PhysiCell_settings.xml 32.5 KB
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<?xml version="1.0" encoding="UTF-8"?>
<!--
/*
###############################################################################
# If you use PhysiCell in your project, please cite PhysiCell and the version #
# number, such as below:                                                      #
#                                                                             #
# We implemented and solved the model using PhysiCell (Version x.y.z) [1].    #
#                                                                             #
# [1] A Ghaffarizadeh, R Heiland, SH Friedman, SM Mumenthaler, and P Macklin, #
#     PhysiCell: an Open Source Physics-Based Cell Simulator for Multicellu-  #
#     lar Systems, PLoS Comput. Biol. 14(2): e1005991, 2018                   #
#     DOI: 10.1371/journal.pcbi.1005991                                       #
#                                                                             #
# See VERSION.txt or call get_PhysiCell_version() to get the current version  #
#     x.y.z. Call display_citations() to get detailed information on all cite-#
#     able software used in your PhysiCell application.                       #
#                                                                             #
# Because PhysiCell extensively uses BioFVM, we suggest you also cite BioFVM  #
#     as below:                                                               #
#                                                                             #
# We implemented and solved the model using PhysiCell (Version x.y.z) [1],    #
# with BioFVM [2] to solve the transport equations.                           #
#                                                                             #
# [1] A Ghaffarizadeh, R Heiland, SH Friedman, SM Mumenthaler, and P Macklin, #
#     PhysiCell: an Open Source Physics-Based Cell Simulator for Multicellu-  #
#     lar Systems, PLoS Comput. Biol. 14(2): e1005991, 2018                   #
#     DOI: 10.1371/journal.pcbi.1005991                                       #
#                                                                             #
# [2] A Ghaffarizadeh, SH Friedman, and P Macklin, BioFVM: an efficient para- #
#     llelized diffusive transport solver for 3-D biological simulations,     #
#     Bioinformatics 32(8): 1256-8, 2016. DOI: 10.1093/bioinformatics/btv730  #
#                                                                             #
###############################################################################
#                                                                             #
# BSD 3-Clause License (see https://opensource.org/licenses/BSD-3-Clause)     #
#                                                                             #
# Copyright (c) 2015-2018, Paul Macklin and the PhysiCell Project             #
# All rights reserved.                                                        #
#                                                                             #
# Redistribution and use in source and binary forms, with or without          #
# modification, are permitted provided that the following conditions are met: #
#                                                                             #
# 1. Redistributions of source code must retain the above copyright notice,   #
# this list of conditions and the following disclaimer.                       #
#                                                                             #
# 2. Redistributions in binary form must reproduce the above copyright        #
# notice, this list of conditions and the following disclaimer in the         #
# documentation and/or other materials provided with the distribution.        #
#                                                                             #
# 3. Neither the name of the copyright holder nor the names of its            #
# contributors may be used to endorse or promote products derived from this   #
# software without specific prior written permission.                         #
#                                                                             #
# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" #
# AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE   #
# IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE  #
# ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE   #
# LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR         #
# CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF        #
# SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS    #
# INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN     #
# CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)     #
# ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE  #
# POSSIBILITY OF SUCH DAMAGE.                                                 #
#                                                                             #
###############################################################################
*/
--> 

<!--
<user_details />
-->

<PhysiCell_settings version="devel-version">
	<domain>
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		<x_min>-400</x_min>
		<x_max>400</x_max>
		<y_min>-400</y_min>
		<y_max>400</y_max>
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		<z_min>-10</z_min>
		<z_max>10</z_max>
		<dx>20</dx>
		<dy>20</dy>
		<dz>20</dz>
		<use_2D>true</use_2D>
	</domain>
	
	<overall>
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		<max_time units="min">8640</max_time> <!-- 5 days * 24 h * 60 min -->
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		<time_units>min</time_units>
		<space_units>micron</space_units>
	
		<dt_diffusion units="min">0.01</dt_diffusion>
		<dt_mechanics units="min">0.1</dt_mechanics>
		<dt_phenotype units="min">6</dt_phenotype>	
	</overall>
	
