Numerical Analysis and Scientific Computing Commons^™

Contrasting Geometric Variations Of Mathematical Models Of Self-Assembling Systems, Michael Sharp

Graduate Theses and Dissertations

Self-assembly is the process by which complex systems are formed and behave due to the interactions of relatively simple units. In this thesis, we explore multiple augmentations of well known models of self-assembly to gain a better understanding of the roles that geometry and space play in their dynamics. We begin in the abstract Tile Assembly Model (aTAM) with some examples and a brief survey of previous results to provide a foundation. We then introduce the Geometric Thermodynamic Binding Network model, a model that focuses on the thermodynamic stability of its systems while utilizing geometrically rigid components (dissimilar to other …

Powers And Behaviors Of Directed Self-Assembly, Trent Allen Rogers

Graduate Theses and Dissertations

In nature there are a variety of self-assembling systems occurring at varying scales which give rise to incredibly complex behaviors. Theoretical models of self-assembly allow us to gain insight into the fundamental nature of self-assembly independent of the specific physical implementation. In Winfree's abstract tile assembly model (aTAM), the atomic components are unit square "tiles" which have "glues" on their four sides. Beginning from a seed assembly, these tiles attach one at a time during the assembly process in an asynchronous and nondeterministic manner.

We can gain valuable insights into the nature of self-assembly by comparing different models of self-assembly …

Theatrical Genre Prediction Using Social Network Metrics, Manisha Shukla

Graduate Theses and Dissertations

With the emergence of digitization, large text corpora are now available online that provide humanities scholars an opportunity to perform literary analysis leveraging the use of computational techniques. This work is focused on applying network theory concepts in the field of literature to explore correlations between the mathematical properties of the social networks of plays and the plays’ dramatic genre, specifically how well social network metrics can identify genre without taking vocabulary into consideration. Almost no work has been done to study the ability of mathematical properties of network graphs to predict literary features. We generated character interaction networks of …

Molecular Dynamics Simulations Of Dna-Functionalized Nanoparticle Building Blocks On Gpus, Tyler Landon Fochtman

Graduate Theses and Dissertations

This thesis discusses massively parallel molecular dynamics simulations of nBLOCKs using graphical processing units. nBLOCKs are nanoscale building blocks composed of gold nanoparticles functionalized with single-stranded DNA molecules. To explore greater simulation time scales we implement our nBLOCK computational model as an extension to the coarse grain molecular simulator oxDNA. oxDNA is parameterized to match the thermodynamics of DNA strand hybridization as well as the mechanics of single stranded DNA and double stranded DNA. In addition to an in-depth review of our implementation details we also provide results of the model validation and performance tests. These validation and performance tests …

Simulating Foodborne Pathogens In Poultry Production And Processing To Defend Against Intentional Contamination, S. Lankford, D. R. Thompson, S. C. Ricke

Journal of the Arkansas Academy of Science

There is a lack of data in recent history of food terrorism attacks, and as such, it is difficult to predict its impact. The food supply industry is one of the most vulnerable industries for terrorist threats while the poultry industry is one of the largest food industries in the United States. A small food terrorism attack against a single poultry processing center has the potential to affect a much larger human population than its immediate consumers. In this work, the spread of foodborne pathogens is simulated in a poultry production and processing system to defend against intentional contamination. An …

A Support Vector Machine Base Model For Predicting Heparin-Binding Proteins Using Biological Metrics And Xb Patterns As Features, Joseph W. Sirrianni

Computer Science and Computer Engineering Undergraduate Honors Theses

Heparin is a highly sulphated and negatively charged polysaccharides belonging to the glycosamino- glycans(GAGs) family. It is widely used in medical treatments as an injectable anticoagulant. Although many heparin-binding proteins have been identified through experimental studies, there are still many proteins needing to be classified as heparin-binding or not. Many studies have been aimed at prediction of heparin binding patterns or motifs in the primary structure of proteins. For example XBBXBX and XBBBXXBX are two well-known patterns or motifs. In spite of intensive studies, still no good model has emerged which reasonably predicts proteins in the protein database as heparin-binding …

Acceleration Of Ddscat Computation By Parallelization On A Supercomputer, Manoj V. Seeram

Chemical Engineering Undergraduate Honors Theses

The DDSCAT software is enabled for use of MPI or OpenMP to distribute calculation of different particle orientations amongst multiple processors on a high performance system. Run times for these simulations have been tested to take hours or days however and simulating varying orientations is not always necessary. If a simulation with only one particle orientation is submitted, DDSCAT could still potentially parallelize the simulation by wavelength calculations but it is unknown if this is the case. In this paper, we will be (i) quantifying the reduction in computation time that MPI provides relative to an equivalent MPI disabled simulation …

Nanoscale Frictional Properties Of Nickel With One-Dimensional And Two-Dimensional Materials, Timothy K. Schlenger

Mechanical Engineering Undergraduate Honors Theses

When looking at the nanoscale, material interface interactions have been observed to exhibit particularly interesting properties. Our research looks into various combinations of carbyne and graphene atop a nickel block to look into the interface friction properties between them. Both the carbyne and graphene are tested using steered molecular dynamics (SMD) in sheering and peeling directions along the surface of the nickel block. These tests are then analyzed by comparing the magnitude of the acting force versus the displacement of the carbon allotrope sample across the nickel block. It is found that as the width of a carbon allotrope sample …

Software Porting Of A 3d Reconstruction Algorithm To Razorcam Embedded System On Chip, Kevin Curtis Gunn

