Analysis and performance of a UPC implementation of a parallel longest common subsequence algorithm

An important problem in computational biology is finding the longest common subsequence (LCS) of two nucleotide sequences. This paper examines the correctness and performance of a recently proposed parallel LCS algorithm that uses successor tables and pruning rules to construct a list of sets from which an LCS can be easily reconstructed. Counterexamples are given for two pruning rules that were given with the original algorithm. Because of these errors, performance measurements originally reported cannot be validated. The work presented here shows that speedup can be reliably achieved by an implementation in Unified Parallel C that runs on an Infiniband cluster. This performance is partly facilitated by exploiting the software cache of the MuPC runtime system. In addition, this implementation achieved speedup without bulk memory copy operations and the associated programming complexity of message passing.

Advanced mechanics of materials with microstructure

The study of advanced materials aimed at improving human life has been performed since time immemorial. Such studies have created everlasting and greatly revered monuments and have helped revolutionize transportation by ushering the age of lighter–than–air flying machines. Hence a study of the mechanical behavior of advanced materials can pave way for their use for mankind’s benefit. In this school of thought, the aim of this dissertation is to broadly perform two investigations. First, an efficient modeling approach is established to predict the elastic response of cellular materials with distributions of cell geometries. Cellular materials find important applications in structural engineering. The approach does not require complex and time-consuming computational techniques usually associated with modeling such materials. Unlike most current analytical techniques, the modeling approach directly accounts for the cellular material microstructure. The approach combines micropolar elasticity theory and elastic mixture theory to predict the elastic response of cellular materials. The modeling approach is applied to the two dimensional balsa wood material. Predicted properties are in good agreement with experimentally determined properties, which emphasizes the model’s potential to predict the elastic response of other cellular solids, such as open cell and closed cell foams. The second topic concerns intraneural ganglion cysts which are a set of medical conditions that result in denervation of the muscles innervated by the cystic nerve leading to pain and loss of function. Current treatment approaches only temporarily alleviate pain and denervation which, however, does not prevent cyst recurrence. Hence, a mechanistic understanding of the pathogenesis of intraneural ganglion cysts can help clinicians understand them better and therefore devise more effective treatment options. In this study, an analysis methodology using finite element analysis is established to investigate the pathogenesis of intraneural ganglion cysts. Using this methodology, the propagation of these cysts is analyzed in their most common site of occurrence in the human body i.e. the common peroneal nerve. Results obtained using finite element analysis show good correlation with clinical imaging patterns thereby validating the promise of the method to study cyst pathogenesis.

Evaluating northern hardwood management using retrospective analysis and diameter distributions

Northern hardwood management was assessed throughout the state of Michigan using data collected on recently harvested stands in 2010 and 2011. Methods of forensic estimation of diameter at breast height were compared and an ideal, localized equation form was selected for use in reconstructing pre-harvest stand structures. Comparisons showed differences in predictive ability among available equation forms which led to substantial financial differences when used to estimate the value of removed timber. Management on all stands was then compared among state, private, and corporate landowners. Comparisons of harvest intensities against a liberal interpretation of a well-established management guideline showed that approximately one third of harvests were conducted in a manner which may imply that the guideline was followed. One third showed higher levels of removals than recommended, and one third of harvests were less intensive than recommended. Multiple management guidelines and postulated objectives were then synthesized into a novel system of harvest taxonomy, against which all harvests were compared. This further comparison showed approximately the same proportions of harvests, while distinguishing sanitation cuts and the future productive potential of harvests cut more intensely than suggested by guidelines. Stand structures are commonly represented using diameter distributions. Parametric and nonparametric techniques for describing diameter distributions were employed on pre-harvest and post-harvest data. A common polynomial regression procedure was found to be highly sensitive to the method of histogram construction which provides the data points for the regression. The discriminative ability of kernel density estimation was substantially different from that of the polynomial regression technique.

The spatial distribution of Copernicia alba (Morong) in the district of Bahia Negra, Paraguay

The Humid Chaco of Northeast Paraguay harbors monoculture palm savannas in which Copernicia alba is the only dominant overstory species. The study’s objective was to provide the complete spatial distribution of a simple ecosystem lacking confounding factors of overstory competition and changes in slope. Palms within six, 50 x 50m plots were marked by their GPS location and measured for dbh and total stem height. The spatial distribution was individually analyzed for each plot at the local scale up to 12 m using Ripley’s K test. For the total population including juvenile and adult plants, the sample plots contained both random and clustered distribution patterns. In each of the six plots, the juvenile populations exhibited more clustered patterns than the adult population of each plot.

