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Prtad: A Database For Protein Residue Torsion Angle Distributions, Xiaoyong Sun, Di Wu, Robert L. Jernigan, Zhijun Wu 2017 Iowa State University

Prtad: A Database For Protein Residue Torsion Angle Distributions, Xiaoyong Sun, Di Wu, Robert L. Jernigan, Zhijun Wu

Robert Jernigan

PRTAD is a dedicated database and structural bioinformatics system for protein analysis and modelling. The database is developed to host and analyse the statistical data for protein residue level 'virtual' bond and torsion angles obtained from their distributions in databases of known protein structures such as in the PDB Data Bank. PRTAD is capable of generating, caching, and displaying the statistical distributions of the angles of various types. The collected information can be used to extract geometric restraints or define statistical potentials for protein structure determination. PRTAD is supported with a friendly designed web interface so that users can easily ...


Low-Communication, Parallel Multigrid Algorithms For Elliptic Partial Differential Equations, Wayne Mitchell 2017 University of Colorado, Boulder

Low-Communication, Parallel Multigrid Algorithms For Elliptic Partial Differential Equations, Wayne Mitchell

Applied Mathematics Graduate Theses & Dissertations

When solving elliptic partial differential equations (PDE's) multigrid algorithms often provide optimal solvers and preconditioners capable of providing solutions with O(N) computational cost, where N is the number of unknowns. As parallelism of modern super computers continues to grow towards exascale, however, the cost of communication has overshadowed the cost of computation as the next major bottleneck for multigrid algorithms. Typically, multigrid algorithms require O((log P)^2) communication steps in order to solve a PDE problem to the level of discretization accuracy, where P is the number of processors. This has inspired the development of new algorithms ...


Information Theoretic Study Of Gaussian Graphical Models And Their Applications, Ali Moharrer 2017 Louisiana State University and Agricultural and Mechanical College

Information Theoretic Study Of Gaussian Graphical Models And Their Applications, Ali Moharrer

LSU Doctoral Dissertations

In many problems we are dealing with characterizing a behavior of a complex stochastic system or its response to a set of particular inputs. Such problems span over several topics such as machine learning, complex networks, e.g., social or communication networks; biology, etc. Probabilistic graphical models (PGMs) are powerful tools that offer a compact modeling of complex systems. They are designed to capture the random behavior, i.e., the joint distribution of the system to the best possible accuracy. Our goal is to study certain algebraic and topological properties of a special class of graphical models, known as Gaussian ...


On The Ramberg-Osgood Stress-Strain Model And Large Deformations Of Cantilever Beams, Ronald J. Giardina Jr 2017 University of New Orleans

On The Ramberg-Osgood Stress-Strain Model And Large Deformations Of Cantilever Beams, Ronald J. Giardina Jr

University of New Orleans Theses and Dissertations

In this thesis the Ramberg-Osgood nonlinear model for describing the behavior of many different materials is investigated. A brief overview of the model as it is currently used in the literature is undertaken and several misunderstandings and possible pitfalls in its application is pointed out, especially as it pertains to more recent approaches to finding solutions involving the model. There is an investigation of the displacement of a cantilever beam under a combined loading consisting of a distributed load across the entire length of the beam and a point load at its end and new solutions to this problem are ...


Euler-Richardson Method Preconditioned By Weakly Stochastic Matrix Algebras: A Potential Contribution To Pagerank Computation, Stefano Cipolla, Carmine Di Fiore, Francesco Tudisco 2017 University of Rome Tor Vergata

Euler-Richardson Method Preconditioned By Weakly Stochastic Matrix Algebras: A Potential Contribution To Pagerank Computation, Stefano Cipolla, Carmine Di Fiore, Francesco Tudisco

Electronic Journal of Linear Algebra

Let S be a column stochastic matrix with at least one full row. Then S describes a Pagerank-like random walk since the computation of the Perron vector x of S can be tackled by solving a suitable M-matrix linear system Mx = y, where M = I − τ A, A is a column stochastic matrix and τ is a positive coefficient smaller than one. The Pagerank centrality index on graphs is a relevant example where these two formulations appear. Previous investigations have shown that the Euler- Richardson (ER) method can be considered in order to approach the Pagerank computation problem by means ...


Eigenfunctions For Partial Differential Equations On Two-Dimensional Domains With Piecewise Constant Coefficients, Abdullah M. Aurko 2017 University of Southern Mississippi

Eigenfunctions For Partial Differential Equations On Two-Dimensional Domains With Piecewise Constant Coefficients, Abdullah M. Aurko

Master's Theses

In this thesis, we develop a highly accurate and efficient algorithm for computing the solution of a partial differential equation defined on a two-dimensional domain with discontinuous coefficients. An example of such a problem is for modeling the diffusion of heat energy in two space dimensions, in the case where the spatial domain represents a medium consisting of two different but homogeneous materials, with periodic boundary conditions.

