Computational Engineering Commons^™

Ms-Reduce: An Ultrafast Technique For Reduction Of Big Mass Spectrometry Data For High-Throughput Processing, Muaaz Gul Awan, Fahad Saeed

Parallel Computing and Data Science Lab Technical Reports

Modern proteomics studies utilize high-throughput mass spectrometers which can produce data at an astonishing rate. These big Mass Spectrometry (MS) datasets can easily reach peta-scale level creating storage and analytic problems for large-scale systems biology studies. Each spectrum consists of thousands of peaks which have to be processed to deduce the peptide. However, only a small percentage of peaks in a spectrum are useful for peptide deduction as most of the peaks are either noise or not useful for a given spectrum. This redundant processing of non-useful peaks is a bottleneck for streaming high-throughput processing of big MS data. One …

Can A Five Minute, Three Question Survey Foretell First-Year Engineering Student Performance And Retention?, Stephanie M. Gratiano, William J. Palm

Engineering, Computing & Construction Management Faculty Publications

This research paper examines first-year student performance and retention within engineering. A considerable body of literature has reported factors influencing performance and retention, including high school GPA and SAT scores,1,2,3 gender,4 self-efficacy,1,5 social status,2,6,7 hobbies,4 and social integration.6,7 Although these factors can help explain and even partially predict student outcomes, they can be difficult to measure; typical survey instruments are lengthy and can be invasive of student privacy. To address this limitation, the present paper examines whether a much simpler survey can be used to understand student motivations and anticipate student outcomes.

The survey was administered to 347 students in …

Modeling Time-Dependent Performance Of Submerged Superhydrophobic Or Slippery Surfaces, Ahmed A. Hemeda

Theses and Dissertations

The goal of this study is to quantify the transient performance of microfabricated superhydrophobic surfaces when used in underwater applications. A mathematical framework is developed and used to predict the stability, longevity, and drag reduction benefits of submerged superhydrophobic surfaces with two- or three-dimensional micro-textures. In addition, a novel design is proposed to improve the drag-reduction benefits of lubricant-infused surfaces, by placing a layer of trapped air underneath the lubricant layer. The new design is referred to as lubricant–infused surfaces with trapped air, and it is designed to eliminate the long-lasting longevity problem of submerged superhydrophobic surfaces. The effectiveness of …

Proactive Biometric-Enabled Forensic Imprinting, Abdulrahman Alruban, Nathan L. Clarke, Fudong Li, Steven M. Furnell

Research outputs 2014 to 2021

Threats to enterprises have become widespread in the last decade. A major source of such threats originates from insiders who have legitimate access to the organization's internal systems and databases. Therefore, preventing or responding to such incidents has become a challenging task. Digital forensics has grown into a de-facto standard in the examination of electronic evidence; however, a key barrier is often being able to associate an individual to the stolen data. Stolen credentials and the Trojan defense are two commonly cited arguments used. This paper proposes a model that can more inextricably links the use of information (e.g. images, …

Use Of Bridging Strategy Between The Ensemble Kalman Filter And Particle Filter For The Measurements With Various Quasi-Gaussian Noise, Sumathi Prabhakaran Jeyakumari

All Graduate Theses, Dissertations, and Other Capstone Projects

Filtering and estimation are two important tools of engineering. Whenever the state of the system needs to be estimated from the noisy sensor measurements, some kind of state estimator is used. If the dynamics of the system and observation model are linear under Gaussian conditions, the root mean squared error can be computed using the Kalman Filter. But practically, noise frequently enters the system as not strictly Gaussian. Therefore, the Kalman Filter does not necessarily provide the better estimate. Hence the estimation of the nonlinear system under non-Gaussian or quasi-Gaussian noise is of an acute interest. There are many versions …

In-Field Fuel Use And Load States Of Agricultural Field Machinery, Santosh Pitla, Joe D. Luck, Jared Werner, Nannan Lin, Scott A. Shearer

Department of Agricultural and Biological Systems Engineering: Faculty Publications

