bi bi reaction ordered mechanism with single central complex (ODE model)

Community: MathModDB

continuous-time model	deterministic model	dimensional model	dynamic model	mathematical model	nonlinear model

Available identifiers

MaRDI QIDQ6675337

bi bi reaction with single central complex model following an ordered mechanism

Description

Ordinary differential equations for the rates of change of all chemical species (substrate 1 and 2, enzyme, enzyme - substrate 1 - complex, enzyme - substrate 1 - substrate 2 = enzyme - product 1 - product 2 - complex, enzyme - product 1 - complex and product 1 and 2 in a Bi Bi Reaction following the Ordered Mechanism with a Single Central Complex. kᵢ with positive or negative i represents the rate constant of the forward- or backward-reaction i-th reaction step.

List of contained entities

bi bi reaction ordered mechanism with single central complex ODE system	$\begin{matrix} \frac{d c_{S_{1}}}{d t} & = k_{- 1} c_{E S_{1}} - k_{1} c_{E} c_{S_{1}} \\ \frac{d c_{S_{2}}}{d t} & = k_{- 2} c_{E S_{1} S_{2} = E P_{1} P_{2}} - k_{2} c_{E S_{1}} c_{S_{2}} \\ \frac{d c_{E S_{1}}}{d t} & = k_{1} c_{E} c_{S_{1}} + k_{- 2} c_{E S_{1} S_{2} = E P_{1} P_{2}} - k_{- 1} c_{E S_{1}} - k_{2} c_{E S_{1}} c_{S_{2}} \\ \frac{d c_{E S_{1} S_{2} = E P_{1} P_{2}}}{d t} & = k_{2} c_{E S_{1}} c_{S_{2}} - k_{- 2} c_{E S_{1} S_{2} = E P_{1} P_{2}} + k_{- 4} c_{E P_{1}} c_{P_{2}} - k_{4} c_{E S_{1} S_{2} = E P_{1} P_{2}} \\ \frac{d c_{E P_{1}}}{d t} & = k_{4} c_{E S_{1} S_{2} = E P_{1} P_{2}} + k_{- 5} c_{E} c_{P_{1}} - k_{- 4} c_{E P_{1}} c_{P_{2}} - k_{5} c_{E P_{1}} \\ \frac{d c_{P_{1}}}{d t} & = k_{5} c_{E P_{1}} - k_{- 5} c_{E} c_{P_{1}} \\ \frac{d c_{P_{2}}}{d t} & = k_{4} c_{E S_{1} S_{2} = E P_{1} P_{2}} - k_{- 4} c_{E P_{1}} c_{P_{2}} \\ \frac{d c_{E}}{d t} & = k_{- 1} c_{E S_{1}} + k_{5} c_{E P_{1}} - k_{1} c_{E} c_{S_{1}} - k_{- 5} c_{E} c_{P_{1}} \end{matrix}$
	$\frac{d c_{E P_{1}}}{d t}$ represents reaction rate of enzyme - product 1 complex
	$\frac{d c_{E S_{1}}}{d t}$ represents reaction rate of enzyme - substrate 1 complex
	$\frac{d c_{E S_{1} S_{2} = E P_{1} P_{2}}}{d t}$ represents reaction rate of enzyme - substrate 1 - substrate 2 = enzyme - product 1 - product 2 complex
	$\frac{d c_{E}}{d t}$ represents reaction rate of enzyme
	$\frac{d c_{P_{1}}}{d t}$ represents reaction rate of product 1
	$\frac{d c_{P_{2}}}{d t}$ represents reaction rate of product 2
	$\frac{d c_{S_{1}}}{d t}$ represents reaction rate of substrate 1
	$\frac{d c_{S_{2}}}{d t}$ represents reaction rate of substrate 2
	$c_{E P_{1}}$ represents enzyme - product 1 complex concentration
	$c_{E S_{1}}$ represents enzyme - substrate 1 complex concentration
	$c_{E S_{1} S_{2} = E P_{1} P_{2}}$ represents enzyme - substrate 1 - substrate 2 = enzyme - product 1 - product 2 complex concentration
	$c_{E}$ represents enzyme concentration
	$c_{P_{1}}$ represents product 1 concentration
	$c_{P_{2}}$ represents product 2 concentration
	$c_{S_{1}}$ represents substrate 1 concentration
	$c_{S_{2}}$ represents substrate 2 concentration
	$k_{- 1}$ represents reaction rate constant
	$k_{- 2}$ represents reaction rate constant
	$k_{- 4}$ represents reaction rate constant
	$k_{- 5}$ represents reaction rate constant
	$k_{1}$ represents reaction rate constant
	$k_{2}$ represents reaction rate constant
	$k_{4}$ represents reaction rate constant
	$k_{5}$ represents reaction rate constant
	$t$ represents time