	<parallel>
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		<omp_num_threads>6</omp_num_threads>
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	</parallel> 
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	<options>
		<legacy_random_points_on_sphere_in_divide>false</legacy_random_points_on_sphere_in_divide>
	</options>	
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	<save>
		<folder>.</folder> <!-- use . for root --> 

		<full_data>
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			<interval units="min">15</interval>
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			<enable>true</enable>
		</full_data>
		
		<SVG>
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			<interval units="min">15</interval>
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			<enable>true</enable>
		</SVG>
		
		<legacy_data>
			<enable>false</enable>
		</legacy_data>
	</save>
	
	<microenvironment_setup>
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		<variable name="virion" units="virion/micron^3" ID="0">
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			<physical_parameter_set>
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				<diffusion_coefficient units="micron^2/min">2.5</diffusion_coefficient> <!-- 10 --> 
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				<decay_rate units="1/min">0</decay_rate>  
			</physical_parameter_set>
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			<initial_condition units="virion/micron^3">0</initial_condition>
			<Dirichlet_boundary_condition units="virion/micron^3" enabled="false">0</Dirichlet_boundary_condition>
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		</variable>

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		<variable name="assembled virion" units="virion/micron^3" ID="1">
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			<physical_parameter_set>
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				<diffusion_coefficient units="micron^2/min">2.5</diffusion_coefficient> <!-- 10 --> 
				<decay_rate units="1/min">0</decay_rate>  
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			</physical_parameter_set>
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			<initial_condition units="virion/micron^3">0</initial_condition>
			<Dirichlet_boundary_condition units="virion/micron^3" enabled="false">0</Dirichlet_boundary_condition>
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		</variable>

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		<variable name="interferon 1" units="mol/micron^3" ID="2">
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			<physical_parameter_set>
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				<diffusion_coefficient units="micron^2/min">555.56</diffusion_coefficient>
				<decay_rate units="1/min">1.02e-2</decay_rate>  
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			</physical_parameter_set>
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			<initial_condition units="mol/micron^3">0</initial_condition>
			<Dirichlet_boundary_condition units="mol/micron^3" enabled="false">0</Dirichlet_boundary_condition>
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		</variable>

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		<variable name="pro-inflammatory cytokine" units="mol/micron^3" ID="3">
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			<physical_parameter_set>
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				<diffusion_coefficient units="micron^2/min">555.56</diffusion_coefficient>
				<decay_rate units="1/min">1.02e-2</decay_rate>  
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			</physical_parameter_set>
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			<initial_condition units="mol/micron^3">0</initial_condition>
			<Dirichlet_boundary_condition units="mol/micron^3" enabled="false">0</Dirichlet_boundary_condition>
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		</variable>
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		<variable name="chemokine" units="mol/micron^3" ID="4">
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			<physical_parameter_set>
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				<diffusion_coefficient units="micron^2/min">555.56</diffusion_coefficient>
				<decay_rate units="1/min">1.02e-2</decay_rate>  
			</physical_parameter_set>
			<initial_condition units="mol/micron^3">0</initial_condition>
			<Dirichlet_boundary_condition units="mol/micron^3" enabled="false">0</Dirichlet_boundary_condition>
		</variable>
		
		<variable name="debris" units="mol/micron^3" ID="5">
			<physical_parameter_set>
				<diffusion_coefficient units="micron^2/min">555.56</diffusion_coefficient>
				<decay_rate units="1/min">1.02e-2</decay_rate>  
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			</physical_parameter_set>
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			<initial_condition units="mol/micron^3">0</initial_condition>
			<Dirichlet_boundary_condition units="mol/micron^3" enabled="false">0</Dirichlet_boundary_condition>
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		</variable>

		<options>
			<calculate_gradients>true</calculate_gradients>
			<track_internalized_substrates_in_each_agent>true</track_internalized_substrates_in_each_agent>
			<!-- not yet supported --> 
			<initial_condition type="matlab" enabled="false">
				<filename>./config/initial.mat</filename>
			</initial_condition>
			<!-- not yet supported --> 
			<dirichlet_nodes type="matlab" enabled="false">
				<filename>./config/dirichlet.mat</filename>
			</dirichlet_nodes>
		</options>
	</microenvironment_setup>	
	