The ability to define in-field tractor load states offers the potential to better specify and characterize fuel consumption rate for various field operations. For the same field operation, the tractor experiences diverse load demands and corresponding fuel use rates as it maneuvers through straight passes, turns, suspended operation for adjustments, repair and maintenance, and biomass or other material transfer operations. It is challenging to determine the actual fuel rate and load states of agricultural machinery using force prediction models, and hence, some form of in-field data acquisition capability is required. Controller Area Networks (CAN) available on the current model tractors …

Growth And Characterization Of Wide Bandgap Quaternary Bemgzno Thin Films And Bemgzno/Zno Heterostructures, Mykyta Toporkov

Theses and Dissertations

This thesis reports a comprehensive study of quaternary BeMgZnO alloy and BeMgZnO/ZnO heterostructures for UV-optoelectronics electronic applications. It was shown that by tuning Be and Mg contents in the heterostructures, high carrier densities of two-dimensional electron gas (2DEG) are achievable and makes its use possible for high power RF applications. Additionally, optical bandgaps as high as 5.1 eV were achieved for single crystal wurtzite material which allows the use of the alloy for solar blind optoelectronics (E_g>4.5eV) or intersubband devices.

A systematic experimental and theoretical study of lattice parameters and bandgaps of quaternary BeMgZnO alloy was performed for …

Project Oasis: Optimizing Aquaponic Systems To Improve Sustainability, Siddharth Nigam, Paige Balcom

Honors Theses and Capstones

Started in Fall 2015, Project OASIS (Optimizing Aquaponic Systems to Improve Sustainability) is an interdisciplinary capstone project with the goal of designing a sustainable and affordable small-scale aquaponic system for use in developing nations to tackle the problems of malnutrition and food insecurity. Aquaponics is a symbiotic relationship between fish and vegetables growing together in a recirculating system. The project’s goals were to minimize energy consumption and construction costs while using universally available materials. The computational fluid dynamics (CFD) software OpenFOAM was used to create transient and steady-state models of fish tanks to visualize velocity profiles, streamlines, and particle movement. …

Solar Photovoltaic System Control Topology Investigation For Power Source Mismatch, Lynette O'Callaghan

Conference papers

An investigation into solar photovoltaic (PV) system control topology selection, when partial shade is anticipated in the solar array, is presented. As available area is maximised in Building Integrated PV (BIPV) systems, shading is an inevitable consequence. The presence of partial shading in a PV array leads to multiple power peaks in the power-voltage curve, due to bypass diode sections being triggered, and an increase in module mismatch losses in the array. A building energy design software, Integrated Environmental Solutions, is used to determine the shadowed area on PV modules throughout the year, incorporating the PV system location and geometrical …

The Next Generation Of Wireless Cyber-Physical Simulator, Xinghan Wang, Kevin Xu

Undergraduate Research Symposium Posters

In order to make Wireless Cyber-Physical Simulator(WCPS) more accessible to people in the research community, and also to improve its accuracy of representing real industrial models, we worked on the dockerization of WCPS, and implemented the multi-rate feature for WCPS, enabling the simulator to have different network rate and plant rate when running a simulation. We created a new version of WCPS by dockerizing run-time libraries and the TOSSIM server and also embedding the multi-rate feature in the old version. This report includes the introduction and dockerization of WCPS, and shows the results of using the new generation of WCPS …

On The Applications Of Interactive Theorem Proving In Computational Sciences And Engineering, Amer Tahat

Dissertations, Master's Theses and Master's Reports

Interactive Theorem Proving (ITP) is one of the most rigorous methods used in

formal verification of computing systems. While ITP provides a high level of confidence in the correctness of the system under verification, it suffers from a steep learning curve and the laborious nature of interaction with a theorem prover. As such, it is desirable to investigate whether ITP can be used in unexplored (but high-impact) domains where other verification methods fail to deliver. To this end, the focus of this dissertation is on two important domains, namely design of parameterized self-stabilizing systems, and mechanical verification of numerical approximations …

Applying Bayesian Machine Learning Methods To Theoretical Surface Science, Shane Carr

McKelvey School of Engineering Graduate Student Theses & Dissertations

Machine learning is a rapidly evolving field in computer science with increasingly many applications to other domains. In this thesis, I present a Bayesian machine learning approach to solving a problem in theoretical surface science: calculating the preferred active site on a catalyst surface for a given adsorbate molecule. I formulate the problem as a low-dimensional objective function. I show how the objective function can be approximated into a certain confidence interval using just one iteration of the self-consistent field (SCF) loop in density functional theory (DFT). I then use Bayesian optimization to perform a global search for the solution. …

