Team:LCG-UNAM-Mexico/Modelling
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==''Summary : Modelling the Defense System''== | ==''Summary : Modelling the Defense System''== | ||
- | [[Image:Modelling_Diagram.png| | + | [[Image:Modelling_Diagram.png|480px|thumb|right|'''Logic diagram of our multi-scale stochastic model''']] |
Bacteriophage infection is a complicated process, once the virus has infected it steals the translation machinery of its host. Bacterium ribosomes synthesize virus proteins and virus assembly takes place. Beyond a phage and time threshold bacterium can’t take it anymore and explodes setting free the newly synthesized bacteriophages. | Bacteriophage infection is a complicated process, once the virus has infected it steals the translation machinery of its host. Bacterium ribosomes synthesize virus proteins and virus assembly takes place. Beyond a phage and time threshold bacterium can’t take it anymore and explodes setting free the newly synthesized bacteriophages. | ||
Let’s take a look at the big picture: biochemical reactions taking place inside infected bacterium, new synthesized phage for each infected bacterium, other bacteria get infected, infection propagation. We need to approach this problem in a multi-scale fashion: molecular scale and population scale. | Let’s take a look at the big picture: biochemical reactions taking place inside infected bacterium, new synthesized phage for each infected bacterium, other bacteria get infected, infection propagation. We need to approach this problem in a multi-scale fashion: molecular scale and population scale. | ||
We designed and implemented a [[Team:LCG-UNAM-Mexico:Molecular_model| Stochastic Molecular Model]] for the essential reactions involved in the infection process: T7’s DNA insertion, transcription, translation, capsid assembly, etc. to create a Wild Type Simulation. Then we added the toxins to the model to simulate the dynamics of the kamikaze system.<br><br> | We designed and implemented a [[Team:LCG-UNAM-Mexico:Molecular_model| Stochastic Molecular Model]] for the essential reactions involved in the infection process: T7’s DNA insertion, transcription, translation, capsid assembly, etc. to create a Wild Type Simulation. Then we added the toxins to the model to simulate the dynamics of the kamikaze system.<br><br> | ||
- | [[Image:Deterministic_model.png| | + | [[Image:Deterministic_model.png|310px|thumb|left|'''Deterministic Molecular Dynamics Model''']] |
With a fairly big number of simulations we are going to generate Probability Distributions for the number of molecules for each metabolite as a function of time. We are particularly interested in the [[Team:LCG-UNAM-Mexico:BSD |Burst-Size Distribution (BSD)]]; the burst-size is the number of phages an infected cell will produce. | With a fairly big number of simulations we are going to generate Probability Distributions for the number of molecules for each metabolite as a function of time. We are particularly interested in the [[Team:LCG-UNAM-Mexico:BSD |Burst-Size Distribution (BSD)]]; the burst-size is the number of phages an infected cell will produce. | ||
Once we have the BSD we are ready for the Spatial Population Model. The kamikaze system we designed is meant to increase the probability that the population as a whole survive an infection process. We make infected-E. Coli commit suicide for the benefit of the population. In case suicide wasn’t altruistic enough we thought an alarm system might be useful: once a bacterium gets infected it will produce AHL to communicate the message that phages are near, advised bacteria will produce antisense RNA against T7’s DNA polymerase. | Once we have the BSD we are ready for the Spatial Population Model. The kamikaze system we designed is meant to increase the probability that the population as a whole survive an infection process. We make infected-E. Coli commit suicide for the benefit of the population. In case suicide wasn’t altruistic enough we thought an alarm system might be useful: once a bacterium gets infected it will produce AHL to communicate the message that phages are near, advised bacteria will produce antisense RNA against T7’s DNA polymerase. |
Revision as of 00:12, 22 October 2009