BSim Features

In this section we outline the main features available in BSim 2009.

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."

BSim 2009 provides a robust implementation of the second and fourth order Runge-Kutta methods for systems of ordinary differential equations. It is possible to easily specify systems of ODEs as objects within the simulation. These ODE systems can be "attached" to objects in the simulation if necessary and can be used to simulate any aspect of the environment to which they are coupled, depending on the user's requirements. An example would be attaching an ODE system to each bacterium and coupling these systems via an external chemical field. See the overview of our ongoing quorum-coupled repressilators simulation for an example application of this.

As a result of the modular nature of the solver implementation it would also be possible to implement stochastic ODEs, and delay differential equations in a similar manner. These features are likely to be implemented soon to assist with the modelling of more complex GRN systems across a population.

Magnetotaxis

Magnetotactic bacteria are gram-negative, motile (by means of a flagella) bacteria. Each one forms a string of intracellular magnetic grains, known as magnetosomes.

Figure 1: Transmission electron micrograph of Magnetospirillum magnetotacticum showing the magnetosomes inside the bacteria. Bar equals 1 micron.[1]

The term magnetotaxis, used to describe the motion of the bacteria in the direction of the magnetic field, denotes the magnetic field effects, solely, on the direction of the bacteria, and not on the speed of the bacteria.

Naturally occurring magnetotactic bacteria will instinctively travel in the direction of the geomagnetic field. It controls the bacteria in the same way as it would control a compass needle, aligning them both to magnetic north pole.

Although the magnetic field forces the alignment of the bacteria, they experience no further magnetic force. All of the propulsion is produced from the flagella force.

The shift of the bacteria towards the magnetic field lines is controlled by the strength of the magnetis field and the magnetic moment of the bacteria. The probability of a moment making an angle between theta and some small increment added on to theta is:

where m = bacteria magnetic moment, B = magnetic field strength, k = Boltzmann constant, T = temperature in Kelvins and where the denominator is the total number of magnetic moments and there is a factor of 2*pi*radius^2 cancelled out.

This equation can be used to generate a distribution of the angles that a group of bacteria make with the magnetic field direction. As shown in the graph below [3]:

This distribution is known as the Maxwell-Boltzmann distribution. Sampling from this provides a more accurate representation of the motion of the magnetotactic e. coli in BSim.

BSim allows the user to control the magnetic field strength, B and the magnetic moment, m of the bacteria.

Insert video

References:

[1] http://www.calpoly.edu/~rfrankel/magbac101.html

[2] Blakemore, RP (1982) Magnetotactic bacteria. Annual Reviews of Microbiology 36: 217-238.

[3] Nicola Ann Spaldin, Magnetic materials: fundamentals and device applications, University Press, Cambridge 2003

Team:BCCS-Bristol/Modeling/BSim Features

From 2009.igem.org

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