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Biomedical Modeling
and Simulation
Presented By
Ahsan Bukhari
CMS: 799-2020
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
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
1
Rotational flow in
airways visualized
Deposit of particulates
related to complexity
of flow revealed
Airway model
Cardiovascular modeling environments
High-performance
computing resources
Connect
Integrate
Models
Computations
Visualization
Predictions
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
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 ODE model
1 CPU
2.0 GHz Pentium 4
21 ODE model
1 CPU
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
78 hours/beat
10 minutes/beat
Data courtesy of the
Cardiac Mechanics Research Group, UCSD
Revolutionizing Prosthetics
Create revolutionary design of forearm/hand prosthesis with realistic
look, feel and action.
Virtual Human Modeling
Example Projects
Use NURBS Software to Design
Pulmonary Airway
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.
Link 3D Imagery to Ontology
Use Foundational Model of Anatomy and Web Services
Web Service Implementation of
Physiology Models
Injury to left ventricle of the heart. Results plotted using tcl/tk.
Model supplied by U. of Washington.
Mathematical Visualization of the Lungs
Using Fractal Geometry
Fractal Tree CAD Model
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

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M&S Presentation.pptx

  • 1. Biomedical Modeling and Simulation Presented By Ahsan Bukhari CMS: 799-2020
  • 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
  • 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 1
  • 4. Rotational flow in airways visualized Deposit of particulates related to complexity of flow revealed Airway model
  • 5. Cardiovascular modeling environments High-performance computing resources Connect Integrate Models Computations Visualization Predictions
  • 6. 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
  • 7. 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 ODE model 1 CPU 2.0 GHz Pentium 4 21 ODE model 1 CPU 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 78 hours/beat 10 minutes/beat Data courtesy of the Cardiac Mechanics Research Group, UCSD
  • 8. Revolutionizing Prosthetics Create revolutionary design of forearm/hand prosthesis with realistic look, feel and action.
  • 10. Use NURBS Software to Design Pulmonary Airway
  • 11. 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.
  • 12. Link 3D Imagery to Ontology Use Foundational Model of Anatomy and Web Services
  • 13. Web Service Implementation of Physiology Models Injury to left ventricle of the heart. Results plotted using tcl/tk. Model supplied by U. of Washington.
  • 14. Mathematical Visualization of the Lungs Using Fractal Geometry Fractal Tree CAD Model
  • 15. 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