La Yeguada volcanic complex, western Panama : an assessment of the geologic hazards using new 40AR/39Ar Ages

La Yeguada volcanic complex is one of three Quaternary volcanic centers in Panama, and is located on the southern slope of the Cordillera Central mountain range in western Panama, province of Veraguas. To assess potential geologic hazards, this study focused on the main dome complex near the village of La Laguna and also examined a cinder cone 10 km to the northwest next to the village of Media Luna. Based on newly obtained 40Ar/39Ar ages, the most recent eruption occurred approximately 32 000 years ago at the Media Luna cinder cone, while the youngest dated eruption at the main dome complex occurred 0.357 ± 0.019 Ma, producing the Castillo dome unit. Cerro Picacho is a separate dome located 1.5 km east of the main complex with a date of 4.47 ± 0.23 Ma, and the El Satro Pyroclastic Flow unit surrounds the northern portion of the volcanic complex and has an age of 11.26 ± 0.17 Ma. No Holocene (10 000 years ago to present) activity is recorded at the La Yeguada volcanic complex and therefore, it is unlikely to produce another eruption. The emergence of a new cinder cone is a possibility, but the associated hazards tend to be low and localized, and this does not pose a significant threat to the small communities scattered throughout the area. The main geologic hazard at the La Yeguada volcanic complex is from landslides coming off the many steep slopes.

Localized annealing of polysilicon microstructures by inductively heated ferromagnetic films

The monolithic integration of dissimilar microsystems is often limited by conflicts in thermal budget. One of the most prevalent examples is the fabrication of active micro-electromechanical systems (MEMS), as structural films utilized for surface micromachining such as polysilicon typically require processing at temperatures unsuitable for microelectronic circuitry. A localized annealing process could provide for the post-deposition heat treatment of integrated structures without compromising active devices. This dissertation presents a new microfabrication technology based on the inductive heating of ferromagnetic films patterned to define regions for heat treatment. Support is provided through theory, finite-element modeling, and experimentation, concluding with the demonstration of inductive annealing on polysilicon inertial sensing structures. Though still in its infancy, the results confirm the technology to be a viable option for integrated MEMS as well as any microsystem fabrication process requiring a thermal gradient.

Effectiveness of a nondestructive evaluation technique for assessing standing timber quality

The research presented in this thesis was conducted to further the development of the stress wave method of nondestructively assessing the quality of wood in standing trees. The specific objective of this research was to examine, in the field, use of two stress wave nondestructive assessment techniques. The first technique examined utilizes a laboratory-built measurement system consisting of commercially available accelerometers and a digital storage oscilloscope. The second technique uses a commercially available tool that incorporates several technologies to determine speed of stress wave propagation in standing trees. Field measurements using both techniques were conducted on sixty red pine trees in south-central Wisconsin and 115 ponderosa pine trees in western Idaho. After in-situ measurements were taken, thirty tested red pine trees were felled and a 15-foot-long butt log was obtained from each tree, while all tested ponderosa pine trees were felled and an 8 1/2 -foot-long butt log was obtained, respectively. The butt logs were sent to the USDA Forest Products Laboratory and nondestructively tested using a resonance stress wave technique. Strong correlative relationships were observed between stress wave values obtained from both field measurement techniques. Excellent relationships were also observed between standing tree and log speed-of-sound values.

Comparison of magnetic properties and petrography between dykes and lava flows from La Cienega, New Mexico and Thunder Bay area, Canada

Data on the evolution of geomagnetic paleointensity are crucial for understanding the geodynamo and Earth’s thermal history. Although basaltic flows are preferred for paleointensity experiments, quickly cooled mafic dykes have also been used. However, the paleointensity values obtained from the dykes are systematically lower than those from lava flows. This bias may originate from the difference in cooling histories and resultant magnetic mineralogies of extrusive and intrusive rocks. To explore this hypothesis, the magnetic mineralogy of two feeder dyke-lave flow systems, from Thunder Bay (Canada) and La Cienega (New-Mexico), has been studied using magnetic and microscopy methods. Within each system, the flow and dyke show different stages of deuteric oxidation of titanomagnetite, but the oxidation stages also differ between the two systems. It is concluded that the tested hypothesis is viable, but the relationships between the magnetic and mineralogical properties of flows and dykes are complex and need a further investigation.

