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Course: CS 314, Fall 2008
School: Purdue
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COMPUTER SCIENCE 314 Spring 2008 January 7 COURSE INFORMATION 1. Course description and prerequisites: Numerical Methods Iterative methods for solving nonlinear equations; direct and iterative methods for solving linear systems; approximations of functions, derivatives, and integrals; error analysis. Prerequisites: Math 265 and one of CS 159, CS 177, or CS 180. Math 265: Linear Algebra Systems of linear equations,...

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COMPUTER SCIENCE 314 Spring 2008 January 7 COURSE INFORMATION 1. Course description and prerequisites: Numerical Methods Iterative methods for solving nonlinear equations; direct and iterative methods for solving linear systems; approximations of functions, derivatives, and integrals; error analysis. Prerequisites: Math 265 and one of CS 159, CS 177, or CS 180. Math 265: Linear Algebra Systems of linear equations, matrix algebra, vector spaces, determinants, eigenvalues and eigenvectors, diagonalization of matrices, applications. Prerequisite: Math 162 or 166 or 173. Math 162 or 166 or 173: Plane Analytic Geometry and Calculus II V...
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Purdue - CS - 314
NUMERICAL METHODSRobert D. Skeel COPYRIGHT c 2008 Robert D. Skeel. All Rights Reserved.Errata ELEMENTARY NUMERICAL COMPUTING with Mathematica1. page 14, top, the last row of the table should be 1.416 1.412 and the result should be 1.414. 2. on pa
Purdue - CS - 314
COMPUTER SCIENCE 314 Numerical MethodsSPRING 2008ASSIGNMENT # 1 (25 points)January 7Announcement Oce hours: Instructor 2:002:30 1:302:00 Teaching Assistant 10:3011:30 10:3011:30, 2:303:30 11:0012:00Tuesdays Thursday FridaysDue Wednesday, Jan
Purdue - CS - 390
CS390S,Week1:Introductionto SecureProgrammingPascalMeunier,Ph.D.,M.Sc.,CISSP January10,2007 DevelopedthankstosupportandcontributionsfromSymantec Corporation,supportfromtheNSFSFSCapacityBuildingProgram (AwardNumber0113725)andthePurdueeEnterpriseCente
Purdue - CS - 390
CS390S,Week2:Assuranceand PrinciplesPascalMeunier,Ph.D.,M.Sc.,CISSP January16,2007 DevelopedthankstosupportandcontributionsfromSymantec Corporation,supportfromtheNSFSFSCapacityBuildingProgram (AwardNumber0113725)andthePurdueeEnterpriseCenterCopyrig
Purdue - CS - 390
CS390S,Week3:Buffer Overflows,Part1PascalMeunier,Ph.D.,M.Sc.,CISSP January23,2008 DevelopedthankstosupportandcontributionsfromSymantec Corporation,supportfromtheNSFSFSCapacityBuildingProgram (AwardNumber0113725)andthePurdueeEnterpriseCenterCopyrigh
Purdue - CS - 390
CS390S,Week4:Buffer Overflows,Part2PascalMeunier,Ph.D.,M.Sc.,CISSP January30,2008 DevelopedthankstosupportandcontributionsfromSymantec Corporation,supportfromtheNSFSFSCapacityBuildingProgram (AwardNumber0113725)andthePurdueeEnterpriseCenterCopyrigh
Purdue - CS - 390
CS390S,Week5:FormatString Vulnerabilities&amp;Integer OverflowsPascalMeunier,Ph.D.,M.Sc.,CISSP February6,2008 DevelopedthankstosupportandcontributionsfromSymantec Corporation,supportfromtheNSFSFSCapacityBuildingProgram (AwardNumber0113725)andthePurdueeE
Purdue - CS - 390
CS390S, Week 6: Shells and EnvironmentPascal Meunier, Ph.D., M.Sc., CISSP February 13, 2008 Developed thanks to support and contributions from Symantec Corporation, support from the NSF SFS Capacity Building Program (Award Number 0113725) and the Pu
Purdue - CS - 390
CS390S, Week 7:Calling Programs, TrustPascal Meunier, Ph.D., M.Sc., CISSP February 20, 2008 Developed thanks to support and contributions from Symantec Corporation, support from the NSF SFS Capacity Building Program (Award Number 0113725) and the Pu
