Bioreactor Modeling

6. Bioreactor Modeling

OBJECTIVES

To acquire the concept of quantitative relationship between input and output of

bioreactors at various conditions to formulate its procedure

To give the concept of the design, modification, and control of bioreactors

6.1. MODEL—WHAT IS IT?

The word 'model' (derived from the Latin word " modus") means to measure some
quantity in a sizeable representation of a planned or existing "object". Modeling is
the mathematical representations of a system. More precisely, it is the
representation of the phenomena in a set of mathematical equations. A
comprehensive list of different tasks of modeling is given in Figure 6.1.

Figure 6.1. Different tasks of models.

A model of a process predicts the behavior of a process. In this regard, a set of
equations that comprise the model is the best approximation of the true process.
Engineers usually seek a compromise between time/cost or effort required to
verify the model. If the model is represented by complex equations, more number
of parameters are involved, which require proper evaluation. This may call for
more experiments to verify the model.

6.1.1. Use of Models

Following are the important uses of models.

Optimization of process operating conditions

Better understanding of the process

Proposing control strategy for a new process or bioreactor operation

For bioreactor operation, control of heat is one of the important factors. This is
a combination of heat generated by metabolic reaction as well as the
contribution from mechanical sources (like agitation, etc.). The control of heat
in the bioreactor can be done by controlling coolant temperature.

Selection of control settings and proposing the control law

Analysis of the safety aspect of the process

Training the plant operating personnel

Analysis of the marketability of the product

6.1.2. Classification of Models

Generally, models are developed from the first principles of physics and
chemistry. They are classified into following categories (Thilakavathi et al., 2007).

6.1.2.1. (A) THEORETICAL MODELS

They are developed from the principles of basic sciences. For example, the Henri-
Michaelis-Menten kinetic model is derived from the first principles.

6.1.2.2. (B) EMPIRICAL MODELS

They are obtained from either mathematical or statistical analysis. These models
might explain the experimental results, but they cannot be derived from the first
principles (Sinclair and Kristiansen, 1987). For example, Monod's model is used to
explain the growth kinetics of cells.

6.1.2.3. (C) SEMI–EMPIRICAL MODELS

This is a compromise between type (a) and type (b) models. One or two
parameters can be evaluated from plant data. The modification of Han and
Levenspiel model for the growth of Trichoderma harzianum growing on chitin to
produce chitinase is an interesting example (Felse, 1999). Other examples are
mixed vessels in series, plug flow with dispersion, etc. These models are
proposed, but the validity of the models on a production scale is questionable.
The basis of these models is RTD.

These models can be applied under dynamic (unsteady state) and steady state
approaches.

Let us take an example of temperature control in a continuous stirred tank

bioreactor model (Fig. 6.2).

Figure 6.2. Schematic of a continuous strried tank bioreactor model

temperature control.

For steady state approach, rate of accumulation term = 0.

Therefore,

(6.1)
Unsteady state (Dynamic) approach

(6.2)

where c is the specific heat capacity (energy/(unit mass)(unit temperature

difference)). Q is the rate of heat transfer (energy/time).

Assuming density and volume to be constant,

(6.3)

Equating the above two expressions for the rate of energy accumulation,

(6.4)

No assumption, except the constant specific heat, has been made for the
variables on the right hand side of the equation.

Relation between steady state and unsteady state approaches

One can derive the expression of steady state approach by considering

accumulation term to be zero.

6.2. DEFINITION OF LUMPED AND DISTRIBUTED PARAMETER

MODELS

6.2.1. Lumped Parameter Models

It assumes variation with time but not with space. For example, in unsteady state
CFSTBR, concentration varies with time, but not with space. The model is
represented by ordinary differential equations (ODEs).

6.2.2. Distributed Parameter Models

The assumed variation is with respect to both time and space. For example, in
unsteady state packed bed reactor (PBR), concentration varies with time and
distance. It has more than one independent variable. The model gives rise to
partial differential equations (PDEs).

6.3. INTRODUCTION TO A FEW TERMINOLOGIES AND THEOREMS

6.3.1. (a) What is a System?

A combination of different pieces of equipment integrated to perform a specific

function is known as system. For the present analysis, bioreactor and heat
exchanger are the systems.

