- Author:
- WeiweiAi <wai484@aucklanduni.ac.nz>
- Date:
- 2021-11-23 11:14:52+13:00
- Desc:
- Add GHK calculation
- Permanent Source URI:
- https://models.cellml.org/workspace/6bc/rawfile/25f702702c1c129fef08faa593ddecb7a368b9d5/Protocols/Patch_clamp_protocol.cellml
<?xml version='1.0' encoding='UTF-8'?>
<model name="Patch_clamp_protocol" xmlns="http://www.cellml.org/cellml/1.1#" xmlns:cellml="http://www.cellml.org/cellml/1.1#" xmlns:cmeta="http://www.cellml.org/metadata/1.0#" xmlns:xlink="http://www.w3.org/1999/xlink">
<!-- clamp the voltage for the activation behaviour-->
<import xlink:href="../Components/units.cellml">
<units name="ms" units_ref="ms"/>
<units name="mV" units_ref="mV"/>
</import>
<component name="sPulse_protocol_ms">
<variable name="time" public_interface="in" units="ms"/>
<variable cmeta:id="steady_state_time" name="t_ss" public_interface="in" units="ms"/>
<variable cmeta:id="activation_holding_potential" name="V_actHolding" public_interface="in" units="mV"/>
<variable cmeta:id="activation_duration" name="t_act" public_interface="in" units="ms"/>
<variable cmeta:id="activation_test_potential" name="V_actTest" public_interface="in" units="mV"/>
<variable name="V" public_interface="out" units="mV"/>
<!--get the model to steady state at the holding potential.-->
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply id="activation_protocol_clamping">
<eq/>
<ci>V</ci>
<piecewise>
<piece>
<ci>V_actHolding</ci>
<apply>
<lt/>
<ci>time</ci>
<ci>t_ss</ci>
</apply>
</piece>
<piece>
<ci>V_actTest</ci>
<apply>
<and/>
<apply>
<geq/>
<ci>time</ci>
<ci>t_ss</ci>
</apply>
<apply>
<lt/>
<ci>time</ci>
<apply>
<plus/>
<ci>t_act</ci>
<ci>t_ss</ci>
</apply>
</apply>
</apply>
</piece>
<otherwise>
<ci>V_actHolding</ci>
</otherwise>
</piecewise>
</apply>
</math>
</component>
<component name="sPulse_protocol_s">
<variable name="time" public_interface="in" units="second"/>
<variable cmeta:id="steady_state_time" name="t_ss" public_interface="in" units="second"/>
<variable cmeta:id="activation_holding_potential" name="V_actHolding" public_interface="in" units="mV"/>
<variable cmeta:id="activation_duration" name="t_act" public_interface="in" units="second"/>
<variable cmeta:id="activation_test_potential" name="V_actTest" public_interface="in" units="mV"/>
<variable name="V" public_interface="out" units="mV"/>
<!--get the model to steady state at the holding potential.-->
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply id="activation_protocol_clamping">
<eq/>
<ci>V</ci>
<piecewise>
<piece>
<ci>V_actHolding</ci>
<apply>
<lt/>
<ci>time</ci>
<ci>t_ss</ci>
</apply>
</piece>
<piece>
<ci>V_actTest</ci>
<apply>
<and/>
<apply>
<geq/>
<ci>time</ci>
<ci>t_ss</ci>
</apply>
<apply>
<lt/>
<ci>time</ci>
<apply>
<plus/>
<ci>t_act</ci>
<ci>t_ss</ci>
</apply>
</apply>
</apply>
</piece>
<otherwise>
<ci>V_actHolding</ci>
</otherwise>
</piecewise>
</apply>
</math>
</component>
<component name="mPulse_protocol_ms">
<variable name="time" public_interface="in" units="ms"/>
<variable cmeta:id="steady_state_time" name="t_ss" public_interface="in" units="ms"/>
<variable cmeta:id="activation_holding_potential" name="V_actHolding" public_interface="in" units="mV"/>
<variable cmeta:id="activation_duration" name="t_act" public_interface="in" units="ms"/>
