The movement of a fluid and solute through a porous medium is of great practical interest because this describes the spread of contaminants through an aquifer. Many contaminants occur at concentrations sufficient to alter the density of the fluid, in which case the physics is typically modelled mathematically by a pair of coupled, nonlinear partial differential equations. There is disagreement as to the exact form of these governing equations. Codes aiming to solve some version of the governing equations are typically tested against the Henry and Elder benchmark problems. Neither benchmark has an analytic solution, so in practice they are treated as exercises in inter code comparison. Different code developers define the boundary conditions of the Henry problem differently, and the Elder problems results are poorly understood. The Henry, Elder and some other problems are simulated on several different codes, which produce widely-varying results. The existing benchmarks are unable to distinguish which code, if any, simulates the problems correctly, illustrating the benchmarks' limitations. To determine whether these discrepancies might be due to numerical error, one popular code, SUTRA, is considered in detail. A numerical analysis of a special case reveals that SUTRA is numerically dispersive. This is confirmed using the Gauss pulse test, a benchmark that does have an analytic solution. To further explain inter code discrepancies, a testcode is developed which allows a choice of numerical methods. Some of the methods are based on SUTRA's while others are finite difference methods of varying levels of accuracy. Simulations of the Elder problem reveal that the benchmark is extremely sensitive to the choice of solution method: qualitative differences are seen in the flow patterns. Finally, the impact of numerical error on a real-world application, the simulation of saline disposals, is considered. Saline disposal basins are used to store saline water away from rivers and agricultural land in parts of Australia. Existing models of disposal basins are assessed in terms of their resemblance to real fieldsite conditions, and in terms of numerical error. This leads to the development of a new model which aims to combine verisimilitude with numerical accuracy. / Thesis (Ph.D.)--School of Mathematical Sciences (Applied Mathematics), 2004.

Delta-Sigma Modulator-based Analog-to-Digital converter design is an active area of research. New topologies require extensive simulations to verify their performance. A series of improvements were made to an existing circuit simulation package in order to speed the simulation process for the designer. Various examples of these improvements are presented in typical applications. / Graduation date: 1992

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Peer-to-Peer (P2P) overlays were initially proposed for use with wired networks. However, the very rapid proliferation of wireless communication technology has prompted a need for adoption of P2P systems in mobile networks too. There are many common characteristics between P2P overlay networks and Mobile Ad-hoc Networks (MANET). Self-organization, decentralization, a dynamic nature and changing topology are the most commonly shared features. Furthermore, when used together, the two approaches complement each other. P2P overlays provide data storage/retrieval functionality and MANET provides wireless connectivity between clients without depending on any pre-existing infrastructure. P2P overlay networks can be deployed over MANET to address content discovery issues. However, previous research has shown that deploying P2P systems straight over MANET does not exhibit satisfactory performance. Bandwidth limitation, limited resources and node mobility are some of the key constraints. This thesis proposes a novel approach, OneHopOverlay4MANET, to exploit the synergies between MANET and P2P overlays through cross-layering. It combines Distributed Hash Table (DHT) based structured P2P overlays with MANET underlay routing protocols to achieve one logical hop between any pair of overlay nodes. OneHopOverlay4MANET constructs a cross-layer channel to permit direct exchange of routing information between the Application layer, where the overlay operates, and the MANET underlay layer. Consequently, underlay routing information can be shared and used by the overlay. Thus, OneHopOverlay4MANET reduces the typical management traffic when deploying traditional P2P systems over MANET. Moreover, as a result of building one hop overlay, OneHopOverlay4MANET can eliminate the mismatching issue between overlay and underlay and hence resolve key lookups in a short time, enhancing the performance of the overlay. v In this thesis, we present OneHopOverlay4MANET and evaluate its performance when combined with different underlay routing protocols. OneHopOverlay4MANET has been combined with two proactive underlays (OLSR and BATMAN) and with three reactive underlay routing protocols (DSR, AODV and DYMO). In addition, the performance of the proposed system over OLSR has been compared to two recent structured P2P over MANET systems (MA-SP2P and E-SP2P) that adopted OLSR as the routing protocol. The results show that better performance can be achieved using OneHopOverlay4MANET.

New hardware devices are continually being released to the public by hardware manufactures around the world. For these new devices to be usable under a PC operating system, device drivers that extend the functionality of the target operating system have to be constructed. This work examines and compares the device driver architectures currently in use by two of the most widely used operating systems, Microsoft’s Windows and Linux. The IEEE1394 (high speed serial bus) device driver stacks on each operating system are examined and compared as an example of a major device driver stack implementation, including driver requirements for the upcoming IEEE1394.1 bridging standard.

For this project the program Walk with Dinosaurs was developed using Keller's Theory of Motivation. Walk with Dinosaurs is a interactive multimedia tool for presenting an integrated thematic unit. As a HyperCard stack, it intoduces students to factual information on dinosaurs in an appealing and motivating way.

