Computational Engineering Commons^™

Accurate Estimation Of Isoform And Gene Expression Levels From Next Generation Sequencing Data, Marius Nicolae

Master's Theses

Massively parallel transcriptome sequencing is quickly replacing microarrays as the technology of choice for performing gene expression profiling due to its wider dynamic range and digital quantitation capabilities. However, accurate estimation of expression levels from sequencing data remains challenging due to the short read length delivered by current sequencing technologies and still poorly understood protocol- and technology-specific biases.

To date, two main transcriptome sequencing protocols have been proposed in the literature. The most commonly used one, referred to as RNA-Seq, generates short (single or paired) sequencing tags from the ends of randomly generated cDNA fragments. An alternative protocol, referred to …

Pandaa: Physical Arrangement Detection Of Networked Devices Through Ambient-Sound Awareness, Zheng Sun, Aveek Purohit, Kaifei Chen, Shijia Pan, Trevor Pering, Pei Zhang

Zheng Sun

Future ubiquitous home environments can contain 10s or 100s of devices. Ubiquitous services running on these devices (i.e. localizing users, routing, security algorithms) will commonly require an accurate location of each device. In order to obtain these locations, existing techniques require either a manual survey, active sound sources, or estimation using wireless radios. These techniques, however, need additional hardware capabilities and are intrusive to the user. Non-intrusive, automatic localization of ubiquitous computing devices in the home has the potential to greatly facilitate device deployments.

This paper presents the PANDAA system, a zero-configuration spatial localization system for networked devices based on …

Pandaa: Physical Arrangement Detection Of Networked Devices Through Ambient-Sound Awareness, Zheng Sun, Aveek Purohit, Kaifei Chen, Shijia Pan, Trevor Pering, Pei Zhang

Aveek Purohit

Future ubiquitous home environments can contain 10s or 100s of devices. Ubiquitous services running on these devices (i.e. localizing users, routing, security algorithms) will commonly require an accurate location of each device. In order to obtain these locations, existing techniques require either a manual survey, active sound sources, or estimation using wireless radios. These techniques, however, need additional hardware capabilities and are intrusive to the user. Non-intrusive, automatic localization of ubiquitous computing devices in the home has the potential to greatly facilitate device deployments.

This paper presents the PANDAA system, a zero-configuration spatial localization system for networked devices based on …

Testing, Modelling And Validation Of Numerical Model Capable Of Predicting Stress Fields Throughout Polyurethane Foam, Conor Briody, Barry Duignan, Stephen Jerrams

Conference Papers

Wheelchair seating systems are specialised for a number of reasons as users can have impaired mobility, which increases the possibility of pressure build up. These areas of high pressure frequently occur in the trunk region under the bony prominences known as the Ischial Tuberosities (IT), pressure ulcers may occur consequently. Polyurethane foam has been in use for some time in wheelchair seating systems as it exhibits good pressure relieving capabilities in most cases. However, little quantitative research has gone into foamed polymers, in comparison with conventional elastomeric materials. This lack of knowledge can ultimately lead to more time being spent …

Pandaa: A Physical Arrangement Detection Technique For Networked Devices Through Ambient-Sound Awareness, Zheng Sun, Aveek Purohit, Philippe De Wagter, Irina Brinster, Chorom Hamm, Pei Zhang

Zheng Sun

This demo presents PANDAA, a zero-configuration automatic spatial localization technique for networked devices based on ambient sound sensing. We will demonstrate that after initial placement of the devices, ambient sounds, such as human speech, music, footsteps, finger snaps, hand claps, or coughs and sneezes, can be used to autonomously resolve the spatial relative arrangement of devices, such as mobile phones, using trigonometric bounds and successive approximation.

A Low Communication Condensation-Based Linear System Solver Utilizing Cramer's Rule, Kenneth C Habgood

Doctoral Dissertations

Systems of linear equations are central to many science and engineering application domains. Given the abundance of low-cost parallel processing fabrics, the study of fast and accurate parallel algorithms for solving such systems is receiving attention. Fast linear solvers generally use a form of LU factorization. These methods face challenges with workload distribution and communication overhead that hinder their application in a true broadcast communication environment.

