// Author: Ronald van Elburg  (RonaldAJ at vanElburg eu)
//  
// Affiliation:
//   Department of Artificial Intelligence
//   Groningen University
//
// Parameter values used in the paper:
//
//   R.A.J. van Elburg and Arjen van Ooyen (2010) `Impact of dendritic size and
//   dendritic topology on burst firing in pyramidal cells', 
//   PLoS Comput Biol 6(5): e1000781. doi:10.1371/journal.pcbi.1000781.
//


Reconstructed cells:
    Temperature:
        celsius   = 37
    
    Passive properties:
        General:
        ra                  = 80            ohm cm
        g_pas               = 3.3333 10^-5  S/cm^2      
        c_m                 = 0.75      uF/cm^2
        
        Exceptions:
        myelin      c_m     = 0.04      uF/cm^2
        axon nodes  g_pas   = 0.02      S/cm^2  
        
    Ion channel densities:
        Soma:   
        gna = 20            pS/um2
        gkv = 200           pS/um2
        gca = .3            pS/um2
        gkm = .1            pS/um2
        gkca = 3            pS/um2
        
        Apical dendrites:
        gna = 20            pS/um2
        gca= .3             pS/um2
        gkm = .1            pS/um2
        gkca = 3            pS/um2
        
        Basal dendrites (passive):
        gna = 0             pS/um2
        gca= 0              pS/um2
        gkm = 0             pS/um2
        gkca = 0            pS/um2
        
        Axon hillock:
        gna = 30000         pS/um2  
        gkv = 2000          pS/um2
    
        Axon initial segment:
        gkv = 2000          pS/um2 
        gna = 30000         pS/um2
        
        Axon nodes:
        gna = 30000         pS/um2
        gkv = 2000          pS/um2
        
        Myelinated axon:
        gna = 20            pS/um2
        
        Reversal potentials:
        Ek = -90                mV
        Ena = 60                mV
        Eca = 140               mV
    
        Dendritic and somatic compartment length:   
        segmentlength=50
        
        Number of myelin and node segments: 5
        

           
        // seems to be necessary for 3d cells to shift Na kinetics -5 mV
        vshift_na = -5
        
    Experiments:
        General:    
            Duration:
                tstop= 10000 ms
            Somatic stimulus:
                I=0.2 nA
                Initial delay stimulus=400 ms  
            Dendritic stimulus:
                synaptic_density=0.05 synapses/ um^2
                mean_interval=1000 ms        
                globSynapseStrength=0.0024  uS
                tau=0.5 ms 
                E_reversal=0    mV
        Pruning:
            Endsegment Pruning probability: p=0.3
            pruneSeed=1:1:20
            pruneDepth=0:1:20
            synaptic density is kept constant during pruning.
            
        ReReconstructed Cells:
            Topologies as shown.
            synaptic density is kept constant
            
        Scaling reconstructed cells:
            Length scaling factor=0.5:0.1:2.5
            For synaptic stimulation the total average current is kept 
            constant by changing the synaptic density.
            
========================================================

Simplified cells:
    Temperature:
        celsius   = 37
     
    Passive properties:
        ra                  = 80            ohm cm
        g_pas               = 3.3333 10^-5  S/cm^2      
        c_m                 = 0.75          uF/cm^2                                       
        
    Active properties:
        Dendrites:
            gca             = 0.3  pS/um2        
            gkca            =   3  pS/um2       
            gna             =  15  pS/um2                                          
            gkm             = 0.1  pS/um2         
        Soma:
            gkv             = 150  pS/um2              
            gna             =3000  pS/um2                                      
    Reversal Potentials:
        ek                  = -90           mV 
        ena                 =  60           mV  
        eca                 =  140          mV
        eleak               = -70           mV     
     
    Morphology:
        Number of Endsegments   =   8     
        somaLength              =   14      um                 
        terminalDiameter        =   0.7     um     
        rallPower               =   3/2                 
    
    Compartimentalization:
        dendNSegLength=50         um         // Maximal segment length of dendritic sections
                                             // as a consequence there are at least 15 compartments 
                                             // which are furtherdivided if the length of a section exceeds 
                                             // 50 um.
        somaNSeg=1                           // Number of segments of axo-somatic section
    Experiments:
        General
            Duration:
                tstop   = 10000 ms
            Somatic stimulus:
                I                       =0.03 nA    
                Initial delay stimulus  =400 ms         
            Dendritic stimulus:
                synapsesPerSection  =40          // number synapses per segment
                mean_interval       =1000 ms        
                globSynapseStrength =0.0024  uS
                tau                 =0.5 ms 
                E_reversal          =0  mV
            
        Rall trees:
            L       =1000:25:4000 um
            Topology=1:1:23
            
        Constant diameter trees:
            L       =500:25:2500 um
            Topology=1:1:23 
            I       =0.1 nA         (Somatic stimulus)