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rheilandrheiland
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‎config/bacteria.xml‎

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<PhysiCell_settings version="devel-version">
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<domain>
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<x_min>-200.0</x_min>
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<x_max>200.0</x_max>
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<y_min>-200.0</y_min>
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<y_max>200.0</y_max>
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<z_min>-10.0</z_min>
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<z_max>10.0</z_max>
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<dx>20.0</dx>
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<dy>20.0</dy>
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<dz>20.0</dz>
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<use_2D>true</use_2D>
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</domain>
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<overall>
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<max_time units="min">5040.0</max_time>
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<time_units>min</time_units>
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<space_units>micron</space_units>
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<dt_diffusion units="min">0.01</dt_diffusion>
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<dt_mechanics units="min">0.1</dt_mechanics>
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<dt_phenotype units="min">6</dt_phenotype>
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</overall>
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<parallel>
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<omp_num_threads>2</omp_num_threads>
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</parallel>
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<save>
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<folder>output_bacteria</folder>
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<full_data>
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<interval units="min">60</interval>
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<enable>true</enable>
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</full_data>
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<SVG>
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<interval units="min">60</interval>
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<enable>true</enable>
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<plot_substrate enabled="false" limits="true">
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<substrate>substrate</substrate>
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<colormap>YlOrRd</colormap>
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<min_conc>0</min_conc>
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<max_conc>1</max_conc>
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</plot_substrate>
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</SVG>
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<legacy_data>
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<enable>false</enable>
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</legacy_data>
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</save>
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<options>
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<legacy_random_points_on_sphere_in_divide>false</legacy_random_points_on_sphere_in_divide>
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<virtual_wall_at_domain_edge>true</virtual_wall_at_domain_edge>
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<disable_automated_spring_adhesions>false</disable_automated_spring_adhesions>
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<random_seed>system_clock</random_seed>
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</options>
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<microenvironment_setup>
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<variable name="substrate" units="dimensionless" ID="0">
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<physical_parameter_set>
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<diffusion_coefficient units="micron^2/min">100000.0</diffusion_coefficient>
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<decay_rate units="1/min">10</decay_rate>
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</physical_parameter_set>
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<initial_condition units="mmHg">0</initial_condition>
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<Dirichlet_boundary_condition units="mmHg" enabled="False">0</Dirichlet_boundary_condition>
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<Dirichlet_options>
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<boundary_value ID="xmin" enabled="False">0</boundary_value>
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<boundary_value ID="xmax" enabled="False">0</boundary_value>
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<boundary_value ID="ymin" enabled="False">0</boundary_value>
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<boundary_value ID="ymax" enabled="False">0</boundary_value>
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<boundary_value ID="zmin" enabled="False">0</boundary_value>
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<boundary_value ID="zmax" enabled="False">0</boundary_value>
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</Dirichlet_options>
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</variable>
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<options>
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<calculate_gradients>true</calculate_gradients>
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<track_internalized_substrates_in_each_agent>true</track_internalized_substrates_in_each_agent>
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<initial_condition type="matlab" enabled="false">
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<filename>./config/initial.mat</filename>
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</initial_condition>
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<dirichlet_nodes type="matlab" enabled="false">
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<filename>./config/dirichlet.mat</filename>
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</dirichlet_nodes>
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</options>
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</microenvironment_setup>
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<cell_definitions>
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<cell_definition name="default" ID="0">
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<phenotype>
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<cycle code="5" name="live">
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<phase_durations units="min">
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<duration index="0" fixed_duration="false">240</duration>
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</phase_durations>
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<standard_asymmetric_division enabled="False">
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<asymmetric_division_probability name="default" units="dimensionless">1.0</asymmetric_division_probability>
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</standard_asymmetric_division>
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</cycle>
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<death>
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<model code="100" name="apoptosis">
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<death_rate units="1/min">0</death_rate>
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<phase_durations units="min">
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<duration index="0" fixed_duration="true">516</duration>
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</phase_durations>
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<parameters>
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<unlysed_fluid_change_rate units="1/min">0.05</unlysed_fluid_change_rate>
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<lysed_fluid_change_rate units="1/min">0</lysed_fluid_change_rate>
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<cytoplasmic_biomass_change_rate units="1/min">1.66667e-02</cytoplasmic_biomass_change_rate>
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<nuclear_biomass_change_rate units="1/min">5.83333e-03</nuclear_biomass_change_rate>
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<calcification_rate units="1/min">0</calcification_rate>
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<relative_rupture_volume units="dimensionless">2.0</relative_rupture_volume>
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</parameters>
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</model>
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<model code="101" name="necrosis">
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<death_rate units="1/min">0.0</death_rate>
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<phase_durations units="min">
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<duration index="0" fixed_duration="true">0</duration>
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<duration index="1" fixed_duration="true">86400</duration>
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</phase_durations>
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<parameters>
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<unlysed_fluid_change_rate units="1/min">1.11667e-2</unlysed_fluid_change_rate>
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<lysed_fluid_change_rate units="1/min">8.33333e-4</lysed_fluid_change_rate>
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<cytoplasmic_biomass_change_rate units="1/min">5.33333e-5</cytoplasmic_biomass_change_rate>
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<nuclear_biomass_change_rate units="1/min">2.16667e-3</nuclear_biomass_change_rate>
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<calcification_rate units="1/min">0</calcification_rate>
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<relative_rupture_volume units="dimensionless">2.0</relative_rupture_volume>
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</parameters>
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</model>
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</death>
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<volume>
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<total units="micron^3">2494</total>
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<fluid_fraction units="dimensionless">0.75</fluid_fraction>
