1. Biomedical Modeling and Simulation
Richard C. Ward
Modeling and Simulation Group
Computational Sciences and Engineering Division
Research supported by the Department of Energy’s Office of Science Office of Advanced Scientific Computing Research
Presented to the RAMS Program Mentoring Meeting
December 10, 2007

2. Geometry models using imaging data
X-ray CT data
(example: National Library of Medicine
Visible Human)
NURBS (nonuniform rational B-spline) model from visible human CT data
Finite element analysis (FEA) from NURBS
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3. Using high-performance computing resources for pulmonary flow modeling
Finite element problem-solving environment
Computational fluid dynamics
Fluid-structure interactions
Equation formulator
Java GUI on user’s desktop computer
Automatic mesh partitioning
Computations routed to high-performance computer using NetSolve
Results returned to user’s desktop computer
Links to client-server visualization software
Automated archiving of scientific data sets
Collaboration with A.J. Baker, UT, and Shawn Ericson, UT/ORNL JICS

4. Rotational flow in airways visualized
Deposit of particulates related to complexity of flow revealed
Airway model
Comen, Kleinstreuer, and Zhang (J Fluid Mech, 435, pp , 2001)

5. Species pulmonary flow modeling
PICMSS (Parallel Interoperable Mechanics System Simulator) used to generate species flow using the airway model
Airway model
Image courtesy of Shawn Ericson, JICS
Comen, Kleinstreuer, and Zhang (J Fluid Mech, 435, pp , 2001)

6. Virtual Human PSE: Rideout Left Heart Model
Model sliders
control simulation

7. Cardiovascular modeling environments
Integrate
Connect
Models
Computations
High-performance computing resources
Visualization
Predictions

8. Modeling toxic exposure: Inhalation of Hg vapor
Promptly
exhaled Hg0
Hg0 exhaled after conversion from Hg++
Respiratory tract model
Red blood cells
Brain
Long-term
Other
Liver
Kidneys
Plasma Hg0
Diffusible
Non- diffusible
Urinary bladder
Urine
Feces
GI tract model
Model developed by
R. W. Leggett, K. F. Eckerman, and N. B. Munro Life Sciences Division

9. Virtual Soldier Project
Support provided by Defense Advanced Research Projects Agency (DARPA) Program Manager: Rick Satava
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10. ORNL contributes to DARPA Virtual Soldier
Preparation
Post-wounding
Assemble detailed individual medical records
Post-wounding information
Pre-wounding information
Use pre- and post-wounding individual data to create predictive model of specific patient
Store records on “dog tags”
Build computer model of “generic” patient
ORNL involved
Computer model provides total informational awareness for forward medical team
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11. High-level integrative physiological models
System
circulation
Circuit models describe blood flow and arterial and venous pressures
Four-Chamber heart model
Airway mechanics
+ -
- +
+ -
Pulmonary system
+ -
Cardiovascular/ pulmonary flow
Computations performed by University of Washington
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12. Finite-element heart simulations
Computations combine biomechanical, electrophysiology, and biochemistry models
Simulations conducted on two 105-node dual Opteron Dell Linux clusters
Typically used only up to 32 nodes per simulation
Overall, obtained substantial speedups by combining new algorithms and high-performance computing
Used pre-computation and interpolation to allow team to develop real-time models for 2 h worth of heartbeats
Conducted by Andrew McCulloch’s Cardiac Mechanics Research Group (University of California in San Diego)
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13. Computational speed up for finite-element simulations
2002
2003
2004
2005
2006
2007
2008
Year
10-6
10-5
10-4
10-3
10-2
10-1
10-0
Computational Speed (beats/second)
300 MHz SGI
Origin 2100
2 ODE model
1 CPU
833 MHz Pentium 3
2.0 GHz Pentium 4
21 ODE model
2.3 GHz Pentium 4
16 dual CPU nodes of Linux cluster
76 ODE model
96 dual CPU nodes of Linux cluster
78 hours/beat
10 minutes/beat
Data courtesy of the Cardiac Mechanics Research Group, UCSD

