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Tutorial 1
Unbounded Diffusion
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This is a simple setup which creates two ligand release sites, red_ligand and blue_ligand. The use of different diffusion constants creates the difference between the two release sites
file run_parameters
/* run_parameters */ /* simple numerical variables */ dt = 1.0e-6 /* exponential notation: 1.0e-6 = 0.000001 */ iterations = 300 /* simple text variables */ viz_output_file = "viz_data" working_directory = "./" /* text expression */ ligand_parameters = working_directory & "June_7_1997"file June_7_1997
/* June_7_1997 */ /* simple numerical variables */ red_ligand_diffusion_constant = 6.0e-6 number_of_ligand_molecules = 5.0e3 release_site_diameter = 0.03 /* simple numerical variables, numerical expressions, and numerical arrays */ red_xy_value = 0.0 red_location = [red_xy_value, red_xy_value, 0.0] blue_x_value = red_xy_value-1.0 blue_location = [blue_x_value, 0.0-1.0, 0.0] blue_ligand_diffusion_constant = red_ligand_diffusion_constant/2.0file unbounded diffusion
/* unbounded diffusion */
INCLUDE_FILE = "run_parameters"
INCLUDE_FILE = ligand_parameters
TIME_STEP = dt
ITERATIONS = iterations
DEFINE_LIGAND red_ligand {DIFFUSION_CONSTANT = red_ligand_diffusion_constant}
DEFINE_LIGAND blue_ligand {DIFFUSION_CONSTANT = blue_ligand_diffusion_constant}
INSTANTIATE microdomain OBJECT {
red_ligand_release_site SPHERICAL_RELEASE_SITE {
LOCATION = red_location
LIGAND = red_ligand
NUMBER_TO_RELEASE = number_of_ligand_molecules
SITE_DIAMETER = release_site_diameter
}
blue_ligand_release_site SPHERICAL_RELEASE_SITE {
LOCATION = blue_location
LIGAND = blue_ligand
NUMBER_TO_RELEASE = number_of_ligand_molecules
SITE_DIAMETER = release_site_diameter
}
}
/*
VIZ_DATA_OUTPUT {
MODE = DX
STATE_VALUES {red_ligand = 1 blue_ligand = 2}
OBJECT_FILE_DESIGNATORS {microdomain = viz_output_file & ".microdomain"}
ITERATION_LIST = [0, [5 TO 70 STEP 10], [100 TO 250 STEP 50], 299]
}
*/
REACTION_DATA_OUTPUT {
STEP = 2*dt
{COUNT[red_ligand,WORLD,FOR_EACH_TIME_STEP]} =>
"unbounded_diffusion.red_ligand"
{COUNT[blue_ligand,WORLD,FOR_EACH_TIME_STEP]} => INPUT_FILE & ".blue_ligand"
}