Purdue - CS - 390
CS390S, Week 9:Meta-Character VulnerabilitiesPascal Meunier, Ph.D., M.Sc., CISSP February 20, 2008 Developed thanks to support and contributions from Symantec Corporation, support from the NSF SFS Capacity Building Program (Award Number 0113725) and
Purdue - CS - 390
CS390S, Week 11:Web Application Security IssuesPascal Meunier, Ph.D., M.Sc., CISSP March 14, 2008 Developed thanks to support and contributions from Symantec Corporation, support from the NSF SFS Capacity Building Program (Award Number 0113725) and
Purdue - CS - 390
CS390S, Week 12: Race ConditionsPascal Meunier, Ph.D., M.Sc., CISSP March 26, 2008 Developed thanks to support and contributions from Symantec Corporation, support from the NSF SFS Capacity Building Program (Award Number 0113725) and the Purdue e-En
Purdue - CS - 390
CS390S, Week 13:File System Vulnerabilities (abridged version)Pascal Meunier, Ph.D., M.Sc., CISSP April 2, 2008 Developed thanks to support and contributions from Symantec Corporation, support from the NSF SFS Capacity Building Program (Award Number
Purdue - CS - 390
CS390S, Week 14:Randomness and CanonicalizationPascal Meunier, Ph.D., M.Sc., CISSP April 9, 2008 Developed thanks to support and contributions from Symantec Corporation, support from the NSF SFS Capacity Building Program (Award Number 0113725) and t
Purdue - DS - 2
Mitigating Attacks AgainstMeasurement-Based Adaptation Mechanisms in Unstructured Multicast Overlay NetworksAAron Walters, David Zage, Cristina Nita-RotaruDepartment of Computer Science and CERIAS Purdue UniversityOverlay NetworksIncreased per
Purdue - DS - 2
A Framework for Role-Based Access Control in Group Communication SystemsCristina Nita-Rotaru and Ninghui LiDepartment of Computer Sciences and CERIAS Purdue UniversityPDCS 2004Why Group Communication? Collaborative applications: computing,
Purdue - CS - 590
COMPUTER SCIENCE 590V Biomolecular SimulationSPRING 2007COURSE INFORMATIONJanuary 8Purpose of course: to explain how to do simulations and computations. The course describes the use of simulation packages and discusses the methodology and select
Purdue - CS - 590
COMPUTER SCIENCE 590V Biomolecular SimulationSPRING 2007ASSIGNMENT # 1 (32 points)January 17Due Wednesday, January 26 in class This assignment covers the VMD tutorial and sections 1.11.3 of the NAMD tutorial, as well as sections 1.11.3 of the le
Purdue - CS - 590
COMPUTER SCIENCE 590V Biomolecular SimulationSPRING 2007ASSIGNMENT # 2 (35 points)January 29Announcements Make up lectures: plans are to hold these Thursdays 9:3010:20 am on Feb 1, Feb 15, and Mar 1. Correction. Page 4 of the class notes, one
Purdue - CS - 590
CHARMM: A users perspectiveV. M. Dadarlat, March 2007CHARMM - a research program developed at Harvard University for energy minimization and dynamics simulation of proteins, nucleic acids and lipids in vacuum, solution or crystal environments (Harv
Purdue - CS - 590
COMPUTER SCIENCE 590V Biomolecular SimulationSPRING 2007ASSIGNMENT # 5 (44 points, 4 pages)March 19Announcement The best reference to statistical mechanics that the instructor has found is the notes at URL http:/www.nyu.edu/classes/tuckerman/sta
Purdue - CS - 590
\documentclass[11pt]{article} \usepackage{fullpage,amsmath} \newcommand{\T}{^{\mathsf{T} % matrix transposition \newcommand{\kb}{k_{\mathrm{B} \newcommand{\rmd}{\mathrm{d} \newcommand{\rme}{\mathrm{e} \begin{document} \begin{center} {\Large COMPUTER
Purdue - CS - 590
Contents1 Getting Started 1.1 Visualization . . . . . . . . . . . 1.2 Structure Building . . . . . . . . 1.3 Molecular Motion and Sampling 1.4 The Canonical Ensemble . . . . . 1.5 Equilibration . . . . . . . . . . . 1.6 Time Correlation Functions .
