Difference between revisions of "Team:Aalto-Helsinki/Modeling synergy"
m (added pathway pic) |
m (fixed some clunkiness in the text) |
||
Line 75: | Line 75: | ||
<p>One big concern in our project was the efficiency of propane production. To solve this problem we wanted to use micelles to hold enzymes together and speed up the reactions. By having two of our most inefficient enzymes close together we try to increase the propane yield. Our only question regarding this is: Does it actually work?</p> | <p>One big concern in our project was the efficiency of propane production. To solve this problem we wanted to use micelles to hold enzymes together and speed up the reactions. By having two of our most inefficient enzymes close together we try to increase the propane yield. Our only question regarding this is: Does it actually work?</p> | ||
− | <p>The idea behind this approach is to get | + | <p>The idea behind this approach is to get the majority of butyraldehyde to ADO and propane production than to other butyraldehyde-eating enzymes. Intuitively this should happen if CAR and ADO are close together.</p> |
<p>To address this not so trivial question of feasibility of this approach, the modeling team assembled and thought about the problem. This problem couldn’t be described easily with simple differential equations since then notions of distance, proximity and their relation with enzyme reaction rates would have to be thoroughly researched as well.</p> | <p>To address this not so trivial question of feasibility of this approach, the modeling team assembled and thought about the problem. This problem couldn’t be described easily with simple differential equations since then notions of distance, proximity and their relation with enzyme reaction rates would have to be thoroughly researched as well.</p> | ||
Line 98: | Line 98: | ||
<p>Now, let’s go through the different phases of the simulation:</p> | <p>Now, let’s go through the different phases of the simulation:</p> | ||
− | <p>Initialization: The program loads a settings file filled with information concerning the simulation, and creates a simulation according these specifications. With this file | + | <p>Initialization: The program loads a settings file filled with information concerning the simulation, and creates a simulation according these specifications. With this file the user can, for example, specify the length of the simulation, the different substrates with their amounts and masses, as well as the different enzymes and the types of substrates and products they either consume or produce.</p> |
<p>Particle movement: The model moves particles according to Brownian motion in water. With particles of this size the governing attribute these particles have is their radius.</p> | <p>Particle movement: The model moves particles according to Brownian motion in water. With particles of this size the governing attribute these particles have is their radius.</p> | ||
Line 133: | Line 133: | ||
<p>Enzymes and substrates only react when they are in close enough proximity with each other. In addition to this, enzymes and substrates only react with the correct type of substrate and enzyme, respectively.</p> | <p>Enzymes and substrates only react when they are in close enough proximity with each other. In addition to this, enzymes and substrates only react with the correct type of substrate and enzyme, respectively.</p> | ||
− | <p>Reaction between enzymes and substrates are difficult to model. Since we don’t have a good way of predicting when a reaction should happen given that an enzyme and a substrate meet, we decide this by giving a reaction a probability to succeed and polling this | + | <p>Reaction between enzymes and substrates are difficult to model. Since we don’t have a good way of predicting when a reaction should happen given that an enzyme and a substrate meet, we decide this by giving a reaction a probability to succeed and polling this probability every time a substrate and enzyme meet.</p> |
<p>Enzyme concentration and therefore particle number stays constant during the simulation. | <p>Enzyme concentration and therefore particle number stays constant during the simulation. | ||
Line 140: | Line 140: | ||
<p>Substrate amounts are either decided in the beginning of the simulation or they are affected by the enzyme reactions.</p> | <p>Substrate amounts are either decided in the beginning of the simulation or they are affected by the enzyme reactions.</p> | ||
− | <p>The model keeps the enzymes and substrates on a 2D plane, as opposed to a 3D space. This is because we assume that the model | + | <p>The model keeps the enzymes and substrates on a 2D plane, as opposed to a 3D space. This is because we assume that the model's behaviour doesn't change much between 2D and 3D space.</p> |
<p>To simplify this model, enzymatic reactions do not take into account cofactors or multiple substrates.</p> | <p>To simplify this model, enzymatic reactions do not take into account cofactors or multiple substrates.</p> |
Revision as of 07:24, 31 August 2015