<variable cmeta:id="activation_test_potential" name="V_actTest" public_interface="in" units="mV"/>
<variable cmeta:id="interpulse" name="t_intp" public_interface="in" units="ms"/>
<variable cmeta:id="period" name="stimPeriod" units="ms"/>
<variable cmeta:id="localTimer" name="t" units="ms"/>
<variable cmeta:id="pulse_number" name="np" public_interface="in" units="dimensionless"/>
<variable name="V" public_interface="out" units="mV"/>
<!--get the model to steady state at the holding potential.-->
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<eq/>
<ci>stimPeriod</ci>
<apply>
<plus/>
<ci>t_act</ci>
<ci>t_intp</ci>
</apply>
</apply>
<apply>
<eq/>
<ci>t</ci>
<apply>
<minus/>
<apply>
<minus/>
<ci>time</ci>
<ci>t_ss</ci>
</apply>
<apply>
<times/>
<ci>stimPeriod</ci>
<apply>
<floor/>
<apply>
<divide/>
<apply>
<minus/>
<ci>time</ci>
<ci>t_ss</ci>
</apply>
<ci>stimPeriod</ci>
</apply>
</apply>
</apply>
</apply>
</apply>
<apply id="activation_protocol_clamping">
<eq/>
<ci>V</ci>
<piecewise>
<piece>
<ci>V_actHolding</ci>
<apply>
<lt/>
<ci>time</ci>
<ci>t_ss</ci>
</apply>
</piece>
<piece>
<ci>V_actTest</ci>
<apply>
<and/>
<apply>
<geq/>
<ci>time</ci>
<ci>t_ss</ci>
</apply>
<apply>
<leq/>
<ci>t</ci>
<ci>t_act</ci>
</apply>
<apply>
<leq/>
<ci>time</ci>
<apply>
<plus/>
<ci>t_ss</ci>
<apply>
<times/>
<ci>stimPeriod</ci>
<ci>np</ci>
</apply>
</apply>
</apply>
</apply>
</piece>
<otherwise>
<ci>V_actHolding</ci>
</otherwise>
</piecewise>
</apply>
</math>
</component>
<component name="mPulse_protocol_s">
<variable name="time" public_interface="in" units="second"/>
<variable cmeta:id="steady_state_time" name="t_ss" public_interface="in" units="second"/>
<variable cmeta:id="activation_holding_potential" name="V_actHolding" public_interface="in" units="mV"/>
<variable cmeta:id="activation_duration" name="t_act" public_interface="in" units="second"/>
<variable cmeta:id="activation_test_potential" name="V_actTest" public_interface="in" units="mV"/>
<variable cmeta:id="interpulse" name="t_intp" public_interface="in" units="second"/>
<variable cmeta:id="period" name="stimPeriod" units="second"/>
<variable cmeta:id="localTimer" name="t" units="second"/>
<variable cmeta:id="pulse_number" name="np" public_interface="in" units="dimensionless"/>
<variable name="V" public_interface="out" units="mV"/>
<!--get the model to steady state at the holding potential.-->
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<eq/>
<ci>stimPeriod</ci>
<apply>
<plus/>
<ci>t_act</ci>
<ci>t_intp</ci>
</apply>
</apply>
<apply>
<eq/>
<ci>t</ci>
<apply>
<minus/>
<apply>
<minus/>
<ci>time</ci>
<ci>t_ss</ci>
</apply>
<apply>
<times/>
<ci>stimPeriod</ci>
<apply>
<floor/>
<apply>
<divide/>
<apply>
<minus/>
<ci>time</ci>
<ci>t_ss</ci>
</apply>
<ci>stimPeriod</ci>
</apply>
</apply>
</apply>
</apply>
</apply>
<apply id="activation_protocol_clamping">
<eq/>
<ci>V</ci>
<piecewise>
<piece>
<ci>V_actHolding</ci>
<apply>
<leq/>
<ci>time</ci>
<ci>t_ss</ci>
</apply>
</piece>
<piece>
<ci>V_actTest</ci>
<apply>
<and/>
<apply>
<gt/>
<ci>time</ci>
<ci>t_ss</ci>
</apply>
<apply>
<leq/>
<ci>t</ci>
<ci>t_act</ci>
</apply>
<apply>
<leq/>
<ci>time</ci>
<apply>
<plus/>
<ci>t_ss</ci>
<apply>
<times/>
<ci>stimPeriod</ci>
<ci>np</ci>
</apply>
</apply>
</apply>
</apply>
</piece>
<otherwise>
<ci>V_actHolding</ci>
</otherwise>
</piecewise>
</apply>
</math>
</component>
</model>