Purdue - CS - 590
10111010101011000111010111010101011110101111010111010101011000001010010100010101000101010101010110101010101000101010010101001010101000101010Scripting Biomolecular Simulations with Tclpart of CS590vMichael McLennan Senior Research Scientist Rosen
Purdue - CS - 590
10111010101011000111010111010101011110101111010111010101011000001010010100010101000101010101010110101010101000101010010101001010101000101010Scripting Biomolecular Simulations with Tclpart of CS590vMichael McLennan Senior Research Scientist Rosen
Purdue - CS - 590
Start up vmd by double clicking its icon. In the Tk console do a cd to the 1-1-build directory. e.g., cd ~/Desktop/namd-tutorial-files/1-1-build/ Do steps 2-4 on pages 3-4 but do not quit VMD. Enter source ubq.tcl where you have prepared ubq.tcl as f
Purdue - CS - 590
Bibliography[ABG+ 03] Mehmet Serkan Apaydin, Douglas L. Brutlag, Carlos Guestrin, David Hsu, JeanClaude Latombe, and Chris Varma. Stochastic roadmap simulation: An ecient representation and algorithm for analyzing molecular motion. J. Comput. Biol.,
Purdue - ANSC - 95
Fatvalue - A computer program for calculating the value of fat D.M. Forsyth Department of Animal Sciences There are two main ways that feeding fat to pigs can be profitable: improved feed conversion (lbs. of feed / lb. of gain) increased rate of ga
Purdue - ANSC - 95
Fatvalue - A computer program for calculating the value of fat D.M. Forsyth Department of Animal Sciences There are two main ways that feeding fat to pigs can be profitable: * improved feed conversion (lbs. of feed / lb. of gain) * increased rate of
Purdue - CS - 515
COMPUTER SCIENCE 515SPRING 2006COURSE INFORMATIONJanuary 13Sta: Instructor Robert Skeel CS 164D 49-49025 skeel at cs.purdue.edu Oce hours: Mondays Tuesdays Wednesdays Thursday Web page: Teaching Assistant Huiying Xu Physics 178 49-62779, 49-6278
Purdue - CS - 515
NUMERICAL LINEAR ALGEBRARobert D. Skeel c 2006 Robert D. Skeel February 10, 20060Chapter 1 DIRECT METHODSPART I1.1 Linear Systems of Equations 1.2 Data Error 1.3 Gaussian Elimination 1.4 LU Factorization 1.5 Symmetric Positive Denite Matrices
Purdue - CS - 515
Chapter 2 DIRECT METHODSPART IIIf we use nite precision arithmetic, the results obtained by the use of direct methods are contaminated with roundo error, which is not always negligible. 2.1 Finite Precision Computation 2.2 Residual vs. Error 2.3 Piv
Purdue - CS - 515
Chapter 3 LEAST SQUARES PROBLEMSE BD C A the sea FOne application is geodesy &amp; surveying. Let z = elevation, and suppose we have the measurements: zA 1., zB 2., zC 3., zB zA 1., zC zB 2., zC zA 1.71This is overdetermined and inconsi
Purdue - CS - 515
Chapter 4 EIGENVALUE PROBLEMThe German word eigen is cognate with the Old English word gen, which became owen in a Middle English and own in modern English. Given A Rnn solve Ax = x where C and 0 = x Cn . 4.1 Mathematics 4.2 Reduction to Upper H
Purdue - CS - 515
5.1Banded Storageu = temperatureu=0 1uh temperature at gridpointsuh =0u=0Laplaces equationuh=0u=0uh =0grid sizeu=1 1u =1hThe ve-point dierence operator uh (x + h, y) 2uh (x, y) + uh (x h, y) uh (x, y + h) 2uh (x, y) + uh
Purdue - CS - 515
Chapter 8 KRYLOV SUBSPACE METHODSA more readable reference is the book by Lloyd N. Trefethen and David Bau. 8.1 Krylov Subspaces 8.2 Arnoldi Orthogonalization 8.3 Generalized Minimal Residual Method 8.4 Conjugate Gradient Method 8.5 Biconjugate Grad
Purdue - CS - 515
Chapter 9 PRECONDITIONING9.1 Preconditioned Krylov Subspace Methods 9.2 Preconditioned Conjugate Gradient 9.3 Preconditioned Generalized Minimal Residual 9.4 Relaxation Method Preconditioners 9.5 Incomplete LU Factorization Preconditioners 9.6 Appro
