Applied Biomedical Engineering

AMME4981

Lecture 1
Introduction to Computational Modelling and
its Application in Biomedical Engineering

Course Web
http://www.aeromech.usyd.edu.au/people/academic/qingli/AMME4981.htm
 Course 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 - Syllabus
Introduction to computational modelling and software
1
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 - Assessment

Assignment 1 – Week 4 (10%)

Assignments Assignment 2 – Week 8 (10%)
Assignment 3 – Week 13 (10%)
1 hour paper (10%) and 1.5 hour in Ansys
Quiz
(10%) – Week 12 (total: 20%)
Seminar 1 – Week 8 (10%)
Seminars Seminar 2 – Week 13 (20%)
Group final report – Week 13 (20%)
Participation Attendance will be counted in individual
Mark project marks of 50%
Project Based Learning

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

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.

Metal, Polyethylene, Ceramic Implantation

Design Related Issues

Biomaterials
• Composites
• metal
• Ceramics
• Polyethylene

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

Three typical steps

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

 Computational Solid Modelling

Geometrical 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.
Reverse Engineering
“Direct” Engineering
Design  Computer Model  Fabrication  Product

“Reverse” Engineering
Product (Bone)  CT  Data
 Computer Model
Reverse Engineering – Application

Model of the prosthesis stem

fitted to the medullary canal.

Slice Solid Model

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

 CT-based Modelling – Procedure

NURBs

Segmentation Stack of sectional Surface Solid Model

of CT images curves fitting

Step 1 selection of CT images that represent the desired anatomy of the bone,
Step 2 segmentation of the desired object(s) through detection of the contours
by determining the value of Hounsfield number CT at points
Step 3 creation of sectional curves along the CT points
Step 4 creation of surface model from the curves
Step 5 generation of the solid model of the femur
 Review 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 – Mimics
Mimics – http://www.materialise.com/materialise/view/en/65854-Homepage.html
CT, MRI images
Allow 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 Remesher
Export Software – Patran neutral, Ansys or Abaqus (surface mesh)
Material Assignment – Continuious
 Review 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$195

Import for CT, MRI via DICOM
Manually generate 3D solid model
Import to Solidworks, Catia, Unigraphics etc
Review on Commercial Software – 3D Doctor

http://www.ablesw.com/3d-doctor/index.html
General-Purpose Software for Solid Modelling

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

– Unigraphics (EDS)
– CATIA (Good free-from surface modeller, Dassault Systems -
IBM)
– SolidWorks (PC version high-end CAD)
– AutoCAD Mechanical Desktop
– I-DEAS (EDS)
– Solid Edge (EDS)
– MicroStation
– Intergraph
– Rhinoceros (NURBS modeling)
General-Purpose FEA Software in AMME
ANSYS (from ANSYS Inc.)
– A growth leader in CAE and integrated design analysis and optimisation
– Covering solid mechanics, kinematics, dynamics, and multi-physics (CFD,
EMAG, HT, Acoustics)
– Interfacing with key CAD systems

 Strand7 (Strand7 - Australian-own FE company, initiated from USYD)

– A powerful structural analysis program for analysing stress, vibration,
dynamic, nonlinear and heat transfer characteristics without node limits.
– Easy to use.

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

 CosmosWorks
– Build-in Solidworks CAD system
– Powerful linear solvers
 Introduction to ANSYS – GUI Layout
Utility Menu
Icon Toolbar Menu
Input Line Raise/Hidden Icon
Output
Window
Abbreviation Toolbar Menu

Main Menu

Graphics Area

User Prompt Info

Current Settings

 Mouse
Left mouse button 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).
Middle mouse button 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.
Right mouse button 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.
 ANSYS 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 Jobname

The 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 Ansys

jobname.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.
 ANSYS File System – Cont’d
 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 Title

This 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
all original graphs)
graphs

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
 ANSYS File System – Cont’d
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 Modelling

 Solid Modeling
Volumes
Be defined as the process of creating solid
models in CAD system.
Areas

 Definitions
Lines
–A solid model is defined by volumes, areas,
lines, and keypoints.
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.
Methods 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 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 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 Operation

 Add: Combines two or more entities A1

A2
A3

into one. Add

 Glue: Attaches two or more entities by

creating a common boundary between A2
A3
A2

them, which is uesful when you want to A1

Glue
maintain the distinction between entities
(such as for different materials).

 Overlap: Same as glue, except that the A2 A3 A4

input entities overlap each other. A1

Overlap A5

 Subtract: Removes the overlapping

portion of one or more entities from a A2
set of “base” entities, which can be A1 A3
Subtract
useful for creating holes or trimming off
portions of an entity.
Boolean Operation – Cont’d
 Divide: Cuts an entity into two or more
pieces that are still connected to each A1
A3
other by common boundaries. The
“cutting tool” may be the working plane, Divide A2
an area, a line, or even a volume. Useful
for “slicing and dicing” a complicated
volume into simpler volumes for brick
meshing.
A2 A3 Intersect A4

 Intersect: Keeps only the overlapping A1 Common

Intersection
portion of two or more entities.

 Partition: Cuts two or more intersecting L2

L6
entities into multiple pieces that are still L1 Intersect L3
L4
connected to each other by common L5

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.)
 ANSYS 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 Methods
There are two main meshing methods: Free and Mapped.
Free Mesh – Has no element shape restrictions.
• The mesh does not follow any pattern.
• 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.

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

hexahedra (volume)
•Typically has a regular pattern with obvious rows of elements.
•Suitable only for “regular” shapes such as rectangles and bricks.

Free meshing Mapped meshing

 Mesh 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 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.
 Unit (SI) – The ANSYS program does not assume a system of units for your
analysis. You can use any system of units
Time Length Mass Force Temperature Energy
s m kg N K J
Density Conductivity Specific Heat Flux Convection Modulus/stress
Kg/m3 J/(smK) J/(KgK) J/(sm2) J/(sm2K) Pa
Tasks 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: Model nail/callus in fractured femur

Upper part of bone

Coating

Implants

Callus

Fracture site

Lower part of bone