- Author:
- termi-official <termi-official@users.noreply.github.com>
- Date:
- 2025-05-15 16:01:20+02:00
- Desc:
- Add documentation for submission
- Permanent Source URI:
- https://staging.physiomeproject.org/workspace/d20/rawfile/8465ce0a385cdc40e2f79b001798d600e9f9e4d2/experiments/channel/ogiermann_2022_piezo1_rect_pacing.cellml
<?xml version='1.0' encoding='UTF-8'?>
<model name="ogiermann_2022_piezo1_rect_pacing" xmlns="http://www.cellml.org/cellml/1.1#" xmlns:cellml="http://www.cellml.org/cellml/1.1#" xmlns:xlink="http://www.w3.org/1999/xlink">
<import xlink:href="../../units.cellml">
<units name="mmHg" units_ref="mmHg"/>
<units name="u_per_m" units_ref="u_per_m"/>
<units name="ms" units_ref="ms"/>
<units name="per_ms" units_ref="per_ms"/>
<units name="mV" units_ref="mV"/>
<units name="per_mV" units_ref="per_mV"/>
<units name="uS_per_nF" units_ref="uS_per_nF"/>
<units name="nA_per_nF" units_ref="nA_per_nF"/>
<units name="molar" units_ref="molar"/>
<units name="mM" units_ref="mM"/>
<units name="uM" units_ref="uM"/>
<units name="mM4" units_ref="mM4"/>
<units name="mV_per_uM" units_ref="mV_per_uM"/>
<units name="uM_per_ms" units_ref="uM_per_ms"/>
<units name="per_uM_per_ms" units_ref="per_uM_per_ms"/>
<units name="J_per_moleK" units_ref="J_per_moleK"/>
<units name="coulomb_per_mmole" units_ref="coulomb_per_mmole"/>
<units name="cm_per_s" units_ref="cm_per_s"/>
<units name="mA_per_cm2" units_ref="mA_per_cm2"/>
<units name="mmole_per_coulomb_cm" units_ref="mmole_per_coulomb_cm"/>
</import>
<import xlink:href="../common/periodic_mechanical_stim_protocol.cellml">
<component component_ref="stimulus_protocol" name="pressure_stim"/>
</import>
<import xlink:href="../common/periodic_electrical_stim_protocol.cellml">
<component component_ref="stimulus_protocol" name="current_stim"/>
</import>
<import xlink:href="../../models/channels/ogiermann_2025_piezo1.cellml">
<component component_ref="kinetics" name="piezo1"/>
</import>
<component name="environment">
<!-- For visibility in the editor.-->
<variable name="P_Open" public_interface="in" units="dimensionless"/>
<variable name="P_Closed" public_interface="in" units="dimensionless"/>
<variable name="P_I1" public_interface="in" units="dimensionless"/>
<variable name="P_I2" public_interface="in" units="dimensionless"/>
<variable initial_value="0.0" name="time" public_interface="out" units="ms"/>
<variable initial_value="-80" name="current_in" public_interface="in" units="nA_per_nF"/>
<variable name="voltage_out" public_interface="out" units="mV"/>
<variable name="transmembranevoltage" public_interface="out" units="mV"/>
<variable name="pressure" public_interface="out" units="mmHg"/>
<variable initial_value="1.0" name="stretch" public_interface="in" units="dimensionless"/>
<variable initial_value="100" name="pressure_stim_offset" public_interface="out" units="ms"/>
<variable initial_value="2000" name="pressure_stim_period" public_interface="out" units="ms"/>
<variable initial_value="5" name="pressure_stim_duration" public_interface="out" units="ms"/>
<variable initial_value="1.1" name="pressure_stim_amplitude" public_interface="out" units="dimensionless"/>
<variable initial_value="100" name="current_stim_offset" public_interface="out" units="ms"/>
<variable initial_value="1000" name="current_stim_period" public_interface="out" units="ms"/>
<variable initial_value="500" name="current_stim_duration" public_interface="out" units="ms"/>
<variable initial_value="80" name="current_stim_amplitude" public_interface="out" units="nA_per_nF"/>
<variable initial_value="999999999999999" name="current_stim_end" public_interface="out" units="ms"/>
<variable initial_value="1" name="current_N_period_total" public_interface="out" units="dimensionless"/>
<variable initial_value="1" name="current_N_period_applied" public_interface="out" units="dimensionless"/>
<!-- If we assume that a stretch of 20% saturates the ion channel response (70 mmHg in the experiment) and a linear relation between stretch and pressure, we get the factor of 350 present here.-->
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<eq/>
<ci>pressure</ci>
<apply>
<times/>
<cn cellml:units="mmHg">350.0</cn>
<apply>
<max/>
<cn cellml:units="dimensionless">0.0</cn>
<apply>
<minus/>
<ci>stretch</ci>
<cn cellml:units="dimensionless">1.0</cn>
</apply>
</apply>
</apply>
</apply>
<apply>
<eq/>
<ci>voltage_out</ci>
<apply>
<times/>
<apply>
<divide/>
<ci>current_in</ci>
<cn cellml:units="nA_per_nF">1.0</cn>
</apply>
<cn cellml:units="mV">1.0</cn>
</apply>
</apply>
<apply>
<eq/>
<ci>transmembranevoltage</ci>
<apply>
<times/>
<apply>
<minus/>
<ci>voltage_out</ci>
<cn cellml:units="mV">5</cn>
</apply>
<ci>P_Open</ci>
</apply>
</apply>
</math>
</component>
<connection>
<map_components component_1="pressure_stim" component_2="environment"/>
<map_variables variable_1="time" variable_2="time"/>
<map_variables variable_1="stretch" variable_2="stretch"/>
<map_variables variable_1="stim_offset" variable_2="pressure_stim_offset"/>
<map_variables variable_1="stim_period" variable_2="pressure_stim_period"/>
<map_variables variable_1="stim_duration" variable_2="pressure_stim_duration"/>
<map_variables variable_1="stim_amplitude" variable_2="pressure_stim_amplitude"/>
</connection>
<connection>
<map_components component_1="current_stim" component_2="environment"/>
<map_variables variable_1="time" variable_2="time"/>
<map_variables variable_1="current" variable_2="current_in"/>
<map_variables variable_1="stim_offset" variable_2="current_stim_offset"/>
<map_variables variable_1="stim_period" variable_2="current_stim_period"/>
<map_variables variable_1="stim_duration" variable_2="current_stim_duration"/>
<map_variables variable_1="stim_amplitude" variable_2="current_stim_amplitude"/>
<map_variables variable_1="stim_t_end" variable_2="current_stim_end"/>
<map_variables variable_1="N_period_total" variable_2="current_N_period_total"/>
<map_variables variable_1="N_period_applied" variable_2="current_N_period_applied"/>
</connection>
<connection>
<map_components component_1="piezo1" component_2="environment"/>
<map_variables variable_1="time" variable_2="time"/>
<map_variables variable_1="pressure" variable_2="pressure"/>
<map_variables variable_1="gradmu" variable_2="voltage_out"/>
<map_variables variable_1="P_Open" variable_2="P_Open"/>
<map_variables variable_1="P_Closed" variable_2="P_Closed"/>
<map_variables variable_1="P_I1" variable_2="P_I1"/>
<map_variables variable_1="P_I2" variable_2="P_I2"/>
</connection>
</model>
