Engineering Commons^™

Exploring Computational Chemistry On Emerging Architectures, David Dewayne Jenkins

Doctoral Dissertations

Emerging architectures, such as next generation microprocessors, graphics processing units, and Intel MIC cards, are being used with increased popularity in high performance computing. Each of these architectures has advantages over previous generations of architectures including performance, programmability, and power efficiency. With the ever-increasing performance of these architectures, scientific computing applications are able to attack larger, more complicated problems. However, since applications perform differently on each of the architectures, it is difficult to determine the best tool for the job. This dissertation makes the following contributions to computer engineering and computational science. First, this work implements the computational chemistry variational …

Parallel For Loops On Heterogeneous Resources, Frederick Edward Weber

Doctoral Dissertations

In recent years, Graphics Processing Units (GPUs) have piqued the interest of researchers in scientific computing. Their immense floating point throughput and massive parallelism make them ideal for not just graphical applications, but many general algorithms as well. Load balancing applications and taking advantage of all computational resources in a machine is a difficult challenge, especially when the resources are heterogeneous. This dissertation presents the clUtil library, which vastly simplifies developing OpenCL applications for heterogeneous systems. The core focus of this dissertation lies in clUtil's ParallelFor construct and our novel PINA scheduler which can efficiently load balance work onto multiple …

Dynamic Task Execution On Shared And Distributed Memory Architectures, Asim Yarkhan

Doctoral Dissertations

Multicore architectures with high core counts have come to dominate the world of high performance computing, from shared memory machines to the largest distributed memory clusters. The multicore route to increased performance has a simpler design and better power efficiency than the traditional approach of increasing processor frequencies. But, standard programming techniques are not well adapted to this change in computer architecture design.

In this work, we study the use of dynamic runtime environments executing data driven applications as a solution to programming multicore architectures. The goals of our runtime environments are productivity, scalability and performance. We demonstrate productivity by …

Structure And Dynamics Of High Temperature Superconductors, Jennifer Lynn Niedziela

Doctoral Dissertations

High temperature superconductivity in iron based compounds has presented a series of complex problems to condensed matter physics since being discovered in 2008. The stalwart basis of condensed matter physics is the “strength in numbers" aspect of crystalline periodicity. Perfect crystalline periodicity has made possible the reduction of the questions of structural and electronic properties to single dimensions, increasing the tractability of these problems. Nevertheless, modern complex materials stretch these assumptions to their limits, and it is at this point where our work starts. Using neutron and x-ray scattering, we have conducted a series of studies on the structural disorder …

Development Of A Novel Technique For Predicting Tumor Response In Adaptive Radiation Therapy, Rebecca Marie Seibert

Doctoral Dissertations

This dissertation concentrates on the introduction of Predictive Adaptive Radiation Therapy (PART) as a potential method to improve cancer treatment. PART is a novel technique that utilizes volumetric image-guided radiation therapy treatment (IGRT) data to actively predict the tumor response to therapy and estimate clinical outcomes during the course of treatment. To implement PART, a patient database containing IGRT image data for 40 lesions obtained from patients who were imaged and treated with helical tomotherapy was constructed. The data was then modeled using locally weighted regression. This model predicts future tumor volumes and masses and the associated confidence intervals based …

A Novel Microfluidic Enrichment Technique For Carbonylated Proteins, Bryant C. Hollins

Doctoral Dissertations

Proteins are the building blocks of cells in living organisms, and are composed of amino acids. The expression of proteins is regulated by the processes of transcription and translation. Proteins undergo post-translational modifications in order to dictate their role physiologically within a cell.

Not all post-translational modifications are beneficial for the protein or the cell. One type of post-translational modification, called carbonylation, irreversibly places a carbonyl group onto an amino acid residue, most commonly proline, lysine, arginine, and threonine. This modification can have severe consequences physiologically, including loss of solubility, loss of function, and protein aggregation.

Carbonylated proteins have commonly …

The Synthesis And Characterization Of Novel Group 13 Nanostructured Building Block Heterogeneous Silicate Catalysts, Joshua G. Abbott

Doctoral Dissertations

A building block approach and sequential addition methodology were utilized to prepare heterogeneous silicate catalysts containing atomically dispersed group 13 metal (B, Al, Ga) centers. The octa(trimethyltin) silsequioxane, Si8[sub]O12[sub](OSnMe3[sub])8[sub], was used as the building block for the synthesis of these materials. Reaction of the building block with a variety of group 13 metal chlorides led to the formation of cross-linked matrices. All prepared materials were characterized by gravimetric analysis, gas absorption, IR, and NMR. In addition, aluminum and boron samples where characterized by 27[sup]Al and 11[sup]B solid state NMR, and gallium samples were studied using x-ray absorption techniques.

Studies found …

Secondary Light Particle Data Base Development Using A Thermodynamic Coalescence Model, Mahmoud Pourarsalan

Doctoral Dissertations

ABSTRACT

As heavy ions are transported through shielding and interact with shielding materials accurate values of total, elastic scattering, reactions cross sections and angular distributions of the emitted nucleons, light high energy particles such as deuteron, triton, helion, alpha particles and other heavy ions are required in order to design appropriate and adequate shielding to protect the human crews and instruments from ionizing radiations during long duration space missions. Double-differential (energy and angle) light energetic particle production cross sections must be known for ion energies from tens of MeV/nucleon to tens of GeV/nucleon for all emitted light energetic particles for …

Hard And Soft Error Resilience For One-Sided Dense Linear Algebra Algorithms, Peng Du

Doctoral Dissertations

Dense matrix factorizations, such as LU, Cholesky and QR, are widely used by scientific applications that require solving systems of linear equations, eigenvalues and linear least squares problems. Such computations are normally carried out on supercomputers, whose ever-growing scale induces a fast decline of the Mean Time To Failure (MTTF). This dissertation develops fault tolerance algorithms for one-sided dense matrix factorizations, which handles Both hard and soft errors.