Presented is an efficient framework for solving large-scale linear systems by means of a novel utilization of Cramer's rule. While the latter is often perceived to be impractical when considered for large systems, it …

Quantitative Characterization Of Microstructure Features For 1st Generation Advanced High Strength Steels, Margarita Vidrio, Ellen Liu, Donsheng Li, Kyoo Sil Choi, Xin Sun

STAR Program Research Presentations

The role of Advanced High Strength Steels (AHSS) in the automotive industry is important because of its affordability and excellent mechanical properties. The 1st generation of AHSS achieves its preferred combination of strength and ductility by embedding harder martensite grains into softer ferritic matrix. Ductility and strength of these steels are important to safety, formability, application, and life. However, a noticeable degree of inconsistent forming behaviors has been observed in the 1st generation AHSS in production, which seems to be related to the microstructure-level inhomogeneity. The objective of this project is to grain fundamental understandings on how different microstructure level …

Design Optimization Using Cad Parameterization Through Capri, William Emerson Brock V

Masters Theses and Doctoral Dissertations

Design optimization is one of the many areas of Computational Engineering that is directly applicable to almost any engineering endeavor. The design cycle is a multi-step process, beginning with a Computer Aided Design (CAD) model and ending with an optimized version of that model relative to some objective function. This is accomplished by parameterizing the model, through one of many different algorithms, and finding the ideal value of those parameters with respect to the specified objective. The purpose of this research is to explore the use of a Computational Analysis PRogramming Interface (CAPRI) for utilizing CAD parameters in design optimization …

Generation And Optimization Of Spacing Fields, Max David Collao

Masters Theses and Doctoral Dissertations

Meshes are used to discretize space for computational fluid dynamics (CFD) simulations. Mesh adaptation through refinement and smoothing can improve the accuracy of the CFD solution. In order to perform adaptive refinement or smoothing a spacing field is needed to define the desired edge sized in mesh. The objectives of this research are to generate spacing fields from existing CFD solutions and optimize this spacing information for efficient use by programs to perform adaptive refinement or smoothing. All work was done on 2D meshes with the intention of gaining knowledge and experience for later application to 3D meshes. The program …

An Adaptive Hybrid Mesh Generation Method For Complex Geometries, Cameron Thomas Druyor

Masters Theses and Doctoral Dissertations

An adaptive hybrid mesh generation method is described to automatically provide spatial discretizations suitable for computational fluid dynamics or other 2D solver applications. This method employs a hierarchical grid generation technique to create a background mesh, an extrusion-type method for inserting boundary layers, and an unstructured triangulation to stitch between the boundary layers and background mesh. This method provides appropriate mesh resolution based on geometry segments from a file, and has the capability of adapting the background mesh based on a spacing field generated from solution data or some other arbitrary source. By combining multiple approaches to the grid generation …

Computational Design For Electromagnetic Simulations, Ryan Steven Glasby

Masters Theses and Doctoral Dissertations

An automatic computational procedure has been developed to efficiently and accurately design the shape of complicated electromagnetic objects. These electromagnetic objects can be simulated for operation at high frequencies (~10 GHz), and can be comprised of dissimilar materials. The automated design procedure consists of linking together an original electromagnetic field simulation tool, an original adjoint routine for obtaining sensitivity derivatives, and an original grid-smoothing tool with an existing optimization package. The electromagnetic field simulation software employs a temporally and spatially higher-order accurate Streamline Upwind/Petrov-Galerkin finite-element method that numerically solves Maxwell’s equations in the time domain using implicit time stepping. The …

Comparison Of Two Methods For Two Dimensional Unstructured Mesh Adaptation With Elliptic Smoothing, Matthew David O'Connell

Masters Theses and Doctoral Dissertations

A new mesh adaptation method for unstructured grids is presented. The technique uses virtual control volumes that are iteratively manipulated to conform the mesh to match either a Riemannianmetric tensor field or an equal distribution of scalar weights. Forcing functions similar to those used for structured grids are employed such that the resulting meshes can be compared with those generated using the new adaptation method. Several test cases using analytic functions to drive the mesh adaptation are also presented and compared with the new method. Mesh adaptation results driven by computed flow field information are also compared to those adapted …

Characterization Of Parallel Application Runtime Sensitivity On Multi-Core High Performance Computing Systems, Padma Priya Veeraraghavan

Purdue Polytechnic Masters Theses

A commonly seen behavior of parallel applications is that their runtime is influenced by network communication load. The way a parallel application is run in a network and the presence of other applications and processes in the network can contribute to a wide range of variations in the runtime. Therefore, in order to achieve consistent and optimal runtimes, it is important to understand and characterize the runtime sensitivity of parallel applications with respect to execution under the presence of network communication load.