Since diffusivity changes based on the material, it will be represented using a piecewise constant function, and this results in the formation of a complicated mathematical model. Such a model is impossible to ...


Numerical Solution Of Partial Differential Equations Using Polynomial Particular Solutions, Thir R. Dangal 2017 University of Southern Mississippi

Numerical Solution Of Partial Differential Equations Using Polynomial Particular Solutions, Thir R. Dangal

Dissertations

Polynomial particular solutions have been obtained for certain types of partial differential operators without convection terms. In this dissertation, a closed-form particular solution for more general partial differential operators with constant coefficients has been derived for polynomial basis functions. The newly derived particular solutions are further coupled with the method of particular solutions (MPS) for numerically solving a large class of elliptic partial differential equations. In contrast to the use of Chebyshev polynomial basis functions, the proposed approach is more flexible in selecting the collocation points inside the domain. Polynomial basis functions are well-known for yielding ill-conditioned systems when their ...


An Investigation Of The Accuracy Of Parallel Analysis For Determining The Number Of Factors In A Factor Analysis, Mandy Matsumoto 2017 Western Kentucky University

An Investigation Of The Accuracy Of Parallel Analysis For Determining The Number Of Factors In A Factor Analysis, Mandy Matsumoto

Honors College Capstone Experience/Thesis Projects

Exploratory factor analysis is an analytic technique used to determine the number of factors in a set of data (usually items on a questionnaire) for which the factor structure has not been previously analyzed. Parallel analysis (PA) is a technique used to determine the number of factors in a factor analysis. There are a number of factors that affect the results of a PA: the choice of the eigenvalue percentile, the strength of the factor loadings, the number of variables, and the sample size of the study. Although PA is the most accurate method to date to determine which factors ...


Shrinkage Function And Its Applications In Matrix Approximation, Toby Boas, Aritra Dutta, Xin Li, Katie Mercier, Eric Niderman 2017 University of Florida, Gainesville

Shrinkage Function And Its Applications In Matrix Approximation, Toby Boas, Aritra Dutta, Xin Li, Katie Mercier, Eric Niderman

Electronic Journal of Linear Algebra

The shrinkage function is widely used in matrix low-rank approximation, compressive sensing, and statistical estimation. In this article, an elementary derivation of the shrinkage function is given. In addition, applications of the shrinkage function are demonstrated in solving several well-known problems, together with a new result in matrix approximation.


Full Wave Modeling Of Ultrasonic Scattering Using Nystrom Method For Nde Applications, Praveen Gurrala, Kun Chen, Jiming Song, Ron Roberts 2017 Iowa State University

Full Wave Modeling Of Ultrasonic Scattering Using Nystrom Method For Nde Applications, Praveen Gurrala, Kun Chen, Jiming Song, Ron Roberts

Jiming Song

Approximate methods for ultrasonic scattering like the Kirchhoff approximation and the geometrical theory of diffraction (GTD) can deliver fast solutions with relatively small computational resources compared to accurate numerical methods. However, these models are prone to inaccuracies in predicting scattered fields from defects that are not very large compared to wavelength. Furthermore, they do not take into account physical phenomena like multiple scattering and surface wave generation on defects. Numerical methods like the finite element method (FEM) and the boundary element method (BEM) can overcome these limitations of approximate models. Commercial softwares such as Abaqus FEA and PZFlex use FEM ...


Fast Algorithms On Random Matrices And Structured Matrices, Liang Zhao 2017 The City University of New York

Fast Algorithms On Random Matrices And Structured Matrices, Liang Zhao

All Graduate Works by Year: Dissertations, Theses, and Capstone Projects

Randomization of matrix computations has become a hot research area in the big data era. Sampling with randomly generated matrices has enabled fast algorithms to perform well for some most fundamental problems of numerical algebra with probability close to 1. The dissertation develops a set of algorithms with random and structured matrices for the following applications: 1) We prove that using random sparse and structured sampling enables rank-r approximation of the average input matrix having numerical rank r. 2) We prove that Gaussian elimination with no pivoting (GENP) is numerically safe for the average nonsingular and well-conditioned matrix preprocessed with ...


Revisiting Assert Use In Github Projects, Pavneet Singh KOCHHAR, David LO 2017 Singapore Management University

Revisiting Assert Use In Github Projects, Pavneet Singh Kochhar, David Lo

Research Collection School Of Information Systems

Assertions are often used to test the assumptions that developers have about a program. An assertion contains a boolean expression which developers believe to be true at a particular program point. It throws an error if the expression is not satisfied, which helps developers to detect and correct bugs. Since assertions make developer assumptions explicit, assertions are also believed to improve under-standability of code. Recently, Casalnuovo et al. analyse C and C++ programs to understand the relationship between assertion usage and defect occurrence. Their results show that asserts have a small effect on reducing the density of bugs and developers ...