A Parabolized Navier-Stokes Method For Wind Farm Applications, Anshul Mittal

Masters Theses and Doctoral Dissertations

Fluid flow simulations play an important role in the wind industry. With the development of large wind farms, flow simulations through an entire wind farm are becoming a necessity. These are required for designing the layout of new wind farms in the development stage and for forecasting power production from the existing ones for operational purposes. Conventional Navier-Stokes simulations (commonly referred to as CFD simulations) are computationally very expensive since they require a supercomputer with runtimes of several weeks. A Parabolized Navier-Stokes (PNS) method is developed and implemented in this study. The developed PNS method requires less stringent approximations as …

Control Of Cation Ordering In Zinc Tin Nitride And In-Situ Monitoring Of Growth, Brian Christopher Durant

Masters Theses

Semiconducting materials with a band gap around 1.5 eV are very much sought after due to their close match to the solar spectrum. However, some compounds that have shown promise for highly efficient solar cells contain rare, expensive, and sometimes toxic elements, such as indium and gallium. As such, a search for earth abundant materials has become more prominent recently. One such earth abundant semiconducting material that has garnered interest is ZnSnN₂. It has been shown through previous studies that there is the possibility of continuously tuning the band gap between 1.0 and 2.0 eV by controlling the …

Novel Software Defined Radio Architecture With Graphics Processor Acceleration, Lalith Narasimhan

Dissertations

Wireless has become one of the most pervasive core technologies in the modern world. Demand for faster data rates, improved spectrum efficiency, higher system access capacity, seamless protocol integration, improved security and robustness under varying channel environments has led to the resurgence of programmable software defined radio (SDR) as an alternative to traditional ASIC based radios. Future SDR implementations will need support for multiple standards on platforms with multi-Gb/s connectivity, parallel processing and spectrum sensing capabilities. This dissertation implemented key technologies of importance in addressing these issues namely development of cost effective multi-mode reconfigurable SDR and providing a framework to …

Face Recognition With Multi-Stage Matching Algorithms, Xianming Chen

Dissertations

For every face recognition method, the primary goal is to achieve higher recognition accuracy and spend less computational costs. However, as the gallery size increases, especially when one probe image corresponds to only one training image, face recognition becomes more and more challenging. First, a larger gallery size requires more computational costs and memory usage. Meanwhile, that the large gallery sizes degrade the recognition accuracy becomes an even more significant problem to be solved.

A coarse parallel algorithm that equally divides training images and probe images into multiple processors is proposed to deal with the large computational costs and huge …

Computational Characterization Of Exogenous Micrornas That Can Be Transferred Into Human Circulation, Jiang Shu, Kevin Chiang, Janos Zempleni, Juan Cui

School of Computing: Faculty Publications

MicroRNAs have been long considered synthesized endogenously until very recent discoveries showing that human can absorb dietary microRNAs from animal and plant origins while the mechanism remains unknown. Compelling evidences of microRNAs from rice, milk, and honeysuckle transported to human blood and tissues have created a high volume of interests in the fundamental questions that which and how exogenous microRNAs can be transferred into human circulation and possibly exert functions in humans. Here we present an integrated genomics and computational analysis to study the potential deciding features of transportable microRNAs. Specifically, we analyzed all publicly available microRNAs, a total of …

Numerical Simulation Of Karst Soil Cave Evolution, Long Jia, Yan Meng, Zhende Guan, Lipeng Liu

Sinkhole Conference 2015

This study is focused on numerical simulation of the formation and development of karst soil caves related to cover-collapse sinkholes. The so-called ‘karst soil cave’ refers to the caves formed in the soil layers above bedrock of sinkhole regions. Because the soil caves are formed and developed under groundwater seepage, studying groundwater level changes can help understand soil cave development and collapse. Based on the improved Terzaghi loosening pressure theory and using excess pore water pressure, two kinds of critical groundwater level decline are discussed. The first, denoted as ∆H0, is the critical groundwater level decline related to soil cave …

