[docs]
class differentiation_rate:
""" This class defines the differentiation rates of the different cell types in the Lemaire bone cell population model.
The following table provides a mapping between the model parameters
and their original names from the publication:
+------------------+------------+----------+
| Parameter Name | Symbol | Units |
+==================+============+==========+
| OBu |:math:`D_R` | pM/day |
+------------------+------------+----------+
| OBp |:math:`d_B` | pM/day |
+------------------+------------+----------+
| OCp |:math:`D_C` | pM/day |
+------------------+------------+----------+
:param OBu: differentiation rate of uncommitted osteoblasts
:type OBu: float
:param OBp: differentiation rate of precursor osteoblasts
:type OBp: float
:param OCp: differentiation rate of precursor osteoclasts
:type OCp: float
"""
def __init__(self):
""" Constructor method. """
self.OBu = 7.00e-4
self.OBp = 7.00e-1
self.OCu = None
self.OCp = 2.10e-3
[docs]
class apoptosis_rate:
""" This class defines the apoptosis rates of the different cell types in the Lemaire bone cell population model.
The following table provides a mapping between the model parameters
and their original names from the publication:
+------------------+-------------+----------------+
| Parameter Name | Symbol | Units |
+==================+=============+================+
| OBa | :math:`k_B` | 1/day |
+------------------+-------------+----------------+
| OCa | :math:`D_A` | pM/day |
+------------------+-------------+----------------+
:param OBa: apoptosis rate of active osteoblasts
:type OBa: float
:param OCa: apoptosis rate of active osteoclasts
:type OCa: float """
def __init__(self):
self.OBa = 1.89e-1
self.OCa = 7.00e-1
[docs]
class activation_coefficient:
""" This class defines the activation coefficients of the different cell types in the Lemaire bone cell population model. """
def __int__(self):
# Activation coefficients related to TGF-beta binding on OBu and OCa [pM]
self.TGFb_OBu = None
self.TGFb_OCa = None
# Activation coefficient related to RANKL binding to RANK [pM]
self.RANKL_OCp = None
# Activation coefficient for RANKL production related to PTH binding to osteoblasts [pM]
self.PTH_OB = None
# Activation coefficient related to MCSF binding on OCu [pM]
self.MCSF_OCu = None
[docs]
class repression_coefficient:
""" This class defines the repression coefficients of the different cell types in the Lemaire bone cell population model. """
def __init__(self):
# Repression coefficient related to TGF-beta binding on OBp [pM]
self.TGFb_OBp = None
# Repression coefficient for OPG production related to PTH binding on osteoblasts [pM]
self.PTH_OB = None
[docs]
class degradation_rate:
""" This class defines the degradation rates of the different factors in the Lemaire bone cell population model.
The following table provides a mapping between the model parameters
and their original names from the publication:
+------------------+-------------+-----------------+
| Parameter Name | Symbol | Units |
+==================+=============+=================+
| PTH | :math:`k_P` | 1/day |
+------------------+-------------+-----------------+
| OPG | :math:`k_O` | 1/day |
+------------------+-------------+-----------------+
:param PTH: degradation rate of PTH
:type PTH: float
:param OPG: degradation rate of OPG
:type OPG: float """
def __init__(self):
self.PTH = 86
self.OPG = 3.50e-1
self.RANKL = None
[docs]
class concentration:
""" This class defines the fixed concentrations of the different factors in the Lemaire bone cell population model.
The following table provides a mapping between the model parameters
and their original names from the publication:
+------------------+-------------------+------------------+
| Parameter Name | Symbol | Units |
+==================+===================+==================+
| OPG_max | :math:`OPG_{\max}`| pM |
+------------------+-------------------+------------------+
| RANK | :math:`K` | pM |
+------------------+-------------------+------------------+
:param OPG_max: Maximum concentration of OPG
:type OPG_max: float
:param RANK: fixed concentration of RANK
:type RANK: float """
def __init__(self):
""" Constructor method. """
self.OPG_max = 2.00e+8 # Maximum concentration of OPG [pM]
self.MCSF = None
# -> K
self.RANK = 1.00e+1 # [pM] fixed concentration of RANK
[docs]
class binding_constant:
""" This class defines the binding constants of the possible receptor-ligand interactions in the Lemaire bone cell population model.