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	<cell_definitions>
		<cell_definition name="default" ID="0">
			<phenotype>
				<cycle code="6" name="flow_cytometry_separated_cycle_model">  
					<!-- using higher than normal significant digits to match divisions in default code -->
					<phase_transition_rates units="1/min"> 
						<!-- G0/G1 to S -->
						<rate start_index="0" end_index="1" fixed_duration="false">0</rate>
						<!-- 0.00334672 --> 
						<!-- S to G2 -->
						<rate start_index="1" end_index="2" fixed_duration="true">0.00208333</rate>
						<!-- G2 to M -->
						<rate start_index="2" end_index="3" fixed_duration="true">0.00416667</rate>
						<!-- M to G0/G1 -->
						<rate start_index="3" end_index="0" fixed_duration="true">0.0166667</rate>
					</phase_transition_rates>
				</cycle>
				
				<death>  
					<model code="100" name="apoptosis"> 
						<death_rate units="1/min">0</death_rate> <!-- 5.31667e-05 --> 
						<phase_transition_rates units="1/min">
							<rate start_index="0" end_index="1" fixed_duration="true">0.00193798</rate>
						</phase_transition_rates>
						<parameters>
							<unlysed_fluid_change_rate units="1/min">0.05</unlysed_fluid_change_rate>
							<lysed_fluid_change_rate units="1/min">0</lysed_fluid_change_rate>
							<cytoplasmic_biomass_change_rate units="1/min">1.66667e-02</cytoplasmic_biomass_change_rate>
							<nuclear_biomass_change_rate units="1/min">5.83333e-03</nuclear_biomass_change_rate>
							<calcification_rate units="1/min">0</calcification_rate>
							<relative_rupture_volume units="dimensionless">2.0</relative_rupture_volume>
						</parameters>
					</model> 

					<model code="101" name="necrosis">
						<death_rate units="1/min">0.0</death_rate>
						<phase_transition_rates units="1/min">
							<rate start_index="0" end_index="1" fixed_duration="false">9e9</rate>
							<rate start_index="1" end_index="2" fixed_duration="true">1.15741e-5</rate>
						</phase_transition_rates>
						<parameters>
							<unlysed_fluid_change_rate units="1/min">0.05</unlysed_fluid_change_rate>
							<lysed_fluid_change_rate units="1/min">0</lysed_fluid_change_rate>
							<cytoplasmic_biomass_change_rate units="1/min">1.66667e-02</cytoplasmic_biomass_change_rate>
							<nuclear_biomass_change_rate units="1/min">5.83333e-03</nuclear_biomass_change_rate>
							<calcification_rate units="1/min">0</calcification_rate>
							<relative_rupture_volume units="dimensionless">2.0</relative_rupture_volume>
						</parameters>
					</model> 
				</death>					

				<volume>  
					<total units="micron^3">2494</total>
					<fluid_fraction units="dimensionless">0.75</fluid_fraction>
					<nuclear units="micron^3">540</nuclear>
					
					<fluid_change_rate units="1/min">0.05</fluid_change_rate>
					<cytoplasmic_biomass_change_rate units="1/min">0.0045</cytoplasmic_biomass_change_rate>
					<nuclear_biomass_change_rate units="1/min">0.0055</nuclear_biomass_change_rate>
					
					<calcified_fraction units="dimensionless">0</calcified_fraction>
					<calcification_rate units="1/min">0</calcification_rate>
					
					<relative_rupture_volume units="dimensionless">2.0</relative_rupture_volume>
				</volume> 				
				
				<mechanics> 
					<cell_cell_adhesion_strength units="micron/min">0.4</cell_cell_adhesion_strength>
					<cell_cell_repulsion_strength units="micron/min">10.0</cell_cell_repulsion_strength>
					<relative_maximum_adhesion_distance units="dimensionless">1.25</relative_maximum_adhesion_distance>
					
					<options>
						<set_relative_equilibrium_distance enabled="false" units="dimensionless">1.8</set_relative_equilibrium_distance>
						<set_absolute_equilibrium_distance enabled="false" units="micron">15.12</set_absolute_equilibrium_distance>
					</options>
				</mechanics>
				
