Lecture4981 1

Applied Biomedical EngineeringAMME4981

Lecture 1Introduction to Computational Modelling and

its Application in Biomedical Engineering

http://www.aeromech.usyd.edu.au/people/academic/qingli/AMME4981.htm

Course Web

Course OutlineCourse Outline - Learning Objectives

Understanding of biomedical engineering design;

• Skills of finite element analysis and application of software (Ansys);

• Overview of modelling techniques in biomedical engineering;

• Project-based-learning, approach to development of biomedical design and optimisation.

Course Outline - Course Outline - SyllabusSyllabus

1Introduction to computational modelling and software in biomedical engineering

2 Biomechanical modelling of musculoskeletal systems

3 Constitutive models of biomaterials

4 Introduction to CT/MRI and image processing

5 Solid modelling and design optimisation

6 Fundamentals of finite element method

7 Finite element modelling issues

8 Seminar 1 (literature review and preliminary studies)

9 Bone remodelling and simulation

10 Modelling of damage, fracture and healing

11 Clinical applications of modelling

12 Quiz (one hour paper and 1.5 hour Ansys)

13 Seminar 2 and Final Report

Course Outline - Course Outline - AssessmentAssessment

AssignmentsAssignment 1 – Week 4 (10%)Assignment 2 – Week 8 (10%)Assignment 3 – Week 13 (10%)

Quiz1 hour paper (10%) and 1.5 hour in Ansys (10%) – Week 12 (total: 20%)

Seminars Seminar 1 – Week 8 (10%)Seminar 2 – Week 13 (20%)Group final report – Week 13 (20%)

Participation Mark

Attendance will be counted in individual project marks of 50%

Project Based LearningProject Based Learning

Tentative Project: Hip Replacement Design (To be finalized by week 2)

Metal, Polyethylene, Ceramic Implantation

Hip replacement is a medical procedure in which the hip joint is replaced by a synthetic implant. It is the most successful, cheapest and safest form of joint replacement surgery.

Design Related Issues Design Related Issues

Biomaterials Biomaterials • Composites• metal• Ceramics• Polyethylene

Design criteriaDesign criteria• Minimize stress shielding• Stimulate positive bone remodelling• Wear resistant• Stiffness• Strength• Biocompatibility

CT or MRI Scanning Acquisition of computer tomographic (CT) data of the femur,

Computational Solid ModellingGeometrical modelling of the femur and design of anatomical prosthesis in a computer-aided design (CAD) system,

Finite Element Modelling and Analysing Verification of the designed prosthesis in the finite element method (FEM) system –– including bone remodeling prediction.

ObjectivesObjectives

Three typical stepsThree typical steps

Reverse EngineeringReverse Engineering

““Direct” EngineeringDirect” EngineeringDesign Computer Model Fabrication Product

““Reverse” EngineeringReverse” EngineeringProduct (Bone) CT Data Computer Model

Reverse Engineering – Application Reverse Engineering – Application

Slice

Model of the prosthesis stem fitted to the medullary canal.

Differences in cross-sections of the three designs of the prosthesis stems:

Solid Model

CT-based Modelling – ProcedureCT-based Modelling – Procedure

Segmentation Segmentation of CT imagesof CT images

Stack of sectional Stack of sectional curvescurves

NURBsNURBs

Surface Surface fittingfitting

Solid ModelSolid Model

Step 1Step 1 selection of CT images that represent the desired anatomy of the bone,selection of CT images that represent the desired anatomy of the bone,

Step 2Step 2 segmentation of the desired object(s) through detection of the contours segmentation of the desired object(s) through detection of the contours by determining the value of Hounsfield number CT at pointsby determining the value of Hounsfield number CT at points

Step 3Step 3 creation of sectional curves along the CT points creation of sectional curves along the CT points

Step 4Step 4 creation of surface model from the curvescreation of surface model from the curves

Step 5Step 5 generation of the solid model of the femurgeneration of the solid model of the femur

Review on Commercial Software – ScanFE/ScanIPReview on Commercial Software – ScanFE/ScanIP

Simpleware (http://www.simpleware.com/index.php) – MRI and CT (US$15K)

ScanIP – image processing tools to assist the user in visualising and segmenting regions of interest from any volumetric 3D data (e.g. MRI, CT, MicroCT). Segmented images can be exported as STL files for CAD analysis and RP manufacturing or imported directly into leading commercial finite element packages.