The following table provides a mapping between the model parameters
and their original names from the publication:
+------------------+-------------+------------------+
| Parameter Name | Symbol | Units |
+==================+=============+==================+
| RANKL_OPG | :math:`k_1` | 1/(pM·day) |
+------------------+-------------+------------------+
| RANKL_RANK | :math:`k_3` | 1/(pM·day) |
+------------------+-------------+------------------+
| TGFb_OC | :math:`C^s` | pM |
+------------------+-------------+------------------+
| PTH_OB | :math:`k_5` | 1/(pM·day) |
+------------------+-------------+------------------+
:param RANKL_OPG: Association binding constant for RANKL-OPG
:type RANKL_OPG: float
:param RANKL_RANK: Association binding constant for RANKL-RANK
:type RANKL_RANK: float
:param TGFb_OC: dissociation binding coefficient of TGFb with its receptor
:type TGFb_OC: float
:param PTH_OB: rate of PTH binding with its receptor on OB
:type PTH_OB: float """
def __init__(self):
""" Constructor method. """
# Association binding constant for RANKL-OPG [(pM day)^{-1}]
# -> k_1
self.RANKL_OPG = 1.00e-2
# Association binding constant for RANKL-RANK [(pM day)^{-1}]
# -> k_3
self.RANKL_RANK = 5.80e-4
# dissociation binding coefficient of TGFb with its receptor
# [pM] value of OC to get half differentiation flux
# -> C^s
self.TGFb_OC = 5.00e-3
# [(pM day)^{-1}] rate of PTH binding with its receptor on OB
# -> k_5
self.PTH_OB = 2.00e-2
[docs]
class unbinding_constant:
""" This class defines the unbinding constants of the possible receptor-ligand interactions in the Lemaire bone cell population model.
The following table provides a mapping between the model parameters
and their original names from the publication:
+------------------+------------+----------+
| Parameter Name | Symbol | Units |
+==================+============+==========+
| RANKL_OPG | :math:`k_2`| 1/day |
+------------------+------------+----------+
| RANKL_RANK | :math:`k_4`| 1/day |
+------------------+------------+----------+
| PTH_OB | :math:`k_6`| 1/day |
+------------------+------------+----------+
:param RANKL_OPG: Unbinding constant for RANKL-OPG
:type RANKL_OPG: float
:param RANKL_RANK: Unbinding constant for RANKL-RANK
:type RANKL_RANK: float
:param PTH_OB: rate of PTH unbinding with its receptor on OB
:type PTH_OB: float """
def __init__(self):
# Association binding constant for RANKL-OPG [1/day]
# -> k_2
self.RANKL_OPG = 1.00e+1
# Association binding constant for RANKL-RANK [1/pM]
# -> k_4
self.RANKL_RANK = 1.70e-2
# dissociation binding coefficient of TGFb with its receptor
self.TGFb_OC = None
# [(day)^{-1}] rate of PTH binding with its receptor on OB
# -> k_6
self.PTH_OB = 3.00e+0
[docs]
class production_rate:
""" This class defines the intrinsic/ endogenous production rates of the different factors in the Lemaire bone cell population model.
