GENESIS: Documentation

Related Documentation:

De Schutter: Purkinje Cell Model

Morphology Discretization

All simulations were performed with a model using the morphology of cell I of Rapp et al. (1994) unless otherwise noted.

Because electrotonic lengths were short, more computationally efficient asymmetric compartments (this GENESIS object corresponds to a three-element segment, as described by [4]) could be used. Simulations done with and without asymmetric compartments confirmed that the difference in input resistance (R_N) and system time constant (τ₀) for a passive membrane model was < 1 %.

In an active membrane compartment the total R_m is variable, resulting in a continuously changing space constant and electrotonic length [1, 3]. The total R_m (RTM_n) of a compartment n at a specific time was computed as the sum of all conductances [G(V, [Ca²⁺],t) from Eqn. (1) and the passive component, RM _n, determined by R_m

(1)

The compartment’s space constant λ_n could be derived from RTM_n, its axial resistance RIn, and its length L_n

(2)

The compartment’s electrotonic length was the ratio of its length, L_n, over the space constant, λ_n. The electronic distance between two compartments was computed as the sum of the electronic lengths of all intervening compartments.

For those simulations that related to granule cell input, the total membrane surface was kept constant by subtracting the membrane surface of modeled spines from the membrane surface of the dendritic compartment to which they were connected. For a spiny dendritic compartment with length L and diameter D, the membrane surface (S in μm²), used for the computation of compartment membrane capacitance and resistance [2, 3], depended thus also on the number of simulated spines (N_s) connected to that compartment

(3)

References