interference pattern through the use of a Michelson interferometer. The slide was placed in the path of one of the beams. The slide could then be rotated through a series of angles, and, from the resulting changes in the interference pattern, the index of refraction of the slide could be extracted. The index of refraction was found to be 1.5±0.02.

The goal of this project was to examine the separatricies that define regions of distinct flow behaviors in realistic time-dependent dynamical systems. In particular, we adapted previously available methods for computing the Finite-Time Lyapunov Exponent (FTLE) to a set of measured wind velocity data in order to visualize the separatricies as ridges of the FTLE field in a section of the atmosphere. This visualization required a number of alterations to the original methods, including interpolation techniques and two different adaptive refinement schemes for producing more detailed results. Overall, there were two computations performed with the wind velocity data: once along a single spherical surface, on which the separatricies could be visualized as material lines, and then along a three-dimensional section of the atmosphere, for which the separatricies were material surfaces. The resulting figures provide an image of the Antarctic polar vortex from the wind velocity data, which is consistent with other data gathered on the same date.

In fan fiction, fans utilize different elements in an original work and incorporate them into their fanfics; elements such as the characters and setting of an original work are frequently used in fan fiction. A different element is investigated: time travel. The physics behind time travel is not yet understood, so authors have to create their own time travel physics in their works to account for this lack of understanding. Therefore, for fan authors to incorporate time travel into their fanfic, they must study the time travel physics in the original work the same way that characters from an original work are studied. Three original works and three fanfics are examined: the television show My Little Pony: Friendship is Magic and its fanfic "The Fall and Rise of the Alicorn", the Harry Potter book series and its fanfic "Back to the Time of the Unknown", and the webcomic Homestuck and its fanfic "Like a Bug on a Windshield".

Covering subsequences with sets of permutations arises in many applications, including event-sequence testing. Given a set of subsequences to cover, one is often interested in knowing the fewest number of permutations required to cover each subsequence, and in finding an explicit construction of such a set of permutations that has size close to or equal to the minimum possible. The construction of such permutation coverings has proven to be computationally difficult. While many examples for permutations of small length have been found, and strong asymptotic behavior is known, there are few explicit constructions for permutations of intermediate lengths. Most of these are generated from scratch using greedy algorithms. We explore a different approach here. Starting with a set of permutations with the desired coverage properties, we compute local changes to individual permutations that retain the total coverage of the set. By choosing these local changes so as to make one permutation less "essential" in maintaining the coverage of the set, our method attempts to make a permutation completely non-essential, so it can be removed without sacrificing total coverage. We develop a post-optimization method to do this and present results on sequence covering arrays and other types of permutation covering problems demonstrating that it is surprisingly effective.