Big Data Proteogenomics And High Performance Computing: Challenges And Opportunities, Fahad Saeed

Parallel Computing and Data Science Lab Technical Reports

Proteogenomics is an emerging field of systems biology research at the intersection of proteomics and genomics. Two high-throughput technologies, Mass Spectrometry (MS) for proteomics and Next Generation Sequencing (NGS) machines for genomics are required to conduct proteogenomics studies. Independently both MS and NGS technologies are inflicted with data deluge which creates problems of storage, transfer, analysis and visualization. Integrating these big data sets (NGS+MS) for proteogenomics studies compounds all of the associated computational problems. Existing sequential algorithms for these proteogenomics datasets analysis are inadequate for big data and high performance computing (HPC) solutions are almost non-existent. The purpose of this …

Using Eye And Head Movements As A Control Mechanism For Tele-Operating A Ground-Based Robot And Its Payload, Kathryn C. Hicks

Computational Modeling & Simulation Engineering Theses & Dissertations

To date, eye and head tracking has been used to indicate users' attention patterns while performing a task or as an aid for disabled persons, to allow hands-free interaction with a computer. The increasing accuracy and the reduced cost of eye- and head-tracking equipment make utilizing this technology feasible for explicit control tasks, especially in cases where there is confluence between the visual task and control.

The goal of this research was to investigate the use of eye-tracking as a more natural interface for the control of a camera-equipped, remotely operated robot in tasks that require the operator to simultaneously …

A Hybrid Approach To General Information Extraction, Marie Belen Grap

Master's Theses

Information Extraction (IE) is the process of analyzing documents and identifying desired pieces of information within them. Many IE systems have been developed over the last couple of decades, but there is still room for improvement as IE remains an open problem for researchers. This work discusses the development of a hybrid IE system that attempts to combine the strengths of rule-based and statistical IE systems while avoiding their unique pitfalls in order to achieve high performance for any type of information on any type of document. Test results show that this system operates competitively in cases where target information …

Software Metrics And Dashboard, Shilpika Shilpika, George K. Thiruvathukal, Saulo Aguiar, Konstantin Läufer, Nicholas J. Hayward

Computer Science: Faculty Publications and Other Works

Software metrics are a critical tool which provide continuous insight to products and processes and help build reliable software in mission critical environments. Using software metrics we can perform calculations that help assess the effectiveness of the underlying software or process. The two types of metrics relevant to our work is complexity metrics and in-process metrics. Complexity metrics tend to focus on intrinsic code properties like code complexity. In-process metrics focus on a higher-level view of software quality, measuring information that can provide insight into the underlying software development process.

Our aim is to develop and evaluate a metrics dashboard …

Optimization Of Blalock-Taussig Shunt And Anastomotic Geometry For Vascular Access Fistula Using A Genetic Algorithm, Guangyu Bao

McKelvey School of Engineering Graduate Student Theses & Dissertations

Blalock-Taussig (BT) shunts are used for defects that affect the flow of blood from the right ventricle, through the pulmonary artery, and to the lungs. Arteriovenous (AV) fistula is one type of vascular access which is a surgically created vein used to remove and return blood during hemodialysis. Plastic grafts used in the above two reconstructions may result in areas of non-physiologic flow in the grafts leading to risk of stenosis (blocked area) and thrombosis, which is the single major cause for access morbidity. The focus of this thesis is to study BT shunts and anastomoses models using Computational Fluid …

Interactive Computer Aided Design Of Electrochemical Systems, Lucas D. Robinson Mr., R. Edwin García Dr., Aniruddha Jana Mr.