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<nuclear units="micron^3">540</nuclear>
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<fluid_change_rate units="1/min">0.05</fluid_change_rate>
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<cytoplasmic_biomass_change_rate units="1/min">0.0045</cytoplasmic_biomass_change_rate>
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<nuclear_biomass_change_rate units="1/min">0.0055</nuclear_biomass_change_rate>
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<calcified_fraction units="dimensionless">0</calcified_fraction>
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<calcification_rate units="1/min">0</calcification_rate>
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<relative_rupture_volume units="dimensionless">2.0</relative_rupture_volume>
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</volume>
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<mechanics>
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<cell_cell_adhesion_strength units="micron/min">0.4</cell_cell_adhesion_strength>
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<cell_cell_repulsion_strength units="micron/min">10.0</cell_cell_repulsion_strength>
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<relative_maximum_adhesion_distance units="dimensionless">1.25</relative_maximum_adhesion_distance>
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<cell_adhesion_affinities>
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<cell_adhesion_affinity name="default">1</cell_adhesion_affinity>
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</cell_adhesion_affinities>
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<options>
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<set_relative_equilibrium_distance enabled="false" units="dimensionless">1.8</set_relative_equilibrium_distance>
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<set_absolute_equilibrium_distance enabled="false" units="micron">15.12</set_absolute_equilibrium_distance>
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</options>
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<attachment_elastic_constant units="1/min">0.01</attachment_elastic_constant>
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<attachment_rate units="1/min">0.0</attachment_rate>
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<detachment_rate units="1/min">0.0</detachment_rate>
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<maximum_number_of_attachments>12</maximum_number_of_attachments>
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</mechanics>
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<motility>
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<speed units="micron/min">1</speed>
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<persistence_time units="min">1</persistence_time>
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<migration_bias units="dimensionless">.5</migration_bias>
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<options>
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<enabled>false</enabled>
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<use_2D>true</use_2D>
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<chemotaxis>
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<enabled>false</enabled>
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<substrate>substrate</substrate>
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<direction>1</direction>
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</chemotaxis>
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<advanced_chemotaxis>
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<enabled>false</enabled>
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<normalize_each_gradient>false</normalize_each_gradient>
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<chemotactic_sensitivities>
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<chemotactic_sensitivity substrate="substrate">0.0</chemotactic_sensitivity>
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</chemotactic_sensitivities>
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</advanced_chemotaxis>
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</options>
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</motility>
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<secretion>
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<substrate name="substrate">
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<secretion_rate units="1/min">0</secretion_rate>
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<secretion_target units="substrate density">1</secretion_target>
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<uptake_rate units="1/min">0</uptake_rate>
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<net_export_rate units="total substrate/min">0</net_export_rate>
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</substrate>
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</secretion>
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<cell_interactions>
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<apoptotic_phagocytosis_rate units="1/min">0</apoptotic_phagocytosis_rate>
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<necrotic_phagocytosis_rate units="1/min">0</necrotic_phagocytosis_rate>
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<other_dead_phagocytosis_rate units="1/min">0</other_dead_phagocytosis_rate>
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<live_phagocytosis_rates>
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<phagocytosis_rate name="default" units="1/min">0</phagocytosis_rate>
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</live_phagocytosis_rates>
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<attack_rates>
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<attack_rate name="default" units="1/min">0</attack_rate>
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</attack_rates>
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<attack_damage_rate units="1/min">1</attack_damage_rate>
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<attack_duration units="min">0.1</attack_duration>
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<fusion_rates>
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<fusion_rate name="default" units="1/min">0</fusion_rate>
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</fusion_rates>
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</cell_interactions>
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<cell_transformations>
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<transformation_rates>
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<transformation_rate name="default" units="1/min">0</transformation_rate>
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</transformation_rates>
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</cell_transformations>
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<cell_integrity>
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<damage_rate units="1/min">0.0</damage_rate>
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<damage_repair_rate units="1/min">0.0</damage_repair_rate>
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</cell_integrity>
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</phenotype>
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<custom_data>
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<theta conserved="false" units="dimensionless" description="">0</theta>
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</custom_data>
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<initial_parameter_distributions enabled="false">
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<distribution enabled="false" type="Log10Normal" check_base="true">
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<behavior>Volume</behavior>
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<mu>4</mu>
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<sigma>2</sigma>
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<upper_bound>100000</upper_bound>
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</distribution>
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<distribution enabled="false" type="LogUniform" check_base="true">
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<behavior>apoptosis</behavior>
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<min>1e-6</min>
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<max>1e-2</max>
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</distribution>
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</initial_parameter_distributions>
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</cell_definition>
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</cell_definitions>
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<initial_conditions>
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<cell_positions type="csv" enabled="true">
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<folder>./config</folder>
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<filename>cells_bacteria.csv</filename>
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</cell_positions>
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</initial_conditions>
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<cell_rules>
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<rulesets>
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<ruleset protocol="CBHG" version="3.0" format="csv" enabled="false">
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<folder>./config</folder>
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<filename>cell_rules.csv</filename>
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</ruleset>
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</rulesets>
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<settings />
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</cell_rules>
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<user_parameters>
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<number_of_cells type="int" units="none" description="initial number of cells (for each cell type)">0</number_of_cells>
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</user_parameters>
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</PhysiCell_settings>

‎config/cells_bacteria.csv‎

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x,y,z,type,custom:theta,volume,cycle entry,custom:GFP
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0.0,-150.0,0.0,default,0
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-12.0,-140.0,0.0,default,2.06
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0.0,-130.0,0.0,default,1.27
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12.0,-140.0,0.0,default,0.49

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