Biomedical Computational Science PREF Outreach Program
Computational Biomedical Science Batmen Camp Outreach Program Dr. Suzanne Shontz Department of Mathematics and Statistics Department of Computer Science and Engineering Center for Computational Sciences Graduate Program in Computational Engineering
June 24, 2014 Todays Agenda You will learn: about computational science and engineering and computational biomedical science; how computational tools can be used to improve treatment of a disease:
deep vein thrombosis; other areas of engineering where these tools can be used; how to design an algorithm. Introduction to Computational Biomedical Science Computational Science and Engineering
What is Computational Biomedical Science? Computational science and engineering: The application of mathematical and computational techniques to simulate a phenomenon in science or engineering. Biomedical science: The application of the principles of the natural sciences to medicine.
Computational biomedical science: The application of mathematical and computational techniques to medicine. Deep Vein Thrombosis Famous People What do these famous people have in common?
Serena Williams (US Tennis Star) Dick Cheney (US Vice President) David Bloom (US NBC Correspondent in Iraq) They all suffered from blood clots. Deep Vein Thrombosis (DVT) Formation of blood clot in deep vein (e.g., leg)
The leg can become swollen, hot, red, warm, and painful. Complication: The clot can break free and travel into the lungs. How would this affect you? Detecting a Pulmonary Embolism
How do doctors treat blood clots? Two main treatment options: 1. Medicine (blood thinners) 2. Insertion of medical device to trap the blood clots (IVC filters) IVC Filters
There are many designs. Here are a few. How does a doctor choose which IVC filter to use? Any thoughts? The decision is typically based on: which device(s) the doctor learned to implant in medical school/residency and
which device the doctor can obtain for the lowest price. How can computational scientists help? Computational scientists can run simulations and advise vascular surgeons on: selection of the appropriate IVC filter placement of the IVC filter.
Why do you think the choice of IVC filter and its placement should depend upon the patient? Simulation Ingredients Patient medical data (CT scans) model of patient veins and blood clots (requires image processing) Model of IVC filter (created via computer-aided design)
Equations for blood flow Simulate the blood flow in the vein with the IVC filter present IVC Filter Simulations The goal is to simulate (on the computer) the effect of placing a particular IVC filter in the vein of a given patient.
Repeat the simulation with different IVC filters and different placements of the IVC filters. Choose the IVC filter and placement that is best for the patient. Sample Simulation Geometric Models Sample Simulation Geometric Models
Mesh Generation Geometric Modeling via Mesh Generation Geometric models must be created for the IVC filter blood flow simulation. The models are created by the generation of meshes on the 3D objects.
What is a Mesh? To simulate blood flow the vein with the IVC filter present, for example, the vein and filter must be represented by a geometric model. This model is represented as a mesh. A mesh is a collection of vertices and elements with certain properties.
Examples of Meshes How are Meshes Generated? Computer software is used to generate meshes. We will see one way in which meshes are generated, i.e., using the advancing front algorithm.
Slides from Steven Owen, 16th IMR Short Course Advancing Front Computational Modeling Sciences Department C A
B Begin with boundary mesh - define as initial front For each edge (face) on front, locate ideal node C based on front AB 26
Advancing Front Computational Modeling Sciences Department r C A
Determine if any other nodes on current front are within search radius r of ideal location C (Choose D instead of C) 27 D B
Advancing Front Computational Modeling Sciences Department D Book-Keeping: New front edges added and deleted from front as triangles are formed
Continue until no front edges remain on front 28 Advancing Front Computational Modeling Sciences Department Book-Keeping: New front edges added and deleted from front as triangles are formed
Continue until no front edges remain on front 29 Advancing Front Computational Modeling Sciences Department Book-Keeping: New front edges added and deleted from front as triangles are formed
Continue until no front edges remain on front 30 Advancing Front Computational Modeling Sciences Department Book-Keeping: New front edges added and deleted from front as triangles are formed
Continue until no front edges remain on front 31 Advancing Front Computational Modeling Sciences Department r
C A B Where multiple choices are available, use best quality (closest shape to equilateral) Reject any that would intersect existing front
Reject any inverted triangles (|AB X AC| > 0) (Lohner,88;96)(Lo,91) 32 Beating Heart Simulation: Dynamic Meshes Canine ventricles (surface mesh)
Canine ventricles (volume mesh) Joint work with Stephen Vavasis, University of Waterloo Some Non-Biomedical Meshing Applications
Summary There are many opportunities for computational scientists to aid doctors. Mesh generation is an important tool for computational biomedical science. Its use extends far beyond computational biomedical science to other areas of engineering and science.
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