IGEM:IMPERIAL/2008/New/Growth Curve: Difference between revisions

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==How to model the growth curve?==
==How to model the growth curve?==


In order to model the growth of ''B. subtilis'', the process was broken down into three main steps where a submodel is produced in MATLAB in each step. Each submodel is an ODE model which can be simulated using MATLAB. The variables in each submodel are modified. So in the final step, a combination of submodel 1 and 2 are incorporated with submodel 3, resulting in a more complex model which illustrates the behaviour of bacterial growth.  For more details about the process of building the model click on the following link: [[Media:Modelling_Growth_Curve.pdf]], for method and results click on [[Tutorial for Growth curve]].
In order to model the growth of ''B. subtilis'', the process was broken down into three main steps, where a separate submodel is produced in MATLAB for each step. Each submodel is an ODE model, which can be simulated using MATLAB. The variables in each submodel can be adjusted according to boundary conditions (from experimental results).  
 
In the final step, a combination of Submodels 1 and 2 are superposed with Submodel 3, resulting in a more complex model, which illustrates bacterial growth.  For more details about the submodels, please click on the following link: [[Media:Modelling_Growth_Curve.pdf]]. For more information on our modelling strategy, please click on [[Tutorial for Growth Curve]].


==The Model==
==The Model==

Revision as of 08:12, 12 September 2008

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Growth Curves

Why model the growth curve?

The aim of modelling the growth curve is to characterise the B. subtilis chassis used in the project. Characterisation increases the predictability of the growth of B.Subtilis by determining, for example, its growth rate and the duration of its distinctive growth phases.

How to model the growth curve?

In order to model the growth of B. subtilis, the process was broken down into three main steps, where a separate submodel is produced in MATLAB for each step. Each submodel is an ODE model, which can be simulated using MATLAB. The variables in each submodel can be adjusted according to boundary conditions (from experimental results).

In the final step, a combination of Submodels 1 and 2 are superposed with Submodel 3, resulting in a more complex model, which illustrates bacterial growth. For more details about the submodels, please click on the following link: Media:Modelling_Growth_Curve.pdf. For more information on our modelling strategy, please click on Tutorial for Growth Curve.

The Model

The model illustrates the main phases a bacteria progresses through during its growth. These are identified as the lag phase, the exponential phase and the stationary phase. The death phase is the constitutive event and it is possible that it exerts an influence in the three phases discussed below. However, to simplify a complicated model, it is less relevant in this case and is, therefore, not included in the model.

LAG PHASE

At this stage, the bacteria is uptaking the nutrients in the medium, thus the lag. An alternative cause is the swtching on of the replication machinery. As the concentration of nutrients in the medium increases, the growth of the bacteria accelerates. As a result, the volume of the bacteria increases, followed by an increases in the number of bacteria.

EXPONENTIAL PHASE

As the name suggests, the growth of the colony in number and in volume is almost exponential. In this model, it is assumed that the concentration of the nutrients inside the bacteria is constant.

STATIONARY PHASE

The growth of the colony ceases in number and in volume due to a finite concentration of nutrients, hence its does not have a gradient. Other causes may be death and cell division.

According to the model, the maximum growth of the bacteria is determined by the value of Cmax (from M-file regarding A plot of nutrient concentration vs time).


To further enhance the accuracy of the model, the following information will be extracted from experimental data

  • Time span of lag phase, stationary phase and exponential phase
  • The growth rate
  • The error of each experiments

Discussion

Dry lab hub

Growth Curve

Genetic Circuit

Motility

Appendices


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