In micro concept, a single unit operation is a system having inputs, states, and
outputs.

6.3.2. (b) What is Simulation?

Modeled equations have many variables. Changing some variables in the

equations while keeping others constant (those variables called parameters) and
finding their dependence on the phenomena is called simulation.

Simulation helps to understand the system behavior and must make sense to be
useful for analysis.

6.3.3. (c) Techniques

Linear System Analysis

The mathematical tools that are used to study the problems of linear dynamic
systems are known as system analysis techniques.

1. Laplace transform

It is applied to analyze single, linear and the nth order ODEs. Annexure to this
chapter summarizes a few Laplace transform of standard useful functions.

2. State-space techniques

This is used to analyze the behavior of multiple first order linear differential
equations. If the differential equations are non-linear, they can be linearized at a
desired steady state point.
6.4. MODELING PRINCIPLES

In general, following principles are used (Bequette, 1998):

Dynamic models consist of differential equations (ODEs or PDEs), often

combined with one or more algebraic equations. For process control problems,
dynamic models are obtained from the application of unsteady state
conservation relations.

Material/energy balances

Force/momentum balances

Algebraic equations in the process model arise from transport and

thermodynamic relations.

Real model should include the important dynamic effects not that much
complicated than needed and keeps the minimal number of equations and
parameters. The model equation must provide unique relationship among all
input and output variables. Degree of freedom is one of such approaches.

Assuming DF stands for degrees of freedom

NV stands for total number of variables (unspecified inputs and outputs)

NE stands for number of independent equations (both differential and algebraic),

Cases:

a. If DF = 0, NV = NE, then it is exactly determined process.

b. If DF > 0, NV > NE, then it is under specified conditions.

c. If DF < 0, NV < NE, it is over-specified conditions.

6.5. STEPS IN MODELING

1. Draw schematic diagram of process and label all process variables.

2. List all assumptions to be used in developing the model.

3. Determine whether independent variable other than time is required.

 4. Write approximate dynamic balance (overall mass, component, energy, etc.).

5. Introduce other relations which may be from the thermodynamics.

6. Identify system parameters.

7. Identify model variables.

8. Calculate degrees of freedom.

9. Specify Nf, total number of input variables.

10. Solve the necessary equations and do the parameter sensitivity analysis.

To understand the procedure, let us take some examples.

Example 6.1  How will you control temperature in a stirred heating device

required for a bioreactor?
Solution  One may recall Figure 6.2 for this purpose.
Assumption: Hold-up is not constant.
Result: Inlet and outlet flows and temperatures differ.
Consideration: Unsteady state mass and energy balances are necessary to
model the change in mass and temperature of the above problem.
Mass balance equation:

(6.5)
At constant density,

(6.6)
The energy balance equation is

(6.7)
where, Ti, Tref , and T are the inlet, reference and outlet temperatures,
respectively.
respectively.
Equations (6.5) and (6.7) are the dynamic model systems. One needs to specify
the conditions for volume and temperature, input variables (wi, w, Q and T) as
a function of time and relationships of an algebraic function (ρ, c).
From Equation (6.7)

Substitute from Equation (6.6), Equation (6.8) is obtained:

(6.8)
Since

Equating (6.7) and (6.8)

Dividing by ρcV

(6.9)

Example 6.2  Non-isothermal CFSTBR may be considered for sterilization

system.
The system description is given below.

The reaction is .

This is nth order with respect to reactant A.

α is the heat of reaction of A reacted (kcal/kmol).

 Heat generated is to be removed by cooling water in circulation.

Solution

1. Schematic representation of the system is given in Figure 6.3.

Figure 6.3. Non-isothermal CFSTBR.

2. Assumptions
a. Both the reactor contents and cooling jacket are perfectly mixed.

b. Heat loss is negligible to the surroundings.

c. Density can be assumed to be constant.

d. Jacket wall has negligible thermal inertia (assuming thin wall in the
jacket).

3. Appropriate dynamic balances

a. Total continuity equation in the bioreactor is described by Equation
(6.10).

(6.10)

b. Continuity equation for component A

(6.11)
where k is the reaction rate constant. kCnA = rate of reaction /unit
volume.
 c. Energy balance equation for the reactor is described below.

