Team:PKU Beijing/Modeling/Result

Modeling > Result

After ODE and Parameters, it's time to see the simulation result.

The Goal of Simulation
Of course, the ultimate goal of modeling is to simulate the circuit as accurate as possible. However, due to the complexity of biological system and very little we have known about it, it's almost impossible to simulate exactly. Thus, we come up a series of standards, which will be the main goals of our modeling. Here're the standards:

As we mentioned in project section, the dog (and of course the model) should react in a specific way under certain circumstances, which has been concluded into a truth table. To simulate perfectly, our model should follow the truth table, which is the primary goal without doubt.
 * The Biological System Should Follow the Truth Table

OK, what we do this year is to simulate Pavlov's dog. Thus, our modeling should not only concentrate on biological mechanism, but also follow a dog's reaction towards certain things. Here're some circumstance we've thought up. If you have new ideas, feel free to email us! Please email to c.z.tian AT gmail.com
 * The Result Should Fit A Dog's Reaction

GFP output should be stronger under a food stimulus Food is a direct stimulus while bell is a more indirect one. Generally, under direct stimulus, the dog will react stronger.

If the dog has memory and is given a bell stimulus, GFP output should have a delay The dog takes time to link BELL with FOOD :]

This is also an attemp to simulate the system as accurately as possible.
 * The Value for Each Parameter Should NOT Be Too Extreme

Now, let's see the result!

Result - T3 RNA Polymerase
Here we'll demonstrate dynamics of GFP(output,shows how strongly the dog reacts), CI and CI434(bistable switch, represents the memory). In the figures below, CI was represented by pink line, CI434 was represented by blue line while yellow line shows the dynamics of GFP output. Since no input, no output. We'll skip the No food+No bell situation.

Now let's see how well this result fit the standards. That means, our model is very successful!
 * Truth Table YES!
 * Fit Dog's Reaction YES!
 * VALUE NOT TOO EXTREME YES!

Result - P2
Then comes the result of P2 model. Just like the case of T3, pink curve represents CI434, blue curve represent CI while yellow curve shows the dynamics of GFP output. Then let's see how this model achieve the goal. Overall, this model is still able to perform well under all the circumstances, which means the P2 model is acceptable.
 * Truth Table YES!
 * Fit Dog's Reaction YES!
 * VALUE NOT TOO EXTREME No. The value for AND Gate 2 is too extreme, which may cause difference between our model and actual process in cells.