				<motility>  
					<speed units="micron/min">4</speed>
					<persistence_time units="min">5</persistence_time>
					<migration_bias units="dimensionless">0.7</migration_bias>
					
					<options>
						<enabled>false</enabled>
						<use_2D>true</use_2D>
						<chemotaxis>
							<enabled>false</enabled>
							<substrate>chemokine</substrate>
							<direction>1</direction>
						</chemotaxis>
					</options>
				</motility>

				<secretion>
					<substrate name="interferon 1">
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						<secretion_target units="dimensionless substrate concentration">1</secretion_target>
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					</substrate> 	
					<substrate name="pro-inflammatory cytokine">
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						<secretion_target units="dimensionless substrate concentration">1</secretion_target>
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					</substrate> 	
					<substrate name="chemokine">
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						<secretion_target units="dimensionless substrate concentration">1</secretion_target>
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					</substrate> 	
					<substrate name="debris">
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						<secretion_target units="dimensionless substrate concentration">1</secretion_target>
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					</substrate> 	
				</secretion>

				<molecular />
			</phenotype>
			<custom_data>  
				<!-- for internal viral dynamics --> 
				<virion units="virions" type="double"
					description="endocytosed virions">0</virion>
				<uncoated_virion units="virions" type="double"
					description="uncoated endocytosed virions">0</uncoated_virion>
				<viral_RNA units="RNA" type="double"
					description="total (functional) viral RNA copies">0</viral_RNA>
				<viral_protein units="protein" type="double"
					description="total assembled sets of viral protein">0</viral_protein>
				<assembled_virion uints="virions" type="double"
					description="total assembled virions">0</assembled_virion>
				
				<virion_uncoating_rate type="double" units="1/min" 
					description="rate at which an internalized virion is uncoated">0.01</virion_uncoating_rate>
				<uncoated_to_RNA_rate type="double" units="1/min" 
					description="rate at which uncoated virion makes its mRNA available">0.01</uncoated_to_RNA_rate> 
				<protein_synthesis_rate type="double" units="1/min" 
					description="rate at mRNA creates complete set of proteins">0.01</protein_synthesis_rate>
				<virion_assembly_rate type="double" units="1/min" 
					description="rate at which viral proteins are assembled into complete virion">0.01</virion_assembly_rate>
 
				<!-- virus adsorption and export -->
				<virion_export_rate type="double" units="1/min" 
					description="rate at which a virion is exported from a live cell">0.01</virion_export_rate> 

				<!-- ACE2 receptor trafficking --> 
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				<unbound_external_ACE2 type="double" units="receptors"
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					description="initial number of unbound ACE2 receptors on surface">1000</unbound_external_ACE2>
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				<bound_external_ACE2 type="double" units="receptors"
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					description="initial number of bound ACE2 receptors on surface">0</bound_external_ACE2>
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				<unbound_internal_ACE2 type="double" units="receptors"
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					description="initial number of internalized unbound ACE2 receptors">0</unbound_internal_ACE2>
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				<bound_internal_ACE2 type="double" units="receptors"
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					description="initial number of internalized bound ACE2 receptors">0</bound_internal_ACE2>
	
				<ACE2_binding_rate type="double" units="1/min" 
					description="ACE2 receptor-virus binding rate">0.001</ACE2_binding_rate> 
				<ACE2_endocytosis_rate type="double" units="1/min" 
					description="ACE2 receptor-virus endocytosis rate">0.01</ACE2_endocytosis_rate> 
				<ACE2_cargo_release_rate type="double" units="1/min" 
					description="ACE2 receptor-virus cargo release rate">0.001</ACE2_cargo_release_rate> 
				<ACE2_recycling_rate type="double" units="1/min" 
					description="ACE2 receptor recycling rate">0.01</ACE2_recycling_rate> 
				
