Spatial gridding and temporal accuracy in NEURON (Hines and Carnevale 2001)

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Accession:53451
A heuristic for compartmentalization based on the space constant at 100 Hz is proposed. The paper also discusses spatio/temporal accuracy and the use of CVODE.
Reference:
1 . Hines ML, Carnevale NT (2001) NEURON: a tool for neuroscientists. Neuroscientist 7:123-35 [PubMed]
Model Information (Click on a link to find other models with that property)
Model Type: Neuron or other electrically excitable cell;
Brain Region(s)/Organism:
Cell Type(s):
Channel(s):
Gap Junctions:
Receptor(s):
Gene(s):
Transmitter(s):
Simulation Environment: NEURON;
Model Concept(s): Tutorial/Teaching; Methods;
Implementer(s): Hines, Michael [Michael.Hines at Yale.edu];
/* trivially modified by Hines to comment out starting the gui at the end
so that we can do our own desired gui for figures 9 and 10
*/

/* --------------------------------------------------------------
   Multi-compartment simulations of neocortical neurons
   DEMO
  
   Z. F. Mainen and T. J. Sejnowski (1996) Influence of dendritic
   structure on firing pattern in model neocortical neurons. 
   Nature 382: 363-366. 
   
   Demo of Figure 1.

   updated: 11/1/96
   author:
   Zach Mainen
   zach@salk.edu or zach@cshl.org


   Corrections to methods of Figure 1 misprinted in paper:

   1. Time step = 25 usec, not 250 usec
   
   2. I_Na rate functions are all shifted 5 mV negative
   m:
   alpha = 0.182(v+30)/(1-exp(-(v+30)/9))
   beta = -0.124(v+30)/(1-exp((v+30)/9))
   h:
   alpha = 0.024(v+45)/(1-exp(-(v+45)/5))
   beta = -0.0091(v+70)/(1-exp((v+70)/5))
   beta_inf = 1/(1+exp(v+60)/6.2)

   3. I_Ca activation not inactivation  is given first 

   4. I_Km rates 
   alpha =  0.001 (v+30)/(1-exp(-(v+30)/9))
   beta =   0.001 (v+30)/(1-exp((v+30)/9)

   5. g_kca = 3 (pS um^-2)

   Correction to Figure 4:

   "transfer impedance" should be "transfer conductance"
   Z^-1 = I/V (uS) 
   
 
   -------------------------------------------------------------- */


objref sh, st, axonal, dendritic, dendritic_only

// needed for my particular version of NEURON--NTC 5/1/2000
strdef tstr
load_file("wingroup.hoc")
// end of patch for my particular version of NEURON

load_proc("nrnmainmenu")

create soma
access soma

tstop = 1000
steps_per_ms = 40
dt = 0.025


// --------------------------------------------------------------
// passive & active membrane 
// --------------------------------------------------------------

ra        = 150
global_ra = ra
rm        = 30000
c_m       = 0.75
cm_myelin = 0.04
g_pas_node = 0.02

v_init    = -70
celsius   = 37

Ek = -90
Ena = 60


gna_dend = 20
gna_node = 30000
gna_soma = gna_dend

gkv_axon = 2000
gkv_soma = 200

gca = .3
gkm = .1
gkca = 3

gca_soma = gca
gkm_soma = gkm
gkca_soma = gkca
 

// --------------------------------------------------------------
// Axon geometry
//
// Similar to Mainen et al (Neuron, 1995)
// --------------------------------------------------------------

n_axon_seg = 5

create soma,iseg,hill,myelin[2],node[2]

proc create_axon() {

  create iseg,hill,myelin[n_axon_seg],node[n_axon_seg]

  soma {
    equiv_diam = sqrt(area(.5)/(4*PI))

    // area = equiv_diam^2*4*PI
  }
  if (numarg()) equiv_diam = $1

  iseg {                // initial segment between hillock + myelin
     L = 15
     nseg = 5
     diam = equiv_diam/10        // see Sloper and Powell 1982, Fig.71
  }

  hill {                
    L = 10
    nseg = 5
    diam(0:1) = 4*iseg.diam:iseg.diam
  }

  // construct myelinated axon with nodes of ranvier

  for i=0,n_axon_seg-1 {
    myelin[i] {         // myelin element
      nseg = 5
      L = 100
      diam = iseg.diam         
    }
    node[i] {           // nodes of Ranvier
      nseg = 1
      L = 1.0           
      diam = iseg.diam*.75       // nodes are thinner than axon
    }
  }

  soma connect hill(0), 0.5
  hill connect iseg(0), 1
  iseg connect myelin[0](0), 1
  myelin[0] connect node[0](0), 1

  for i=0,n_axon_seg-2  { 
      node[i] connect myelin[i+1](0), 1 
      myelin[i+1] connect node[i+1](0), 1
  }
}

