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Biomedical Modeling and Simulation

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

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Biomedical Modeling and Simulation

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

  2. 2 Ward_BioModelSim_0611 Geometry models using imaging data X-ray CT data (example: NationalLibrary of Medicine Visible Human) NURBS (nonuniformrational B-spline) modelfrom visible human CT data Finite elementanalysis (FEA)from NURBS

  3. Collaboration with A.J. Baker, UT, and Shawn Ericson, UT/ORNL JICS Using high-performance computingresources 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

  4. Deposit of particulatesrelated to complexityof flow revealed Rotational flow inairways visualized Airway model Comen, Kleinstreuer, and Zhang(J Fluid Mech, 435, pp. 25-52, 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 ofShawn Ericson, JICS Comen, Kleinstreuer, and Zhang(J Fluid Mech, 435, pp. 25-52, 2001)

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

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

  8. Hg0 exhaled after conversion from Hg++ Promptly exhaled Hg0 Promptly exhaled Hg0 Respiratory tract model Red blood cells PlasmaHg0 PlasmaHg0 Brain Long-term Diffusible Other Long-term Liver Long-term Non-diffusible Kidneys Long-term Urine Urinarybladder GI tract model Feces Modeling toxic exposure: Inhalation of Hg vapor Model developed by R. W. Leggett, K. F. Eckerman, and N. B. MunroLife Sciences Division

  9. 9 Ward_BioModelSim_0611 Virtual Soldier Project Support provided byDefense Advanced Research Projects Agency (DARPA)Program Manager: Rick Satava

  10. Post-wounding information Pre-wounding information Use pre- and post-wounding individual data to create predictive model of specific patient ORNL contributes toDARPA Virtual Soldier Preparation Post-wounding Assemble detailed individual medical records Store records on “dog tags” Build computer model of “generic” patient ORNLinvolved Computer model provides total informational awareness for forward medical team 10 Ward_BioModelSim_0611

  11. Cardiovascular/pulmonary flow High-level integrative physiological models System circulation Circuit models describe blood flow and arterial and venous pressures Four-Chamberheart model Airway mechanics + - - + Pulmonarysystem + - + - Computations performed by University of Washington 11 Ward_BioModelSim_0611

  12. Finite-element heart simulations • Computations combine biomechanical, electrophysiology, and biochemistry models • Simulations conducted on two 105-nodedual Opteron Dell Linux clusters • Typically used only up to 32 nodesper simulation • Overall, obtained substantial speedups by combining new algorithms and high-performancecomputing • Used pre-computation and interpolation to allow team to develop real-time models for 2 h worth of heartbeats Conducted byAndrew McCulloch’s Cardiac Mechanics Research Group(University of California in San Diego) 12 Ward_BioModelSim_0611

  13. 10-0 10-1 10 minutes/beat 10-2 2.3 GHz Pentium 4 21 ODE model 16 dual CPU nodes of Linux cluster 2.3 GHz Pentium 4 76 ODE model 96 dual CPU nodes of Linux cluster Computational Speed (beats/second) 10-3 78 hours/beat 2.0 GHz Pentium 4 21 ODE model 1 CPU 10-4 300 MHz SGI Origin 2100 2 ODE model 1 CPU 833 MHz Pentium 3 2 ODE model 1 CPU 10-5 10-6 2002 2003 2004 2005 2006 2007 2008 Year Computational speed up for finite-element simulations Data courtesy of the Cardiac Mechanics Research Group, UCSD

  14. Taxonomy Simulation Results Results Results Results Ontology Results ORNL developed middleware architecture 3D segmentedanatomy model Wound trajectorydatabase Experimentaldata Prediction software An early plan VSP middleware WS WS WS Data repository WS = Web services

  15. ORNL HotBox integrates all the DARPA Virtual Soldier windows Predicted locationof wound SCIRun Net Anatomical ontology: Foundational model of anatomy HotBox interface Physiology display Geometry window with thorax model 15 Ward_BioModelSim_0611

  16. 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 ORNL solves biomedical problems 16 Ward_BioModelSim_0611

  17. Virtual Human ModelingRichard C. WardComputational 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. Erica Sherritze Use NURBS Software to Design Pulmonary Airway

  24. 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. Gary Atkins Display Surfaces of Organ Segments using VTK Software

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

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

  28. 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 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_BioModelSim_0611

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