- Author:
- Weiwei Ai <wai484@aucklanduni.ac.nz>
- Date:
- 2024-04-19 17:04:11+12:00
- Desc:
- Add bond graph models for ref 2005 fig 3B
- Permanent Source URI:
- http://models.cellml.org/workspace/b65/rawfile/ca447f870d3be12963a885d5acd8da79af2a683d/Facilitated transporter/CellMLV2/GLUT1_BG.py
# The content of this file was generated using the Python profile of libCellML 0.5.0.
from enum import Enum
from math import *
__version__ = "0.4.0"
LIBCELLML_VERSION = "0.5.0"
STATE_COUNT = 4
VARIABLE_COUNT = 48
class VariableType(Enum):
VARIABLE_OF_INTEGRATION = 0
STATE = 1
CONSTANT = 2
COMPUTED_CONSTANT = 3
ALGEBRAIC = 4
VOI_INFO = {"name": "t", "units": "second", "component": "GLUT1_BG", "type": VariableType.VARIABLE_OF_INTEGRATION}
STATE_INFO = [
{"name": "q_1", "units": "fmol", "component": "GLUT1_BG", "type": VariableType.STATE},
{"name": "q_2", "units": "fmol", "component": "GLUT1_BG", "type": VariableType.STATE},
{"name": "q_3", "units": "fmol", "component": "GLUT1_BG", "type": VariableType.STATE},
{"name": "q_4", "units": "fmol", "component": "GLUT1_BG", "type": VariableType.STATE}
]
VARIABLE_INFO = [
{"name": "q_init_Ao", "units": "fmol", "component": "params_BG", "type": VariableType.COMPUTED_CONSTANT},
{"name": "g_o", "units": "mM", "component": "params_BG", "type": VariableType.CONSTANT},
{"name": "V_o", "units": "pL", "component": "params_BG", "type": VariableType.CONSTANT},
{"name": "q_init_Ai", "units": "fmol", "component": "params_BG", "type": VariableType.COMPUTED_CONSTANT},
{"name": "g_i", "units": "mM", "component": "params_BG", "type": VariableType.CONSTANT},
{"name": "V_i", "units": "pL", "component": "params_BG", "type": VariableType.CONSTANT},
{"name": "R", "units": "J_per_K_mol", "component": "params_BG", "type": VariableType.CONSTANT},
{"name": "T", "units": "kelvin", "component": "params_BG", "type": VariableType.CONSTANT},
{"name": "K_Ai", "units": "per_fmol_1", "component": "params_BG", "type": VariableType.CONSTANT},
{"name": "K_Ao", "units": "per_fmol_1", "component": "params_BG", "type": VariableType.CONSTANT},
{"name": "K_1", "units": "per_fmol_1", "component": "params_BG", "type": VariableType.CONSTANT},
{"name": "q_init_1", "units": "fmol", "component": "params_BG", "type": VariableType.CONSTANT},
{"name": "K_2", "units": "per_fmol_1", "component": "params_BG", "type": VariableType.CONSTANT},
{"name": "q_init_2", "units": "fmol", "component": "params_BG", "type": VariableType.CONSTANT},
{"name": "K_3", "units": "per_fmol_1", "component": "params_BG", "type": VariableType.CONSTANT},
{"name": "q_init_3", "units": "fmol", "component": "params_BG", "type": VariableType.CONSTANT},
{"name": "K_4", "units": "per_fmol_1", "component": "params_BG", "type": VariableType.CONSTANT},
{"name": "q_init_4", "units": "fmol", "component": "params_BG", "type": VariableType.CONSTANT},
{"name": "kappa_r1", "units": "fmol_per_s_1", "component": "params_BG", "type": VariableType.CONSTANT},
{"name": "kappa_r2", "units": "fmol_per_s_1", "component": "params_BG", "type": VariableType.CONSTANT},
{"name": "kappa_r3", "units": "fmol_per_s_1", "component": "params_BG", "type": VariableType.CONSTANT},