For hard errors, we propose methods based on diskless checkpointing and Algorithm Based Fault Tolerance (ABFT) to provide full matrix protection, including the left and right factor that are normally seen in …

Morphology-Properties Studies In Laser Synthesized Nanostructured Materials, Nozomi Shirato

Doctoral Dissertations

Synthesis of well-defined nanostructures by pulsed laser melting is an interesting subject from both a funda- mental and technological point of view. In this thesis, the synthesis and functional properties of potentially useful materials were studied, such as tin dioxide nanostructured arrays, which have potential applications in hydrogen gas sensing, and ferromagnetic Co nanowire and nanomagnets, which are fundamentally im- portant towards understanding magnetism in the nanoscale. First, the formation of 1D periodic tin dioxide nanoarrays was investigated with the goal of forming nanowires for hydrogen sensing. Experimental obser- vations combined with theoretical modeling successfully explained the mechanisms of structure …

Reliability Models For Hpc Applications And A Cloud Economic Model, Thanadech Thanakornworakij

Doctoral Dissertations

With the enormous number of computing resources in HPC and Cloud systems, failures become a major concern. Therefore, failure behaviors such as reliability, failure rate, and mean time to failure need to be understood to manage such a large system efficiently.

This dissertation makes three major contributions in HPC and Cloud studies. First, a reliability model with correlated failures in a k-node system for HPC applications is studied. This model is extended to improve accuracy by accounting for failure correlation. Marshall-Olkin Multivariate Weibull distribution is improved by excess life, conditional Weibull, to better estimate system reliability. Also, the univariate …

Development And Experimental Analysis Of Wireless High Accuracy Ultra-Wideband Localization Systems For Indoor Medical Applications, Michael Joseph Kuhn

Doctoral Dissertations

This dissertation addresses several interesting and relevant problems in the field of wireless technologies applied to medical applications and specifically problems related to ultra-wideband high accuracy localization for use in the operating room. This research is cross disciplinary in nature and fundamentally builds upon microwave engineering, software engineering, systems engineering, and biomedical engineering. A good portion of this work has been published in peer reviewed microwave engineering and biomedical engineering conferences and journals. Wireless technologies in medicine are discussed with focus on ultra-wideband positioning in orthopedic surgical navigation. Characterization of the operating room as a medium for ultra-wideband signal transmission …

Towards Sustainable Development Of Nanomanufacturing, Sasikumar Ramdas Naidu

Doctoral Dissertations

"Sustainability" is a buzz word these days not just among regulatory agencies but even with corporations, as evident by the release of annual sustainability report by a large number of firms. Companies are starting to portray profit making along with corporate environmental responsibility.

Nanotechnology and nanomanufacturing which holds a lot of promise for development in a multitude of fields in science and engineering is the new kid on the block and carries a lot of apprehension due to public concern about their potential unwanted side effects that may result in the case of an untoward incident or lack of oversight. …

Derivation Of Correction Terms To The Eikonal Approximations In The Formulation Of Analytical Abrasion-Ablation Model, Santosh Bhatt

Doctoral Dissertations

Analytical models for the quantitative predictions of spectra from the neutrons and light ions produced from the high energy, heavy ion (HZE) reactions are extremely important in assessment of the radiation damage during long duration deep space missions, and for various accelerator applications. The fundamental physics of the secondary particle production and transport from these HZE reactions is described using the abrasion-ablation model. The abrasion part of the model is based on the Glauber multiple scattering theory while the ablation process is based on statistical decay based on an evaporation model. The current formulations for the abrasion process are based …

Numerical Simulation Of Nanopulse Penetration Of Biological Matter Using The Adi-Fdtd Method, Fei Zhu

Doctoral Dissertations

Nanopulses are ultra-wide-band (UWB) electromagnetic pulses with pulse duration of only a few nanoseconds and electric field amplitudes greater than 105 V/m. They have been widely used in the development of new technologies in the field of medicine. Therefore, the study of the nanopulse bioeffects is important to ensure the appropriate application with nanopulses in biomedical and biotechnological settings. The conventional finite-difference time-domain (FDTD) method for solving Maxwell's equations has been proven to be an effective method to solve the problems related to electromagnetism. However, its application is restricted by the Courant, Friedrichs, and Lewy (CFL) stability condition that confines …

The Search For An Optimal Means Of Determining The Minmax Control Parameter Using Sensitivity Analysis, John Teye Brown

Doctoral Dissertations

The use of computational methods for design and simulation of control systems allows for a cost-effective trial and error approach. In this work, we are concerned with the robust, real-time control of physical systems whose state space is infinite-dimensional. Such systems are known as Distributed Parameter Systems (DPS). A body whose state is heterogeneous is a distributed parameter. In particular, this work focuses on DPS systems that are governed by linear Partial Differential Equations, such as the heat equation. We specifically focus on the MinMax controller, which is regarded as being a very robust controller. The mathematical formulation of the …

Mathematical Modeling Of Pipeline Features For Robotic Inspection, Yang Gao

Doctoral Dissertations

Underground pipeline systems play an indispensable role in transporting liquids in both developed and developing countries. The associated social and economic cost to repair a pipe upon abrupt failure is often unacceptable. Regular inspection is a preventative action that aims to monitor pipe conditions, catch abnormalities and reduce the chance of undesirable surprises. Robots with CCTV video cameras have been used for decades to inspect pipelines, yielding only qualitative information. It is becoming necessary and preferable for municipalities, project managers and engineers to also quantify the 3-D geometry of underground pipe networks. Existing robots equipped specialized hardware and software algorithms …