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Collection Description

Collection of student theses and dissertations from as early as 1939, but mainly from 2010 to present.

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A comparison of the efficiency of an atomic component operation versus primitive operations for building a real-time collaborative editing API
Includes bibliographical references (pages 27-28)., Real-time collaborative editing is a productive way to work in groups and drive innovation. A software application is more likely to be adopted by its users if it is familiar to them and something they already know how to use. Thus, an API that would allow a development team to turn a single-user application into a collaborative application is needed. Such an API would need to find a balance between complexity from the perspective of the developers building the API and the developers using the API to build a real time collaborative editor. The API should be flexible and include enough operations so as to be useful, but not so many operations as to make the operation transformations overly complex. This paper presents a comparison of the efficiency of primitive algorithms versus atomic component algorithms in the context of building a real-time collaborative editing API. The atomic component operations perform better, both in terms of CPU clock cycles as well as in terms of ease of use for a developer building an application.
A comparison of the pattern of herb and shrub growth in comparable sites in Chile and California
A comparison of the pattern of herb and shrub growth was undertaken in two similar appearing but floristically unrelated brush land areas, the Fundo Santa Laura, Chile and Echo Dell, California. Within each study site four types of areas were sampled to evaluate the change in herb-shrub relationship with disturbance. These were: Undisturbed, Semi-disturbed, Disturbed (cleared), and a First-year burn. The point-quarter and line intercept methods were used t o gather data in both sites. The results of the study and the conclusions reached were: (1) The two herbaceous vegetations appear at different times and in different relationships to the shrub overstories. In Chile the herbs and shrubs are found concurrently, the herbs growing directly beneath specific shrub canopies. The destruction of the shrubs by fire is coupled with the loss of the herbs. In California the herbaceous vegetation is homogeneously distributed within and between the canopies and the high levels of herb growth are associated with the lack of a shrubby overstory. (2) The types of herbs commonly found are different in the two systems. In Chile 75% of the major species are herbaceous perennials, in California when the herbaceous vegetation is at its peak, following fire, 75% of the species are annuals. (3) Slight amounts of disturbance altfrs the vegetation in both countries but in Chile disturbance only serves to reinforce the pattern of herb and shrub association. In California slight amounts of disturbance allow for a greater proliferation of herbs but there is no apparent change in the distribution of the herbs, they remain relatively homogeneously distributed. (4) Extreme disturbance such as clearing causes apparently similar destruction of the vegetations. In both Chile and California clearing reduced the number of shrubs and opened the area to colonization by mediterranean weeds. (5) The role of fire in the two areas is apparently different. Fire does not appear to be common in the mattoral, now or in the past, but it is common in the chaparral system. (6) The climatic stresses appear to be somewhat different in the two countries. While both Chile and California have mediterranean climates the fluctuations in temperatures and humidities appears to be less in Chile than California, the maritime influences in Chile seem to damp out climatic variations producing an overall more constant climate. The type of perennial vegetation found in central Chile provides support for this idea. The more widely fluctuating and less predictable climate in southern California is reflected in the annual type herbaceous flora. In conclusion the two systems are superficially similar but represent different climatic and ecological types, with different fire histories. Chilean mattoral appears to be a derivative of a former forest type vegetation where fire type disturbance was uncommon, while in California the chaparral appears to be a true xerophytic scrub vegetation, constantly influenced by fire., California State University, San Diego, Digitization of this archival thesis was made possible through a generous donation from Robin B. Luby.