				<!-- cell virus response --> 
				<max_infected_apoptosis_rate type="double" units="1/min" 
					description="maximum rate of cell apoptosis due to viral infection">0.001</max_infected_apoptosis_rate>
				<max_apoptosis_half_max type="double" units="virion" 
					description="viral load at which cells reach half max apoptosis rate">250</max_apoptosis_half_max> <!-- 500 -->
				<apoptosis_hill_power type="double" units="none" 
					description="Hill power for viral load apoptosis response">1</apoptosis_hill_power> 
				<virus_fraction_released_at_death type="double" units="none" 
					description="fraction of internal virus released at cell death">0</virus_fraction_released_at_death>
				<infected_cell_chemokine_secretion_rate units="1/min" type="double"
					description="max rate that infected cells secrete chemokine">1</infected_cell_chemokine_secretion_rate>
				<debris_secretion_rate units="1/min" type="double"
					description="rate that dead cells release debris">1</debris_secretion_rate>
				
				<infected_cell_chemokine_secretion_activated units="none" type="double"
					description="used internally to track activation of chemokine secretion">0</infected_cell_chemokine_secretion_activated>

				<!-- for the immune model --> 
				<TCell_contact_time type="double" units="min"
					description="tracks total contact time with CD8 T cells">0.0</TCell_contact_time>
				<cell_attachment_rate units="1/min" type="double"
					description="the rate at which the cell attaches to cells in contact">0</cell_attachment_rate>
				<cell_attachment_lifetime units="min" type="double"
					description="the mean duration of a cell-cell attachment">0</cell_attachment_lifetime>
				
				<TCell_contact_death_threshold units="min" type="double"
					description="threshold CD8 T cell contact time to trigger apoptosis">50</TCell_contact_death_threshold> <!-- 50 -->
				<max_attachment_distance units="micron" type="double"
					desription="max distance at which to form a cell-cell attachment">15</max_attachment_distance>
				<elastic_attachment_coefficient units="1/min" type="double"
					description="elastic coefficient for cell-cell attachment">0.01</elastic_attachment_coefficient>
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<!--
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				<relative_maximum_volume units="dimensionless" type="double"
					description="max tolerated volume (relative to normal volume) before triggering apoptosis">1.8</relative_maximum_volume>
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--> <!-- disable in v 3.2 -->

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				<!-- more immmune cell parameters  -->
				<phagocytosis_rate units="1/min" type="double" 
					desription="rate of phagocytosing a nearby target">0.167</phagocytosis_rate>
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<!-- 					
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				<phagocytosis_relative_target_cutoff_size unit="dimensionless" type="double"
					desription="do not phagocytose anything over this size (relative to cell's volume)">1.1</phagocytosis_relative_target_cutoff_size>
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--> <!-- disable in v 3.2 -->

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				<sensitivity_to_debris_chemotaxis units="dimensionless" type="double" 
					description="relative sensitivity to debris in chemotaxis">1.0</sensitivity_to_debris_chemotaxis>
				<sensitivity_to_chemokine_chemotaxis units="dimensionless" type="double" 
					description="relative sensitivity to chemokine in chemotaxis">10.0</sensitivity_to_chemokine_chemotaxis> 

				<activated_speed units="micron/min" type="double" 
					description="speed after activation">0.4</activated_speed>
				<activated_cytokine_secretion_rate units="1/min" type="double" 
					description="rate of secreting pro-inflamatory cytokine after activation">1</activated_cytokine_secretion_rate>

				<activated_immune_cell units="dimensionless" type="double" 
					description="used internally to track activation state">0.0</activated_immune_cell>

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				<virus_expression_threshold units="dimensionless" type="double"
					description="minimal quantity of virus to activate virus_expression node">10.0</virus_expression_threshold>

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				<!-- your custom data and parameters go here (for new submodels) --> 
				
			
			</custom_data>
		</cell_definition>
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		<cell_definition name="lung epithelium" parent_type="default" ID="1">
			<phenotype>
				<death>
					<model code="100" name="apoptosis"> 
						<death_rate units="1/min">0</death_rate> <!-- 5.31667e-05 --> 
					</model> 
				</death>
				<motility>  
					<options>
						<enabled>false</enabled>
					</options>
				</motility>
				<secretion>
				</secretion>
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				<intracellular type="maboss">
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					<bnd_filename>../data/boolean_network/epithelial_cell_2.bnd</bnd_filename>
					<cfg_filename>../data/boolean_network/epithelial_cell_2.cfg</cfg_filename>
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					<time_step units="min">12</time_step>
				</intracellular>
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			</phenotype>
			<custom_data>
			</custom_data>
		</cell_definition>

