modelAllostery

Change of macromolecule state - providing specific subunit forms (e.g. relaxed<->tensed deoxygenated hemoglobin change)

Extends from Chemical.Processes.Internal.PartialSpeciationWithSubunitsDefinition (Chemical speciation), Chemical.Interfaces.ConditionalKinetics (Input of kinetics coefficient vs. parametric kinetics coefficient).

Information

s₁·S₁ + .. + s_nS·S_nS <-> p₁·P₁ + .. + p_nP·P_nP

By redefinition of stoichometry as v_i = -s_i, A_i = S_i for i=1..nS v_i = p_i-nS, A_i = P_i-nS for i=nS+1..nS+nP

So the reaction can be written also as 0 = ∑ (v_i · A_i)

Equilibrium equation

K = product(a(S).^s) / product( a(P).^s ) = product(a(A).^v)	dissociation constant
Δ_rG = ∑ (v_i · Δ_fG_i) = Δ_rH - T·Δ_rS = -R·T·log(K)	molar Gibb's energy of the reaction
Δ_rH = ∑ (v_i · Δ_fH_i)	molar enthalpy of the reaction
Δ_rS = ∑ (v_i · Δ_fS_i) = k·log(Δ_rω)	molar entropy of the reaction

Notations

A_i	i-th substance
v_i	stochiometric coefficients of i-th substance
K	dissociation constant (activity based)
a(A_i)=f_i*x_i	activity of the substance A
f_i	activity coefficient of the substance A
x_i	mole fraction of the substance A
Δ_fH_i	molar enthalpy of formation of i-th substance
Δ_fG_i	molar Gibbs energy of formation of i-th substance
Δ_fS_i	molar entropy of formation of i-th substance
Δ_rω	change of number of microstates of particles by reaction

Parameters

Type	Name	Default	Description
Chemical.Interfaces.Definition	firstForeSubunit (from PartialSpeciationWithSubunitsDefinition)	dropOfCommons.DefaultSubstance	First product definition
Chemical.Interfaces.Definition[:]	nextForeSubunits (from PartialSpeciationWithSubunitsDefinition)	fill(dropOfCommons.DefaultSubstance, max(1, nP - 1))	Definitions of next subunit_fore
Chemical.Interfaces.Definition	process (from PartialSpeciationWithSubunitsDefinition)	Chemical.Interfaces.processData(1)	Process changes of Gibbs energy, enthalpy, volume and heat capacity (subunit_fore - reactants)
Real	k_forward (from ConditionalKinetics)	1	Forward rate coefficient (mole-fraction based)
Advanced
Modelica.Units.SI.MolarFlowRate	n_flow_reg (from PartialSpeciation)	dropOfCommons.n_flow_reg	Regularization threshold of mass flow rate
StateSelect	n_flowStateSelect (from PartialSpeciation)	StateSelect.default	State select for n_flow
Modelica.Units.SI.Time	TC (from PartialSpeciation)	0.1	Time constant for electro-chemical potential adaption
Utilities.Units.Inertance	L (from PartialSpeciation)	dropOfCommons.L	Inertance of the flow
Initialization › Molar flow
InitializationMethods	initN_flow (from PartialSpeciation)	Chemical.Utilities.Types.InitializationMethods.none	Initialization method for n_flow
Modelica.Units.SI.MolarFlowRate	n_flow_0 (from PartialSpeciation)	0	Initial value for n_flow
Utilities.Units.MolarFlowAcceleration	n_acceleration_0 (from PartialSpeciation)	0	Initial value for der(n_flow)
General › Ports
Integer	nS (from PartialSpeciation)	0	Number of subunits in rear macromolecule state
Integer	nP (from PartialSpeciation)	0	Number of subunits in fore macromolecule state
Conditional inputs
FirstProductChoice	firstForeSubunitFrom (from PartialSpeciationWithSubunitsDefinition)	FirstProductChoice.Process	First product definition comes from?
Advanced › Conditional inputs
Boolean	useForwardRateInput (from ConditionalKinetics)	false	Forward rate coefficient from input?

Connectors

Type	Name	Default	Description
Chemical.Interfaces.Rear[nS]	subunit_rear (from PartialSpeciation)		Subunits in rear macromolecule state
Chemical.Interfaces.Fore[nP]	subunit_fore (from PartialSpeciation)		Subunits in fore macromolecule state
Interfaces.SolutionPort	solution_rear (from PartialSpeciation)		To connect solution of subunits with rear state of macromolecule
Interfaces.SolutionPort	solution_fore (from PartialSpeciation)		To connect solution of subunits with fore state of macromolecule
Chemical.Interfaces.SolutionPort	solution (from PartialSpeciation)		To connect substance with solution, where is pressented
Modelica.Blocks.Interfaces.RealInput	kfInput (from ConditionalKinetics)	kf

Components

Type	Name	Description
Modelica.Units.SI.MolarFlowRate	rr (from PartialSpeciation)	Molar flow rate of change macromolecule from rear state to fore state
Modelica.Units.SI.AmountOfSubstance	nm_fore (from PartialSpeciation)	Amount of the macromolecule in fore state
Modelica.Units.SI.AmountOfSubstance	nm_rear (from PartialSpeciation)	Amount of the macromolecule in rear state
Modelica.Units.SI.MoleFraction	xm_fore (from PartialSpeciation)	Mole fraction of the macromolecule in fore state
Modelica.Units.SI.MoleFraction	xm_rear (from PartialSpeciation)	Mole fraction of the macromolecule in rear state
Chemical.Interfaces.SolutionState	solutionState (from PartialSpeciation)
Chemical.Interfaces.Definition	macromolecule_rear (from PartialSpeciation)	Specific rear state of macromolecule composed only with connected subunits
Chemical.Interfaces.Definition	macromolecule_fore (from PartialSpeciation)	Specific fore state of macromolecule composed only with connected subunits
Real	i (from PartialSpeciation)
Real	dH (from PartialSpeciation)
Real	dV (from PartialSpeciation)
Real	nj (from PartialSpeciation)
Real	mj (from PartialSpeciation)
Real	Vj (from PartialSpeciation)
Real	Gj (from PartialSpeciation)
Real	Qj (from PartialSpeciation)
Real	Ij (from PartialSpeciation)
Real[nS]	RTlnxm_rear (from PartialSpeciation)
Real[nP]	RTlnxm_fore (from PartialSpeciation)
Real	kf (from ConditionalKinetics)	Current forward rate coefficient

Name	Description
uDiff

Revisions

2013-2020 by Marek Matejak, Charles University, Prague, Czech Republic