High cycle fatigue of AA6082 and AA6063 aluminum extrusions

The high cycle fatigue behavior of hollow extruded AA6082 and AA6063 aluminum extrusions has been studied. Hollow extruded aluminum profiles can be processed into intricate shapes, and may be suitable replacements for fatigue critical automotive applications requiring reduced weight. There are several features inherent in hollow aluminum extrusions, such as seam welds, charge welds, microstructural variations and die lines. The effects of such extrusion variables on high cycle fatigue properties were studied by taking specimens from an actual car bumper extrusion. It appears that extrusion die lines create large anisotropy differences in fatigue properties, while welds themselves have little effect on fatigue lives. Removal of die lines greatly increased fatigue properties of AA6082 specimens taken transverse to the extrusion direction. Without die lines, anisotropy in fatigue properties between AA6082 specimens taken longitudinal and transverse to the extrusion direction, was significantly reduced, and properties associated with the orientation of the microstructure appears to be isotropic. A fibrous microstructure for AA6082 specimens showed great improvements in fatigue behavior. The effects of elevated temperatures and exposure of specimens to NaCl solutions was also studied. Exposure to the salt solution greatly reduced the fatigue lives of specimens, while elevated temperatures showed more moderate reductions in fatigue lives.

Parallel algorithm for solving integer linear programs

Linear programs, or LPs, are often used in optimization problems, such as improving manufacturing efficiency of maximizing the yield from limited resources. The most common method for solving LPs is the Simplex Method, which will yield a solution, if one exists, but over the real numbers. From a purely numerical standpoint, it will be an optimal solution, but quite often we desire an optimal integer solution. A linear program in which the variables are also constrained to be integers is called an integer linear program or ILP. It is the focus of this report to present a parallel algorithm for solving ILPs. We discuss a serial algorithm using a breadth-first branch-and-bound search to check the feasible solution space, and then extend it into a parallel algorithm using a client-server model. In the parallel mode, the search may not be truly breadth-first, depending on the solution time for each node in the solution tree. Our search takes advantage of pruning, often resulting in super-linear improvements in solution time. Finally, we present results from sample ILPs, describe a few modifications to enhance the algorithm and improve solution time, and offer suggestions for future work.

In-situ electrical, mechanical and electrochemical characterizations of one-dimensional nanostructures

One-dimensional nanostructures initiated new aspects to the materials applications due to their superior properties compared to the bulk materials. Properties of nanostructures have been characterized by many techniques and used for various device applications. However, simultaneous correlation between the physical and structural properties of these nanomaterials has not been widely investigated. Therefore, it is necessary to perform in-situ study on the physical and structural properties of nanomaterials to understand their relation. In this work, we will use a unique instrument to perform real time atomic force microscopy (AFM) and scanning tunneling microscopy (STM) of nanomaterials inside a transmission electron microscopy (TEM) system. This AFM/STM-TEM system is used to investigate the mechanical, electrical, and electrochemical properties of boron nitride nanotubes (BNNTs) and Silicon nanorods (SiNRs). BNNTs are one of the subjects of this PhD research due to their comparable, and in some cases superior, properties compared to carbon nanotubes. Therefore, to further develop their applications, it is required to investigate these characteristics in atomic level. In this research, the mechanical properties of multi-walled BNNTs were first studied. Several tests were designed to study and characterize their real-time deformation behavior to the applied force. Observations revealed that BNNTs possess highly flexible structures under applied force. Detailed studies were then conducted to understand the bending mechanism of the BNNTs. Formations of reversible ripples were observed and described in terms of thermodynamic energy of the system. Fracture failure of BNNTs were initiated at the outermost walls and characterized to be brittle. Second, the electrical properties of individual BNNTs were studied. Results showed that the bandgap and electronic properties of BNNTs can be engineered by means of applied strain. It was found that the conductivity, electron concentration and carrier mobility of BNNTs can be tuned as a function of applied stress. Although, BNNTs are considered to be candidate for field emission applications, observations revealed that their properties degrade upon cycles of emissions. Results showed that due to the high emission current density, the temperature of the sample was increased and reached to the decomposition temperature at which the B-N bonds start to break. In addition to BNNTs, we have also performed in-situ study on the electrochemical properties of silicon nanorods (SiNRs). Specifically, lithiation and delithiation of SiNRs were studied by our STM-TEM system. Our observations showed the direct formation of Li22Si5 phases as a result of lithium intercalation. Radial expansion of the anode materials were observed and characterized in terms of size-scale. Later, the formation and growth of the lithium fibers on the surface of the anode materials were observed and studied. Results revealed the formation of lithium islands inside the ionic liquid electrolyte which then grew as Li dendrite toward the cathode material.

Topological changes in 2D simplicial meshes for the simulation of fractures

A method for the introduction of strong discontinuities into a mesh will be developed. This method, applicable to a number of eXtended Finite Element Methods (XFEM) with intra-element strong discontinuities will be demonstrated with one specific method: the Generalized Cohesive Element (GCE) method. The algorithm utilizes a subgraph mesh representation which may insert the GCE either adaptively during the course of the analysis or a priori. Using this subgraphing algorithm, the insertion time is O(n) to the number of insertions. Numerical examples are presented demonstrating the advantages of the subgraph insertion method.