adding correct parameters for the pulse and rates for the processes

sample_projects_intracellular/boolean/spheroid_tnf_model_mpi/config/PhysiCell_settings_1M.xml

@@ -171,13 +171,9 @@
 				<death>  
 					<model code="100" name="apoptosis"> 
 						<death_rate units="1/min">5.31667e-05</death_rate>
-						<phase_durations units="min">
-							<duration index="0" fixed_duration="true">516</duration>
-						</phase_durations>
-						<!--
-						<phase_transition_rates units="1/min">
-							<rate start_index="0" end_index="1" fixed_duration="false">0.00193798</rate>
-						</phase_transition_rates> -->
+                        <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>
@@ -190,16 +186,10 @@
 
 					<model code="101" name="necrosis">
 						<rate units="1/min">0.0</rate>
-						<phase_durations units="min">
-							<duration index="0" fixed_duration="true">0</duration>
-							<duration index="1" fixed_duration="true">86400</duration>
-						</phase_durations>
-						<!--
 						<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>
 						</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>
@@ -238,9 +228,9 @@
 				<next_physiboss_run units="dimensionless">10.</next_physiboss_run>
 				
 				<!-- Molecular model internal variables-->
-				<TNFR_binding_rate type="double" units="1/min" description="TNF receptor binding rate">0.243</TNFR_binding_rate> <!-- 0.243 -->
-				<TNFR_endocytosis_rate type="double" units="1/min" description="TNF receptor-TNF endocytosis rate">0.128</TNFR_endocytosis_rate>
-				<TNFR_recycling_rate type="double" units="1/min" description="TNF receptor recycling">0.293</TNFR_recycling_rate>
+				<TNFR_binding_rate type="double" units="1/min" description="TNF receptor binding rate">0.3</TNFR_binding_rate> <!-- 0.243 -->
+				<TNFR_endocytosis_rate type="double" units="1/min" description="TNF receptor-TNF endocytosis rate">0.2</TNFR_endocytosis_rate>
+				<TNFR_recycling_rate type="double" units="1/min" description="TNF receptor recycling">0.6</TNFR_recycling_rate>
 				<TNFR_activation_threshold type="double" units="" description="TNFR threshold to update booleano model input">0.5</TNFR_activation_threshold>
 				<TNFR_receptors_per_cell type="double" units="dimensionless" description="number of TNFR receptors per cell">1.0</TNFR_receptors_per_cell>
 				<TNF_net_production_rate type="double" units="TNF/cell/min" description="The total TNF produced by the cell when NFkB is active">0</TNF_net_production_rate> <!-- 0.5 ng/mL -->
@@ -266,9 +256,9 @@
 		<cfg_file type="string" units="">./config/boolean_network/TNF_conf.cfg</cfg_file>
 		<maboss_time_step type="double" units="dimensionless">10.</maboss_time_step> -->
 
-		<time_add_tnf type="int" units="min">50</time_add_tnf> <!-- 150 -->
-		<duration_add_tnf type="int" units="min">10</duration_add_tnf> <!-- 10 -->
-		<concentration_tnf type="double" units="TNF/um^3"> 0.0 </concentration_tnf> <!-- 0.5 ng/mL -->
+		<time_add_tnf type="int" units="min">247</time_add_tnf> <!-- 150 -->
+		<duration_add_tnf type="int" units="min">12</duration_add_tnf> <!-- 10 -->
+		<concentration_tnf type="double" units="TNF/um^3"> 0.0389 </concentration_tnf> <!-- 0.5 ng/mL -->
 		<time_remove_tnf type="int" units="min">100000</time_remove_tnf> <!-- 8000 -->
 		<membrane_length type="int" units=""> 170 </membrane_length> <!-- 470 -->