exercise inhibition

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exercise inhibition

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This exercise is designed to introduce you to nonlinear fitting technique and application of Monod

equation:

𝐶𝑠

𝜇 = 𝜇 max

𝐾𝑚 + 𝐶𝑠

1. Analyze equation using fundamental analytical techniques:

a. What is lim 𝜇? What kind of information can you gain using this result?

𝐶𝑠 → ∞

𝜇max

b. Prove that 𝜇(𝐶𝑠 ) in the limit of small 𝐶𝑠 tends to 𝜇(𝐶𝑠 ) = 𝐶𝑠 (Hint: use Taylor’s

𝐾𝑚

series expansion). What kind of information can you gain using this result?

c. Prove that the equation can be transformed to:

1 1 𝐾𝑚 1

= +

𝜇 𝜇 max 𝜇 max 𝐶𝑠

2. Using provided data:

a. Give first estimation of 𝜇 max and 𝐾𝑚 using only raw data plot.

b. Using Lineweaver-Burk relationship to appropriate data set estimate 𝜇 max and 𝐾𝑚 ,

c. Plot your data and model on one plot. Confirm correctness of your model. Give at least

two reasons (mathematical) why you think the model is correct.

d. Compute SSE of your model.

e. Using cftool perform nonlinear fit of the Monod equation. What is the most appropriate

choice of initial values of your parameters?

f. Compare SSE of the first and second fit. What do you observe?

Figure. Relationship between growth rate (weight increase) and nitrate concentration in juvenile

sporangial plants collected from 2 sites in Nova Scotia. Means and 95% confidence limits are given.

Curves fitted to the Monod equation (after Espinoza and Chapman, 1983).

This exercise is designed to familiarize you with fundamental analytical techniques and data analysis

process in biochemical engineering exemplified by analysis of the growth kinetics of Pseudomonas

fluorescens.

1. For given relation between time and log of biomass concentration find specific growth rate

(Suplement A).

a. Using analytical techniques (derivative, R 2 or others) find the range where data are

linearly dependent

b. Use linear regression to calculate specific growth rate using the relation

1 𝑑𝑋 𝑑𝑙𝑛𝑋

𝜇= =

𝑋 𝑑𝑡 𝑑𝑡

2. For given set of data of specific growth rate as a function of substrate (Suplement B)

concentration fit and validate five different models of growth kinetics with inhibi tion:

a. Analyze each equation. For example you can prove that Haldane model for small

concentration is a Monod equation. What kind of information can you deduce from it?

b. Remember that nonlinear fitting is a iterative procedure that may not converge. Choice

of initial parameters is crucial. Can you transform Haldane model to functional form that

enables use of least squared method (e.x. polynomial)?

c. Use estimates of the initial parameters to perform nonlinear fit of your model.

No Author Model

1 Haldane 𝜇 max 𝑆

𝜇=

𝑆2

𝐾𝑆 + 𝑆 +

𝐾𝑖

2 Webb 𝑆

𝜇 max 𝑆 (1 + )

𝜇= 𝐾

𝑆2

𝐾𝑆 + 𝑆 +

𝐾𝑖

3 Aiba 𝜇 max 𝑆 −𝐾𝑆

𝜇= 𝑒 𝑖

𝐾𝑆 + 𝑆

4 Teisser 𝑆 𝑆

− −

𝜇 = 𝜇 max (𝑒 𝐾𝑖 −𝑒 𝐾𝑠 )

5 Yano-Koga 𝑆

𝜇 max 𝑆 (1 + )

𝜇= 𝐾

𝑆2 𝑆3

𝐾𝑆 + 𝑆 + + 2

𝐾1 𝐾2

And fill the table below:

No Author 𝜇 max 𝐾𝑠 𝐾𝑖 𝐾 𝐾1 𝐾2 𝑒𝑌

1 Haldane

2 Webb

3 Aiba

4 Teisser

5 Yano-Koga

1 𝜇𝑒𝑥𝑝,𝑖−𝜇𝑐𝑎𝑙𝑐,𝑖

Where 𝑒𝑌 = ∑𝑁

𝑖=1 | |

𝑁 𝜇𝑒𝑥𝑝,𝑖

a) Estimate initial values of parameters 𝜇 max and 𝐾𝑠 by fitting Monode equation to

data from the range where 𝜇 is increasing

b) Using this estimates perform nonlinear regression using cftool toolbox

c) Calculate relative error

d) Using relative error and distribution of residuals analysis determine which model is

the most suitable and why

e) Using the model calculate optimal substrate concentration

Suplement A

t log(X)

0 -9.41667

0.184463 -9.41795

0.320608 -9.39411

0.546572 -9.39274

0.755965 -9.37947

0.891862 -9.35695

1.028505 -9.33047

1.256707 -9.31719

1.428979 -9.30128

1.614835 -9.31314

1.748244 -9.30385

1.942311 -9.27206

2.131402 -9.26673

2.471218 -9.26004

2.778888 -9.22426

3.137514 -9.21757

3.503355 -9.17251

3.821873 -9.17906

4.166914 -9.14459

4.484686 -9.1551

4.826244 -9.13915

5.204425 -9.12849

5.525929 -9.11916

5.808073 -9.11909

6.110767 -9.10977

6.473623 -9.08059

6.77159 -9.09639

7.108669 -9.10426

7.467046 -9.09889

7.789794 -9.08294

8.133342 -9.05641

8.448377 -9.08147

8.863183 -9.07609

9.109946 -9.06413

9.430455 -9.06009

9.806149 -9.06266

10.10835 -9.05598

10.40905 -9.05723

10.83744 -9.07963

11.04634 -9.069

Suplement B

S μ

0.792079 -0.07574

18.86423 6.782315

25.15534 6.051417

30.92751 6.146005

37.10937 7.36521

47.03312 7.605906

62.21008 6.516678

77.16854 7.077654

80.23671 6.499778

93.46535 6.812376

109.0702 6.897747

124.7115 7.083083

156.3583 6.203414

186.5301 5.775128

216.6655 5.246876

281.7799 3.985831

310.3494 3.659047

370.684 2.777484

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