Team:LCG-UNAM-Mexico:Population

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(INTRODUCTION TO POPULATION MODEL)
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=Population Scale Modelling=
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=='''Summary: Population Scale Modelling'''==
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==Contents==
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<br>
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#Summary
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#Multi-Scale integration using Cellular Automaton
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Some bacteriophages are parasites of bacteria, and as such, must prudently exploit their resources (in this case bacteria) to avoid killing bacterium before reproduce enough copies of itself. It has been suggested that parasites have evolved to tune their degree of virulence (amount of damage the parasite causes to the host) to achieve a balance between rapid reproduction and a prudent use of resources[1]. It is this fine balance which we intend to break increasing the virulence of phage in such a way that kills the bacterium so fast that the phage is unable to assemble their own copies
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#Mathematical Modelling using Delay Differential Equations
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#Agent Based Simulation Applet
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Bacteria-phage interaction essentially is a fight for survival between two POPULATIONS.
 
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Although we modified ''E. coli'' at molecular level to defend itself against certain phages, our ultimate goal is that ''E. coli'' can contend against infection at population level.
 
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For this reason we decided to simulate, at population level, phage infection and the effectiveness of our genetic circuit.
 
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<br><br>
 
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For this purpose, we use three different approaches:
 
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* [https://2009.igem.org/Team:LCG-UNAM-Mexico:odes Modelling population dynamics with a system of differential equations. ]
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==Sumary==
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* [https://2009.igem.org/Team:LCG-UNAM-Mexico:ABmodel Spatial agent-based model.]
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Population Modelling is concerned with the dynamics in population size  as a consequence of interactions of organisms with the physical environment, with individuals of their own species, and with organisms of other species. <br>We designed a dynamical population model in which we simulate the behaviour of bacteria.  
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* [https://2009.igem.org/Team:LCG-UNAM-Mexico:CA Modeling bacteria behaviour and Bacteriophage infection using Cellular Automata.]
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<br><br>We want to gain insight into the dynamics of bacteriophage infection, bacteria-phage interaction essentially is a fight for survival between two populations. By adding a phage invasion in our simulated bacteria population we can simulate the whole infection process. The modelling of infectious processes is a tool which has been used to study the mechanisms by which diseases spread, to predict the future course of an outbreak and to evaluate strategies to control an epidemic (Daley & Gani, 2005). Our kamikaze construction was designed to sabotage the phage lytic cycle, but our final goal is to contend the infection at the Population Scale. <br>
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We used 3 different approaches to model the population dynamics:
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#Multi-Scale integration using Cellular Automata: Using this system we can simulate spatial interactions as movement and biomolecules diffusion. In our model spatial dynamics are of vital importance: Quorum Sensing dynamics is one of the main aspects of the Defense System, infected E.Coli will produce AHL and will warn it’s neighbours. Using the Cellular Automata we can make direct sampling from the distributions generated by the [[Team:LCG-UNAM-Mexico:Molecular |modemolecular simulations]] in real time linking the molecular and population scales.
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#Delay Differential Equations System: Deterministic 1
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==References==
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Daley, D. J. & Gani, J. (2005). Epidemic Modeling and Introduction. NY: Cambridge University Press.
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S. Goel. Stochastic Models in Biology. 2003
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Istas. Mathematical Modeling for the Life Sciences.2005

Revision as of 01:31, 22 October 2009

Population Scale Modelling

Contents

  1. Summary
  2. Multi-Scale integration using Cellular Automaton
  3. Mathematical Modelling using Delay Differential Equations
  4. Agent Based Simulation Applet



Sumary

Population Modelling is concerned with the dynamics in population size as a consequence of interactions of organisms with the physical environment, with individuals of their own species, and with organisms of other species.
We designed a dynamical population model in which we simulate the behaviour of bacteria.

We want to gain insight into the dynamics of bacteriophage infection, bacteria-phage interaction essentially is a fight for survival between two populations. By adding a phage invasion in our simulated bacteria population we can simulate the whole infection process. The modelling of infectious processes is a tool which has been used to study the mechanisms by which diseases spread, to predict the future course of an outbreak and to evaluate strategies to control an epidemic (Daley & Gani, 2005). Our kamikaze construction was designed to sabotage the phage lytic cycle, but our final goal is to contend the infection at the Population Scale.
We used 3 different approaches to model the population dynamics:

  1. Multi-Scale integration using Cellular Automata: Using this system we can simulate spatial interactions as movement and biomolecules diffusion. In our model spatial dynamics are of vital importance: Quorum Sensing dynamics is one of the main aspects of the Defense System, infected E.Coli will produce AHL and will warn it’s neighbours. Using the Cellular Automata we can make direct sampling from the distributions generated by the modemolecular simulations in real time linking the molecular and population scales.
  2. Delay Differential Equations System: Deterministic 1

References

Daley, D. J. & Gani, J. (2005). Epidemic Modeling and Introduction. NY: Cambridge University Press. S. Goel. Stochastic Models in Biology. 2003 Istas. Mathematical Modeling for the Life Sciences.2005


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