Graduate Theses and Dissertations

A method is presented to calculate depth information for a UAV navigation system from Keypoints in two consecutive image frames using a monocular camera sensor as input and the OpenCV library. This method was first implemented in software and run on a general-purpose Intel CPU, then ported to the RazorCam Embedded Smart-Camera System and run on an ARM CPU onboard the Xilinx Zynq-7000. The results of performance and accuracy testing of the software implementation are then shown and analyzed, demonstrating a successful port of the software to the RazorCam embedded system on chip that could potentially be used onboard a …

Directed Percolation And The Abstract Tile Assembly Model, Tyler Garrett Moore

Graduate Theses and Dissertations

Self-assembly is a process by which simple components build complex structures through local interactions. Directed percolation is a statistical physical model for describing competitive spreading processes on lattices. The author describes an algorithm which can transform a tile assembly system in the abstract Tile Assembly Model into a directed percolation problem, and then shows simulations of the aTAM which support this algorithm. The author also investigates two new constructs designed for Erik Winfree's abstract Tile Assembly Model called the NULL tile and temperature 1.5. These constructs aid the translation between self-assembly and directed percolation and may assist self-assembly researchers in …

A Domain Specific Model For Generating Etl Workflows From Business Intents, Wesley Deneke

Graduate Theses and Dissertations

Extract-Transform-Load (ETL) tools have provided organizations with the ability to build and maintain workflows (consisting of graphs of data transformation tasks) that can process the flood of digital data. Currently, however, the specification of ETL workflows is largely manual, human time intensive, and error prone. As these workflows become increasingly complex, the users that build and maintain them must retain an increasing amount of knowledge specific to how to produce solutions to business objectives using their domain's ETL workflow system. A program that can reduce the human time and expertise required to define such workflows, producing accurate ETL solutions with …

Comparing Methods For Interpolation To Improve Raster Digital Elevation Models, J. C. Guarneri, R. C. Weih Jr.

Journal of the Arkansas Academy of Science

Digital elevation models (DEMs) are available as raster files at 100m, 30m, and 10m resolutions for the contiguous United States and are used in a variety of geographic analyses. Some projects may require a finer resolution. GIS software offers many options for interpolating data to higher resolutions. We compared ten interpolation methods using 10m sample data from the Ouachita Mountains in central Arkansas. We interpolated the 10m DEM to 5m, 2.5m, and 1m resolutions and compared the absolute mean difference (AMD) for each using surveyed control points. Overall, there was little difference in the accuracy between interpolation methods at the …

Parallelizing Scale Invariant Feature Transform On A Distributed Memory Cluster, Stanislav Bobovych

Computer Science and Computer Engineering Undergraduate Honors Theses

Scale Invariant Feature Transform (SIFT) is a computer vision algorithm that is widely-used to extract features from images. We explored accelerating an existing implementation of this algorithm with message passing in order to analyze large data sets. We successfully tested two approaches to data decomposition in order to parallelize SIFT on a distributed memory cluster.

Understanding Sources And Consequences Of Variation In Self-Assembly, Arjun Dasgupta

Computer Science and Computer Engineering Undergraduate Honors Theses

Self-assembly is the process of constructing a larger structure from small component parts that randomly collide and bond through weak interactions [2]. It is a potentially important method in the field of nanoscale manufacturing. However, because of the nature of self-assembly, randomness and the design of self-assembly compete with each other, and unforeseen things can be produced. In this thesis, the tiling assembly model of Winfree [7] was simulated. The tiling assembly model has two bonds which assemble planar nanostructures. The goal of the simulations was to determine what probabilities would produce an average degree of four (the ideal) for …

Visualizing Electrostatic Phenomena Using Mathematica, Eric Mayes

Journal of the Arkansas Academy of Science

A set of packages for visualizing electrostatic phenomena was developed using Mathematica as a programming language. These packages allow users to plot potential fields, equipotential lines, 2-D and 3-D vector fields in order to gain a visual understanding of electrostatic charges. They would be useful in accompanying undergraduate physics labs pertaining to electrostatics, as they would enable students to connect experiment with mathematics through open-ended visual exploration

Data Acquisition And Control Program For Chromatographic And Spectroscopic Studies, M. Keith Hudson, William G. Hood, Robert Henson

Journal of the Arkansas Academy of Science

An IBMPC compatible computer was interfaced to an Ithaco 3962 lock-in-amplifier. The computer controlled the functions of the lock-in-amplifier, acquired and stored data, and allowed for real time or off-line processing of data. Computer/amplifier connection was made via RS-232-C serial interface. Programmed in Microsoft Quick BASIC, the computer assumed the role of a dedicated chromatographic integrator. This reduced the overall instrumentation expense by eliminating a dedicated chromatographic integrator. The computer program supplied much greater flexibility in control and data interpretation. To show its utility, the program was applied to a study of the infrared emission from a flame upon the …

Impact Of Microprocessor Protected Mode Programming On Undergraduate Education N Engineering Technology, Robert L. Douglas

Journal of the Arkansas Academy of Science

No abstract provided.

Effects Of Changes In Surface Water Regime And/Or Land Use On The Vertical Distribution Of Water Available For Wetland Vegetation: Dynamic Model Of The Zone Of Aeration (Appendix To Part 1 Of Completion Report For Project A-023-Ark), Robert N. Maccallum, R. A. Sims

Arkansas Water Resources Center Technical Reports

Appendix to Part 1 of Completion Report for Project A-023-ARK