A competitive analysis of the small format printing media market in the North American retail chain
Over the past five years dramatic improvements in quality and technology, along with fast falling average selling prices, have led to a rapidly growing installed base of home and office printers. These trends have caused an explosion in the variety and types of media on which to print, such as photo papers, greeting cards, brochure paper and art paper. This growth opportunity has attracted many players and has resulted in a hotly competitive market. The North American retail channel is now highly fragmented with 34 players vying for a share of the opportunity. This paper focuses on developing a competitive analysis methodology that utilizes two important measures: market commonality as proposed by Chen (1996) and market posture, as described by the author. This analysis is based on data collected monthly by ARS, Inc., a market research firm. This data tracks monthly placements of stock keeping units (SKUs) in each of 14 major retail chains that sell printing media. Based on this data, a new competitor map for the focal firm, Hewlett-Packard (HP), is proposed that addresses these two measures. HP's main rivals are identified on the map and this is then followed by a discussion of generic strategies as well as specific actions. HP's primary focus should be on the three competitors contained in Zone I of the competitor map: Epson, Avery, and International Paper (IP). An aggressive response is required against Epson and Avery, while a more cautious and cooperative approach is appropriate against IP. HP must defend against Epson by using a printing system message which addresses photo printing and that is targeted to the end-user. HP must use an aftermarket approach to defend against Avery by offering a broad product line in the card category, and an approach that is targeted toward the reseller., San Diego State University, Digitization of this archival thesis was made possible through a generous donation from Robin B. Luby.
A comprehensive nonlinear mathematical modeling of smart flow distribution network
In this study, we will detail the physics of a solenoid-actuated butterfly valve. We will then develop a comprehensive formula to describe the pressure drops across valves in a system of many valves. We then use this formula to perform a case study of a network of three valves subject to the laminar flow. We then analyze the system as each of the valves is subjected to external noise with the intent to understand the behavior of the system as one valve is disturbed. Additionally, we capture chaotic dynamics of the system, showing that chaos can be induced in this system. The findings of the work show that a general formula of many valves can be used in simulating a system of three valves. Additionally, it is shown that when each of the valves is subjected to an external disturbance, the other ones behave different in each case.
A computational method for classifying phages
Viruses that that infect bacteria are called bacteriophages, or phages. It is estimated that there are 10³⁰ bacterial cells in biosphere. Given that typical ratios of bacteria to phage are on the order of 10:1, it is estimated that there exist 10³¹ phage particles on the planet. Viruses thus are the most abundant biological entities on the planet. Phages are ubiquitous and can be found in any environment where their bacterial hosts are present, yet only a small fraction of phages have so far been characterized. Phages are not placed on the universal tree of life, however they are classified into Order, Family, Subfamily, Genus and Species. All phages either fall under the Order Caudovirales or have yet to be assigned to an Order. Below the hierarchy of Order 14 phage Families have been created. There are also two distinct lifestyles of phages: lytic and lysogenic. The lytic lifestyle has many implications for phage therapy, genomics, and climate change. Classifying the Family and lifestyle of phages is currently performed through culturing and isolation in the lab, and is not only time consuming but costly. Classifying phages computationally has always been difficult due to the highly mosaic organization of their genomes. As such, a Phage Classification Tool Set (PHACTS) was developed to classify phages by using the known phage genomes in The PHANTOME database. PHACTS utilizes these known genomes to find similarities in the unknown phage genome. A supervised Random Forest classifier then determines which class a phage falls into. To test the classifier the phage Family, phage lifestyle and Gram stain of host were manually curated by hand for phages in the PHANTOME database. Each phage was sequentially removed from the annotated datasets one at a time and treated as an unknown. PHACTS was then used to predicted which classes that phage belonged to. When predicting the lifestyle of a phage, PHACTS had a 99% accuracy rate, and when predicting the Gram stain of the host PHACTS had a 95% accuracy rate. For the non-binary classification of phage Family the protocols were modified, and PHACTS had a 99% accuracy rate for predicting the Family of a phage. PHACTS was not able to confidently predict the classes of some phages, however it is thought that as more known phages are added to the PHANTOME database, PHACTS will be able to more accurately predict classes.