{"name": "kappa_r4", "units": "fmol_per_s_1", "component": "params_BG", "type": VariableType.CONSTANT},
{"name": "mu_Ai", "units": "J_per_mol", "component": "GLUT1_BG", "type": VariableType.COMPUTED_CONSTANT},
{"name": "q_Ai", "units": "fmol", "component": "GLUT1_BG", "type": VariableType.COMPUTED_CONSTANT},
{"name": "mu_Ao", "units": "J_per_mol", "component": "GLUT1_BG", "type": VariableType.COMPUTED_CONSTANT},
{"name": "q_Ao", "units": "fmol", "component": "GLUT1_BG", "type": VariableType.COMPUTED_CONSTANT},
{"name": "mu_1", "units": "J_per_mol", "component": "GLUT1_BG", "type": VariableType.ALGEBRAIC},
{"name": "v_1", "units": "fmol_per_s", "component": "GLUT1_BG", "type": VariableType.ALGEBRAIC},
{"name": "mu_2", "units": "J_per_mol", "component": "GLUT1_BG", "type": VariableType.ALGEBRAIC},
{"name": "v_2", "units": "fmol_per_s", "component": "GLUT1_BG", "type": VariableType.ALGEBRAIC},
{"name": "mu_3", "units": "J_per_mol", "component": "GLUT1_BG", "type": VariableType.ALGEBRAIC},
{"name": "v_3", "units": "fmol_per_s", "component": "GLUT1_BG", "type": VariableType.ALGEBRAIC},
{"name": "mu_4", "units": "J_per_mol", "component": "GLUT1_BG", "type": VariableType.ALGEBRAIC},
{"name": "v_4", "units": "fmol_per_s", "component": "GLUT1_BG", "type": VariableType.ALGEBRAIC},
{"name": "v_r1", "units": "fmol_per_s", "component": "GLUT1_BG", "type": VariableType.ALGEBRAIC},
{"name": "A_f_r1", "units": "J_per_mol", "component": "GLUT1_BG", "type": VariableType.ALGEBRAIC},
{"name": "A_r_r1", "units": "J_per_mol", "component": "GLUT1_BG", "type": VariableType.ALGEBRAIC},
{"name": "v_r2", "units": "fmol_per_s", "component": "GLUT1_BG", "type": VariableType.ALGEBRAIC},
{"name": "A_f_r2", "units": "J_per_mol", "component": "GLUT1_BG", "type": VariableType.ALGEBRAIC},
{"name": "A_r_r2", "units": "J_per_mol", "component": "GLUT1_BG", "type": VariableType.ALGEBRAIC},
{"name": "v_r3", "units": "fmol_per_s", "component": "GLUT1_BG", "type": VariableType.ALGEBRAIC},
{"name": "A_f_r3", "units": "J_per_mol", "component": "GLUT1_BG", "type": VariableType.ALGEBRAIC},
{"name": "A_r_r3", "units": "J_per_mol", "component": "GLUT1_BG", "type": VariableType.ALGEBRAIC},
{"name": "v_r4", "units": "fmol_per_s", "component": "GLUT1_BG", "type": VariableType.ALGEBRAIC},
{"name": "A_f_r4", "units": "J_per_mol", "component": "GLUT1_BG", "type": VariableType.ALGEBRAIC},
{"name": "A_r_r4", "units": "J_per_mol", "component": "GLUT1_BG", "type": VariableType.ALGEBRAIC},
{"name": "v_Ai", "units": "fmol_per_s", "component": "GLUT1_BG", "type": VariableType.ALGEBRAIC},
{"name": "v_Ao", "units": "fmol_per_s", "component": "GLUT1_BG", "type": VariableType.ALGEBRAIC}
]
def create_states_array():
return [nan]*STATE_COUNT
def create_variables_array():
return [nan]*VARIABLE_COUNT
def initialise_variables(states, rates, variables):
variables[1] = 1.0e-5
variables[2] = 0.09
variables[4] = 10.0
variables[5] = 0.09
variables[6] = 8.31
variables[7] = 273.15
variables[8] = 149.65
variables[9] = 149.65
variables[10] = 33.20
variables[11] = 0.0017
variables[12] = 4.25e+03
variables[13] = 0.0017
variables[14] = 344.59
variables[15] = 0.0017
variables[16] = 1.99
variables[17] = 0.0017
variables[18] = 0.36
variables[19] = 0.26
variables[20] = 1.01e+05