		<!-- generic immune cell type --> 
		<cell_definition name="immune" parent_type="default" ID="2">
			<phenotype>
				<mechanics> 
					<cell_cell_adhesion_strength units="micron/min">0</cell_cell_adhesion_strength>
					<cell_cell_repulsion_strength units="micron/min">10</cell_cell_repulsion_strength>
				</mechanics>
				<death>
					<model code="100" name="apoptosis"> 
						<death_rate units="1/min">5e-4</death_rate> <!-- 5e-4 --> 
					</model> 
				</death>
				<motility>  
					<speed units="micron/min">4</speed>
					<persistence_time units="min">5</persistence_time>
					<migration_bias units="dimensionless">0.70</migration_bias>
					<options>
						<enabled>true</enabled>
						<use_2D>true</use_2D>
						<chemotaxis>
							<enabled>true</enabled>
							<substrate>chemokine</substrate>
							<direction>1</direction>
						</chemotaxis>
					</options>
				</motility>

				<secretion>
					<substrate name="pro-inflammatory cytokine">
						<uptake_rate units="1/min">0.01</uptake_rate>
					</substrate> 	
					<substrate name="chemokine">
						<uptake_rate units="1/min">0.01</uptake_rate>
					</substrate> 	
					<substrate name="debris">
						<uptake_rate units="1/min">0.1</uptake_rate>
					</substrate> 	
				</secretion>

			</phenotype>
			<custom_data>
			</custom_data>
		</cell_definition>
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		<cell_definition name="CD8 Tcell" parent_type="immune" ID="3">
			<phenotype>
				<death>
					<model code="100" name="apoptosis"> 
						<death_rate units="1/min">2.8e-4</death_rate> 
					</model> 
				</death>			
			
				<motility>
					<migration_bias units="dimensionless">0.70</migration_bias>
					<options>
						<enabled>true</enabled>
						<use_2D>true</use_2D>
						<chemotaxis>
							<enabled>true</enabled>
							<substrate>chemokine</substrate>
							<direction>1</direction>
						</chemotaxis>
					</options>
				</motility>
				<volume>
					<total units="micron^3">478</total>
					<nuclear units="micron^3">47.8</nuclear>
				</volume>
	
				<secretion>
					<substrate name="debris">
						<uptake_rate units="1/min">0</uptake_rate>
					</substrate> 	
				</secretion>
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				<intracellular type="maboss">
					<bnd_filename>../data/boolean_network/cd8t_cell.bnd</bnd_filename>
					<cfg_filename>../data/boolean_network/cd8t_cell.cfg</cfg_filename>
					<time_step units="min">12</time_step>
				</intracellular>
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			</phenotype>
			<custom_data>
				<cell_attachment_rate units="1/min">0.2</cell_attachment_rate> <!-- 0.2 --> 
				<cell_attachment_lifetime units="min">8.5</cell_attachment_lifetime> 
			</custom_data>
		</cell_definition>
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		<cell_definition name="macrophage" parent_type="immune" ID="4">
			<phenotype>
				<death>
					<!-- death is about 5x slower --> 
					<model code="100" name="apoptosis"> 
						<death_rate units="1/min">2.1e-4</death_rate>  
					</model> 
				</death>
				<motility>  
					<migration_bias>0.7</migration_bias> 
					<persistence_time>5</persistence_time>
					<options>
						<enabled>true</enabled>
						<use_2D>true</use_2D>					
						<chemotaxis>
							<enabled>true</enabled>
							<substrate>debris</substrate> 
							<direction>1</direction>
						</chemotaxis>
					</options>
				</motility>
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				<volume>
					<total units="micron^3">4849</total>
					<nuclear units="micron^3">485</nuclear>
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					<cytoplasmic_biomass_change_rate units="1/min">0.01</cytoplasmic_biomass_change_rate> 
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					<!-- set this higher so that cells "digest" phagocytosed materials faster -->
				</volume>
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				<intracellular type="maboss">
					<bnd_filename>../data/boolean_network/macrophage.bnd</bnd_filename>
					<cfg_filename>../data/boolean_network/macrophage.cfg</cfg_filename>
					<time_step units="min">12</time_step>
				</intracellular>
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			</phenotype>
			<custom_data>
				<phagocytosis_rate units="1/min" type="double" 
					desription="rate of phagocytosing a nearby target">0.167</phagocytosis_rate>
				<sensitivity_to_debris_chemotaxis units="dimensionless" type="double" 
					description="relative sensitivity to debris in chemotaxis">1.0</sensitivity_to_debris_chemotaxis>
				<sensitivity_to_chemokine_chemotaxis units="dimensionless" type="double" 
					description="relative sensitivity to chemokine in chemotaxis">10.0</sensitivity_to_chemokine_chemotaxis> <!-- 1 -->
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				<activated_speed units="micron/min" type="double" 
					description="speed after activation">0.4</activated_speed> <!-- 0.4 --> 
				<activated_cytokine_secretion_rate units="1/min" type="double" 
					description="rate of secreting pro-inflamatory cytokine after activation">1</activated_cytokine_secretion_rate>

