beaucheminTrack {celltrackR}

Simulate a 3D Cell Track Using the Beauchemin Model

Description

The Beauchemin model is a simple, particle-based description of T cell motion in lymph node in the absence of antigen, which is similar to a random walk (Beauchemin et al, 2007).

Usage

beaucheminTrack(
  sim.time = 10,
  delta.t = 1,
  p.persist = 0,
  p.bias = 0.9,
  bias.dir = c(0, 0, 0),
  taxis.mode = 1,
  t.free = 2,
  v.free = 18.8,
  t.pause = 0.5
)

Arguments

sim.time

specifies the duration of the track to be generated

delta.t

change in time between each timepoint.

p.persist

indicates how probable a change in direction is. With p.persist = 1, the direction never changes between steps and with p.persist = 0, a new direction is sampled at every step.

p.bias

strength of movement in the direction of bias.dir.

bias.dir

a 3D vector indicating the direction along which there is a preference for movement.

taxis.mode

specified mode of movement. 1 := orthotaxis, 2 := topotaxis, 3 := klinotaxis.

t.free

time interval for how long the cell is allowed to move between turns.

v.free

speed of the cell during the free motion.

t.pause

time that it takes the cell to adjust movement to new direction.

Details

In the Beauchemin model, cells move into a fixed direction for a fixed time t.free at a fixed speed v.free. They then switch to a different direction, which is sampled at uniform from a sphere. The change of direction takes a fixed time t.pause, during which the cell does not move. Thus, the Beauchemin model is identical to the freely jointed chain model of polymer physics, except for the explicit "pause phase" between subsequent steps.

The default parameters implemented in this function were found to most accurately describe 'default' T cell motion in lymph nodes using least-squares fitting to the mean displacement plot (Beauchemin et al, 2007).

This function implements an extended version of the Beauchemin model, which can also simulate directionally biased motion. For details, see Textor et al (2013).

Value

A track, i.e., a matrix with t/delta.t rows and 4 columns.

References

Catherine Beauchemin, Narendra M. Dixit and Alan S. Perelson (2007), Characterizing T cell movement within lymph nodes in the absence of antigen. Journal of Immunology 178(9), 5505-5512. doi:10.4049/jimmunol.178.9.5505

Johannes Textor, Mathieu Sinn and Rob J. de Boer (2013), Analytical results on the Beauchemin model of lymphocyte migration. BMC Bioinformatics 14(Suppl 6), S10. doi:10.1186/1471-2105-14-S6-S10

Examples

## Create track with model parameters and return matrix of positions
out <- beaucheminTrack(sim.time=20,p.persist = 0.3,taxis.mode = 1)
## Plot X-Y projection
plot( wrapTrack(out) )

## Create 20 tracks and plot them all
out <- simulateTracks( 20, beaucheminTrack(sim.time=10,
  bias.dir=c(-1,1,0),p.bias=10,taxis.mode = 2,
  p.persist = 0.1,delta.t = 1) )
plot( out )