variables[21] = 1.01e+04
states[0] = variables[11]
states[1] = variables[13]
states[2] = variables[15]
states[3] = variables[17]
def compute_computed_constants(variables):
variables[0] = variables[1]*variables[2]
variables[3] = variables[4]*variables[5]
variables[22] = variables[6]*variables[7]*log(variables[8]*variables[23])
variables[23] = variables[3]
variables[24] = variables[6]*variables[7]*log(variables[9]*variables[25])
variables[25] = variables[0]
def compute_rates(voi, states, rates, variables):
variables[32] = variables[6]*variables[7]*log(variables[16]*states[3])
variables[35] = variables[32]
variables[26] = variables[6]*variables[7]*log(variables[10]*states[0])
variables[36] = variables[26]
variables[34] = variables[18]*(exp(variables[35]/(variables[6]*variables[7]))-exp(variables[36]/(variables[6]*variables[7])))
variables[28] = variables[6]*variables[7]*log(variables[12]*states[1])
variables[42] = variables[28]
variables[41] = variables[24]+variables[26]
variables[40] = variables[20]*(exp(variables[41]/(variables[6]*variables[7]))-exp(variables[42]/(variables[6]*variables[7])))
variables[27] = variables[34]-variables[40]
rates[0] = variables[27]
variables[38] = variables[28]
variables[30] = variables[6]*variables[7]*log(variables[14]*states[2])
variables[39] = variables[30]
variables[37] = variables[19]*(exp(variables[38]/(variables[6]*variables[7]))-exp(variables[39]/(variables[6]*variables[7])))
variables[29] = variables[40]-variables[37]
rates[1] = variables[29]
variables[44] = variables[30]
variables[45] = variables[22]+variables[32]
variables[43] = variables[21]*(exp(variables[44]/(variables[6]*variables[7]))-exp(variables[45]/(variables[6]*variables[7])))
variables[31] = variables[37]-variables[43]
rates[2] = variables[31]
variables[33] = variables[43]-variables[34]
rates[3] = variables[33]
def compute_variables(voi, states, rates, variables):
variables[26] = variables[6]*variables[7]*log(variables[10]*states[0])
variables[28] = variables[6]*variables[7]*log(variables[12]*states[1])
variables[30] = variables[6]*variables[7]*log(variables[14]*states[2])
variables[32] = variables[6]*variables[7]*log(variables[16]*states[3])
variables[35] = variables[32]
variables[36] = variables[26]
variables[34] = variables[18]*(exp(variables[35]/(variables[6]*variables[7]))-exp(variables[36]/(variables[6]*variables[7])))
variables[38] = variables[28]
variables[39] = variables[30]
variables[37] = variables[19]*(exp(variables[38]/(variables[6]*variables[7]))-exp(variables[39]/(variables[6]*variables[7])))
variables[42] = variables[28]
variables[41] = variables[24]+variables[26]
variables[40] = variables[20]*(exp(variables[41]/(variables[6]*variables[7]))-exp(variables[42]/(variables[6]*variables[7])))
variables[44] = variables[30]
variables[45] = variables[22]+variables[32]
variables[43] = variables[21]*(exp(variables[44]/(variables[6]*variables[7]))-exp(variables[45]/(variables[6]*variables[7])))
variables[46] = variables[43]
variables[47] = -variables[40]
variables[27] = variables[34]-variables[40]
variables[29] = variables[40]-variables[37]
variables[31] = variables[37]-variables[43]
variables[33] = variables[43]-variables[34]