Purdue - CS - 515
COMPUTER SCIENCE 515 Numerical Linear AlgebraSPRING 2006ASSIGNMENT # 1 (30 points)January 18Due Friday, January 27 in class 0. Look over Sections 1.11.4 of the class notes and Sections 1.11.6 and 1.13 of the textbook. As a general rule, for prob
Purdue - CS - 515
\documentclass[11pt]{article} \usepackage{fullpage,amsmath} \newcommand{\T}{^{\mathsf{T} % matrix transposition \newcommand{\bfy}{\mathbf{y} \newcommand{\rmd}{\mathrm{d} \begin{document} \begin{center} {\Large COMPUTER SCIENCE 515}\ {\Large Numerical
Purdue - CS - 515
COMPUTER SCIENCE 515 Numerical Linear AlgebraSPRING 2006ASSIGNMENT # 1 (30 points maximum) solutionsJanuary 301. (2 points) Assuming that A is nonsingular, prove that (A1 )T = (AT )1 . Organize your proof logically. Hence, the notation AT may be
Purdue - CS - 515
COMPUTER SCIENCE 515 Numerical Linear AlgebraSPRING 2006ASSIGNMENT # 2 (30 points)January 27Announcements The rst examination is Wednesday, February 15 in class (from 12:30 pm to 1:20 pm). It is a closed book exam, and only pens, pencils, and e
Purdue - CS - 515
\documentclass[11pt]{article} \usepackage{fullpage,amsmath} \newcommand{\T}{^{\mathsf{T} % matrix transposition \begin{document} \begin{center} {\Large COMPUTER SCIENCE 515}\ {\Large Numerical Linear Algebra} \ {\large SPRING 2006} \ ASSIGNMENT \# 2
Purdue - CS - 515
COMPUTER SCIENCE 515 Numerical Linear AlgebraSPRING 2006ASSIGNMENT # 2 (30 points)January 27Due Friday, February 10 in class 0. Look over Sections 1.52.5 of the class notes and Section 1.11 of the textbook. 1. (15 points) Write a recursive progr
Purdue - CS - 515
COMPUTER SCIENCE 515 Numerical Linear AlgebraSPRING 2006ASSIGNMENT # 3 (25 points)February 10Due Friday, February 24 in class 0. Look over Chapter 3 of the class notes and Sections 1.7 and 1.12 of the textbook. 1. (5 points) Construct the orthog
Purdue - CS - 515
\documentclass[11pt]{article} \usepackage{fullpage,amsmath} \newcommand{\T}{^{\mathsf{T} % matrix transposition \begin{document} \begin{center} {\Large COMPUTER SCIENCE 515}\ {\Large Numerical Linear Algebra} \ {\large SPRING 2006} \ ASSIGNMENT \# 3
Purdue - CS - 515
COMPUTER SCIENCE 515 Numerical Linear AlgebraSPRING 2006ASSIGNMENT # 3 (25 points)February 10Due Friday, February 24 in class 1. (5 points) Construct the orthogonal projector onto the plane through (0,0,0), (1,1,0), (1,0,1). 1 1 This plane ha
Purdue - CS - 515
COMPUTER SCIENCE 515 Numerical Linear AlgebraSPRING 2006ASSIGNMENT # 4 (39 points)February 27Announcements The second examination is Wednesday, March 22 in class (from 12:30 pm to 1:20 pm). It is a closed book exam, and only pens, pencils, and
Purdue - CS - 515
\documentclass[11pt]{article} \usepackage{fullpage,amsmath,amssymb} \newcommand{\T}{^{\mathsf{T} % matrix transposition \begin{document} \begin{center} {\Large COMPUTER SCIENCE 515}\ {\Large Numerical Linear Algebra} \ {\large SPRING 2006} \ ASSIGNME
Purdue - CS - 515
COMPUTER SCIENCE 515 Numerical Linear AlgebraSPRING 2006ASSIGNMENT # 4 (39 points)February 27Due Friday, March 10 in class 1. (22 points) The goal is to compare the eectiveness of ve dierent techniques for orthogonalizing the columns of a matrix
Purdue - CS - 515
COMPUTER SCIENCE 515 Numerical Linear AlgebraSPRING 2006March 10ASSIGNMENT # 5 (17 points)Due Friday, March 31 in class 0. Look over Sections 5.1 and 5.36.2 of the class notes and Section 3.2.1, Section 3.3.2, pp. 82 84, Section 3.4, Section 3.
