/* ===========================================================

        Author: Daniel Keller
	Institution: Ecole Polytechnique Federale de Lausanne
	Reference: Keller D, Babai N, Kochubey O, Han Y, Markram H, Schürmann F, et al. (2015) An Exclusion Zone for Ca2+ Channels around Docked Vesicles Explains Release Control by Multiple Channels at a CNS Synapse. PLoS Comput Biol 11(5): e1004253. doi:10.1371/journal.pcbi.1004253

============================================================= */

/* ----- Geometrical Parameters for Cell ---- */

fuzz=1e-5
gap_size=0.02
dendrite_width=1.0
dendrite_length=2.0
spine_head_width=0.5
spine_head_length=0.5
spine_head_size=spine_head_length
spine_neck_width=0.2
spine_neck_length=0.5
head_n_neck_size=spine_head_size+spine_neck_length

bouton_width=0.8
bouton_height=1.2

mesh_width=0.5
active_zone_width=0.05
vesicle_diameter=0.03

height = -0.5*gap_size
psd_size = 0.7*spine_head_size
psd_corner = 0.5*(spine_head_size-psd_size)

connector_volume=(0.225*spine_head_size+ 0.2*spine_neck_width)*(0.225*spine_head_size+ 0.2*spine_neck_width)* 0.2 *spine_head_size 
spine_apparatus_head_volume=(0.45*spine_head_size)^2*(0.45*spine_head_size)+connector_volume
spine_apparatus_neck_volume=0.4*spine_neck_width*0.4*spine_neck_width*(spine_neck_length-2*fuzz)
spine_apparatus_volume=spine_apparatus_head_volume+spine_apparatus_neck_volume
spine_head_volume=spine_head_width^2 * spine_head_length
spine_neck_volume=spine_neck_width*spine_neck_width*spine_neck_length

spine_and_neck_volume_no_apparatus=spine_head_volume+spine_neck_volume

spine_and_neck_volume_with_apparatus=spine_head_volume-spine_apparatus_head_volume+spine_neck_volume- spine_apparatus_neck_volume
dendrite_volume=dendrite_width * dendrite_width * dendrite_length

post_synaptic_density_volume = (psd_size-2*fuzz)*(psd_size-2*fuzz)*0.05