Biomedical Modeling and Simulation Presented by Richard C

Biomedical Modeling and Simulation Presented by 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

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 2 Ward_Bio. Model. Sim_0611 Finite element analysis (FEA) from NURBS

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 highperformance computer using Net. Solve · 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 3

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. 25 -52, 2001) 4

Species pulmonary flow modeling PICMSS (Parallel Interoperable Mechanics System Simulator) used to generate species flow using the airway model Airway model Comen, Kleinstreuer, and Zhang (J Fluid Mech, 435, pp. 25 -52, 2001) 5 Image courtesy of Shawn Ericson, JICS

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

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

Modeling toxic exposure: Inhalation of Hg vapor Promptly exhaled Hg 0 exhaled after conversion from Hg++ Respiratory tract model Red blood cells Plasma Hg 0 Brain Long-term Other Long-term Liver Long-term Kidneys Long-term Urine Urinary bladder GI tract model Plasma Hg 0 Diffusibl e Nondiffusible Feces Model developed by R. W. Leggett, K. F. Eckerman, and N. B. Munro Life Sciences Division 8

Virtual Soldier Project Support provided by Defense Advanced Research Projects Agency (DARPA) Program Manager: Rick Satava 9 Ward_Bio. Model. Sim_0611

ORNL contributes to DARPA Virtual Soldier Preparation Post-wounding Assemble detailed individual medical records Postwounding information Use pre- and post-wounding individual data to create predictive model of specific patient Store records on “dog tags” Build compute r model of “generic ” patient 10 10 Ward_Bio. Model. Sim_0611 Prewounding information ORNL involved Computer model provides total informational awareness forward medical team

High-level integrative physiological models Circuit models describe blood flow and arterial and venous pressures System circulation Four-Chamber heart model Airway mechanics + + - - + + - Cardiovascular/ Computations performed by pulmonary flow University of Washington 11 Ward_Bio. Model. Sim_0611 Pulmonary system

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 Mc. Culloch’s Cardiac Mechanics Research Group (University of California in San Diego) 12 Ward_Bio. Model. Sim_0611

Computational Speed (beats/second) Computational speed up for finite-element simulations 10 -0 10 minutes/beat 10 -1 10 -2 2. 3 GHz Pentium 4 21 ODE model 16 dual CPU nodes of Linux cluster 10 -3 78 hours/beat 2. 0 GHz Pentium 4 21 ODE model 1 CPU 10 -4 10 -5 300 MHz SGI Origin 2100 2 ODE model 1 CPU 10 -6 2002 2003 833 MHz Pentium 3 2 ODE model 1 CPU 2004 2005 Year 13 2. 3 GHz Pentium 4 76 ODE model 96 dual CPU nodes of Linux cluster Data courtesy of the Cardiac Mechanics Research Group, UCSD 2006 2007 2008

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

ORNL Hot. Box integrates all the DARPA Virtual Soldier windows Predicted location of wound SCIRun Net Anatomical ontology: Foundational model of anatomy Hot. Box interface Physiology display Geometry window with thorax model 15 Ward_Bio. Model. Sim_0611

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 16 Ward_Bio. Model. Sim_0611

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) 17

Virtual Soldier Or Combat Medical Support Enters the Information Age 18

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

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

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 Mc. Murray, 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 21

Virtual Human Modeling Example Projects 22

Erica Sherritze Use NURBS Software to Design Pulmonary Airway 23

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

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

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

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

Jennifer Bennett Visualize Arterial Fluid Flow · Data supplied by Pearl Flath · Convert original data to HDF 5 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 28

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

Contacts Richard Ward Senior Research Scientist Computational Sciences and Engineering Division (865) 574 -5449 wardrc@ornl. gov Barbara Beckerman Program Manager, Biomedical Engineering Computational Sciences and Engineering Division (865) 576 -2681 beckermanbg@ornl. gov 30 Ward_Bio. Model. Sim_0611