Aroli Marcellinus

Computation Medicine Lab

Kumoh National Institute of Technology
Gumi, South Korea
CONTENTS
Brief introduction about the Cardiac Simulation.
Explanation about the system of the simulation,
limitation in the development, and so on.
Code Presentation.
WHY WE NEED TO CREATE IT?
Analyze the symptoms that happened in the
cardiovascular organ without dissecting the real one.
We can reuse the simulation data of the cardiac
simulation for multiple research, so we can save time
not to do repetitive steps to get some data.
As a platform for testing a medicine that impacts the
cardiovascular system.
CURRENT CARDIAC SIMULATION
Using pre-coded cell model to do the single-cell
simulation (included the initial value).
Using some PDE solver and ODE solver to create the
cardiac meshes (for the ODE, using hardcoded Euler
BDF).
Return some numerical data as files, such as the action
potential and the ionic current.
Also, we will get the animation of the cardiac movement, so
we can see the animation result of cardiac movement and
action potential during the time.
Moreover, we have some features to include the mutation
to the simulation, so we can observe the condition when
the heart become mutated.
IMPROVEMENT PLAN
Use the CellML files as the input for single-cell
simulation.
Change the ODE solver from manual Euler to use
CVODE as the solver.
Create some mutated condition of the single-cell
simulation using CellML files.
Create the 3D simulation using the CellML files as the
input.
OBJECTIVES
Create a single-cell simulation using CellML files
as the input.
PROPOSED SCHEMATICS
METHODS
Using CellML file based on the ten Tusscher 2006.
Using the OpenCOR to convert the CellML files into a
C++ source code files.
The simulator will be built using C++ language.
The method of solving the ODE will use Euler BDF or
using CVODE, with Newton Iteration and CVDiag
solver.
Simulation Workflow
SIMULATION RESULT (ACTION
POTENTIAL)
PERFORMANCE REPORT
450
Simulator Performance, using dt = 0.1
T
400 400
i 350
m
e 300

250
(

s 232
e 200 New Euler
c
150 New CVODE
o
n 100
d 89
50 43
)

5 9 23
0 1 2 11
50 100 500 1000 10000
N
LIMITATION
The simulator should be using CellML files directly as
the input. However, the API/library documentations
and examples related to the CellML are limited.
Because of that, we use the OpenCOR as the
alternatives to convert the CellML files into a source
code.
SUMMARY
We can build a simulator that use the CellML
information.
However, because of the lack of documentation for
using the CellML files, we need to convert the CellML
files into source codes.
As we can see, the result from OpenCOR and from the
simulation is same, so the result is valid.
Although we can use both of the Euler BDF and
CVODE, the Euler BDF still has better performance.
FURTHER WORKS
Applying mutation to the simulation.
Using libCellML to use CellML files directly to the
simulator program.
Apply the CellML as the input to the 3D simulation.