Compartmental models of growing neurites (Graham and van Ooyen 2004)

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Accession:59582
Simulator for models of neurite outgrowth. The principle model is a biophysical model of neurite outgrowth described in Graham and van Ooyen (2004). In the model, branching depends on the concentration of a branch-determining substance in each terminal segment. The substance is produced in the cell body and is transported by active transport and diffusion to the terminals. The model reveals that transport-limited effects may give rise to the same modulation of branching as indicated by the stochastic BESTL model. Different limitations arise if transport is dominated by active transport or by diffusion.
References:
1 . Graham BP, van Ooyen A (2004) Transport limited effects in a model of dendritic branching. J Theor Biol 230:421-32 [PubMed]
2 . Graham BP, van Ooyen A (2006) Mathematical modelling and numerical simulation of the morphological development of neurons. BMC Neurosci 7 Suppl 1:S9 [PubMed]
Model Information (Click on a link to find other models with that property)
Model Type: Axon; Dendrite;
Brain Region(s)/Organism:
Cell Type(s):
Channel(s):
Gap Junctions:
Receptor(s):
Gene(s):
Transmitter(s):
Simulation Environment: Java;
Model Concept(s): Development;
Implementer(s): Graham, Bruce [B.Graham at cs.stir.ac.uk];
# Neurite version JTB1

# MODEL PARAMETERS
# MODEL: AD
1
# Branching scale factor (Kbr):
0.01925
# Diffusion rate (D):
0
# Active transport rate (f):
100
# Soma production rate (I):
10
# Soma uptake rate (G0):
9
# Terminal uptake rate (Gn):
100
# Conc. calc. length (dL):
1.0
# Minimum length (minL):
5.0
# Branching phase rate (Vbr):
0.22
# Elongation phase rate (Vel):
0.51
# Rate coefficient of variation (rCV):
0.28
# Time branching stops (Tbstop):
264
# Soma length:
10.0
# Soma diameter:
10.0
# Terminal diameter:
1.0
# Branch power (e):
8

# SIMULATION PARAMETERS
# Number of trees:
1
# Time step (dt):
0.001
# Simulation time (Tstop):
200
# Store statistics (1=yes):
0
# Statistics file stem:
AD
# Store concentrations (1=yes):
0
# Concentration file stem:
AD
# Store lengths (1=yes):
0
# Length file stem:
AD
# Store no. terminals over time (1=yes):
0
# Storage interval (time):
1

# DISPLAY PARAMETERS
# Display width:
600
# Display height:
350
# Display parameter:
Cbr
# Maximum display value:
1.0
# Display interval (steps):
1000
# Display delay (msecs):
0
# Maximum path length (um):
100
# Initial branch angle (deg):
20
# Angle scaling factor:
-0.4
# Soma scaling factor:
1.0
# Dendrite scaling factor:
5.0

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