High Performance Computation Of Cardiac Models In Real-Time Using Webgl, Abouzar Kaboudian, Flavio H. Fenton 2017 Georgia Institute of Technology

High Performance Computation Of Cardiac Models In Real-Time Using Webgl, Abouzar Kaboudian, Flavio H. Fenton

Biology and Medicine Through Mathematics Conference

No abstract provided.


A Large Reaction-Diffusion Model For Cell Polarization In Yeast, Marissa Renardy 2017 The Ohio State University

A Large Reaction-Diffusion Model For Cell Polarization In Yeast, Marissa Renardy

Biology and Medicine Through Mathematics Conference

No abstract provided.


Evolution Of Influenza H3n2: A Random Walk In High Dimensions, James R. Moore 2017 Emory University

Evolution Of Influenza H3n2: A Random Walk In High Dimensions, James R. Moore

Biology and Medicine Through Mathematics Conference

No abstract provided.


Building And Validating A Model For Investigating The Dynamics Of Isolated Water Molecules, Grant Cates 2017 Linfield College

Building And Validating A Model For Investigating The Dynamics Of Isolated Water Molecules, Grant Cates

Senior Theses

Understanding how water molecules behave in isolation is vital to understand many fundamental processes in nature. To that end, scientists have begun studying crystals in which single water molecules become trapped in regularly occurring cavities in the crystal structure. As part of that investigation, numerical models used to investigate the dynamics of isolated water molecules are sought to help bolster our fundamental understanding of how these systems behave. To that end, the efficacy of three computational methods—the Euler Method, the Euler-Aspel Method and the Beeman Method—is compared using a newly defined parameter, called the predictive stability coefficient ρ ...


Accuracy And Stability Of Integration Methods For Neutrino Transport In Core Collapse Supernovae, Kyle A. Gregory 2017 kgrego12

Accuracy And Stability Of Integration Methods For Neutrino Transport In Core Collapse Supernovae, Kyle A. Gregory

University of Tennessee Honors Thesis Projects

No abstract provided.


Efficient Denoising And Sharpening Of Color Images Through Numerical Solution Of Nonlinear Diffusion Equations, Linh T. Duong 2017 The University of Southern Mississippi

Efficient Denoising And Sharpening Of Color Images Through Numerical Solution Of Nonlinear Diffusion Equations, Linh T. Duong

Honors Theses

The purpose of this project is to enhance color images through denoising and sharpening, two important branches of image processing, by mathematically modeling the images. Modifications are made to two existing nonlinear diffusion image processing models to adapt them to color images. This is done by treating the red, green, and blue (RGB) channels of color images independently, contrary to the conventional idea that the channels should not be treated independently. A new numerical method is needed to solve our models for high resolution images since current methods are impractical. To produce an efficient method, the solution is represented as ...


Hawking Radiation And Classical Tunneling: A Numerical Study, Dmitriy Zhigunov 2017 College of William and Mary

Hawking Radiation And Classical Tunneling: A Numerical Study, Dmitriy Zhigunov

Undergraduate Honors Theses

Unruh [1] demonstrated that black holes have an analogy in acoustics. Under this analogy the acoustic event horizon is defined by the set of points in which the local background flow exceeds the local sound speed. In past work [2], we demonstrated that under a white noise source, the acoustic event horizon will radiate at a thermal spectrum via a classical tunneling process. In this work, I summarize the theory presented in [2] and nondimensionalize it in order to reduce the dynamical equations to one parameter, the coupling coefficient η2. Since η2 is the sole parameter of the system, we ...


Jet-Hadron Correlations Relative To The Event Plane Pb--Pb Collisions At The Lhc In Alice, Joel Anthony Mazer 2017 University of Tennessee, Knoxville

Jet-Hadron Correlations Relative To The Event Plane Pb--Pb Collisions At The Lhc In Alice, Joel Anthony Mazer

Doctoral Dissertations

In relativistic heavy ion collisions at the Large Hadron Collider (LHC), a hot, dense and strongly interacting medium known as the Quark Gluon Plasma (QGP) is produced. Quarks and gluons from incoming nuclei collide to produce partons at high momenta early in the collisions. By fragmenting into collimated sprays of hadrons, these partons form 'jets'. Within the framework of perturbative Quantum Chromodynamics (pQCD), jet production is well understood in pp collisions. We can use jets measured in pp interactions as a baseline reference for comparing to heavy ion collision systems to detect and study jet quenching. The jet quenching mechanism ...


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