In this research, runtime sensitivities for various parallel applications were studied by applying additional network communication load. In …

Coughloc: Location-Aware Indoor Acoustic Sensing For Non-Intrusive Cough Detection, Zheng Sun, Aveek Purohit, Kathleen Yang, Neha Pattan, Dan Siewiorek, Asim Smailagic, Ian Lane, Pei Zhang

Zheng Sun

Pervasive medical monitoring has become an ideal alter- native to nursing care for elderly people and patients in hospitals. Existing systems using single body-worn sensors are often intrusive and less reliable. By contrast, ubiqui- tous acoustic sensing techniques can support non-intrusive and robust medical monitoring. In this paper, we describe CoughLoc, a ubiquitous acoustic sensing system for con- tinuous cough detection using a wireless sensor network. We show how knowledge of sound source locations can be leveraged to improve the detection accuracy of sound events caused by mobile users. Experiments in indoor environ- ments show our system achieves over 90% …

Cavitation Modelling Based On Eulerian-Eulerian Multiphase Flow, Rachid Bannari Ph.D

Rachid BANNARI

Cavitation is a physical phenomenon encountered in the normal operation of hydraulic turbines. It can lead to loss in efficiency, vibrations and blade erosion damages. It is crucial to accurately predict cavitation development and evolution to make confident predictive results for hydraulic turbines in a cavitating regime. The cavity closure is a critical region that is characterized by its unsteady and unstable behavior. In this region, liquid and vapor are highly mixed and experienced a strong interaction between the cavity and the outer flow. Most of the published work is based on the mixture multiphase model. An important limitation of …

Cal Poly Wow: Week Of Welcome’S Leader Android Application, Eric Cerney

Computer Engineering

The Week of Welcome Android application aims to improve the efficiency and ease at which Orientation Leaders function during the week long program designed to aid in new student
assimilation to the San Luis Obispo campus and community. It focuses on four utilities combined in
one easy location that Leaders use on a regular basis. They are maps, the online guidebook, budget keeper, and contact list. These four utilities are commonly used by Leaders in their day to day
guidance of new students, making one single application with each tool very desirable to the WOW Program.

Currently there are no …

The Ergo Knife Manufacturability Project: A Prosthetic Device, Caleb Sarris

Industrial and Manufacturing Engineering

Millions of Americans’ upper extremities have been rendered useless or amputated due to injury or illness. Without strength and dexterity in the hand or wrist, these people are in need of tools to help them in everyday activities. The Ergo Knife offers these individuals a way to cope with this way of life as a device that can assist them, primarily in food consumption and can also be expanded to many other applications. The purpose of this project is to further develop the Ergo Knife so that it can better assist these individuals and improve the necessary processes used to …

Chinese To English Introductory Cover Letter Generator, Jason L. Stine

Liberal Arts and Engineering Studies

The Chinese to English Introductory Cover Letter Generator allows Chinese computer users who know little to no English automatically generate a self-introductory cover letter in good English. As an example, professors in English-speaking countries are increasingly receiving emails from students abroad in countries like China, and these students often need to introduce themselves in order to support their reasons for their message. Unfortunately, more often than not these letters contain poorly written English. This software aims to help solve this issue. Using a combination of a “sentence template” system and intelligent natural language processing software, the program assembles each paragraph …

An Evaluation Of The Eeg Alpha-To-Theta And Theta-To-Alpha Band Ratios As Indexes Of Mental Workload, Bujar Raufi, Luca Longo

Articles

Many research works indicate that EEG bands, specifically the alpha and theta bands, have been potentially helpful cognitive load indicators. However, minimal research exists to validate this claim. This study aims to assess and analyze the impact of the alpha-to-theta and the theta-to-alpha band ratios on supporting the creation of models capable of discriminating self-reported perceptions of mental workload. A dataset of raw EEG data was utilized in which 48 subjects performed a resting activity and an induced task demanding exercise in the form of a multitasking SIMKAP test. Band ratios were devised from frontal and parietal electrode clusters. …

News Media Environment, Selective Perception, And The Survival Of Preference Diversity Within Communication Networks, Frank C.S. Liu, Paul E. Johnson

JITP 2011: The Future of Computational Social Science

There is a natural tension between the effects on public opinion of social networks and the news media. It is widely believed that social networks tend to harmonize opinions within them, but the presence of media may accentuate diversity by inserting discordant messages. On the other hand, in a totalitarian state where the government controls the media, social networks may mitigate the homogenizing pressure of a regime’s propaganda. The tendency of opinion to follow the “official line” may be mitigated because opponents of the government interact on a personal level and bolster one another’s views. This paper employs agent-based modeling—an …