Team:BCCS-Bristol/Modeling/Population Dynamics

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Revision as of 09:54, 24 July 2009

BCCS-Bristol
iGEM 2009

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?
  - What is the growth rate of the bacterium?
- Maximum size
  - When the bacterium will be to the maximum size?
- What is the 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 between 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.
- 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?

[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?

@@ Line 10: / Line 10: @@
 **Minimum size
 ***When the bacterium will be at the minimum size?
-***How fast the bacterium increase its dimension?
+***What is the [[Team:BCCS-Bristol/Modeling/Growth_Rate|growth rate]] of the bacterium?
 **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] ?
+**What is the 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
+**Relationship between size/time/growth rate
 ----
 *Separation.
@@ Line 24: / Line 24: @@
 **Motion properties after the separation.
 ***Velocity after separation.
-**The two bacteria after the separation have the same size?
+**Are the two bacteria, after replication, the same size?
 ----
 *Genetic information
-**After the separation the two bacteria have the same genetic properties:
+**After separation, the two bacteria have the same genetic properties:
-***same replication time distribution?
+***Same replication time distribution?
-***or the new one has a normal/uniform distribution on the normal/uniform distribution of the oldest one?
+***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]