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Week 14Review + What I Do

Paul ChewCS 212 – Spring 2004

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AnnouncementsPart 4

There is no type-casting in Bali4, but you can assign to a supertype

If A is a supertype of B and aa and bb are declared as types A and B, respectively then

aa = bb; // is legalbb = aa; // is not

Reminder: Download the latest SaM Simulator

Part 4 regradesGrades available by WednesdayRegrade requests must be in by Friday

CMS cleaningIf you are still in the course, but have been removed from CMS, let me know right away

SectionsThere is a Section meeting today (7:30 in 205 Upson)There is one Section meeting on Monday (12:20 in ???)

Please participate in the online Course Evaluation

There is also a paper survey to fill out today

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Quick OverviewIntroduction

Computer architectureMachine language & assembly languageIntro to SaM

CompilersLexical analysis & parsingAbstract Syntax TreesRecursive descent parsing & code generation

Software EngineeringUse of abstractionSpecification & validationTesting & debuggingModels for software developmentTop-down vs. bottom-up designEvaluating a design

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More OverviewImplementing recursive functions

Stack frames

Implementing arrays

Implementing objectsUse of the HeapDispatch vectors

Software Engineering ToolsUnixProgramming languagesScripting languagesRegular expressionsMakefilesVersion controlUMLProfiling

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What I Do: Computational GeometryUsing a computer to solve geometric problems

Get to use lots of data structure ideasExample

Given n line segments in the plane, report all intersectionsUses both a PQ and a Balanced Tree

Areas I work inMotion PlanningMeshingShape Matching

computer visionprotein matching

More theoretical questions

sweepline

The Delaunay TriangulationHas the “Empty Circle Property” (each Delaunay triangle’s circumcircle is empty)

Is commonly used for meshing

initial sitesinitial sites

a Delaunay triangulationa Delaunay triangulation

an empty circle

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Adaptive Software Project (ASP)Adaptivity at three levels

Application LevelChoosing among physical models

Algorithm LevelChoosing among algorithms

System LevelUsing system resources effectively

Problem domainsfracture mechanicsreactive fluid flows

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Necessary ToolsGeometric modelers

Existing modelers are mostly inadequate

Mesh generatorsNeed quality guarantees

Visualization toolsComponents for different physical models

Different domainsfluid flow, structural mechanics, heat flow

Different scalesatomic scale, grain scale, structural scale

Components for different solution techniques (algorithms)

finite elements, boundary elements, finite differences, …

Framework for combining componentsSystem tools

Runtime environmentDynamic load balancingFault tolerance (processor failure)Compiler support

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ASP Meshing RequirementsControl of element density

Small elements (in “interesting” regions) for accuracyLarge elements (elsewhere) for efficiency

Allow internal boundariesNeeded to represent, e.g., a crack

Ideally: guarantee of element quality

Nice, but unnecessary for a single meshBut we have many meshes as geometry changes over time

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Initial Crude Mesh

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During Improvement

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Final Mesh

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Protein Shape and URMSProtein function is largely based on the protein’s geometric shapeHow do we analyze protein shape?Our technique: URMS (Unit-vector Root Mean Square distance)Advantages

Insensitive to outliersEfficient to computeEqual weight for all portions

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Protein Families & Consensus ShapeEvolution theory ⇒ a protein ancient ancestor evolved into a family of proteins

Membership in a protein family is expressed by sequence similarity, but is more strongly expressed by structure similarity

25-30% sequence resemblance (almost always) ensures shape resemblance

Goal: Create a Consensus Shape Algorithm that produces

a multiple alignment of structures, and

a single (core) structure that summarizes the structural information for a protein family

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An Alpha Protein Family (Globins)

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A Beta Protein Family

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Unrelated Proteins