ScanFE – generates volume and/or surface meshes, contact surfaces and material properties from segmented data.

Software Export – ABAQUS, ANSYS

Segmentation Hip meshed with ScanFE Analysis

Review on Commercial Software – MimicsReview on Commercial Software – Mimics

Mimics – http://www.materialise.com/materialise/view/en/65854-Homepage.htmlCT, MRI imagesAllow segmentation, solid modelling and FEA or export

MedCAD Module – a bridge between medical imaging (CT, MRI) and CAD.Allow a two-way interface from the imaging system to the CAD system and vice versa.

FEA – Build-in FEA module: Remesh the 3D object with the Mimics RemesherExport Software – Patran neutral, Ansys or Abaqus (surface mesh)Material Assignment – Continuious

Review on Commercial Software – Amira and Rhino3DReview on Commercial Software – Amira and Rhino3D

Amira – http://www.amiravis.com/Import for CT, MRI, Ultrasound images from current scanning devices via DICOM,

Rhino3D – http://www.rhino3d.com/ US$195Import for CT, MRI via DICOM

Manually generate 3D solid model Import to Solidworks, Catia, Unigraphics etc

Review on Commercial Software – 3D DoctorReview on Commercial Software – 3D Doctor

http://www.ablesw.com/3d-doctor/index.html

– – Pro/EPro/E (first feature based design tool, PTC) (first feature based design tool, PTC)

– – Unigraphics Unigraphics (EDS)(EDS)

–– CATIACATIA (Good free-from surface modeller, Dassault Systems - (Good free-from surface modeller, Dassault Systems - IBM)IBM)

– – SolidWorksSolidWorks (PC version high-end CAD) (PC version high-end CAD)

– – AutoCADAutoCAD Mechanical Desktop Mechanical Desktop

– – I-DEAS (EDS)I-DEAS (EDS)

– – Solid Edge (EDS)Solid Edge (EDS)

– – MicroStationMicroStation

– – IntergraphIntergraph

– – Rhinoceros (NURBS modeling)Rhinoceros (NURBS modeling)

General-Purpose Software for Solid ModellingGeneral-Purpose Software for Solid Modelling

ANSYS (from ANSYS Inc.)ANSYS (from ANSYS Inc.)– – A growth leader in CAE and integrated design analysis and optimisationA growth leader in CAE and integrated design analysis and optimisation– – Covering solid mechanics, kinematics, dynamics, and multi-physics (CFD, Covering solid mechanics, kinematics, dynamics, and multi-physics (CFD, EMAG, HT, Acoustics)EMAG, HT, Acoustics)– – Interfacing with key CAD systemsInterfacing with key CAD systems

Strand7Strand7 (Strand7 - Australian-own FE company, initiated from USYD) (Strand7 - Australian-own FE company, initiated from USYD)– – A powerful structural analysis program for analysing stress, vibration, A powerful structural analysis program for analysing stress, vibration, dynamic, nonlinear and heat transfer characteristics without node limits.dynamic, nonlinear and heat transfer characteristics without node limits.– – Easy to use.Easy to use.