14. ORNL developed middleware architecture
3D segmented anatomy model
Wound trajectory database
Experimental data
Prediction
software
An early plan
VSP middleware
Taxonomy
Results
Ontology
Simulation
Results WS WS WS
Data repository
WS = Web services

15. ORNL HotBox integrates all the DARPA Virtual Soldier windows
Predicted location of wound
SCIRun Net
Anatomical ontology:
Foundational model of anatomy
HotBox interface
Physiology display
Geometry window with thorax model
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16. ORNL solves biomedical problems
Convert CT slice data to finite-element mesh
Abdominal aneurysms
Prediction of wounds
Data repositories
Parallel computations
Computational tools for toxicants
Agent technologies
Ontologies and informatics
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17. Virtual Human Modeling Richard C
Virtual Human Modeling Richard C. Ward Computational Sciences and Engineering Division
Virtual Human Computational Environment
Integrated Respiratory System Modeling
Virtual Soldier Project (DARPA)
Virtual Autopsy Project (DARPA)
Revolutionizing Prosthetics (DARPA)

18. Virtual
Soldier Or
Combat Medical Support
Enters the Information Age

19. One Goal of Virtual Soldier Project: Create a
Holographic Medical Electronic Representation
The HotBox connects:
Physiology display
Geometry window
Anatomical ontology
SCIRun Net
Physiology Monitor
The HotBox interface
Thorax model

20. Revolutionizing Prosthetics
Create revolutionary design of forearm/hand prosthesis with realistic look, feel and action.

21. Students Contribute Significantly to Virtual Human Modeling
Virtual Human Computational Environment
Eduardo Difilippo, SULI 1999
Dan Price, SULI 2000
Joy Wright, PST, 2000
Ming Gu, GLCA 2001
Integrated Respiratory System Modeling
Jacob McMurray, SULI 2000
Todd Miller, CCT 2000
Erica Sherritze, PST 2003
Human Abdominal Aortic Aneurysm (Kara Kruse)
Wiliam Jenkins, SULI 2001
Joel Outten, SULI 2002
Virtual Soldier Project (DARPA)
Gary Atkins, RAMS 2004
Sarah Wing, SULI 2004
Pearl Flath, SULI 2005
Jennifer Bennett, RAMS 2005
Matt Woerner, HERE 2005

22. Virtual Human Modeling
Example Projects

23. Use NURBS Software to Design
Erica Sherritze
Use NURBS Software to Design
Pulmonary Airway

24. Display Surfaces of Organ Segments using VTK Software
Gary Atkins
Display Surfaces of Organ Segments using VTK Software
Simulate a fragment wound to the right ventricle.
Display each organ segment as fragment traverses that segment.
Surfaces rendered using VTK.
Work with program obtained GE Global Research.

25. Link 3D Imagery to Ontology
Gary Atkins
Link 3D Imagery to Ontology
Use Foundational Model of Anatomy and Web Services

26. Web Service Implementation of
Sarah Wing
Web Service Implementation of
Physiology Models
Injury to left ventricle of the heart. Results plotted using tcl/tk.
Model supplied by U. of Washington.

27. Mathematical Visualization of the Lungs Using Fractal Geometry
Matt Woerner
Mathematical Visualization of the Lungs
Using Fractal Geometry
Fractal Tree
CAD Model

28. Visualize Arterial Fluid Flow
Jennifer Bennett
Visualize Arterial Fluid Flow
Data supplied by Pearl Flath
Convert original data to HDF5 format
Create a SCIRun network of modules to compute and interpret data
Launch the SCIRun Viewer module, a GUI (Graphical User Interface)
Network makes possible interactive exploration of scalar and vector flow fields

29. Summary
Students Have Contributed Significantly to Virtual Human Modeling!
Students learned:
Visualization
Representations of information in ontologies
Practical programming (Java, Tcl/Tk and VTK)
Integration of software components
Concepts learned are applicable to real world
IT Industry
e-Commerce
Games and animation industry
Modeling and simulation

30. Contacts Richard Ward Barbara Beckerman Senior Research Scientist
Computational Sciences and Engineering Division
(865)
Barbara Beckerman
Program Manager, Biomedical Engineering
Computational Sciences and Engineering Division
(865)
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