// --------------------------------------------------------------
// Spines
// --------------------------------------------------------------

      // Based on the "Folding factor" described in
      // Jack et al (1989), Major et al (1994)
      // note, this assumes active channels are present in spines 
      // at same density as dendrites

spine_dens = 1
      // just using a simple spine density model due to lack of data on some 
      // neuron types.

spine_area = 0.83 // um^2  -- K Harris

proc add_spines() { local a, i
  forsec $o1 {
    a =0
    for(x) a=a+area(x)

    F = (L*spine_area*spine_dens + a)/a

    L = L * F^(2/3)
    for(x) diam(x) = diam(x) * F^(1/3)
    //for i=0, n3d()-1 pt3dchange(i, diam3d(i)*F^(1/3))
  }
}



proc init_cell() {

  // passive
  forall {
    insert pas
    Ra = ra 
    cm = c_m 
    g_pas = 1/rm
    e_pas = v_init
  }

  // exceptions along the axon
  forsec "myelin" cm = cm_myelin
  forsec "node" g_pas = g_pas_node

  // na+ channels
  forall insert na
  forsec dendritic gbar_na = gna_dend
  forsec "myelin" gbar_na = gna_dend
  hill.gbar_na = gna_node
  iseg.gbar_na = gna_node
  forsec "node" gbar_na = gna_node

  // kv delayed rectifier channels
  iseg { insert kv  gbar_kv = gkv_axon }
  hill { insert kv  gbar_kv = gkv_axon }
  soma { insert kv  gbar_kv = gkv_soma }

  // dendritic channels
  forsec dendritic {
    insert km    gbar_km  = gkm
    insert kca   gbar_kca = gkca
    insert ca    gbar_ca = gca
    insert cad
  }

  soma {
    gbar_na = gna_soma
    gbar_km = gkm_soma
    gbar_kca = gkca_soma
    gbar_ca = gca_soma
  }

 
  forall if(ismembrane("k_ion")) ek = Ek
  forall if(ismembrane("na_ion")) {
    ena = Ena
    // seems to be necessary for 3d cells to shift Na kinetics -5 mV
    vshift_na = -5
  }
  forall if(ismembrane("ca_ion")) {
    eca = 140
//    ion_style("ca_ion",0,1,0,0,0)
    ion_style("ca_ion", 3,1,0,0,0)
	//cai is a STATE (from cad.mod)
	// and the initialization with cainit turns out to be
	// early enough (before kca.mod) that initialization of n(cai)
	// is ok. Otherwise we would need a different ion_style (last
	//arg = 1) and 	cai0_ca_ion = cainit in an proc init()
	// note that eca is explicitly held constant. If the default
	// ion style was used to compute this, for fcurrent() to give
	// consistent currents it would be necessary to initialize
	// in a proc init() since nernst is computed befor cad.
   vshift_ca = 0
  }
}

proc load_3dcell() {

// $s1 filename

  aspiny = 0
  forall delete_section()
  xopen($s1)
  access soma

  dendritic = new SectionList()

  // make sure no compartments exceed 50 uM length
  forall {
    diam_save = diam
    n = L/50
    nseg = n + 1
    if (n3d() == 0) diam = diam_save
    dendritic.append()
  }    


  // show cell
//  sh = new PlotShape()
//  sh.size(-300,300,-300,300)

  dendritic_only = new SectionList()
  forsec dendritic dendritic_only.append()
  soma  dendritic_only.remove()

  create_axon()

  init_cell()

  if (!aspiny) add_spines(dendritic_only,spine_dens)

  st=new IClamp(.5)
  st.dur = 900
  st.del = 5
}


proc fig1a() {
  load_3dcell("cells/lcAS3.hoc")
  st.amp = 0.05
}

proc fig1b() {
  load_3dcell("cells/j7.hoc")  
  st.amp = 0.07
}

proc fig1c() {
  load_3dcell("cells/j8.hoc")
  st.amp = 0.1
}

proc fig1d() {
  load_3dcell("cells/j4a.hoc") 
  st.amp = 0.2
}

/*
xpanel("Figure 1")
xbutton("a. L3 Aspiny","fig1a()")
xbutton("b. L4 Stellate","fig1b()")
xbutton("c. L3 Pyramid","fig1c()")
xbutton("d. L5 Pyramid","fig1d()")
xpanel()

nrnmainmenu()
nrncontrolmenu()
newPlotV()
*/


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