ABAQUSABAQUS– – FEA software for highly nonlinear complex problems (Standard/Explicit).FEA software for highly nonlinear complex problems (Standard/Explicit).– – High-end parallelised program in super-computersHigh-end parallelised program in super-computers– – ABAQUS/CAE interface with CAD systemsABAQUS/CAE interface with CAD systems

CosmosWorksCosmosWorks– – Build-in Solidworks CAD systemBuild-in Solidworks CAD system– – Powerful linear solversPowerful linear solvers

General-Purpose FEA Software in AMMEGeneral-Purpose FEA Software in AMME

Introduction to ANSYS – Introduction to ANSYS – GUI Layout

Output

Window

Output

Window

Icon Toolbar MenuIcon Toolbar Menu

Abbreviation Toolbar MenuAbbreviation Toolbar Menu

Utility MenuUtility Menu

Graphics AreaGraphics Area

Main MenuMain Menu

Input LineInput Line Raise/Hidden IconRaise/Hidden Icon

Current SettingsCurrent SettingsUser Prompt InfoUser Prompt Info

MouseMouse

Left mouse buttonLeft mouse button picks (or unpicks) the entity or location closest to the mouse pointer. picks (or unpicks) the entity or location closest to the mouse pointer. Pressing and dragging allows you to “preview” the item being picked (or unpicked).Pressing and dragging allows you to “preview” the item being picked (or unpicked).

Middle mouse buttonMiddle mouse button does an Apply. Saves the time required to move the mouse over to does an Apply. Saves the time required to move the mouse over to the Picker and press the Apply button. Use Shift-Right button on a two-button mouse.the Picker and press the Apply button. Use Shift-Right button on a two-button mouse.

Right mouse buttonRight mouse button toggles between pick and unpick mode. Note, the Shift-Right button on toggles between pick and unpick mode. Note, the Shift-Right button on a two-button mouse is equivalent to the Middle mouse button on a three-button mouse.a two-button mouse is equivalent to the Middle mouse button on a three-button mouse.

ANSYS File SystemANSYS File System

Database and Files: The term ANSYS database refers to the data ANSYS maintains in memory as you build, solve, and postprocess your model. The database stores both your input data and ANSYS results data:– Input data -- info you must enter, such as dimensions, material properties, and load data.– Results data -- quantities that ANSYS calculates, such as displacements and stresses.

Defining the Jobname: Utility Menu > File> Change JobnameThe jobname is a name up to 32 characters that identifies the ANSYS job. When you define a jobname for an analysis, the jobname becomes the first part of the name of all files the analysis creates. (The extension or suffix for these files' names is a file identifier such as .DB.) By using a jobname for each analysis, you ensure that no files are overwritten.

Typical files in Ansysjobname.db, .dbb: Database file, binary. Compatible across all supported platforms.jobname.log: Log file, ASCII. Contains a log of every command issued during the session. If you start a second session with the same jobname in the same working directory, ANSYS will append to the previous log file (with a time stamp).jobname.err: Error file, ASCII. Contains all errors and warnings encountered during the session. ANSYS will also append to an existing error file.jobname.rst, .rth, .rmg, .rfl: Results files, binary. Contains results data calculated by ANSYS during solution.Compatible across all supported platforms.

File Management Tips:• Run each analysis project in a separate working directory.• Use different jobnames to differentiate various analysis runs.• You should keep the following files after any ANSYS analysis: log file ( .log); database file ( .db); results files (.rst, .rth, …); load step files, if any (.s01, .s02, ...)

Defining an Analysis Title: Utility Menu> File> Change TitleThis will define a title for the analysis. ANSYS includes the title on all graphics displays and on the solution output. (Please include your name and student ID in the analysis title for Please include your name and student ID in the analysis title for all original graphsall original graphs)

ANSYS File System – Cont’dANSYS File System – Cont’d

Tips on SAVE and RESUME:

Periodically save the database as you progress through an analysis. ANSYS does NOT do automatic saves.

You should definitely SAVE the database before attempting an unfamiliar operation (such as a Boolean or meshing) or an operation that may cause major changes (such as a delete).

RESUME can then be used as an “undo” if you don’t like the results of that operation. SAVE is also recommended before doing a solver.

Exiting ANSYS Two ways to exit ANSYS, either: Toolbar > QUIT or Utility Menu > File > Exit

Save and ResumeSince the database is stored in the computer’s memory (RAM), it is good practice to save it to disk frequently so that you can restore the information in the event of a computer crash or power failure. The SAVE operation copies the database from memory to a file called the database file (or db file for short).

