Team:BCCS-Bristol/Modeling/Population Dynamics

From 2009.igem.org

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==BSim ToDO List==
==BSim ToDO List==
*CentrePosition
*CentrePosition
 +
**Class BSimObject
 +
**Method setPosition
 +
**Usage: linearMotion:run:BSimCollisionPhysicsThread
==BSim Fixed Problems==
==BSim Fixed Problems==

Revision as of 10:25, 23 July 2009

BCCS-Bristol
iGEM 2009

Contents

Population Dynamics

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

[http://www.pubmedcentral.nih.gov/picrender.fcgi?artid=98908&blobtype=pdf Morphogenesis E.Coli]

  • Bacteria change [http://www.pubmedcentral.nih.gov/picrender.fcgi?artid=2134870&blobtype=pdf size].
    • Minimum size
      • When the bacterium will be at the minimum size?
      • How fast the bacterium increase its dimension?
    • Maximum size
      • When the bacterium will be to the maximum size?
    • There is same relationship between [http://books.google.co.uk/books?id=0SPMLpTxGpMC&pg=PA51&lpg=PA51&dq=e.coli+size+velocity+motion&source=bl&ots=rqCBRQ1IN1&sig=__zft5KeWbLpUodXwGcyvnOBQtM&hl=en&ei=ZUhkSprSKcaZjAeN6IUC&sa=X&oi=book_result&ct=result&resnum=5 velocity and size] ?
    • Relationship beetwen size/time/growth rate
  • Separation.
    • When this happen?
    • Where the bacterium get placed?
      • Maybe following the [http://books.google.co.uk/books?id=DjdgXGLoJY8C&printsec=frontcover&dq=E.+coli+in+motion++By+Howard+C.+Berg&source=gbs_similarbooks_s&cad=1 bacterium motion] ?
      • Random?
      • Fluid dynamics?
    • Motion properties after the separation.
      • Velocity after separation.
    • The two bacteria after the separation have the same size?
  • Genetic information
    • After the 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?
  • [http://aem.asm.org/cgi/reprint/71/12/7920 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...
  • [http://jon.visick.faculty.noctrl.edu/research/aging.htm Growth Phase]
  • [http://www.science-projects.com/SteadyState/SSProjects.htm Steady State]
  • [http://www.ecoli-model.com/index_files/Page382.html Growth and Environments]

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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