			</custom_data>
		</cell_definition>		

		<cell_definition name="neutrophil" parent_type="immune" ID="5">
			<phenotype>
				<death>
					<model code="100" name="apoptosis"> 
						<death_rate units="1/min">8.9e-4</death_rate>  
					</model> 
				</death>
				
				<motility>  
					<speed units="micron/min">19</speed>
					<migration_bias>0.91</migration_bias>  
					<persistence_time>5</persistence_time>
					<options>
						<enabled>true</enabled>
						<use_2D>true</use_2D>					
						<chemotaxis>
							<enabled>true</enabled>
							<substrate>debris</substrate>  
							<direction>1</direction>							
						</chemotaxis>
					</options>
				</motility>

				<secretion>
					<substrate name="virion">
						<uptake_rate units="1/min">0.1</uptake_rate> <!-- 0.001 --> 
					</substrate> 	
				</secretion>

				<volume>
					<total units="micron^3">1437</total>
					<nuclear units="micron^3">143.7</nuclear>
					
					<cytoplasmic_biomass_change_rate units="1/min">0.045</cytoplasmic_biomass_change_rate> 
					<!-- set this higher so that cells "digest" phagocytosed materials faster -->
				</volume>
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				<intracellular type="maboss">
					<bnd_filename>../data/boolean_network/neutrophil.bnd</bnd_filename>
					<cfg_filename>../data/boolean_network/neutrophil.cfg</cfg_filename>
					<time_step units="min">12</time_step>
				</intracellular>
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			</phenotype>
			<custom_data>
				<phagocytosis_rate units="1/min" type="double" 
					desription="rate of phagocytosing a nearby target">0.117</phagocytosis_rate>
				<sensitivity_to_debris_chemotaxis units="dimensionless" type="double" 
					description="relative sensitivity to debris in chemotaxis">1.0</sensitivity_to_debris_chemotaxis> 
				<sensitivity_to_chemokine_chemotaxis units="dimensionless" type="double" 
					description="relative sensitivity to chemokine in chemotaxis">10.0</sensitivity_to_chemokine_chemotaxis> 

				<activated_speed units="micron/min" type="double" 
					description="speed after activation">0.4</activated_speed>
				<activated_cytokine_secretion_rate units="1/min" type="double" 
					description="rate of secreting pro-inflamatory cytokine after activation">0</activated_cytokine_secretion_rate>
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			</custom_data>
		</cell_definition>
		
	</cell_definitions>
	
	
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	<user_parameters>
		<random_seed type="int" units="dimensionless">0</random_seed> 
		<!-- example parameters from the template --> 
		
		<div_immune type="divider" description="--Immune activation parameters--"/>
			<immune_dt type="double" units="min" description="how often we check to introduce immune cells">10</immune_dt> 
			
			<immune_z_offset type="double" units="micron" 
				description="immune cell position over the epithelium">0</immune_z_offset>