enzyme conservation	$c_{E_{0}} = c_{E} + c_{E X}$
	$c_{E X}$ represents complexed enzyme concentration
	$c_{E_{0}}$ represents enzyme concentration
	$c_{E}$ represents enzyme concentration

initial enzyme - product 1 - complex concentration (bi bi reaction ordered - ODE model)	$c_{E P_{1}} (t = 0) = c_{E P_{1_{0}}}$	initial condition
	$c_{E P_{1}}$ represents concentration
	$t$ represents time

initial enzyme - substrate 1 - complex concentration (bi bi reaction ordered - ODE model)	$c_{E S_{1}} (t = 0) = c_{{E S_{1}}_{0}}$	initial condition
	$c_{E S_{1}}$ represents concentration
	$t$ represents time

initial enzyme - substrate 1 - substrate 2 = enzyme product 1 - product 2 - complex concentration (bi bi reaction ordered with single central compelx - ODE model)	$c_{E S_{1} S_{2} = E P_{1} P_{2}} (t = 0) = c_{{E S_{1} S_{2} = E P_{1} P_{2}}_{0}}$	initial condition
	$c_{E S_{1} S_{2} = E P_{1} P_{2}}$ represents concentration
	$t$ represents time

initial enzyme concentration (bi bi reaction ordered - ODE model)	$c_{E} (t = 0) = c_{E_{0}}$	initial condition
	$c_{E}$ represents concentration
	$t$ represents time

initial product 1 concentration (bi bi reaction ordered - ODE model)	$c_{P_{1}} (t = 0) = c_{P_{1, 0}}$	initial condition
	$c_{P_{1}}$ represents concentration
	$t$ represents time

initial product 2 concentration (bi bi reaction ordered - ODE model)	$c_{P_{2}} (t = 0) = c_{P_{2, 0}}$	initial condition
	$c_{P_{2}}$ represents concentration
	$t$ represents time

initial substrate 1 concentration (bi bi reaction ordered - ODE model)	$c_{S_{1}} (t = 0) = c_{S_{1, 0}}$	initial condition
	$c_{S_{1}}$ represents concentration
	$t$ represents time

initial substrate 2 concentration (bi bi reaction ordered - ODE model)	$c_{S_{2}} (t = 0) = c_{S_{2, 0}}$	initial condition
	$c_{S_{2}}$ represents concentration
	$t$ represents time

law of mass action	$v = k \prod_{i = 1}^{n} c_{i}$
	$c_{i}$ represents concentration
	$k$ represents reaction rate constant
	$n$ represents molecularity
	$v$ represents reaction rate

mass balance	$δ_{t} + \nabla F = 0$

List of computational tasks

parameter estimation of enzyme kinetics
sensitivity analysis of complex kinetic systems
simulation of complex kinetic systems

Mathematical models specializing bi bi reaction ordered mechanism with single central complex (ODE model)

bi bi reaction ordered mechanism Michaelis Menten model with product 1 and single central complex (steady state assumption)	assumes	steady state assumption
bi bi reaction ordered mechanism Michaelis Menten model with product 2 and single central complex (steady state assumption)	assumes	steady state assumption
bi bi reaction ordered mechanism Michaelis Menten model with products 1 and 2 and single central complex (steady state assumption)	assumes	steady state assumption
bi bi reaction ordered mechanism Michaelis Menten model without products and single central complex (steady state assumption)	assumes	steady state assumption

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