The following table provides a mapping between the model parameters
and their original names from the publication:
+---------------------+-------------+------------------+
| Parameter Name | Symbol | Units |
+=====================+=============+==================+
| intrinsic_PTH | :math:`S_P` | pM/day |
+---------------------+-------------+------------------+
| intrinsic_RANKL |:math:`r_L` | pM/day |
+---------------------+-------------+------------------+
| min_OPG_per_cell |:math:`K^P_O`| pM/day |
+---------------------+-------------+------------------+
| max_RANKL_per_cell |:math:`K^P_L`| pM/pM |
+---------------------+-------------+------------------+
:param intrinsic_PTH: Intrinsic production rate of PTH
:type intrinsic_PTH: float
:param intrinsic_RANKL: Intrinsic production rate of RANKL
:type intrinsic_RANKL: float
:param min_OPG_per_cell: Minimal rate of OPG production per cell
:type min_OPG_per_cell: float
:param max_RANKL_per_cell: Production rate of RANKL per cell
:type max_RANKL_per_cell: float"""
def __init__(self):
""" Constructor method. """
# Intrinsic production rate of PTH [pM/day] (assumed to be constant)
# -> S_P
self.intrinsic_PTH = 250
# Intrinsic production rate of RANKL [pM/day]
# -> r_L
self.intrinsic_RANKL = 1.0e+3
# Minimal rate of OPG production per cell
# -> K^P_O
self.min_OPG_per_cell = 2.00e+5
# Boolean variables determining which cells produce OPG
self.bool_OPGprod_OBp = None # 0=no
self.bool_OPGprod_OBa = None # 1=yes
# Constant describing how much RANK is produced per cell [pM/pM]
self.RANKrate_per_cell = None
# Production rate of RANKL per cell [pM/pM]
# -> K^P_L
self.max_RANKL_per_cell = 3.00e+6
# Boolean variables determining which cells produce RANKL
self.bool_RANKLprod_OBp = None # 1=yes
self.bool_RANKLprod_OBa = None # 0=no
[docs]
class correction_factor:
""" This class defines the correction factors for the Lemaire bone cell population model. They are used to adjust the model parameters.
:param f0: correction factor for OBp differentiation rate and TGFb activation function
:type f0: float """
def __init__(self):
""" Constructor method. """
# -> f_0
self.f0 = 5.00e-2 # correction factor for OBp differentiation rate and TGFb activation function
[docs]
class bone_volume:
""" This class defines the parameters relevant for bone volume of the bone model.
:param formation_rate: rate of bone formation
:type formation_rate: float
:param resorption_rate: rate of bone resorption
:type resorption_rate: float """
def __init__(self):
self.formation_rate = 1.571/ 100
self.resorption_rate = None
[docs]
class Lemaire_Parameters:
""" This class defines the parameters of the Lemaire bone cell population model.
:param differentiation_rate: differentiation rates of the different cell types, see :class:`differentiation_rate` for details
:type differentiation_rate: differentiation_rate
:param apoptosis_rate: apoptosis rates of the different cell types, see :class:`apoptosis_rate` for details
:type apoptosis_rate: apoptosis_rate
:param activation_coefficient: activation coefficients of the different cell types, see :class:`activation_coefficient` for details
:type activation_coefficient: activation_coefficient
:param repression_coefficient: repression coefficients of the different cell types, see :class:`repression_coefficient` for details
:type repression_coefficient: repression_coefficient
:param correction_factor: correction factors for the model, see :class:`correction_factor` for details
:type correction_factor: correction_factor
:param degradation_rate: degradation rates of the different factors, see :class:`degradation_rate` for details
:type degradation_rate: degradation_rate
:param concentration: fixed concentrations of the different factors, see :class:`concentration` for details
:type concentration: concentration
:param binding_constant: binding constants of the receptor-ligand interactions, see :class:`binding_constant` for details
:type binding_constant: binding_constant
:param unbinding_constant: unbinding constants of the receptor-ligand interactions, see :class:`unbinding_constant` for details
:type unbinding_constant: unbinding_constant
:param production_rate: intrinsic production rates of the different factors, see :class:`production_rate` for details
:type production_rate: production_rate
:param bone_volume: parameters relevant for bone volume, see :class:`bone_volume` for details
:type bone_volume: bone_volume
:param differentiation_rate.OBp: corrected differentiation rate of precursor osteoblasts
:type differentiation_rate.OBp: float """
def __init__(self):
self.differentiation_rate = differentiation_rate()
self.apoptosis_rate = apoptosis_rate()
self.activation_coefficient = activation_coefficient()
self.repression_coefficient = repression_coefficient()
self.correction_factor = correction_factor()
self.degradation_rate = degradation_rate()
self.concentration = concentration()
self.binding_constant = binding_constant()
self.unbinding_constant = unbinding_constant()
self.production_rate = production_rate()
# self.capacity = capacity()
self.bone_volume = bone_volume()
self.differentiation_rate.OBp = self.differentiation_rate.OBp * self.correction_factor.f0