Computational Engineering Commons^™

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.

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 …

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 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 …

Accuracy Comparison Of Numerical Integration Algorithms For Real-Time Hybrid Simulations, Ganesh Anant Reddy

Civil & Environmental Engineering Theses & Dissertations

The use of accurate numerical integration algorithms is one of the key factors for a successful real-time hybrid simulation (RTHS). In RTHSs, explicit integration algorithms are preferred more than implicit methods since all calculations need to be completed within a given time step during simulation. Explicit methods require the use of effective stiffness and damping for experimental substructures, which are incorporated into the calculation of the integration parameters. In general, those values that are greater than the expected stiffness and damping of the experimental substructure are used to ensure the stability of simulation. If a rate-dependent and nonlinear experimental substructure …

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 …

A Modified Rank Ordered Logit Model To Analyze Injury Severity Of Occupants In Multi-Vehicle Crashes, Shelley Bogue

Civil & Environmental Engineering Theses & Dissertations

Research on methodological approaches to model injury severity has become important in order to prevent crash fatalities. Roadways have always been dangerous, with significant congestion and uncontrollable variables, such as weather, coupled with road users' decisions including seat belt and alcohol/drug use. These decisions can influence the severity of injuries sustained by vehicle occupants in the event of a crash. Few studies have examined the potential impacts of comprehensive roadway user injury severity profiles of all occupants ( drivers as well as passengers) in all vehicles involved in a crash. The focus of past studies has been on examining the …

Computational Fluid Dynamics Study Of Balloon System Tethered To A Stratosail, Jayakanth Loganathan, Kian-Meng Lim, Heow Pueh Lee, Boo Cheong Khoo

2017 Academic High Altitude Conference

In this paper, we present a numerical study of a stratospheric balloon system tethered to a passive device, known as the Stratosail, for station-keeping operation. For scientific applications, stratospheric balloons that operate at altitudes between 15 and 20 km will need to maintain station over a fixed point above the earth for a prescribed period of time. This is a challenging problem due to the limitation of payloads and lack of an energy source. The present study uses computational fluid dynamics (CFD) simulations to analyze the drift velocity of such a balloon-Stratosail system under typical wind conditions in the stratosphere. …

Cooperative 3-D Map Generation Using Multiple Uavs, Andrew Erik Lawson

University Scholar Projects

This report aims to demonstrate the feasibility of building a global 3-D map from multiple UAV robots in a GPS-denied, indoor environment. Presented are the design of each robot and the reasoning behind choosing its hardware and software components, the process in which a single robot obtains a individual 3-D map entirely onboard, and lastly how the mapping concept is extended to multiple robotic agents to form a global 3-D map using a centralized server. In the latter section, this report focuses on two algorithms, Online Mapping and Map Fusion, developed to facilitate the cooperative approach. A limited selection …

What Is The Right Context For An Engineering Problem: Finding Such A Context Is Np-Hard, Martine Ceberio, Vladik Kreinovich, Hung T. Nguyen, Songsak Sriboonchitta, Rujira Ouncharoen

Departmental Technical Reports (CS)

In the general case, most computational engineering problems are NP-hard. So, to make the problem feasible, it is important to restrict this problem. Ideally, we should use the most general context in which the problem is still feasible. In this paper, we prove that finding such most general context is itself an NP-hard problem. Since it is not possible to find the appropriate context by utilizing some algorithm, it is therefore necessary to be creative -- i.e., to use some computational intelligence techniques. On three examples, we show how such techniques can help us come up with the appropriate context. …

Semi-Automated Test Generation With Spest, Adam Mozek

Computer Science and Software Engineering

Automated black box test generation is a useful tool for developers that allows them to

quickly generate a large number of tests with a wide range of values tested. The current most

popular tool for black box test generation in Java, JML, is lacking in a number of features.

SPEST aims to improve upon existing tools, and provide a black box test generation tool that

can create human readable tests from simple pre and post conditions added as comments to

the Java source code.