Team:BCCS-Bristol/Modeling/Population Dynamics

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BCCS-Bristol
iGEM 2009

Contents

Population Dynamics

We are trying to find answers to these problems and questions:

Morphogenesis E.Coli

  • Bacteria change size.
    • Minimum size
      • When the bacterium will be at the minimum size?
      • What is the growth rate of the bacterium?
    • Maximum size
      • When the bacterium will be to the maximum size?
    • What is the relationship between velocity and size ?
    • Relationship between size/time/growth rate
  • Separation.
    • When this happen?
    • Where the bacterium get placed?
    • Motion properties after the separation.
      • Velocity after separation.
    • Are the two bacteria, after replication, the same size?
  • Genetic information
    • After separation, the two bacteria have the same genetic properties:
      • Same replication time distribution?
      • Or the new one has a normal/uniform distribution on the normal/uniform distribution of the oldest one?
  • Growth
    • Rate of growth
    • Connection between the rate of duplication and the growth phase.
  • Standing phase
    • One bacterium can "kill" another one to make its replication?
      • If yes which one is going to die?
  • Environment
    • we can try to model a variable condition of the environment:
      • 100% Suitable for the replication of the bacteria
      • 80% Suitable for the replication of the bacteria
      • and so on...

BSim Verify Some Concepts

  • Collision (Distance calculation)
  • Draw an element smoller than bacterium
    • Rescale all BSim? (Maybe solution found!
  • Increase the lifeTime for each bacterium every timeStep?
  • Direction aid?

BSim ToDO List

  • CentrePosition
    • Class BSimObject
    • Method setPosition
    • Usage: linearMotion:run:BSimCollisionPhysicsThread

BSim Fixed Problems

  • Now we can draw shape using a "double" precision and not "int" precision

Problems

The most popular replication time for an E.Coli is about 20/25 minutes.
Can our simulation take so long time?
How can we simulate on "world" day with 400 bacteria?

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