Sequence similarity searching is commonly used to help clarify the biochemical and physiological features of newly discovered genes or proteins. An efficient similarity search relies on the choice of tools and their associated subprograms and numerous parameter settings. To assist researchers in selecting optimal programs and parameter settings for efficient sequence similarity searches, the web-based expert system, Smart Sequence Similarity Search (S4) was developed.

Hadoop is a popular software framework written in Java that performs data-intensive distributed computations on a cluster. It includes Hadoop MapReduce and the Hadoop Distributed File System (HDFS). HDFS has known scalability limitations due to its single NameNode which holds the entire file system namespace in RAM on one computer. Therefore, the NameNode can only store limited amounts of file names depending on the RAM capacity. The solution to furthering scalability is distributing the namespace similar to how file is data divided into chunks and stored across cluster nodes. Hadoop has an abstract file system API which is extended to integrate HDFS, but has also been extended for integrating file systems S3, CloudStore, Ceph and PVFS. File systems Ceph and PVFS already distribute the namespace, while others such as Lustre are making the conversion. Google previously announced in 2009 they have been implementing a Google File System distributed namespace to achieve greater scalability. The Generic Hadoop API is created from Hadoop's abstract file system API. It speaks a simple communication protocol that can integrate any file system which supports TCP sockets. By providing a file system agnostic API, future work with other file systems might provide ways for surpassing Hadoop 's current scalability limitations. Furthermore, the new API eliminates the need for customizing Hadoop's Java implementation, and instead moves the implementation to the file system itself. Thus, developers wishing to integrate their new file system with Hadoop are not responsible for understanding details ofHadoop's internal operation. The API is tested on a homogeneous, four-node cluster with OrangeFS. Initial OrangeFS I/0 throughputs compared to HDFS are 67% ofHDFS' write throughput and 74% percent of HDFS' read throughput. But, compared with an alternate method of integrating with OrangeFS (a POSIX kernel interface), write and read throughput is increased by 23% and 7%, respectively

We study fundamental graph problems under parallel computing models. In particular, we consider two parallel computing models: Parallel Random Access Machine (PRAM) and Massively Parallel Computation (MPC). The PRAM model is a classic model of parallel computation. The efficiency of a PRAM algorithm is measured by its parallel time and the number of processors needed to achieve the parallel time. The MPC model is an abstraction of modern massive parallel computing systems such as MapReduce, Hadoop and Spark. The MPC model captures well coarse-grained computation on large data --- data is distributed to processors, each of which has a sublinear (in the input data) amount of local memory and we alternate between rounds of computation and rounds of communication, where each machine can communicate an amount of data as large as the size of its memory. We usually desire fully scalable MPC algorithms, i.e., algorithms that can work for any local memory size. The efficiency of a fully scalable MPC algorithm is measured by its parallel time and the total space usage (the local memory size times the number of machines). Consider an 𝑛-vertex 𝑚-edge undirected graph 𝐺 (either weighted or unweighted) with diameter 𝐷 (the largest diameter of its connected components). Let 𝑁=𝑚+𝑛 denote the size of 𝐺. We present a series of efficient (randomized) parallel graph algorithms with theoretical guarantees. Several results are listed as follows: 1) Fully scalable MPC algorithms for graph connectivity and spanning forest using 𝑂(𝑁) total space and 𝑂(log 𝐷loglog_{𝑁/𝑛} 𝑛) parallel time. 2) Fully scalable MPC algorithms for 2-edge and 2-vertex connectivity using 𝑂(𝑁) total space where 2-edge connectivity algorithm needs 𝑂(log 𝐷loglog_{𝑁/𝑛} 𝑛) parallel time, and 2-vertex connectivity algorithm needs 𝑂(log 𝐷⸱log²log_{𝑁/𝑛} n+\log D'⸱loglog_{𝑁/𝑛} 𝑛) parallel time. Here 𝐷' denotes the bi-diameter of 𝐺. 3) PRAM algorithms for graph connectivity and spanning forest using 𝑂(𝑁) processors and 𝑂(log 𝐷loglog_{𝑁/𝑛} 𝑛) parallel time. 4) PRAM algorithms for (1 + 𝜖)-approximate shortest path and (1 + 𝜖)-approximate uncapacitated minimum cost flow using 𝑂(𝑁) processors and poly(log 𝑛) parallel time. These algorithms are built on a series of new graph algorithmic primitives which may be of independent interests.

This paper presents a means of modulating timbre in digital sound synthesis using additive processes . A major portion of the paper is a computer program, written in Pl/1, which combines this additive method of timbre modulation with several other sound manipulation ideas to form a compositional program. This program-which is named CART for Computer Aided Rotational Translation-provides input for the Music 360 digital sound synthesis program. The paper contains three major parts: (1) a discussion of the CART program's evolution; (2) a manual describing in detail the use of CART; and (3) two tape compositions realized using the program. An appendix contains the program listing and listing of the input cards that were used to produce the two compositions.