A computational model of mucus
We created a computational model of mucus using the LAMMPS molecular dynamics simulation software. The model recreates the properties of MUC5AC which is one of the most common varieties of mucins. The model was validated against real-world data. We plan to use the model to study processes in the mucosal environment, such as the motion of bacteriaphage through mucus., San Diego State University
A computational pipeline for novel phage discovery in metagenomic samples
Viruses make up the most abundant biological entities on the planet, but the high levels of variability between viral sequences and lack of known hosts have left a large majority of these sequences undocumented using traditional laboratory techniques. Through metagenomic sampling and computational analysis, it is now possible for DNA sequences to be isolated and identified as phages. This was proven in the 2014 discovery of crAssphage, a highly abundant bacteriophage present in the majority of human guts. The amount of publicly available sequencing data since then has grown exponentially, and there are now over 4,000 human fecal metagenomes available on the Sequence Read Archive (SRA). We developed a computational pipeline to extract data from the SRA, perform a cross-assembly, identify abundant, co-occurring contigs, and sort these contigs into genome bins. The contigs contained in these genome bins can then be compared to a database of all documented phage genes to date. All of the metagenomes in the SRA can then be scanned for this collection of contigs, and runs containing the contigs most similar to phage genes are repeatedly put through the pipeline. This method exploits the fact that contigs belonging to the same phage-like entity will occur together, and cross assembly of runs containing the largest abundance of such contigs should reveal the complete genome. These methods are promising for the discovery of novel phages in the human gut, which can improve our knowledge of human health., San Diego State University
A computational study and statistical analysis of Santa Ana winds in Rancho Bernardo, San Diego
Wildfires are devastating natural disasters that cause massive physical, ecological, and economic damage. In Southern California, wildfires are strongly impacted by Santa Ana wind events. Current research funded by NIST, the National Institute of Standards and Technology, is focused on studying the behavior of winds within the Rancho Bernardo Trails community in San Diego County, which was the victim of the Witch and Guejito wildfires in 2007. The goal of the research project is to understand the effects that Santa Ana winds have upon the spread of wildfires as the fires transition from a wildland environment to an urban environment across what is called the wildland-urban interface. Within the Trails community in Rancho Bernardo and the neighboring San Dieguito River Valley, there exist 18 different locations monitoring wind speed, wind direction, temperature, and humidity using various methods. In conjunction with experimental field data, the project utilizes a CFD model developed by NIST called Fire Dynamics Simulator (FDS) in order to simulate wind flow and fire spread under specified conditions. A statistical analysis was done on experimental data from both a Santa Ana event on February 8, 2016 and typical wind behavior on February 1, 2016. The goal of this analysis was to study how the local terrain within the Rancho Bernardo Trails community and the surrounding area affected wind flow during a Santa Ana event. Correlation between different Trails sites were calculated to quantify this affect, and time graphs and boundary layer profiles were created to visualize the data collected. FDS has three methods by which wind flow can be implemented within the domain. Before fire can be modeled accurately within FDS, it must first be determined which wind flow method is best suited for the purposes of this project. Testing was done within a simplified domain to study how various boundary conditions and imposed synthetic turbulence affect the wind flow using each method. It was determined that the Coriolis Force method is the most promising method to use for complex simulations, but still requires some validation testing., San Diego State University
A computational study of wind turbine wake models and their application in wind farm layout optimization
With the ongoing climate crisis, supporting a sustainable future has been a priority worldwide. Generating power that does not produce greenhouse gas emissions and reducing the dependence on imported fuel sources made the use of renewable energy resources skyrocket in recent years. Wind energy specically is one of the fastest growing renewable energy resources. In this study, we answer important mathematical questions in the development of a wind project. We compare various analytical models to better understand the wake created by a turbine, and how the wake-interaction within a wind farm affects overall energy production. With a better understanding of wake modeling, we further analyze how the various wake models affect the wind farm layout optimization problem, with the goal of minimizing wake interaction and therefore maximizing energy production. These results are important to consider when developing a wind project because they govern the overall nancial viability of a potential wind farm., San Diego State University
A computerized proof of hypergeometric identities with Gosper and Zeilberger algorithms
This paper discusses Gosper and Zeilberger algorithms which are the cornerstone of proving the hypergeometric identities. Solving the hypergeometric identities that involve binomial coefficients, factorials, rational functions, and power functions is simplified immensely with computer algebra. Computer algebra started to develop with the Gosper algorithm for indefinite sums in 1978 and the Zeilberger algorithm for definite sums in 1990. I first analyze how the algorithms work explicitly. I then present a derivation of Gosper's algorithm which allows the generalization to high-order recurrence. Next I analyze how the computer finds whether or not a given hypergeometric sum is expressible in simple closed form. After some preliminary examples, I give the computerized short proofs of hypergeometric identities with the Maple., San Diego State University