(6.12)
where h is the enthalpy Q is the heat removed from the system.
Balances for jacket
i. Energy balance
Enthalpy accumulation,

(6.13)

ii. Heat transfer from reactor to the cooling water

(6.14)
where AH is the heat transfer area.

4. Other balances
i. Expression for rate constant

(6.15)

ii. Hydraulic relationship

(6.16)
where kv is valve coefficient and (V – Vmin) drop in volume across the
valve.
This is not required if a pump is used for feeding.
Assuming enthalpy

5. Simplification of model equations

(6.17)
 (6.18)

(6.19)

(6.20)

(6.21)

6. Analysis of degrees of freedom

Hence, five variables have to be specified for the analysis.

6.6. FUNDAMENTAL LAWS USED IN PROCESS MODELING

Continuity Equation – law of conservation of mass

Conservation of energy – First law of thermodynamics

Diffusion of mass – Transport law

Heat transfer – Transport law

Newton's law of viscosity – Transport law

Equation of motion

Equation of state (density, heat capacity)

Rate of reaction
 Thermodynamic equilibrium

In bioreactor, dynamic analysis is more important for the design consideration

(Fish et al., 1989; Volesky and Votruba 1992). So the basic concept of first order
and second order kinetics are described here.

6.7. FIRST–ORDER SYSTEMS

The schematic diagram is given in Figure 6.4.

Figure 6.4. A typical CFSTBR.

The overall balance equations are given below.

(6.22)

Component balance is

(6.23)

At steady state,

(6.24)

At steady state
(6.25)

(6.26)

(6.27)

where,

Taking Laplace transform

(6.28)

If the input change is a step change,

Then
(6.29)

Taking the inverse of Laplace transform

(6.30)

6.8. SECOND-ORDER SYSTEMS

This comes from a concept of two reactors in series. In this case, the overall
transfer function of the system will be the product of each transfer function. The
scheme is given in Figure 6.5.

Figure 6.5. Schematic diagram of a second order system.

where

Q i(t), Q 1(t), Q 2(t) are flow rates.

V1, V2 are volume of the reactors.

k, R2 are gain.

H1 and H2 are height of the fluid in the first and second reactor, respectively.

Transfer function for a second-order system is given in Equation (6.31).

(6.31)

Here, for reactor (1),

Assuming gain, k = 1,

(6.32)

For reactor (2), Q 2 is dependent on H2.

(6.33)

Responses for a second-order system is described here.

Consider a linear second order ODE with constant parameters.

(6.34)

This equation can be written as

(6.35)

where,

(6.36)

where, ξ is the damping factor.

Taking Laplace transform for the above Equation (6.35)

Rearranging,

(6.37)

The roots of the characteristic equation

(6.38)

For step response, values of the roots depend on ξ, which are discussed by
Coughanour (1991) with proper Equations (6.39)–(6.43).

When    ξ = 1, the roots of the equation are real and equal.

(6.39)
The response of the system is critically damped.

If ξ < 1, the roots of the equation are complex, indicating underdamped or

oscillatory response.

(6.40)

For ξ > 1, the roots of the equation are real, resulting in overdamped or non-
oscillatory response.

(6.41)

For sinusoidal response

(6.42)

(6.43)

In Chapters 4 and 5, we have discussed about batch and continuous flow

bioreactors. Some of the mathematical treatments are directly used for bioreactor
modeling. Here, a few specific examples are discussed in detail.

6.9. COMPLEXITY OF THE MODEL

Simple model is better to understand and is easily applied in modeling. This may
not accommodate enough information of the system. For this reason, models are
sometimes complicated which results in cumbersome solution. Such type of
diffcult model may not find real applications. For examples, most of the models
related to fungal morphological parameters are complicated models.

A suitable model should have a balance between simplicity and reliability.

To achieve the goals of a desired mathematical model, computer applications are
necessary. A preferred applications of computer in this aspect is described here in
the flow diagram.

6.10. PARAMETER SENSITIVITY

A proper comparison between a mathematical model and experimental results

can be made if the proper values are known for the different parameters in the
model. Of course, the determination of parameters in the model is very much
time consuming as there may have interaction of different parameters in the
model.