–The easiest way to do a save is to click on: Toolbar > SAVE_DB

–Or use: • Utility Menu > File > Save as Jobname.db

• Utility Menu > File > Save as… To restore the database from the db file back into memory, use the RESUME operation. –Toolbar > RESUME_DB –or use: • Utility Menu>File>Resume Jobname.db

• Utility Menu > File > Resume from… The default file name for SAVE and RESUME is jobname.db, but you can choose a different name by using the “Save as” or “Resume from” functions. –Choosing the “Save as” or “Resume from” function does NOT change the current jobname. If you save to the default file name and a jobname.db already exists, ANSYS will first copy the “old” file to jobname.dbb as a back-up.

ANSYS File System – Cont’dANSYS File System – Cont’d

ANSYS ModellingANSYS Modelling

Solid Modeling Be defined as the process of creating solid models in CAD system. Definitions

–A solid model is defined by volumes, areas, lines, and keypoints.

–Volumes are bounded by areas, areas by lines, and lines by keypoints.

–Hierarchy of entities from low to high as

keypoints < lines < areas < volumes

–You cannot delete an entity if a higher-order entity is attached to it. Also, a model with just areas and below, such as a shell or 2-D plane model, is still considered a solid model in ANSYS terminology.

Keypoints

Lines

Areas

Volumes

Keypoints

Lines

Areas

Volumes

Keypoints

Lines

Areas

Volumes

Methods of Solid ModelingMethods of Solid Modeling

There are two approaches to creating a solid model in ANSYS, Top-down and Bottom-up

Top-down modeling starts with a definition of volumes (or areas), which are then combined in some fashion to create the final shape.

add

Input entities Boolean operation Output entity(ies) Bottom-up modeling

starts with keypoints, from which you “build up” lines, areas, etc.

Ansys PrimitivesAnsys Primitives

The volumes or areas that you initially define are called primitives, which are basic entities for the top-down method. ANSYS contains the following 2D and 3D primitives:

Rectangle Circle Polygon

Block Cylinder Prism Sphere Cone Torus

Top-Down method – Boolean OperationTop-Down method – Boolean Operation

The final shape of an object is usually not as simple as primitives. However, it is likely doable to combine a number of primitives through a series of proper Boolean operations. The “input” to Boolean operations can be any geometric entity, ranging from simple primitives to complicated volumes generated in previous steps.

Boolean operations are computations involving combinations of geometric entities. ANSYS Boolean operations include add, subtract, intersect, divide, glue, and overlap. •All Boolean operations are available in the GUI: Main Menu > Preprocessor > Modeling > Operate > Booleans

Boolean OperationBoolean Operation

Add: Combines two or more entities

into one.

Glue: Attaches two or more entities by creating a common boundary between them, which is uesful when you want to maintain the distinction between entities (such as for different materials).

Overlap: Same as glue, except that the

input entities overlap each other. Subtract: Removes the overlapping

portion of one or more entities from a set of “base” entities, which can be useful for creating holes or trimming off portions of an entity.

A1

A2A3

Add

A1

A2A3

Glue

A2

A1

A2

A5Overlap

A4A3

A1

A2

A3Subtract

Boolean Operation – Cont’dBoolean Operation – Cont’d

Divide: Cuts an entity into two or more pieces that are still connected to each other by common boundaries. The “cutting tool” may be the working plane, an area, a line, or even a volume. Useful for “slicing and dicing” a complicated volume into simpler volumes for brick meshing.

Intersect: Keeps only the overlapping

portion of two or more entities. Partition: Cuts two or more intersecting

entities into multiple pieces that are still connected to each other by common boundaries, e.g., to find the intersection point of two lines and still retain all four line segments, as shown. (An intersection operation would return the common keypoint and delete both lines.)