The Summer Undergraduate Research Fellowship (SURF) Symposium

The most popular and widely used rechargeable battery numerical model, the dualfoil, was developed in fortran by John Newman and coworkers1-3, and enables the user to describe the time-dependent electrochemical transport of lithium and charge, through the application of concentrated solution theory in porous media. Such a model has enabled the design of many advanced lithium-ion batteries for hybrid and plug-in electric vehicles that can operate under high current densities. Historically, however, the dualfoil and other subsequently derived models are cumbersome and unwieldy when used, and offer limited flexibility regarding parameter variability, integration into more sophisticated numerical descriptions, coupling to …

A Parallel Algorithm For Compression Of Big Next-Generation Sequencing Datasets, Sandino N. Vargas Perez, Fahad Saeed

Parallel Computing and Data Science Lab Technical Reports

With the advent of high-throughput next-generation sequencing (NGS) techniques, the amount of data being generated represents challenges including storage, analysis and transport of huge datasets. One solution to storage and transmission of data is compression using specialized compression algorithms. However, these specialized algorithms suffer from poor scalability with increasing size of the datasets and best available solutions can take hours to compress gigabytes of data. In this paper we introduce paraDSRC, a parallel implementation of DSRC algorithm using a message passing model that presents reduction of the compression time complexity by a factor of O(1/p ). Our experimental results show …

Tetrahedral Mesh Optimization And Generation Via Topological Transformations And Gradient Based Node Perturbation, Christopher B. Hilbert

Masters Theses and Doctoral Dissertations

A general tetrahedral mesh optimization scheme utilizing both topological changes (i.e. flips) and gradient-based vertex optimization (i.e. smoothing) is demonstrated. This scheme is used in the optimization of tetrahedral meshes created by third-party software as well as a grid generation methodology created for this work. The particular algorithms involved are explained in detail including, an explication of the primary optimization metric, weighted condition number. In addition, a thorough literature review regarding tetrahedral mesh generation is given.

On The Selection Of A Good Shape Parameter For Rbf Approximation And Its Application For Solving Pdes, Lei-Hsin Kuo

Dissertations

Meshless methods utilizing Radial Basis Functions~(RBFs) are a numerical method that require no mesh connections within the computational domain. They are useful for solving numerous real-world engineering problems. Over the past decades, after the 1970s, several RBFs have been developed and successfully applied to recover unknown functions and to solve Partial Differential Equations (PDEs).
However, some RBFs, such as Multiquadratic (MQ), Gaussian (GA), and Matern functions, contain a free variable, the shape parameter, c. Because c exerts a strong influence on the accuracy of numerical solutions, much effort has been devoted to developing methods for determining shape parameters which provide …

A Stratified Turbulence Formulation And A Turbulent Inflow Boundary Condition For Large-Eddy Simulation Of Complex Terrain Winds, Clancy Umphrey

Boise State University Theses and Dissertations

There has been an increased interest to forecast winds over complex terrain under realistic stability conditions using spatial resolutions that are much finer than the current practice. This goal is realizable thanks to the computational power of graphics processing units (GPUs). This thesis investigates an immersed boundary (IB) formulation and a turbulent inflow boundary condition within a multi-GPU parallel incompressible wind solver. Katabatic flows over a sloped complex terrain surface under stable stratification remain to be one of the least understood subjects in atmospheric turbulence. Prandtl’s analytical solution for laminar katabatic flow is used to develop an IB formulation to …

A Numerical Investigation Of A Solidification Model For Snow Micro-Structure Metamorphosis, Micah Johnson

Boise State University Theses and Dissertations

Understanding the way snow changes during environmental events has wide spread benefits ranging from avalanche prediction to water conservation. Snow on a micro-structural level constantly changes from the moment it forms. Snow metamorphosis is driven by the transport of water vapor. Thus far it has only been investigated as a pure diffusion process in dry snow, despite observations that suggest that natural convection may have a role in the heat and mass transport in snow packs. This thesis research numerically explores the role of transport processes in the context of snow metamorphism. An existing solidification model is reformulated to simulate …

Classification Of Digital Communication Signal Modulation Schemes In Multipath Environments Using Higher Order Statistics, Meena Sreekantamurthy

Electrical & Computer Engineering Theses & Dissertations

Automatic identification and classification of modulation schemes in communication signals and decoding of information from the captured signals has assumed great importance recently in the wireless communication industry. Advancements in communications have introduced a large variety of modulation schemes in the transmitted signals; consequently, reliable detection of the modulation scheme in the intercepted signal has become an important issue in communications. It is the aim of this thesis to address this issue of reliable detection. Therefore, this research is focused on modeling and simulation of an automatic modulation classifier and, in particular, on the development of algorithms to use higher …