Analysis to obtain an insight into the influence of parameters is called parameter

sensitivity analysis. This guides us to avoid unnecessary efforts in obtaining
accurate values of less important parameters. Simple way to do this analysis one
may practice the following.

Step 1: To get first estimate of the values of the parameters in the model.

Step 2: Substitute these parameter values into the model and solve.

Step 3: Vary the values of the parameters and record the influence on the most
important output variable of the model.

Kossen and Oosterhuis (1985) defined parameter sensitivity (PS) in the following
way.
Example 6.3  Batch growth with oxygen limitation
Considerations are listed below.

1. The concentration of oxygen in the liquid phase is zero in oxygen-limited

growth.

2. Oxygen is transferred from the gas phase to the liquid phase by inter-phase
mass transfer.

(6.44)
where

CL* is solubility of oxygen in the medium, and

kLa is the volumetric oxygen transfer coefficient.

The equation for growth is

(6.45)
Upon integration

(6.46)
This equation suggests that the growth is linear. In real system, exponential
growth occurs as the growth is limited by reactants.

Example 6.4  CFSTBR with oxygen limited growth

Figure 6.6. CFSTBR with oxygen limited growth.

Cell balance equation is

(6.47)
Reactant balance equation is

(6.48)
Oxygen balance equation is

(6.49)
where,

D = (F/V), and is the dilution rate,

is the number of moles of oxygen transfered from gas phase to liquid

phase,

C is the concentration of oxygen in the reaction fluid,

Co is the concentration of oxygen in the medium inlet,

CS is the concentration of reactant in the reaction fluid, and

CSo is the concentration of reactant in the inlet.

If oxygen is growth limiting

(6.50)
As

(6.51)
From oxygen balance, we get
(6.52)
where C* = Concentration of oxygen in the bulk (0 ≤ C* ≤ CL). CL is the
saturation level of oxygen in reaction phase.
∴ From Equations (6.47), (6.49), and (6.52), Equation (6.53) is obtained

(6.53)

Example 6.5  Model for plug flow reactor

The model equation for ideal plug flow will be the same as the batch reactor
equation except the real time is changed to residence time.

Example 6.6  Modeling of fed batch reactor

Fed-batch culture has two different concepts suggested by Yoshida et al.
(1973) and Suga et al. (1980). In chemical engineering practice, this is referred
to as semi-batch reactors. They are also called "extended cultures" and
"repeated fed-batch cultures". We have discussed about fed batch reactor in
Chapters 3 and 4.
For the modeling purpose, we consider three terminologies.

Simple fed batch

Repeated fed batch

Dialysis culture

We need to develop model equations in this aspect to predict

Cell concentration,

Product concentration, and

Residual reactant concentration as a function of time (Wang and

Stephanopoulos, 1984; Roels, 1983).

Model equations are listed below.

Volume balance equation
(6.54)
Reactant, cell, and product balances are given as

(6.55)

(6.56)

(6.57)
Under quasi-steady state conditions,

(6.58)
In a fed-batch reactor, the rate of consumption of reactants = rate of reactant
addition.
Under quasi-steady state condition,

(6.59)
The dilution rate, D and, therefore, μ decreases with time in a fed batch
culture.
To compare with other basic reactors let us consider the following figures.

Figure 6.7. μ vs. time plot for various reactors. (a) Batch bioreactor, (b)
CFSTBR (c) Fed-batch bioreactor.

Cell Concentration

(6.60)
where
where

Product Concentration
Two expressions are suggested here.

a. YP/S is constant
Therefore,

(6.61)
and hence,

(6.62)
Total product is

(6.63)

b. Specific product formation rate, qp is constant

(6.64)
We know

Substituting CXt into Equation (6.64), we get

(6.65)
Therefore, the product per unit volume of culture from Equations (6.61) and
(6.63)

(6.66)

where,

Vi is the initial volume

 Vi is the initial volume

CXm is the final cell concentration.

