BSim Features

In Progress...

Simulation Features

Bacteria

Heavy basis on literature
Run and tumble by default (flagellar motor)
chemotaxis!
brownian motion and fluid forces implemented
easily adaptable.

Interactions and actions

easily specified and adaptable
can do whatever you want:
- Collision
- Merging (vesicle/bacterium)
- GRNs
other interactions:
- Everything can interact! chemical fields, GRNs, vesicles...

Vesicles

Small, but size based on growth
Size and creation rate based on rate of change of surface area [ref - steve?]
Vesicle movement - brownian motion in a viscous fluid environment
Interaction can be specified

Chemical Fields

diffusion
decay
physical units

GRN modelling

BSim 2008: "Each of the modelling approaches [GRNs and agent-based modelling] have been considered in separate contexts, mainly due to the differing aspects of the system they are concerned with. Now, having working models for each, it would be possible to bring these together with the aim of improving simulation accuracy and allowing for the internal cellular dynamics to be studied in an ever changing physical environment. Such a hybrid model may also help shed light on the critical aspects of project as a whole."

ODE(s) can be attached to bacteria
Can interact with chemical fields etc

Magnetotaxis

an alternative to chemotaxis?
- Allow tuning of the field strength and direction
- Include both naturally magnetic bacteria and/or magnetic beads
- Include both uniform magnetic field and/or also variable magnetic field (to affect motion as well as orientation)

Other Features

Separate the physical and biological aspects of features into 2 sections?

Team:BCCS-Bristol/Modeling/BSim Features

From 2009.igem.org

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