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Copais and continuous rectors

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COPASI

Filipe Gama Freire

Department of Chemical Engineering

ISTUniversidade de Lisboa

Lisboa, Av. Rovisco Pais, 1 Portugal

December 5, 2014

Abstract

This article aims to fill an important gap in COPASI documentation and examples.

The most helpful example was Model of oscillating NF-kappaB signaling [1].

We implement and solve, in detail, a continuous flow stirred tank reactor (CSTR)

and validate the solution.

1

Contents

1 Introduction 3

4 Conclusions 13

2

1 Introduction

COPASI is a software application for simulation and analysis of chemical/biochemical net-

works and their dynamics [2].

Its development concerned primarily batch systems. However, COPASI can be used to

analyse reactions conducted in open systems. For instance, due to its analogy to a batch

reactor, ideal tubular reactors can already be studied using COPASI. With only small tricks

we can also analyse the kinetics of reactions performed during CSTR startup.

d(V Ci ) 1

= Q(Cio Ci ) + r(Cin )V

dt i

where:

V - reactor volume

Ci - Concentration of i species

Q - Volumetric flow rate

i - Stoichiometric coeficiente of the i species in the stoichiometric equation

r(Cin ) - rate of reaction

n - reaction order

dV d(V Ci ) d(Ci )

1. Liquid System. We can consider dt

= 0 and dt

=V dt

3. The system is isothermic,

dCi

= Q/V Cio Q/V Ci k Ci

dt

where we can identify three terms: a source Q/V Cio , a sink Q/V Ci and a reaction k Ci

Validation

Analitical Solution This example is very simple and has a analytical solution for Ci (t =

0) = Co that is:

1

Ci = Cio (Cio Co(1 + k V /Q))e(Q/V +k)t

1 + k V /Q

3

Other Solutions For more complex systems, like reaction orders different from zero or

one, or more than one reaction, we need numerical methods to solve them, but its always

possible to achieve a stationary state solution, given by:

dCi

= Q/V (Cio CiS ) k CiS = 0

dt

That for first order is easy to solve in order to Ci .

!

k V /Q

CiS = Cio 1 (1)

1 + k V /Q

For orders (n) different from zero or one, we need to solve the equation

n

Q/V (Cio CiS ) k CiS = 0

The V /Q, spatial time, will be a tricky part to input to COPASI, has we will see on the

implementation later on.

Lets assume the following system:

1. k = 0.15 s1

COPASI implementation.

4

Figure 1: Defining units and time interval in COPASI

First we need to define the units Figure 1. For our case time is in s, volume in L, quantity

is mol and time interval 10 (20 times the spacial time, a stiff thing!).

Secondly, lets create a compartment, say for instance, reactor, with fixed type and volume

1 L, Figure 2.

5

Figure 2: Defining the reactor

AB

we need four species (A, B, In and Out) and the tricky part, four reactions (reaction, SourceA,

OutA and OutB).

Lets introduce first the reaction itself as seen in Figure 3.

The second is not really a reaction but the inlet of A (SourceA) to the reactor as seen in

Figure 4.

6

Figure 4: Defining the inlet of A. Name, Rate Law and Parameter SV

SV is a global quantity and is the spatial velocity (Q/V). We can introduce a numerical

value or for commodity we can define it in Global Quantities section as seen in Figure 5

Figure 5: Defining SV the spatial velocity, in our case SV=2 but we use in the image a

Q/V=4.0/2.0 to demonstrate the possibility of putting equations here to achieve proper

understanding

7

If nothing more comes to the reactor its now necessary to define the sink, the outlets of

A and B, like in Figures 6 and 7.

Figure 6: Defining the outlet of A, of course that will be with the same parameter k1=SV,

because the volume and the volumetric flow rate are to be constant.

8

Figure 7: Defining the outlet of B with the same SV.

And finally defining the initial condition, the concentration of A inside the reactor at

time=0, Figure 9.

9

Figure 9: Defining the initial concentration of A inside the reactor Cio .

Now, we can solve the system Runing the task Time Course after the creation of a output

with the Output Assistant (plots - Concentrations, Volumes and ...), Figure 10.

10

Figure 11: Plot of the concentration of A in the reactor and outlet with time compared with

the inlet and product concentration.

The easiest way to validate the result is to calculate the stationary concentration of A

that in Figure 11 is shown as approx. 1.86 mol/l and can be calculated as said before eq. 1,

!

k V /Q

CiS = Cio 1 = 2(1 0.15 1/2/(1 + 0.15 1/2) = 1.860

1 + k V /Q

For simplicity, let say that everything stays the same with the late example of first order

except, obviously, the kinetic equation, which will now be

2A B

The only thing to do is to change the reaction in the Reaction section to have a rate

expression of second order, Figure 12

11

Figure 12: Defining a second order reaction is the only thing to change to the last example.

Run again the Time Course Task and the automatic generated plot will appear, Figure

13.

12

Figure 13: Plot of the concentration of A in the reactor and outlet with time compared with

the inlet and product concentration for a second order system.

We can now validate the results by solving the system with a ODE solver like the odeint

of the scipy.integrate of Python gets a CiS = 1.611 that is fully compatible with the COPASI

solution (CiS = 1.61).

By solving the ODE with other mean, it is necessary to emphasise that COPASI resolved

the mass balance

dA

= SV (Cio A) 2 k1 A2 with : A(t = 0) = 1, Cio = 2 and k1 = 0.15

dt

4 Conclusions

The first example seemed to take a lot of work for such an easy task as to solve an ODE.

But the reader must pay attention to the possibilities of COPASI, namely the easy imple-

mentation of other systems, as we made the order change, with very complex mechanisms

and its strong ability to make Parameter Estimation with standard error determination.

We regret the absence of an easy implementation of non-isothermal systems but we

understand that is not usually on biochemical problem.

13

This paper is only intended to explain how to extend the huge COPASI capacity to

CSTRs and perhaps other open systems of Chemical Engineering.

References

[1] NF-kappaB signaling pathway oscillations, as published by Nelson et al. (2004), following

the one of Hoffman et al. (2002).

14

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