Purdue - CS - 515
\documentclass[11pt]{article} \usepackage{fullpage,amsmath} \usepackage[dvips]{graphicx} \newcommand{\T}{^{\mathsf{T} % matrix transposition \begin{document} \begin{center} {\Large COMPUTER SCIENCE 515}\ {\Large Numerical Linear Algebra} \ {\large SP
Purdue - CS - 515
COMPUTER SCIENCE 515 Numerical Linear AlgebraSPRING 2006March 31ASSIGNMENT # 5 SOLUTIONS (17 points)Due Friday, March 31 in class 1. (4 points) Complete the following algorithm for performing Gaussian elimination with partial pivoting on a trid
Purdue - CS - 515
COMPUTER SCIENCE 515 Numerical Linear AlgebraSPRING 2006March 29ASSIGNMENT # 6 (39 points)Announcements The third examination is Wednesday, April 19 in class (from 12:30 pm to 1:20 pm). It is a closed book exam, and only pens, pencils, and era
Purdue - CS - 515
\documentclass[11pt]{article} \usepackage{fullpage,amsmath,amssymb} \usepackage[dvips]{graphicx} \newcommand{\T}{^{\mathsf{T} % matrix transposition \begin{document} \begin{center} {\Large COMPUTER SCIENCE 515}\ {\Large Numerical Linear Algebra} \ {\
Purdue - CS - 515
COMPUTER SCIENCE 515 Numerical Linear AlgebraSPRING 2006Solution of Assignment # 6 (39 points)April 17Due Friday, April 14 in class 1. (20 points) The goal is to write a routine to nd roots of a polynomial using Rayleigh quotient iteration. You
Purdue - CS - 501
COMPUTER SCIENCE 501/590C Computing for Science and EngineeringFALL 2008TENTATIVE ASSIGNMENT # 2 (32 points)September 5Due Saturday, September 27 at 6:00 am Eastern Time Section 4.2 of the class notes.This assignment covers through1. (7 poi
Purdue - CS - 501
COMPUTER SCIENCE 501 Computing for Science and EngineeringFALL 2008COURSE INFORMATIONAugust 29CS 590C:See page 4 for modications pertaining to CS 590C.Course description: Computational concepts, tools, and skills for computational science an
Purdue - CS - 501
COMPUTING FOR SCIENCE AND ENGINEERINGCOPYRIGHT c 2008 Robert D. Skeel. All Rights Reserved.Contents1 Introduction 1.1 Nature of Computational Science and Engineering 1.2 Approximation . . . . . . . . . . . . . . . . . . . . 1.3 Error Propagation
Purdue - CS - 501
COMPUTER SCIENCE 501/590C Computing for Science and EngineeringFALL 2008ASSIGNMENT # 1 (32 points)September 1Due Saturday, September 13 at 6:00 am Eastern Time This assignment covers through Section 3.1 of the class notes. The rst question exerc
Purdue - CS - 501
COMPUTING FOR SCIENCE AND ENGINEERINGCOPYRIGHT c 2007 Robert D. Skeel. All Rights Reserved.Contents1 Introduction 1.1 Nature of Computational Science and Engineering 1.2 Approximation . . . . . . . . . . . . . . . . . . . . 1.3 Error Propagation
Purdue - CYTO - 1
Lecture 1First Lecture: (3rd year students) Phagocytic Cells and their function This lecture will discuss the principles of phagocytosis and neutrophil function. We will discuss the basic principles of how phagocytic cells function to bind, ingest a