			<macrophage_max_recruitment_rate type="double" units="cells/min/micron^3"
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				description="max macrophage recruitment rate (for saturated signal)">4e-9</macrophage_max_recruitment_rate> <!-- 4e-9 debug -->
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			<macrophage_recruitment_min_signal type="double" units="substrate/micron^3"
				description="min concentration to attract macrophages">0.1</macrophage_recruitment_min_signal> <!--0.1 debug -->
			<macrophage_recruitment_saturation_signal type="double" units="substrate/micron^3"
				description="saturating concentration to attract macrophages">0.3</macrophage_recruitment_saturation_signal> <!-- 0.3 debug -->
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			<neutrophil_max_recruitment_rate type="double" units="cells/min/micron^3"
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				description="max neutrophil recruitment rate (for saturated signal)">4e-9</neutrophil_max_recruitment_rate> <!-- 4e-9 debug -->
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			<neutrophil_recruitment_min_signal type="double" units="substrate/micron^3"
				description="min concentration to attract neutrophils">0.1</neutrophil_recruitment_min_signal> <!--0.1 debug -->
			<neutrophil_recruitment_saturation_signal type="double" units="substrate/micron^3"
				description="saturating concentration to attract neutrophils">0.3</neutrophil_recruitment_saturation_signal> <!-- 0.3 debug -->
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			<CD8_Tcell_max_recruitment_rate type="double" units="cells/min/micron^3"
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				description="max CD8 T cell recruitment rate (for saturated signal)">4e-9</CD8_Tcell_max_recruitment_rate> <!-- 4e-9 debug -->
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			<CD8_Tcell_recruitment_min_signal type="double" units="substrate/micron^3"
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				description="min concentration to attract CD8 T cells">0.4</CD8_Tcell_recruitment_min_signal> <!-- 0.3 debug -->
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			<CD8_Tcell_recruitment_saturation_signal type="double" units="substrate/micron^3"
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				description="saturating concentration to attract CD8 T cells">0.7</CD8_Tcell_recruitment_saturation_signal> <!-- 0.7 debug -->	
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		<div_initialization type="divider" description="---Initialization Options--"/>
			<multiplicity_of_infection type="double" units="none" 
				description="multiplicity of infection: virions/cells at t=0">0.1</multiplicity_of_infection> <!-- 0.01 debug -->
			<use_single_infected_cell type="bool" units="none" 
				description="Infect center cell with one virion (overrides MOI)">false</use_single_infected_cell>
			
			<number_of_CD8_Tcells type="int" units="none" 
				description="initial number of CD8 T cells">0</number_of_CD8_Tcells>
			<number_of_macrophages type="int" units="none" 
				description="initial number of macrophages">50</number_of_macrophages>
			<number_of_neutrophils type="int" units="none" 
				description="initial number of neutrophils">0</number_of_neutrophils>
			
			<perecentage_tissue_vascularized units="percentage" type="double"
				description="percentage of tissue sitting above blood vessels">8.8</perecentage_tissue_vascularized>			
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			<m_inhibition_percentage units="dimensionless" type="double"
				description="ratio of the population capable of inhibiting M protein">0.0</m_inhibition_percentage>
			
			<fadd_inhibition_percentage units="dimensionless" type="double"
				description="ratio of the population capable of inhibiting FADD protein">0.0</fadd_inhibition_percentage>
			
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		<div_colors type="divider" description="---Cell Color Options--"/>
			<color_variable type="string" description="color cells based on this variable">assembled_virion</color_variable>
			
			<apoptotic_epithelium_color type="string" 
				description="apoptotic epithelial cell color">black</apoptotic_epithelium_color>
			<apoptotic_immune_color type="string" 
				description="apoptotic immune cell color">rosybrown</apoptotic_immune_color>
		
<!---			<lung_epithelium_color type="string" 
				description="lung epithelium color">blue</lung_epithelium_color> -->
			<CD8_Tcell_color type="string" 
				description="CD8 T cell color">red</CD8_Tcell_color>
			<Macrophage_color type="string" 
				description="macrophage color">lime</Macrophage_color>
			<activated_macrophage_color type="string" 
				description="color of activated macrophage">fuchsia</activated_macrophage_color>
			<Neutrophil_color type="string" description="neutrophil color">cyan</Neutrophil_color>
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	</user_parameters>
	
</PhysiCell_settings>