6.11. EXERCISES

6.1 The system is described with gas phase enzymatic reaction

The CSFTBR is filled with gases. The forward and reverse reactions are of
different orders. The mole fraction of A is ξ. Both pressure and ξ vary with
time. The product stream flows into another reactor through a restriction valve.
The second reactor is maintained at pressure of P2 (absolute). The feed stream
has a density of ρo and a mole fraction of yi of reactant A. Assume both the
gases are perfectly mixed and the system is isothermal. Molecular weights of A
and B are MA and MB, respectively. Calculate degrees of freedom in the system.

6.2 Consider the statement given in worked out Example 6.2, but flow in the
jacket is plug flow. Write the model equations and estimate the degrees of
freedom.

6.3 Model the following CFSTBR with recycle (Fig. 6.8):

Figure 6.8. CFSTBR with recycle

where subscript 'o' for initial/input conditions and R for recycle condition.

6.4 Model the bioreactor given in Figure 6.9.

Figure 6.9. Two stage single input CFSTBR in series

6.5 In modeling of a bioprocess, the following equations are to be used

where

X is the cell concentration

S is the substrate concentration

P is the product concentration

μ is the specific growth rate

qp is the specific production rate

YX/S, YP/S are the yield coefficients

Discuss on the difficulties you expect in the estimation of the yield coefficients.

6.6 No mathematical model in bio-system is unique one. Explain

6.7 Comment on the following:

a. Structured and unstructured models.

b. Asymmetric dynamic response of cells to changes in substrate

concentration.
 c. Relaxation – time criterion in modeling.

6.12. REFERENCES

Bequette BW (Ed.) (1998) Process Dynamics: Modeling, Analysis, and

Simulation, Prentice-Hall Int., Inc., New Jersey.

Coughanour DR (Ed.) (1991) Process System Analysis and Control, 2nd edn.,
McGraw-Hill International edn.

Felse PA (1999) "Process development for extracellular chitinase production by

Trichoderma harzianum", Ph.D. Thesis, IIT Madras, India.

Fish NM, Fox RI and Thornhill NF (Eds.) (1989) Computer applications in

fermentation technology: Modeling and control of biological processes, Society
of Chemical Industry and Elsevier Applied Science, London.

Kossen NWF and Oosterhuis, NMG (1985) "Modeling and scaling-up of

bioreactors" in, Biotechnology, Vol 2, (Brauer H, Editor), VCH, Weinheim. pp
571-605,

Roels JA (Ed.) (1983) Energetics and Kinetics in Biotechnology , Elsevier

Biomedical Press, Amsterdam.

Sinclair GG and Kristiansen B (1987) Fermentation Kinetics and Modelling,

Bu'Lock JD (Ed.), Open University Press.

Suga K, Waki T, Kumano M, Chimange P, Shin SB and Ichikawa K (1980)

Production of cellulose in fed-batch system, pp 371-392, Proceedings of
Bioconversion and Biochemical engineering , Symposium 2, vol II, Ghose TK
(ed) IITDelhi, New Delhi.

Thilakavathi M, Basak T and Panda T (2007) "Modeling of enzyme production

kinetics", Applied Microbiology and Biotechnology, 73, 991-1007.

Volesky B and Votruba J (Eds.) Modeling and Optimization of Fermentation

Processes, Elsevier, Amsterdam (1992).

Wang NS and Stephanopoulos GN (1984) "Computer applications to

fermentation processes". CRC critical reviews in Biotechnology, 2, 1-103.
 Yoshida F, Yamane T and Nakamoto K (1973) "Fed-batch hydrocarbon
fermentation with colloidal emulsion feed", Biotechnology and Bioengineering,
15, 257-270.

6.13. APPENDIX 6

6.13.1. LAPLACE TRANSFORM

Let us consider a time domain function f(t). Laplace transform of f(t) = L(f(t)).

This transforms time domain to's' domain.

In other words, inverse of Laplace transform is

6.13.1.1. APPLICATION

Laplace transform is used for linear operation, to solve linear partial differential
equations, exponential function, step function, time delay, integral and impulse
functions. Some standard Laplace transforms are summarized in Table 6.1 to help
solve the problems.
Table 6.1. Some standard Laplace transforms

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Professor Tapobrata Panda: Bioreactors: Analysis and Design. Bioreactor
Modeling, Chapter (McGraw-Hill Professional, 2011), AccessEngineering

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