A3A1

A2Divide

CommonIntersection

A1

A4IntersectA2 A3

L1

L2

L3L6

L5L4

Intersect

ANSYS Element TypeANSYS Element Type

Element Type The element type is an important choice that determines the following element characteristics:

Degree of Freedom (DOF) set. A thermal element type, for example, has one dof: TEMP, whereas a structural element type may have up to six dof: UX, UY, UZ, ROTX, ROTY, ROTZ.

Element shape -- brick, tetrahedron, quadrilateral, triangle, etc. Dimensionality -- 2-D solid (X-Y plane only), or 3-D solid. Assumed displacement shape -- linear vs. quadratic.

To define an element: Main Menu>Preprocessor>Element Type> Add/Edit/Delete>Add

Meshing MethodsMeshing Methods

There are two main meshing methods: Free and Mapped.There are two main meshing methods: Free and Mapped.

Free MeshFree Mesh – Has no element shape restrictions. – Has no element shape restrictions.

• The mesh does not follow any pattern.The mesh does not follow any pattern.

• Suitable for complex shaped areas and volumes.Suitable for complex shaped areas and volumes.

• Suitable for complex shaped areas and volumes.Suitable for complex shaped areas and volumes.

• Volume meshes consist of high order tetrahedral (10 nodes), large dof.Volume meshes consist of high order tetrahedral (10 nodes), large dof.

Mapped MeshMapped Mesh – Restricts element shapes to quadrilaterals (areas) and – Restricts element shapes to quadrilaterals (areas) and hexahedra (volume) hexahedra (volume)

•Typically has a regular pattern with obvious rows of elements.Typically has a regular pattern with obvious rows of elements.

•Suitable only for “regular” shapes such as rectangles and bricks.Suitable only for “regular” shapes such as rectangles and bricks.

Free meshing Mapped meshing

Mesh Density ControlMesh Density Control Mesh Density Control ANSYS provides many tools to control mesh density, on a global and local level: –Global controls: SmartSizing; Global element sizing; Default sizing –Local controls: Keypoint sizing; Line sizing; Area sizing To bring up the MeshTool:

Main Menu > Preprocessor > Meshing > MeshTool SmartSizing: by turning on SmartSizing, and set the desired size level. Size level ranges from 1 (fine) to 10 (coarse), defaults to 6. Then mesh all volumes (or all areas) at once, rather than one-by-one.Advanced SmartSize controls, such as mesh expansion and transition factors, are available by Main Menu>Preprocessor>Meshing>Size Cntrls>SmartSize>Adv Opts Global Element Sizing: Allows you to specify a maximum element edge length for the entire model (or number of divisions per line): Go to “Size Controls”, “Global” ,and click [Set] or Main Menu>Preprocessor>Meshing>Size Cntrls > ManualSize >Global >Size

Material Property and UnitMaterial Property and Unit

Material Properties Every analysis requires some material property input: Young’s modulus (EX), Poisson’s ratio (PRXY) for structural elements, thermal conductivity (KXX) for thermal elements, etc. To define the material properties:

Main Menu>Preprocessor>Material Props>Material Models

More than one set of material properties can be defined when needed.

Time Length Mass Force Temperature Energy

s m kg N K J Density Conductivity Specific Heat Flux Convection Modulus/stress Kg/m3 J/(smK) J/(KgK) J/(sm2) J/(sm2K) Pa

Unit (SI) – Unit (SI) – The ANSYS program does not assume a system of units for your The ANSYS program does not assume a system of units for your analysis. You can use any system of units analysis. You can use any system of units

Tasks of Week 1Tasks of Week 1

Discussion for forming a team (shaft and cup)

Read papers and further literature review

Ansys online tutorial (login Ansys Help > tutorial)

Ansys tutorial in biomedical engineering (see handout)

Ansys tutorial: Ansys tutorial: Model nail/callus in fractured femurModel nail/callus in fractured femur

Upper part of bone

Lower part of bone

Callus

Fracture site

Coating

Implants